From b71d430af6025cb46ac574e91e516bc5c4caf048 Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 28 Jun 2016 17:59:34 +0200 Subject: [PATCH 001/126] module : can regenerate single module files, homogenized cli options spack module : - refresh accepts a constraint - find and refresh share common cli options - ask for confirmation before refreshing - deleting the module file tree is now optional --- lib/spack/spack/cmd/module.py | 136 ++++++++++++++++++++++------------ lib/spack/spack/modules.py | 8 +- share/spack/csh/spack.csh | 8 +- share/spack/setup-env.sh | 8 +- 4 files changed, 101 insertions(+), 59 deletions(-) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 5292d422255..c71e615d1c7 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -32,73 +32,115 @@ from spack.modules import module_types from spack.util.string import * -description = "Manipulate modules and dotkits." +from spack.cmd.uninstall import ask_for_confirmation + +description = "Manipulate module files" + + +def _add_common_arguments(subparser): + type_help = 'Type of module files' + subparser.add_argument('--module-type', help=type_help, required=True, choices=module_types) + constraint_help = 'Optional constraint to select a subset of installed packages' + subparser.add_argument('constraint', nargs='*', help=constraint_help) def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command') + # spack module refresh + refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.') + refresh_parser.add_argument('--delete-tree', help='Delete the module file tree before refresh', action='store_true') + _add_common_arguments(refresh_parser) - sp.add_parser('refresh', help='Regenerate all module files.') - + # spack module find find_parser = sp.add_parser('find', help='Find module files for packages.') - find_parser.add_argument('module_type', - help="Type of module to find file for. [" + - '|'.join(module_types) + "]") - find_parser.add_argument('spec', - nargs='+', - help='spec to find a module file for.') + _add_common_arguments(find_parser) -def module_find(mtype, spec_array): - """Look at all installed packages and see if the spec provided - matches any. If it does, check whether there is a module file - of type there, and print out the name that the user - should type to use that package's module. +class MultipleMatches(Exception): + pass + + +class NoMatch(Exception): + pass + + +def module_find(mtype, specs, args): + """ + Look at all installed packages and see if the spec provided + matches any. If it does, check whether there is a module file + of type there, and print out the name that the user + should type to use that package's module. """ - if mtype not in module_types: - tty.die("Invalid module type: '%s'. Options are %s" % - (mtype, comma_or(module_types))) - - specs = spack.cmd.parse_specs(spec_array) - if len(specs) > 1: - tty.die("You can only pass one spec.") - spec = specs[0] - - specs = spack.installed_db.query(spec) if len(specs) == 0: - tty.die("No installed packages match spec %s" % spec) + raise NoMatch() if len(specs) > 1: - tty.error("Multiple matches for spec %s. Choose one:" % spec) - for s in specs: - sys.stderr.write(s.tree(color=True)) - sys.exit(1) + raise MultipleMatches() - mt = module_types[mtype] - mod = mt(specs[0]) + mod = module_types[mtype](specs.pop()) if not os.path.isfile(mod.file_name): tty.die("No %s module is installed for %s" % (mtype, spec)) print(mod.use_name) -def module_refresh(): - """Regenerate all module files for installed packages known to - spack (some packages may no longer exist).""" - specs = [s for s in spack.installed_db.query(installed=True, known=True)] +def module_refresh(name, specs, args): + """ + Regenerate all module files for installed packages known to + spack (some packages may no longer exist). + """ + # Prompt a message to the user about what is going to change + if not specs: + tty.msg('No package matches your query') + return - for name, cls in module_types.items(): - tty.msg("Regenerating %s module files." % name) - if os.path.isdir(cls.path): - shutil.rmtree(cls.path, ignore_errors=False) - mkdirp(cls.path) - for spec in specs: - cls(spec).write() + tty.msg('You are about to regenerate the {name} module files for the following specs:'.format(name=name)) + for s in specs: + print(s.format(color=True)) + ask_for_confirmation('Do you want to proceed ? ') + + cls = module_types[name] + tty.msg('Regenerating {name} module files'.format(name=name)) + if os.path.isdir(cls.path) and args.delete_tree: + shutil.rmtree(cls.path, ignore_errors=False) + mkdirp(cls.path) + for spec in specs: + cls(spec).write() + +# Qualifiers to be used when querying the db for specs +constraint_qualifiers = { + 'refresh': { + 'installed': True, + 'known': True + }, + 'find': { + } +} + +# Dictionary of callbacks based on the value of module_command +callbacks = { + 'refresh': module_refresh, + 'find': module_find +} def module(parser, args): - if args.module_command == 'refresh': - module_refresh() - - elif args.module_command == 'find': - module_find(args.module_type, args.spec) + module_type = args.module_type + # Query specs from command line + qualifiers = constraint_qualifiers[args.module_command] + specs = [s for s in spack.installed_db.query(**qualifiers)] + constraint = ' '.join(args.constraint) + if constraint: + specs = [x for x in specs if x.satisfies(constraint, strict=True)] + # Call the appropriate function + try: + callbacks[args.module_command](module_type, specs, args) + except MultipleMatches: + message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context' + tty.error(message.format(query=constraint)) + for s in specs: + sys.stderr.write(s.format(color=True) + '\n') + raise SystemExit(1) + except NoMatch: + message = 'the constraint \'{query}\' match no package, and this is not allowed in this context' + tty.die(message.format(query=constraint)) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index ce46047fa3f..068179c0cee 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -454,7 +454,7 @@ def remove(self): class Dotkit(EnvModule): name = 'dotkit' - + path = join_path(spack.share_path, 'dotkit') environment_modifications_formats = { PrependPath: 'dk_alter {name} {value}\n', SetEnv: 'dk_setenv {name} {value}\n' @@ -466,7 +466,7 @@ class Dotkit(EnvModule): @property def file_name(self): - return join_path(spack.share_path, "dotkit", self.spec.architecture, + return join_path(self.path, self.spec.architecture, '%s.dk' % self.use_name) @property @@ -494,7 +494,7 @@ def prerequisite(self, spec): class TclModule(EnvModule): name = 'tcl' - + path = join_path(spack.share_path, "modules") environment_modifications_formats = { PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n', AppendPath: 'append-path --delim "{delim}" {name} \"{value}\"\n', @@ -514,7 +514,7 @@ class TclModule(EnvModule): @property def file_name(self): - return join_path(spack.share_path, "modules", self.spec.architecture, self.use_name) + return join_path(self.path, self.spec.architecture, self.use_name) @property def header(self): diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh index d64ce8935b6..5acd1904499 100644 --- a/share/spack/csh/spack.csh +++ b/share/spack/csh/spack.csh @@ -74,25 +74,25 @@ case unload: # tool's commands to add/remove the result from the environment. switch ($_sp_subcommand) case "use": - set _sp_full_spec = ( "`\spack $_sp_flags module find dotkit $_sp_spec`" ) + set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" ) if ( $? == 0 ) then use $_sp_module_args $_sp_full_spec endif breaksw case "unuse": - set _sp_full_spec = ( "`\spack $_sp_flags module find dotkit $_sp_spec`" ) + set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" ) if ( $? == 0 ) then unuse $_sp_module_args $_sp_full_spec endif breaksw case "load": - set _sp_full_spec = ( "`\spack $_sp_flags module find tcl $_sp_spec`" ) + set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" ) if ( $? == 0 ) then module load $_sp_module_args $_sp_full_spec endif breaksw case "unload": - set _sp_full_spec = ( "`\spack $_sp_flags module find tcl $_sp_spec`" ) + set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" ) if ( $? == 0 ) then module unload $_sp_module_args $_sp_full_spec endif diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 8aa259cf159..3975672e7b7 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -105,19 +105,19 @@ function spack { # If spack module command comes back with an error, do nothing. case $_sp_subcommand in "use") - if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then use $_sp_module_args $_sp_full_spec fi ;; "unuse") - if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then unuse $_sp_module_args $_sp_full_spec fi ;; "load") - if _sp_full_spec=$(command spack $_sp_flags module find tcl $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then module load $_sp_module_args $_sp_full_spec fi ;; "unload") - if _sp_full_spec=$(command spack $_sp_flags module find tcl $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then module unload $_sp_module_args $_sp_full_spec fi ;; esac From 6f69c01915aad8bb2d4b242ab7e5b185adf08b7d Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 27 Apr 2016 15:00:47 -0400 Subject: [PATCH 002/126] bootstrap: fall back to the default upstream URL Fixes #352. --- lib/spack/spack/cmd/bootstrap.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index bec11439b5c..9fd428e6b1e 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -31,6 +31,8 @@ import spack from spack.util.executable import which +_SPACK_UPSTREAM = 'https://github.com/llnl/spack' + description = "Create a new installation of spack in another prefix" def setup_parser(subparser): @@ -40,9 +42,15 @@ def setup_parser(subparser): def get_origin_url(): git_dir = join_path(spack.prefix, '.git') git = which('git', required=True) - origin_url = git( - '--git-dir=%s' % git_dir, 'config', '--get', 'remote.origin.url', - output=str) + try: + origin_url = git( + '--git-dir=%s' % git_dir, + 'config', '--get', 'remote.origin.url', + output=str) + except ProcessError: + origin_url = _SPACK_UPSTREAM + tty.warn('No git repository found; ' + 'using default upstream URL: %s' % origin_url) return origin_url.strip() From 7ec191ce0b82827013485a98db84cd66aa2ca1b4 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 10:44:01 -0400 Subject: [PATCH 003/126] bootstrap: use the currently checked out branch The `master` branch is not really where Spack development happens, so default to it, but use the user's current branch if it's there. --- lib/spack/spack/cmd/bootstrap.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 9fd428e6b1e..16808b30b88 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -39,9 +39,14 @@ def setup_parser(subparser): subparser.add_argument('prefix', help="names of prefix where we should install spack") -def get_origin_url(): +def get_origin_info(): git_dir = join_path(spack.prefix, '.git') git = which('git', required=True) + try: + branch = git('symbolic-ref', '--short', 'HEAD', output=str) + except ProcessError: + branch = 'develop' + tty.warn('No branch found; using default branch: %s' % branch) try: origin_url = git( '--git-dir=%s' % git_dir, @@ -51,11 +56,11 @@ def get_origin_url(): origin_url = _SPACK_UPSTREAM tty.warn('No git repository found; ' 'using default upstream URL: %s' % origin_url) - return origin_url.strip() + return (origin_url.strip(), branch.strip()) def bootstrap(parser, args): - origin_url = get_origin_url() + origin_url, branch = get_origin_info() prefix = args.prefix tty.msg("Fetching spack from origin: %s" % origin_url) @@ -81,8 +86,9 @@ def bootstrap(parser, args): git = which('git', required=True) git('init', '--shared', '-q') git('remote', 'add', 'origin', origin_url) - git('fetch', 'origin', 'master:refs/remotes/origin/master', '-n', '-q') - git('reset', '--hard', 'origin/master', '-q') + git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch), + '-n', '-q') + git('reset', '--hard', 'origin/%s' % branch, '-q') tty.msg("Successfully created a new spack in %s" % prefix, "Run %s/bin/spack to use this installation." % prefix) From 89bf5f4045eebdc1f40561dbb70a56e170411c20 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 10:49:24 -0400 Subject: [PATCH 004/126] bootstrap: allow using alternate remotes If you want to bootstrap from a fork, the `--remote` option may be used to select it. Also limit the branches to 'develop' and 'master' if the remote is 'origin' since those are the actual integration branches used (other branches on 'origin' are just PR branches). --- lib/spack/spack/cmd/bootstrap.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 16808b30b88..3480c96f39a 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -36,10 +36,13 @@ description = "Create a new installation of spack in another prefix" def setup_parser(subparser): + subparser.add_argument( + '-r', '--remote', action='store', dest='remote', + help="name of the remote to bootstrap from", default='origin') subparser.add_argument('prefix', help="names of prefix where we should install spack") -def get_origin_info(): +def get_origin_info(remote): git_dir = join_path(spack.prefix, '.git') git = which('git', required=True) try: @@ -47,10 +50,14 @@ def get_origin_info(): except ProcessError: branch = 'develop' tty.warn('No branch found; using default branch: %s' % branch) + if remote == 'origin' and \ + branch not in ('master', 'develop'): + branch = 'develop' + tty.warn('Unknown branch found; using default branch: %s' % branch) try: origin_url = git( '--git-dir=%s' % git_dir, - 'config', '--get', 'remote.origin.url', + 'config', '--get', 'remote.%s.url' % remote, output=str) except ProcessError: origin_url = _SPACK_UPSTREAM @@ -60,10 +67,10 @@ def get_origin_info(): def bootstrap(parser, args): - origin_url, branch = get_origin_info() + origin_url, branch = get_origin_info(args.remote) prefix = args.prefix - tty.msg("Fetching spack from origin: %s" % origin_url) + tty.msg("Fetching spack from '%s': %s" % (args.remote, origin_url)) if os.path.isfile(prefix): tty.die("There is already a file at %s" % prefix) From e3e94f0ac96db3c1ddd51555fec5a2bf71b867bf Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 10:55:14 -0400 Subject: [PATCH 005/126] bootstrap: name the current branch the same as the remote --- lib/spack/spack/cmd/bootstrap.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 3480c96f39a..04892e258db 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -96,6 +96,7 @@ def bootstrap(parser, args): git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch), '-n', '-q') git('reset', '--hard', 'origin/%s' % branch, '-q') + git('checkout', '-B', branch, 'origin/%s' % branch, '-q') tty.msg("Successfully created a new spack in %s" % prefix, "Run %s/bin/spack to use this installation." % prefix) From 5f720f9b7c0e507c2a0335ce9840036ad0b9262f Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 9 Jun 2016 10:51:29 -0400 Subject: [PATCH 006/126] flake8: appease the style checker --- lib/spack/spack/cmd/bootstrap.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py index 04892e258db..60e2bd3a114 100644 --- a/lib/spack/spack/cmd/bootstrap.py +++ b/lib/spack/spack/cmd/bootstrap.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -from subprocess import check_call import llnl.util.tty as tty from llnl.util.filesystem import join_path, mkdirp @@ -35,11 +34,14 @@ description = "Create a new installation of spack in another prefix" + def setup_parser(subparser): subparser.add_argument( '-r', '--remote', action='store', dest='remote', help="name of the remote to bootstrap from", default='origin') - subparser.add_argument('prefix', help="names of prefix where we should install spack") + subparser.add_argument( + 'prefix', + help="names of prefix where we should install spack") def get_origin_info(remote): @@ -82,7 +84,8 @@ def bootstrap(parser, args): files_in_the_way = os.listdir(prefix) if files_in_the_way: - tty.die("There are already files there! Delete these files before boostrapping spack.", + tty.die("There are already files there! " + "Delete these files before boostrapping spack.", *files_in_the_way) tty.msg("Installing:", From 1b7eedbb7df7c6dee9ab84217e75dc8ec54dcee1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 30 Jun 2016 12:56:47 +0200 Subject: [PATCH 007/126] modules.yaml : added hash_length as a new keyword config : - added `hash_length` under the modules section EnvModules : - take into consideration hash_length when constructing `file_name` - added logic to warn and skip module file writing in case of file name clash --- lib/spack/spack/config.py | 5 +++++ lib/spack/spack/modules.py | 16 ++++++++++++++-- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index 84179e14696..3a66e9f2a60 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -328,6 +328,11 @@ 'anyOf': [ { 'properties': { + 'hash_length': { + 'type': 'integer', + 'minimum': 0, + 'default': 7 + }, 'whitelist': {'$ref': '#/definitions/array_of_strings'}, 'blacklist': {'$ref': '#/definitions/array_of_strings'}, 'naming_scheme': { diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 068179c0cee..82016feb843 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -188,6 +188,7 @@ def parse_config_options(module_generator): ##### # Automatic loading loads + module_file_actions['hash_length'] = module_configuration.get('hash_length', 7) module_file_actions['autoload'] = dependencies( module_generator.spec, module_file_actions.get('autoload', 'none')) # Prerequisites @@ -295,7 +296,9 @@ def use_name(self): if constraint in self.spec: suffixes.append(suffix) # Always append the hash to make the module file unique - suffixes.append(self.spec.dag_hash()) + hash_length = configuration.pop('hash_length', 7) + if hash_length != 0: + suffixes.append(self.spec.dag_hash(length=hash_length)) name = '-'.join(suffixes) return name @@ -338,7 +341,7 @@ def blacklisted(self): return False - def write(self): + def write(self, overwrite=False): """ Writes out a module file for this object. @@ -399,6 +402,15 @@ def write(self): for line in self.module_specific_content(module_configuration): module_file_content += line + # Print a warning in case I am accidentally overwriting + # a module file that is already there (name clash) + if not overwrite and os.path.exists(self.file_name): + message = 'Module file already exists : skipping creation\n' + message += 'file : {0.file_name}\n' + message += 'spec : {0.spec}' + tty.warn(message.format(self)) + return + # Dump to file with open(self.file_name, 'w') as f: f.write(module_file_content) From ba87937fffc5843b5f32246571b79d499dafeba3 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 30 Jun 2016 13:44:49 +0200 Subject: [PATCH 008/126] module : added detection of file name clashes --- lib/spack/spack/cmd/module.py | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index c71e615d1c7..4f6b4764b6c 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -25,6 +25,7 @@ import os import shutil import sys +import collections import llnl.util.tty as tty import spack.cmd @@ -100,12 +101,32 @@ def module_refresh(name, specs, args): ask_for_confirmation('Do you want to proceed ? ') cls = module_types[name] + + # Detect name clashes + writers = [cls(spec) for spec in specs] + file2writer = collections.defaultdict(list) + for item in writers: + file2writer[item.file_name].append(item) + + if len(file2writer) != len(writers): + message = 'Name clashes detected in module files:\n' + for filename, writer_list in file2writer.items(): + if len(writer_list) > 1: + message += 'file : {0}\n'.format(filename) + for x in writer_list: + message += 'spec : {0}\n'.format(x.spec.format(color=True)) + message += '\n' + tty.error(message) + tty.error('Operation aborted') + raise SystemExit(1) + + # Proceed regenerating module files tty.msg('Regenerating {name} module files'.format(name=name)) if os.path.isdir(cls.path) and args.delete_tree: shutil.rmtree(cls.path, ignore_errors=False) mkdirp(cls.path) - for spec in specs: - cls(spec).write() + for x in writers: + x.write(overwrite=True) # Qualifiers to be used when querying the db for specs constraint_qualifiers = { From a770151359a9c573bfd967f79eab26670d499af0 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 30 Jun 2016 16:49:24 +0200 Subject: [PATCH 009/126] module : minor improvement to output formatting --- bin/spack | 2 +- lib/spack/spack/cmd/module.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/spack b/bin/spack index e9307d1485a..9b1276a8666 100755 --- a/bin/spack +++ b/bin/spack @@ -77,7 +77,7 @@ import llnl.util.tty as tty from llnl.util.tty.color import * import spack from spack.error import SpackError -import argparse +from external import argparse # Command parsing parser = argparse.ArgumentParser( diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 4f6b4764b6c..4f0593e45e5 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -95,9 +95,10 @@ def module_refresh(name, specs, args): tty.msg('No package matches your query') return - tty.msg('You are about to regenerate the {name} module files for the following specs:'.format(name=name)) + tty.msg('You are about to regenerate the {name} module files for the following specs:\n'.format(name=name)) for s in specs: print(s.format(color=True)) + print('') ask_for_confirmation('Do you want to proceed ? ') cls = module_types[name] @@ -112,10 +113,9 @@ def module_refresh(name, specs, args): message = 'Name clashes detected in module files:\n' for filename, writer_list in file2writer.items(): if len(writer_list) > 1: - message += 'file : {0}\n'.format(filename) + message += '\nfile : {0}\n'.format(filename) for x in writer_list: message += 'spec : {0}\n'.format(x.spec.format(color=True)) - message += '\n' tty.error(message) tty.error('Operation aborted') raise SystemExit(1) From 6793a54748246efcda302b1fba24239ca5e19c2d Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 30 Jun 2016 23:18:32 +0200 Subject: [PATCH 010/126] --prefix : defaults to empty string --- lib/spack/spack/cmd/module.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 916bb656466..0d980bc9182 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -65,7 +65,7 @@ def setup_parser(subparser): help='Generate shell script (instead of input for module command)') find_parser.add_argument( - '-p', '--prefix', dest='prefix', + '-p', '--prefix', dest='prefix', default='', help='Prepend to module names when issuing module load commands') _add_common_arguments(find_parser) From fe4ef286f2887c27b7fe18a594a11eb4647c5cf3 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 1 Jul 2016 12:38:04 +0200 Subject: [PATCH 011/126] module : added the command 'load-list' --- lib/spack/spack/cmd/module.py | 119 ++++++++++++++++++---------------- 1 file changed, 62 insertions(+), 57 deletions(-) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 0d980bc9182..5628ab17a5a 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from __future__ import print_function + import os import shutil import sys @@ -41,7 +42,7 @@ def _add_common_arguments(subparser): type_help = 'Type of module files' - subparser.add_argument('--module-type', help=type_help, required=True, choices=module_types) + subparser.add_argument('--module-type', help=type_help, default='tcl', choices=module_types) constraint_help = 'Optional constraint to select a subset of installed packages' subparser.add_argument('constraint', nargs='*', help=constraint_help) @@ -55,19 +56,26 @@ def setup_parser(subparser): # spack module find find_parser = sp.add_parser('find', help='Find module files for packages.') - find_parser.add_argument( + _add_common_arguments(find_parser) + + # spack module env + loadlist_parser = sp.add_parser( + 'load-list', + help='Prompt the list of modules associated with packages that satisfy a contraint' + ) + loadlist_parser.add_argument( '-r', '--dependencies', action='store_true', dest='recurse_dependencies', help='Recursively traverse dependencies for modules to load.') - find_parser.add_argument( + loadlist_parser.add_argument( '-s', '--shell', action='store_true', dest='shell', help='Generate shell script (instead of input for module command)') - find_parser.add_argument( + loadlist_parser.add_argument( '-p', '--prefix', dest='prefix', default='', help='Prepend to module names when issuing module load commands') - _add_common_arguments(find_parser) + _add_common_arguments(loadlist_parser) class MultipleMatches(Exception): @@ -78,7 +86,45 @@ class NoMatch(Exception): pass -def module_find(mtype, specs, args): +def load_list(mtype, specs, args): + + # Get a comprehensive list of specs + if args.recurse_dependencies: + specs_from_user_constraint = specs[:] + specs = [] + # FIXME : during module file creation nodes seem to be visited multiple + # FIXME : times even if cover='nodes' is given. This work around permits + # FIXME : to get a unique list of spec anyhow. Do we miss a merge + # FIXME : step among nodes that refer to the same package? + # FIXME : (same problem as in spack/modules.py) + seen = set() + seen_add = seen.add + for spec in specs_from_user_constraint: + specs.extend( + [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))] + ) + + module_cls = module_types[mtype] + modules = [(spec, module_cls(spec).use_name) for spec in specs if os.path.exists(module_cls(spec).file_name)] + + module_commands = { + 'tcl': 'module load ', + 'dotkit': 'dotkit use ' + } + + d = { + 'command': '' if not args.shell else module_commands[mtype], + 'prefix': args.prefix + } + + prompt_template = '{comment}{command}{prefix}{name}' + for spec, mod in modules: + d['comment'] = '' if not args.shell else '# {0}\n'.format(spec.format()) + d['name'] = mod + print( prompt_template.format(**d)) + + +def find(mtype, specs, args): """ Look at all installed packages and see if the spec provided matches any. If it does, check whether there is a module file @@ -92,56 +138,12 @@ def module_find(mtype, specs, args): raise MultipleMatches() spec = specs.pop() - if not args.recurse_dependencies: - mod = module_types[mtype](spec) - if not os.path.isfile(mod.file_name): - tty.die("No %s module is installed for %s" % (mtype, spec)) + mod = module_types[mtype](spec) + if not os.path.isfile(mod.file_name): + tty.die("No %s module is installed for %s" % (mtype, spec)) + print(mod.use_name) - print(mod.use_name) - else: - - def _find_modules(spec, modules_list): - """Finds all modules and sub-modules for a spec""" - if str(spec.version) == 'system': - # No Spack module for system-installed packages - return - - if args.recurse_dependencies: - for dep in spec.dependencies.values(): - _find_modules(dep, modules_list) - - mod = module_types[mtype](spec) - if not os.path.isfile(mod.file_name): - tty.die("No %s module is installed for %s" % (mtype, spec)) - modules_list.append((spec, mod)) - # -------------------------------------- - - modules = set() # Modules we will load - seen = set() - - # ----------- Chase down modules for it and all its dependencies - modules_dups = list() - _find_modules(spec, modules_dups) - - # Remove duplicates while keeping order - modules_unique = list() - for spec, mod in modules_dups: - if mod.use_name not in seen: - modules_unique.append((spec,mod)) - seen.add(mod.use_name) - - # Output... - if args.shell: - module_cmd = {'tcl': 'module load', 'dotkit': 'dotkit use'}[mtype] - for spec, mod in modules_unique: - if args.shell: - print('# %s' % spec.format()) - print('%s %s%s' % (module_cmd, args.prefix, mod.use_name)) - else: - print(mod.use_name) - - -def module_refresh(name, specs, args): +def refresh(name, specs, args): """ Regenerate all module files for installed packages known to spack (some packages may no longer exist). @@ -191,13 +193,16 @@ def module_refresh(name, specs, args): 'known': True }, 'find': { + }, + 'load-list':{ } } # Dictionary of callbacks based on the value of module_command callbacks = { - 'refresh': module_refresh, - 'find': module_find + 'refresh': refresh, + 'find': find, + 'load-list': load_list } From f0f7b23c8a6804da6d215e15712c99a6d72e782a Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 1 Jul 2016 14:27:55 +0200 Subject: [PATCH 012/126] module : added rm subcommand, encapsulated logic for constraints in argarse.Action subclass --- lib/spack/spack/cmd/module.py | 127 +++++++++++++++++++++++----------- 1 file changed, 88 insertions(+), 39 deletions(-) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 5628ab17a5a..6f9ede21acf 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -28,6 +28,7 @@ import shutil import sys import collections +import argparse import llnl.util.tty as tty import spack.cmd @@ -40,33 +41,76 @@ description = "Manipulate module files" +# Qualifiers to be used when querying the db for specs +constraint_qualifiers = { + 'refresh': { + 'installed': True, + 'known': True + }, + 'find': { + }, + 'load-list':{ + }, + 'rm': { + } +} + + +class ConstraintAction(argparse.Action): + qualifiers = {} + + def __call__(self, parser, namespace, values, option_string=None): + # Query specs from command line + d = self.qualifiers.get(namespace.subparser_name, {}) + specs = [s for s in spack.installed_db.query(**d)] + values = ' '.join(values) + if values: + specs = [x for x in specs if x.satisfies(values, strict=True)] + namespace.specs = specs + +# TODO : this needs better wrapping to be extracted +ConstraintAction.qualifiers.update(constraint_qualifiers) + + def _add_common_arguments(subparser): type_help = 'Type of module files' - subparser.add_argument('--module-type', help=type_help, default='tcl', choices=module_types) + subparser.add_argument('-m', '--module-type', help=type_help, default='tcl', choices=module_types) constraint_help = 'Optional constraint to select a subset of installed packages' - subparser.add_argument('constraint', nargs='*', help=constraint_help) + subparser.add_argument('constraint', nargs='*', help=constraint_help, action=ConstraintAction) def setup_parser(subparser): - sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command') + sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name') # spack module refresh refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.') refresh_parser.add_argument('--delete-tree', help='Delete the module file tree before refresh', action='store_true') _add_common_arguments(refresh_parser) + refresh_parser.add_argument( + '-y', '--yes-to-all', action='store_true', dest='yes_to_all', + help='Assume "yes" is the answer to every confirmation asked to the user.' + ) # spack module find find_parser = sp.add_parser('find', help='Find module files for packages.') _add_common_arguments(find_parser) - # spack module env + # spack module rm + rm_parser = sp.add_parser('rm', help='Find module files for packages.') + _add_common_arguments(rm_parser) + rm_parser.add_argument( + '-y', '--yes-to-all', action='store_true', dest='yes_to_all', + help='Assume "yes" is the answer to every confirmation asked to the user.' + ) + + # spack module load-list loadlist_parser = sp.add_parser( 'load-list', help='Prompt the list of modules associated with packages that satisfy a contraint' ) loadlist_parser.add_argument( - '-r', '--dependencies', action='store_true', + '-d', '--dependencies', action='store_true', dest='recurse_dependencies', - help='Recursively traverse dependencies for modules to load.') + help='Recursively traverse spec dependencies') loadlist_parser.add_argument( '-s', '--shell', action='store_true', dest='shell', @@ -87,7 +131,6 @@ class NoMatch(Exception): def load_list(mtype, specs, args): - # Get a comprehensive list of specs if args.recurse_dependencies: specs_from_user_constraint = specs[:] @@ -121,7 +164,7 @@ def load_list(mtype, specs, args): for spec, mod in modules: d['comment'] = '' if not args.shell else '# {0}\n'.format(spec.format()) d['name'] = mod - print( prompt_template.format(**d)) + print(prompt_template.format(**d)) def find(mtype, specs, args): @@ -143,7 +186,29 @@ def find(mtype, specs, args): tty.die("No %s module is installed for %s" % (mtype, spec)) print(mod.use_name) -def refresh(name, specs, args): + +def rm(mtype, specs, args): + module_cls = module_types[mtype] + modules = [module_cls(spec) for spec in specs if os.path.exists(module_cls(spec).file_name)] + + if not modules: + tty.msg('No module file matches your query') + return + + # Ask for confirmation + if not args.yes_to_all: + tty.msg('You are about to remove the following module files:\n') + for s in modules: + print(s.file_name) + print('') + ask_for_confirmation('Do you want to proceed ? ') + + # Remove the module files + for s in modules: + s.remove() + + +def refresh(mtype, specs, args): """ Regenerate all module files for installed packages known to spack (some packages may no longer exist). @@ -153,13 +218,14 @@ def refresh(name, specs, args): tty.msg('No package matches your query') return - tty.msg('You are about to regenerate the {name} module files for the following specs:\n'.format(name=name)) - for s in specs: - print(s.format(color=True)) - print('') - ask_for_confirmation('Do you want to proceed ? ') + if not args.yes_to_all: + tty.msg('You are about to regenerate the {name} module files for the following specs:\n'.format(name=mtype)) + for s in specs: + print(s.format(color=True)) + print('') + ask_for_confirmation('Do you want to proceed ? ') - cls = module_types[name] + cls = module_types[mtype] # Detect name clashes writers = [cls(spec) for spec in specs] @@ -179,48 +245,31 @@ def refresh(name, specs, args): raise SystemExit(1) # Proceed regenerating module files - tty.msg('Regenerating {name} module files'.format(name=name)) + tty.msg('Regenerating {name} module files'.format(name=mtype)) if os.path.isdir(cls.path) and args.delete_tree: shutil.rmtree(cls.path, ignore_errors=False) mkdirp(cls.path) for x in writers: x.write(overwrite=True) -# Qualifiers to be used when querying the db for specs -constraint_qualifiers = { - 'refresh': { - 'installed': True, - 'known': True - }, - 'find': { - }, - 'load-list':{ - } -} - -# Dictionary of callbacks based on the value of module_command +# Dictionary of callbacks based on the value of subparser_name callbacks = { 'refresh': refresh, 'find': find, - 'load-list': load_list + 'load-list': load_list, + 'rm': rm } def module(parser, args): module_type = args.module_type - # Query specs from command line - qualifiers = constraint_qualifiers[args.module_command] - specs = [s for s in spack.installed_db.query(**qualifiers)] - constraint = ' '.join(args.constraint) - if constraint: - specs = [x for x in specs if x.satisfies(constraint, strict=True)] - # Call the appropriate function + constraint = args.constraint try: - callbacks[args.module_command](module_type, specs, args) + callbacks[args.subparser_name](module_type, args.specs, args) except MultipleMatches: message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context' tty.error(message.format(query=constraint)) - for s in specs: + for s in args.specs: sys.stderr.write(s.format(color=True) + '\n') raise SystemExit(1) except NoMatch: From 0e171127b99e06d05631fe6391cb20b813bc1747 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 1 Jul 2016 14:30:01 +0200 Subject: [PATCH 013/126] module : reverted typo introduced in a previous commit --- bin/spack | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/spack b/bin/spack index 9b1276a8666..e9307d1485a 100755 --- a/bin/spack +++ b/bin/spack @@ -77,7 +77,7 @@ import llnl.util.tty as tty from llnl.util.tty.color import * import spack from spack.error import SpackError -from external import argparse +import argparse # Command parsing parser = argparse.ArgumentParser( From d10fceaacc7a1f8349f249c8700381f858b359b1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 1 Jul 2016 23:06:07 +0200 Subject: [PATCH 014/126] spack commands : refactoring of cli arguments and common utiities. Implemented suggestions on `spack module loads` - Common cli arguments now are in their own module - Moved utilities that can be reused by different commands into spack.cmd.__init__.py - Modifications to `spack module loads` --- lib/spack/spack/cmd/__init__.py | 101 ++++++++++++++++- lib/spack/spack/cmd/common/__init__.py | 24 ++++ lib/spack/spack/cmd/common/arguments.py | 88 +++++++++++++++ lib/spack/spack/cmd/find.py | 85 +------------- lib/spack/spack/cmd/module.py | 142 +++++++++--------------- lib/spack/spack/cmd/uninstall.py | 20 +--- lib/spack/spack/test/cmd/find.py | 6 +- lib/spack/spack/util/pattern.py | 6 + 8 files changed, 272 insertions(+), 200 deletions(-) create mode 100644 lib/spack/spack/cmd/common/__init__.py create mode 100644 lib/spack/spack/cmd/common/arguments.py diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 672999159c0..02f6f5b98a2 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -27,11 +27,12 @@ import sys import llnl.util.tty as tty -from llnl.util.lang import attr_setdefault - import spack -import spack.spec import spack.config +import spack.spec +from llnl.util.lang import * +from llnl.util.tty.colify import * +from llnl.util.tty.color import * # # Settings for commands that modify configuration @@ -145,3 +146,97 @@ def disambiguate_spec(spec): tty.die(*args) return matching_specs[0] + + +def ask_for_confirmation(message): + while True: + tty.msg(message + '[y/n]') + choice = raw_input().lower() + if choice == 'y': + break + elif choice == 'n': + raise SystemExit('Operation aborted') + tty.warn('Please reply either "y" or "n"') + + +def gray_hash(spec, length): + return colorize('@K{%s}' % spec.dag_hash(length)) + + +def display_specs(specs, **kwargs): + mode = kwargs.get('mode', 'short') + hashes = kwargs.get('long', False) + namespace = kwargs.get('namespace', False) + flags = kwargs.get('show_flags', False) + variants = kwargs.get('variants', False) + + hlen = 7 + if kwargs.get('very_long', False): + hashes = True + hlen = None + + nfmt = '.' if namespace else '_' + ffmt = '$%+' if flags else '' + vfmt = '$+' if variants else '' + format_string = '$%s$@%s%s' % (nfmt, ffmt, vfmt) + + # Make a dict with specs keyed by architecture and compiler. + index = index_by(specs, ('architecture', 'compiler')) + + # Traverse the index and print out each package + for i, (architecture, compiler) in enumerate(sorted(index)): + if i > 0: + print + + header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color, + architecture, spack.spec.compiler_color, + compiler) + tty.hline(colorize(header), char='-') + + specs = index[(architecture, compiler)] + specs.sort() + + abbreviated = [s.format(format_string, color=True) for s in specs] + if mode == 'paths': + # Print one spec per line along with prefix path + width = max(len(s) for s in abbreviated) + width += 2 + format = " %%-%ds%%s" % width + + for abbrv, spec in zip(abbreviated, specs): + if hashes: + print(gray_hash(spec, hlen), ) + print(format % (abbrv, spec.prefix)) + + elif mode == 'deps': + for spec in specs: + print(spec.tree( + format=format_string, + color=True, + indent=4, + prefix=(lambda s: gray_hash(s, hlen)) if hashes else None)) + + elif mode == 'short': + # Print columns of output if not printing flags + if not flags: + + def fmt(s): + string = "" + if hashes: + string += gray_hash(s, hlen) + ' ' + string += s.format('$-%s$@%s' % (nfmt, vfmt), color=True) + + return string + + colify(fmt(s) for s in specs) + # Print one entry per line if including flags + else: + for spec in specs: + # Print the hash if necessary + hsh = gray_hash(spec, hlen) + ' ' if hashes else '' + print(hsh + spec.format(format_string, color=True) + '\n') + + else: + raise ValueError( + "Invalid mode for display_specs: %s. Must be one of (paths," + "deps, short)." % mode) # NOQA: ignore=E501 diff --git a/lib/spack/spack/cmd/common/__init__.py b/lib/spack/spack/cmd/common/__init__.py new file mode 100644 index 00000000000..ed1ec23bcab --- /dev/null +++ b/lib/spack/spack/cmd/common/__init__.py @@ -0,0 +1,24 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py new file mode 100644 index 00000000000..a50bac5ac5d --- /dev/null +++ b/lib/spack/spack/cmd/common/arguments.py @@ -0,0 +1,88 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +import argparse + +import spack.modules +from spack.util.pattern import Bunch +__all__ = ['add_common_arguments'] + +_arguments = {} + + +def add_common_arguments(parser, list_of_arguments): + for argument in list_of_arguments: + if argument not in _arguments: + message = 'Trying to add the non existing argument "{0}" to a command' + raise KeyError(message.format(argument)) + x = _arguments[argument] + parser.add_argument(*x.flags, **x.kwargs) + + +class ConstraintAction(argparse.Action): + """Constructs a list of specs based on a constraint given on the command line + + An instance of this class is supposed to be used as an argument action in a parser. + + It will read a constraint and will attach a list of matching specs to the namespace + """ + qualifiers = {} + + def __call__(self, parser, namespace, values, option_string=None): + # Query specs from command line + d = self.qualifiers.get(namespace.subparser_name, {}) + specs = [s for s in spack.installed_db.query(**d)] + values = ' '.join(values) + if values: + specs = [x for x in specs if x.satisfies(values, strict=True)] + namespace.specs = specs + +_arguments['constraint'] = Bunch(flags=('constraint',), + kwargs={ + 'nargs': '*', + 'help': 'Optional constraint to select a subset of installed packages', + 'action': ConstraintAction + }) + +_arguments['module_type'] = Bunch(flags=('-m', '--module-type'), + kwargs={ + 'help': 'Type of module files', + 'default': 'tcl', + 'choices': spack.modules.module_types + }) + +_arguments['yes_to_all'] = Bunch(flags=('-y', '--yes-to-all'), + kwargs={ + 'action': 'store_true', + 'dest': 'yes_to_all', + 'help': 'Assume "yes" is the answer to every confirmation asked to the user.' + }) + +_arguments['recurse_dependencies'] = Bunch(flags=('-r', '--dependencies'), + kwargs={ + 'action': 'store_true', + 'dest': 'recurse_dependencies', + 'help': 'Recursively traverse spec dependencies' + }) diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py index 3ec671f93f6..d3ea38c573f 100644 --- a/lib/spack/spack/cmd/find.py +++ b/lib/spack/spack/cmd/find.py @@ -31,7 +31,7 @@ from llnl.util.lang import * from llnl.util.tty.colify import * from llnl.util.tty.color import * -from llnl.util.lang import * +from spack.cmd import display_specs description = "Find installed spack packages" @@ -104,89 +104,6 @@ def setup_parser(subparser): help='optional specs to filter results') -def gray_hash(spec, length): - return colorize('@K{%s}' % spec.dag_hash(length)) - - -def display_specs(specs, **kwargs): - mode = kwargs.get('mode', 'short') - hashes = kwargs.get('long', False) - namespace = kwargs.get('namespace', False) - flags = kwargs.get('show_flags', False) - variants = kwargs.get('variants', False) - - hlen = 7 - if kwargs.get('very_long', False): - hashes = True - hlen = None - - nfmt = '.' if namespace else '_' - ffmt = '$%+' if flags else '' - vfmt = '$+' if variants else '' - format_string = '$%s$@%s%s' % (nfmt, ffmt, vfmt) - - # Make a dict with specs keyed by architecture and compiler. - index = index_by(specs, ('architecture', 'compiler')) - - # Traverse the index and print out each package - for i, (architecture, compiler) in enumerate(sorted(index)): - if i > 0: - print - - header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color, - architecture, spack.spec.compiler_color, - compiler) - tty.hline(colorize(header), char='-') - - specs = index[(architecture, compiler)] - specs.sort() - - abbreviated = [s.format(format_string, color=True) for s in specs] - if mode == 'paths': - # Print one spec per line along with prefix path - width = max(len(s) for s in abbreviated) - width += 2 - format = " %%-%ds%%s" % width - - for abbrv, spec in zip(abbreviated, specs): - if hashes: - print(gray_hash(spec, hlen), ) - print(format % (abbrv, spec.prefix)) - - elif mode == 'deps': - for spec in specs: - print(spec.tree( - format=format_string, - color=True, - indent=4, - prefix=(lambda s: gray_hash(s, hlen)) if hashes else None)) - - elif mode == 'short': - # Print columns of output if not printing flags - if not flags: - - def fmt(s): - string = "" - if hashes: - string += gray_hash(s, hlen) + ' ' - string += s.format('$-%s$@%s' % (nfmt, vfmt), color=True) - - return string - - colify(fmt(s) for s in specs) - # Print one entry per line if including flags - else: - for spec in specs: - # Print the hash if necessary - hsh = gray_hash(spec, hlen) + ' ' if hashes else '' - print(hsh + spec.format(format_string, color=True) + '\n') - - else: - raise ValueError( - "Invalid mode for display_specs: %s. Must be one of (paths," - "deps, short)." % mode) # NOQA: ignore=E501 - - def query_arguments(args): # Check arguments if args.explicit and args.implicit: diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 6f9ede21acf..2c47e9fcb6f 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -24,102 +24,59 @@ ############################################################################## from __future__ import print_function +import collections import os import shutil import sys -import collections -import argparse import llnl.util.tty as tty import spack.cmd +import spack.cmd.common.arguments as arguments from llnl.util.filesystem import mkdirp from spack.modules import module_types -from spack.util.string import * - -from spack.cmd.uninstall import ask_for_confirmation +#from spack.util.string import * description = "Manipulate module files" - -# Qualifiers to be used when querying the db for specs -constraint_qualifiers = { - 'refresh': { - 'installed': True, - 'known': True - }, - 'find': { - }, - 'load-list':{ - }, - 'rm': { - } -} +callbacks = {} -class ConstraintAction(argparse.Action): - qualifiers = {} - - def __call__(self, parser, namespace, values, option_string=None): - # Query specs from command line - d = self.qualifiers.get(namespace.subparser_name, {}) - specs = [s for s in spack.installed_db.query(**d)] - values = ' '.join(values) - if values: - specs = [x for x in specs if x.satisfies(values, strict=True)] - namespace.specs = specs - -# TODO : this needs better wrapping to be extracted -ConstraintAction.qualifiers.update(constraint_qualifiers) - - -def _add_common_arguments(subparser): - type_help = 'Type of module files' - subparser.add_argument('-m', '--module-type', help=type_help, default='tcl', choices=module_types) - constraint_help = 'Optional constraint to select a subset of installed packages' - subparser.add_argument('constraint', nargs='*', help=constraint_help, action=ConstraintAction) +def subcommand(subparser_name): + """Registers a function in the callbacks dictionary""" + def decorator(callback): + callbacks[subparser_name] = callback + return callback + return decorator def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name') # spack module refresh - refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.') + refresh_parser = sp.add_parser('refresh', help='Regenerate module files') refresh_parser.add_argument('--delete-tree', help='Delete the module file tree before refresh', action='store_true') - _add_common_arguments(refresh_parser) - refresh_parser.add_argument( - '-y', '--yes-to-all', action='store_true', dest='yes_to_all', - help='Assume "yes" is the answer to every confirmation asked to the user.' - ) + arguments.add_common_arguments(refresh_parser, ['constraint', 'module_type', 'yes_to_all']) # spack module find - find_parser = sp.add_parser('find', help='Find module files for packages.') - _add_common_arguments(find_parser) + find_parser = sp.add_parser('find', help='Find module files for packages') + arguments.add_common_arguments(find_parser, ['constraint', 'module_type']) # spack module rm - rm_parser = sp.add_parser('rm', help='Find module files for packages.') - _add_common_arguments(rm_parser) - rm_parser.add_argument( - '-y', '--yes-to-all', action='store_true', dest='yes_to_all', - help='Assume "yes" is the answer to every confirmation asked to the user.' + rm_parser = sp.add_parser('rm', help='Remove module files') + arguments.add_common_arguments(rm_parser, ['constraint', 'module_type', 'yes_to_all']) + + # spack module loads + loads_parser = sp.add_parser( + 'loads', + help='Prompt the list of modules associated with packages that satisfy a constraint' ) + loads_parser.add_argument( + '--input-only', action='store_false', dest='shell', + help='Generate input for module command (instead of a shell script)') - # spack module load-list - loadlist_parser = sp.add_parser( - 'load-list', - help='Prompt the list of modules associated with packages that satisfy a contraint' - ) - loadlist_parser.add_argument( - '-d', '--dependencies', action='store_true', - dest='recurse_dependencies', - help='Recursively traverse spec dependencies') - - loadlist_parser.add_argument( - '-s', '--shell', action='store_true', dest='shell', - help='Generate shell script (instead of input for module command)') - - loadlist_parser.add_argument( + loads_parser.add_argument( '-p', '--prefix', dest='prefix', default='', help='Prepend to module names when issuing module load commands') - _add_common_arguments(loadlist_parser) + arguments.add_common_arguments(loads_parser, ['constraint', 'module_type', 'recurse_dependencies']) class MultipleMatches(Exception): @@ -129,8 +86,8 @@ class MultipleMatches(Exception): class NoMatch(Exception): pass - -def load_list(mtype, specs, args): +@subcommand('loads') +def loads(mtype, specs, args): # Get a comprehensive list of specs if args.recurse_dependencies: specs_from_user_constraint = specs[:] @@ -166,7 +123,7 @@ def load_list(mtype, specs, args): d['name'] = mod print(prompt_template.format(**d)) - +@subcommand('find') def find(mtype, specs, args): """ Look at all installed packages and see if the spec provided @@ -187,9 +144,11 @@ def find(mtype, specs, args): print(mod.use_name) +@subcommand('rm') def rm(mtype, specs, args): module_cls = module_types[mtype] - modules = [module_cls(spec) for spec in specs if os.path.exists(module_cls(spec).file_name)] + specs_with_modules = [spec for spec in specs if os.path.exists(module_cls(spec).file_name)] + modules = [module_cls(spec) for spec in specs_with_modules] if not modules: tty.msg('No module file matches your query') @@ -197,21 +156,20 @@ def rm(mtype, specs, args): # Ask for confirmation if not args.yes_to_all: - tty.msg('You are about to remove the following module files:\n') - for s in modules: - print(s.file_name) + tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype)) + spack.cmd.display_specs(specs_with_modules, long=True) print('') - ask_for_confirmation('Do you want to proceed ? ') + spack.cmd.ask_for_confirmation('Do you want to proceed ? ') # Remove the module files for s in modules: s.remove() +@subcommand('refresh') def refresh(mtype, specs, args): - """ - Regenerate all module files for installed packages known to - spack (some packages may no longer exist). + """Regenerate module files for installed packages + """ # Prompt a message to the user about what is going to change if not specs: @@ -219,11 +177,10 @@ def refresh(mtype, specs, args): return if not args.yes_to_all: - tty.msg('You are about to regenerate the {name} module files for the following specs:\n'.format(name=mtype)) - for s in specs: - print(s.format(color=True)) + tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype)) + spack.cmd.display_specs(specs, long=True) print('') - ask_for_confirmation('Do you want to proceed ? ') + spack.cmd.ask_for_confirmation('Do you want to proceed ? ') cls = module_types[mtype] @@ -252,16 +209,17 @@ def refresh(mtype, specs, args): for x in writers: x.write(overwrite=True) -# Dictionary of callbacks based on the value of subparser_name -callbacks = { - 'refresh': refresh, - 'find': find, - 'load-list': load_list, - 'rm': rm -} - def module(parser, args): + # Qualifiers to be used when querying the db for specs + constraint_qualifiers = { + 'refresh': { + 'installed': True, + 'known': True + }, + } + arguments.ConstraintAction.qualifiers.update(constraint_qualifiers) + module_type = args.module_type constraint = args.constraint try: diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index a6f08d09ed8..92de33873b2 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -30,7 +30,6 @@ import spack import spack.cmd import spack.repository -from spack.cmd.find import display_specs description = "Remove an installed package" @@ -47,17 +46,6 @@ } -def ask_for_confirmation(message): - while True: - tty.msg(message + '[y/n]') - choice = raw_input().lower() - if choice == 'y': - break - elif choice == 'n': - raise SystemExit('Operation aborted') - tty.warn('Please reply either "y" or "n"') - - def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', dest='force', @@ -99,7 +87,7 @@ def concretize_specs(specs, allow_multiple_matches=False, force=False): if not allow_multiple_matches and len(matching) > 1: tty.error("%s matches multiple packages:" % spec) print() - display_specs(matching, **display_args) + spack.cmd.display_specs(matching, **display_args) print() has_errors = True @@ -179,7 +167,7 @@ def uninstall(parser, args): tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True)) print('') print("The following packages depend on it:") - display_specs(lst, **display_args) + spack.cmd.display_specs(lst, **display_args) print('') has_error = True elif args.dependents: @@ -193,9 +181,9 @@ def uninstall(parser, args): if not args.yes_to_all: tty.msg("The following packages will be uninstalled : ") print('') - display_specs(uninstall_list, **display_args) + spack.cmd.display_specs(uninstall_list, **display_args) print('') - ask_for_confirmation('Do you want to proceed ? ') + spack.cmd.ask_for_confirmation('Do you want to proceed ? ') # Uninstall everything on the list do_uninstall(uninstall_list, args.force) diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py index 371e9650e04..fa82db77337 100644 --- a/lib/spack/spack/test/cmd/find.py +++ b/lib/spack/spack/test/cmd/find.py @@ -27,11 +27,7 @@ import spack.cmd.find import unittest - -class Bunch(object): - - def __init__(self, **kwargs): - self.__dict__.update(kwargs) +from spack.util.pattern import Bunch class FindTest(unittest.TestCase): diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py index 6d4bcb10396..6af39c87d88 100644 --- a/lib/spack/spack/util/pattern.py +++ b/lib/spack/spack/util/pattern.py @@ -114,3 +114,9 @@ def getter(*args, **kwargs): return wrapper_class return cls_decorator + + +class Bunch(object): + """Carries a bunch of named attributes (from Alex Martelli bunch)""" + def __init__(self, **kwargs): + self.__dict__.update(kwargs) From 3100c5948a7278bd1429c316a1c78264b5fafcb3 Mon Sep 17 00:00:00 2001 From: alalazo Date: Sat, 2 Jul 2016 12:14:30 +0200 Subject: [PATCH 015/126] module : added unit tests --- lib/spack/spack/cmd/module.py | 28 ++++++---- lib/spack/spack/test/__init__.py | 2 +- lib/spack/spack/test/cmd/module.py | 82 ++++++++++++++++++++++++++++++ 3 files changed, 101 insertions(+), 11 deletions(-) create mode 100644 lib/spack/spack/test/cmd/module.py diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 2c47e9fcb6f..374e71a4d8c 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -32,12 +32,16 @@ import llnl.util.tty as tty import spack.cmd import spack.cmd.common.arguments as arguments -from llnl.util.filesystem import mkdirp +import llnl.util.filesystem as filesystem from spack.modules import module_types -#from spack.util.string import * description = "Manipulate module files" +# Dictionary that will be populated with the list of sub-commands +# Each sub-command must be callable and accept 3 arguments : +# - mtype : the type of the module file +# - specs : the list of specs to be processed +# - args : namespace containing the parsed command line arguments callbacks = {} @@ -51,6 +55,7 @@ def decorator(callback): def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name') + # spack module refresh refresh_parser = sp.add_parser('refresh', help='Regenerate module files') refresh_parser.add_argument('--delete-tree', help='Delete the module file tree before refresh', action='store_true') @@ -71,11 +76,12 @@ def setup_parser(subparser): ) loads_parser.add_argument( '--input-only', action='store_false', dest='shell', - help='Generate input for module command (instead of a shell script)') - + help='Generate input for module command (instead of a shell script)' + ) loads_parser.add_argument( '-p', '--prefix', dest='prefix', default='', - help='Prepend to module names when issuing module load commands') + help='Prepend to module names when issuing module load commands' + ) arguments.add_common_arguments(loads_parser, ['constraint', 'module_type', 'recurse_dependencies']) @@ -86,8 +92,10 @@ class MultipleMatches(Exception): class NoMatch(Exception): pass + @subcommand('loads') def loads(mtype, specs, args): + """Prompt the list of modules associated with a list of specs""" # Get a comprehensive list of specs if args.recurse_dependencies: specs_from_user_constraint = specs[:] @@ -123,6 +131,7 @@ def loads(mtype, specs, args): d['name'] = mod print(prompt_template.format(**d)) + @subcommand('find') def find(mtype, specs, args): """ @@ -146,13 +155,14 @@ def find(mtype, specs, args): @subcommand('rm') def rm(mtype, specs, args): + """Deletes module files associated with items in specs""" module_cls = module_types[mtype] specs_with_modules = [spec for spec in specs if os.path.exists(module_cls(spec).file_name)] modules = [module_cls(spec) for spec in specs_with_modules] if not modules: tty.msg('No module file matches your query') - return + raise SystemExit(1) # Ask for confirmation if not args.yes_to_all: @@ -168,9 +178,7 @@ def rm(mtype, specs, args): @subcommand('refresh') def refresh(mtype, specs, args): - """Regenerate module files for installed packages - - """ + """Regenerate module files for item in specs""" # Prompt a message to the user about what is going to change if not specs: tty.msg('No package matches your query') @@ -205,7 +213,7 @@ def refresh(mtype, specs, args): tty.msg('Regenerating {name} module files'.format(name=mtype)) if os.path.isdir(cls.path) and args.delete_tree: shutil.rmtree(cls.path, ignore_errors=False) - mkdirp(cls.path) + filesystem.mkdirp(cls.path) for x in writers: x.write(overwrite=True) diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index fb91f247214..dfbd73b91f8 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -40,7 +40,7 @@ 'cc', 'link_tree', 'spec_yaml', 'optional_deps', 'make_executable', 'configure_guess', 'lock', 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', - 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd'] + 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd', 'cmd.module'] def list_tests(): diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py new file mode 100644 index 00000000000..52628f5b3b8 --- /dev/null +++ b/lib/spack/spack/test/cmd/module.py @@ -0,0 +1,82 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import argparse +import os.path + +import spack.cmd.module as module +import spack.modules as modules +import spack.test.mock_database + + +class TestModule(spack.test.mock_database.MockDatabase): + def _get_module_files(self, args): + return [ + modules.module_types[args.module_type](spec).file_name for spec in args.specs + ] + + def test_module_common_operations(self): + parser = argparse.ArgumentParser() + module.setup_parser(parser) + # Try to remove a non existing module [tcl] + args = parser.parse_args(['rm', 'doesnotexist']) + self.assertRaises(SystemExit, module.module, parser, args) + # Remove existing modules [tcl] + args = parser.parse_args(['rm', '-y', 'mpileaks']) + module_files = self._get_module_files(args) + for item in module_files: + self.assertTrue(os.path.exists(item)) + module.module(parser, args) + for item in module_files: + self.assertFalse(os.path.exists(item)) + # Add them back [tcl] + args = parser.parse_args(['refresh', '-y', 'mpileaks']) + module.module(parser, args) + for item in module_files: + self.assertTrue(os.path.exists(item)) + # TODO : test the --delete-tree option + # TODO : this requires having a separate directory for test modules + # Try to find a module with multiple matches + args = parser.parse_args(['find', 'mpileaks']) + self.assertRaises(SystemExit, module.module, parser, args) + # Try to find a module with no matches + args = parser.parse_args(['find', 'doesnotexist']) + self.assertRaises(SystemExit, module.module, parser, args) + # Try to find a module + args = parser.parse_args(['find', 'libelf']) + module.module(parser, args) + # Remove existing modules [dotkit] + args = parser.parse_args(['rm', '-y', '-m', 'dotkit', 'mpileaks']) + module_files = self._get_module_files(args) + for item in module_files: + self.assertTrue(os.path.exists(item)) + module.module(parser, args) + for item in module_files: + self.assertFalse(os.path.exists(item)) + # Add them back [dotkit] + args = parser.parse_args(['refresh', '-y', '-m', 'dotkit', 'mpileaks']) + module.module(parser, args) + for item in module_files: + self.assertTrue(os.path.exists(item)) + # TODO : add tests for loads and find to check the prompt format From 6d988dde8dcc2d666631151e5dab429811ffed37 Mon Sep 17 00:00:00 2001 From: alalazo Date: Sat, 2 Jul 2016 12:54:36 +0200 Subject: [PATCH 016/126] qa : fixed flake8 issues --- lib/spack/spack/cmd/__init__.py | 19 +++---- lib/spack/spack/cmd/common/arguments.py | 64 ++++++++++++---------- lib/spack/spack/cmd/module.py | 46 ++++++++++------ lib/spack/spack/cmd/uninstall.py | 42 +++++++++------ lib/spack/spack/modules.py | 4 +- lib/spack/spack/test/__init__.py | 6 ++- lib/spack/spack/test/cmd/module.py | 3 +- lib/spack/spack/util/pattern.py | 72 +++++++++++++++---------- 8 files changed, 153 insertions(+), 103 deletions(-) diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 02f6f5b98a2..230115df50a 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -37,7 +37,8 @@ # # Settings for commands that modify configuration # -# Commands that modify confguration By default modify the *highest* priority scope. +# Commands that modify confguration By default modify the *highest* +# priority scope. default_modify_scope = spack.config.highest_precedence_scope().name # Commands that list confguration list *all* scopes by default. default_list_scope = None @@ -49,7 +50,7 @@ ignore_files = r'^\.|^__init__.py$|^#' SETUP_PARSER = "setup_parser" -DESCRIPTION = "description" +DESCRIPTION = "description" command_path = os.path.join(spack.lib_path, "spack", "cmd") @@ -72,7 +73,7 @@ def get_module(name): module_name, fromlist=[name, SETUP_PARSER, DESCRIPTION], level=0) - attr_setdefault(module, SETUP_PARSER, lambda *args: None) # null-op + attr_setdefault(module, SETUP_PARSER, lambda *args: None) # null-op attr_setdefault(module, DESCRIPTION, "") fn_name = get_cmd_function_name(name) @@ -102,17 +103,17 @@ def parse_specs(args, **kwargs): specs = spack.spec.parse(args) for spec in specs: if concretize: - spec.concretize() # implies normalize + spec.concretize() # implies normalize elif normalize: spec.normalize() return specs - except spack.parse.ParseError, e: + except spack.parse.ParseError as e: tty.error(e.message, e.string, e.pos * " " + "^") sys.exit(1) - except spack.spec.SpecError, e: + except spack.spec.SpecError as e: tty.error(e.message) sys.exit(1) @@ -128,7 +129,7 @@ def elide_list(line_list, max_num=10): [1, 2, 3, '...', 6] """ if len(line_list) > max_num: - return line_list[:max_num-1] + ['...'] + line_list[-1:] + return line_list[:max_num - 1] + ['...'] + line_list[-1:] else: return line_list @@ -139,8 +140,8 @@ def disambiguate_spec(spec): tty.die("Spec '%s' matches no installed packages." % spec) elif len(matching_specs) > 1: - args = ["%s matches multiple packages." % spec, - "Matching packages:"] + args = ["%s matches multiple packages." % spec, + "Matching packages:"] args += [" " + str(s) for s in matching_specs] args += ["Use a more specific spec."] tty.die(*args) diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py index a50bac5ac5d..af041708243 100644 --- a/lib/spack/spack/cmd/common/arguments.py +++ b/lib/spack/spack/cmd/common/arguments.py @@ -35,7 +35,7 @@ def add_common_arguments(parser, list_of_arguments): for argument in list_of_arguments: if argument not in _arguments: - message = 'Trying to add the non existing argument "{0}" to a command' + message = 'Trying to add the non existing argument "{0}" to a command' # NOQA: ignore=E501 raise KeyError(message.format(argument)) x = _arguments[argument] parser.add_argument(*x.flags, **x.kwargs) @@ -44,9 +44,9 @@ def add_common_arguments(parser, list_of_arguments): class ConstraintAction(argparse.Action): """Constructs a list of specs based on a constraint given on the command line - An instance of this class is supposed to be used as an argument action in a parser. - - It will read a constraint and will attach a list of matching specs to the namespace + An instance of this class is supposed to be used as an argument action + in a parser. It will read a constraint and will attach a list of matching + specs to the namespace """ qualifiers = {} @@ -59,30 +59,38 @@ def __call__(self, parser, namespace, values, option_string=None): specs = [x for x in specs if x.satisfies(values, strict=True)] namespace.specs = specs -_arguments['constraint'] = Bunch(flags=('constraint',), - kwargs={ - 'nargs': '*', - 'help': 'Optional constraint to select a subset of installed packages', - 'action': ConstraintAction - }) +parms = Bunch( + flags=('constraint',), + kwargs={ + 'nargs': '*', + 'help': 'Constraint to select a subset of installed packages', + 'action': ConstraintAction + }) +_arguments['constraint'] = parms -_arguments['module_type'] = Bunch(flags=('-m', '--module-type'), - kwargs={ - 'help': 'Type of module files', - 'default': 'tcl', - 'choices': spack.modules.module_types - }) +parms = Bunch( + flags=('-m', '--module-type'), + kwargs={ + 'help': 'Type of module files', + 'default': 'tcl', + 'choices': spack.modules.module_types + }) +_arguments['module_type'] = parms -_arguments['yes_to_all'] = Bunch(flags=('-y', '--yes-to-all'), - kwargs={ - 'action': 'store_true', - 'dest': 'yes_to_all', - 'help': 'Assume "yes" is the answer to every confirmation asked to the user.' - }) +parms = Bunch( + flags=('-y', '--yes-to-all'), + kwargs={ + 'action': 'store_true', + 'dest': 'yes_to_all', + 'help': 'Assume "yes" is the answer to every confirmation asked to the user.' # NOQA: ignore=E501 + }) +_arguments['yes_to_all'] = parms -_arguments['recurse_dependencies'] = Bunch(flags=('-r', '--dependencies'), - kwargs={ - 'action': 'store_true', - 'dest': 'recurse_dependencies', - 'help': 'Recursively traverse spec dependencies' - }) +parms = Bunch( + flags=('-r', '--dependencies'), + kwargs={ + 'action': 'store_true', + 'dest': 'recurse_dependencies', + 'help': 'Recursively traverse spec dependencies' + }) +_arguments['recurse_dependencies'] = parms diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 374e71a4d8c..a10e36e077a 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -58,8 +58,14 @@ def setup_parser(subparser): # spack module refresh refresh_parser = sp.add_parser('refresh', help='Regenerate module files') - refresh_parser.add_argument('--delete-tree', help='Delete the module file tree before refresh', action='store_true') - arguments.add_common_arguments(refresh_parser, ['constraint', 'module_type', 'yes_to_all']) + refresh_parser.add_argument( + '--delete-tree', + help='Delete the module file tree before refresh', + action='store_true' + ) + arguments.add_common_arguments( + refresh_parser, ['constraint', 'module_type', 'yes_to_all'] + ) # spack module find find_parser = sp.add_parser('find', help='Find module files for packages') @@ -67,12 +73,14 @@ def setup_parser(subparser): # spack module rm rm_parser = sp.add_parser('rm', help='Remove module files') - arguments.add_common_arguments(rm_parser, ['constraint', 'module_type', 'yes_to_all']) + arguments.add_common_arguments( + rm_parser, ['constraint', 'module_type', 'yes_to_all'] + ) # spack module loads loads_parser = sp.add_parser( 'loads', - help='Prompt the list of modules associated with packages that satisfy a constraint' + help='Prompt the list of modules associated with a constraint' ) loads_parser.add_argument( '--input-only', action='store_false', dest='shell', @@ -82,7 +90,9 @@ def setup_parser(subparser): '-p', '--prefix', dest='prefix', default='', help='Prepend to module names when issuing module load commands' ) - arguments.add_common_arguments(loads_parser, ['constraint', 'module_type', 'recurse_dependencies']) + arguments.add_common_arguments( + loads_parser, ['constraint', 'module_type', 'recurse_dependencies'] + ) class MultipleMatches(Exception): @@ -100,20 +110,20 @@ def loads(mtype, specs, args): if args.recurse_dependencies: specs_from_user_constraint = specs[:] specs = [] - # FIXME : during module file creation nodes seem to be visited multiple - # FIXME : times even if cover='nodes' is given. This work around permits - # FIXME : to get a unique list of spec anyhow. Do we miss a merge - # FIXME : step among nodes that refer to the same package? + # FIXME : during module file creation nodes seem to be visited + # FIXME : multiple times even if cover='nodes' is given. This + # FIXME : work around permits to get a unique list of spec anyhow. # FIXME : (same problem as in spack/modules.py) seen = set() seen_add = seen.add for spec in specs_from_user_constraint: specs.extend( - [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))] + [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))] # NOQA: ignore=E501 ) module_cls = module_types[mtype] - modules = [(spec, module_cls(spec).use_name) for spec in specs if os.path.exists(module_cls(spec).file_name)] + modules = [(spec, module_cls(spec).use_name) + for spec in specs if os.path.exists(module_cls(spec).file_name)] module_commands = { 'tcl': 'module load ', @@ -127,7 +137,8 @@ def loads(mtype, specs, args): prompt_template = '{comment}{command}{prefix}{name}' for spec, mod in modules: - d['comment'] = '' if not args.shell else '# {0}\n'.format(spec.format()) + d['comment'] = '' if not args.shell else '# {0}\n'.format( + spec.format()) d['name'] = mod print(prompt_template.format(**d)) @@ -157,7 +168,8 @@ def find(mtype, specs, args): def rm(mtype, specs, args): """Deletes module files associated with items in specs""" module_cls = module_types[mtype] - specs_with_modules = [spec for spec in specs if os.path.exists(module_cls(spec).file_name)] + specs_with_modules = [ + spec for spec in specs if os.path.exists(module_cls(spec).file_name)] modules = [module_cls(spec) for spec in specs_with_modules] if not modules: @@ -166,7 +178,7 @@ def rm(mtype, specs, args): # Ask for confirmation if not args.yes_to_all: - tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype)) + tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype)) # NOQA: ignore=E501 spack.cmd.display_specs(specs_with_modules, long=True) print('') spack.cmd.ask_for_confirmation('Do you want to proceed ? ') @@ -185,7 +197,7 @@ def refresh(mtype, specs, args): return if not args.yes_to_all: - tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype)) + tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype)) # NOQA: ignore=E501 spack.cmd.display_specs(specs, long=True) print('') spack.cmd.ask_for_confirmation('Do you want to proceed ? ') @@ -233,11 +245,11 @@ def module(parser, args): try: callbacks[args.subparser_name](module_type, args.specs, args) except MultipleMatches: - message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context' + message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context' # NOQA: ignore=E501 tty.error(message.format(query=constraint)) for s in args.specs: sys.stderr.write(s.format(color=True) + '\n') raise SystemExit(1) except NoMatch: - message = 'the constraint \'{query}\' match no package, and this is not allowed in this context' + message = 'the constraint \'{query}\' match no package, and this is not allowed in this context' # NOQA: ignore=E501 tty.die(message.format(query=constraint)) diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index 92de33873b2..a17b7c685c3 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -42,7 +42,7 @@ display_args = { 'long': True, 'show_flags': True, - 'variants':True + 'variants': True } @@ -53,32 +53,37 @@ def setup_parser(subparser): subparser.add_argument( '-a', '--all', action='store_true', dest='all', help="USE CAREFULLY. Remove ALL installed packages that match each " + - "supplied spec. i.e., if you say uninstall libelf, ALL versions of " + - "libelf are uninstalled. This is both useful and dangerous, like rm -r.") + "supplied spec. i.e., if you say uninstall libelf, ALL versions of " + # NOQA: ignore=E501 + "libelf are uninstalled. This is both useful and dangerous, like rm -r.") # NOQA: ignore=E501 subparser.add_argument( '-d', '--dependents', action='store_true', dest='dependents', - help='Also uninstall any packages that depend on the ones given via command line.' + help='Also uninstall any packages that depend on the ones given via command line.' # NOQA: ignore=E501 ) subparser.add_argument( '-y', '--yes-to-all', action='store_true', dest='yes_to_all', - help='Assume "yes" is the answer to every confirmation asked to the user.' + help='Assume "yes" is the answer to every confirmation asked to the user.' # NOQA: ignore=E501 ) - subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall") + subparser.add_argument( + 'packages', + nargs=argparse.REMAINDER, + help="specs of packages to uninstall" + ) def concretize_specs(specs, allow_multiple_matches=False, force=False): - """ - Returns a list of specs matching the non necessarily concretized specs given from cli + """Returns a list of specs matching the non necessarily + concretized specs given from cli Args: specs: list of specs to be matched against installed packages - allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted) + allow_multiple_matches : if True multiple matches are admitted Return: list of specs """ - specs_from_cli = [] # List of specs that match expressions given via command line + # List of specs that match expressions given via command line + specs_from_cli = [] has_errors = False for spec in specs: matching = spack.installed_db.query(spec) @@ -104,8 +109,8 @@ def concretize_specs(specs, allow_multiple_matches=False, force=False): def installed_dependents(specs): - """ - Returns a dictionary that maps a spec with a list of its installed dependents + """Returns a dictionary that maps a spec with a list of its + installed dependents Args: specs: list of specs to be checked for dependents @@ -135,7 +140,7 @@ def do_uninstall(specs, force): try: # should work if package is known to spack packages.append(item.package) - except spack.repository.UnknownPackageError as e: + except spack.repository.UnknownPackageError: # The package.py file has gone away -- but still # want to uninstall. spack.Package(item).do_uninstall(force=True) @@ -157,14 +162,17 @@ def uninstall(parser, args): with spack.installed_db.write_transaction(): specs = spack.cmd.parse_specs(args.packages) # Gets the list of installed specs that match the ones give via cli - uninstall_list = concretize_specs(specs, args.all, args.force) # takes care of '-a' is given in the cli - dependent_list = installed_dependents(uninstall_list) # takes care of '-d' + # takes care of '-a' is given in the cli + uninstall_list = concretize_specs(specs, args.all, args.force) + dependent_list = installed_dependents( + uninstall_list) # takes care of '-d' # Process dependent_list and update uninstall_list has_error = False if dependent_list and not args.dependents and not args.force: for spec, lst in dependent_list.items(): - tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True)) + tty.error("Will not uninstall %s" % + spec.format("$_$@$%@$#", color=True)) print('') print("The following packages depend on it:") spack.cmd.display_specs(lst, **display_args) @@ -176,7 +184,7 @@ def uninstall(parser, args): uninstall_list = list(set(uninstall_list)) if has_error: - tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well') + tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well') # NOQA: ignore=E501 if not args.yes_to_all: tty.msg("The following packages will be uninstalled : ") diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 82016feb843..e648c6140f1 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -188,7 +188,8 @@ def parse_config_options(module_generator): ##### # Automatic loading loads - module_file_actions['hash_length'] = module_configuration.get('hash_length', 7) + module_file_actions['hash_length'] = module_configuration.get( + 'hash_length', 7) module_file_actions['autoload'] = dependencies( module_generator.spec, module_file_actions.get('autoload', 'none')) # Prerequisites @@ -238,6 +239,7 @@ class EnvModule(object): formats = {} class __metaclass__(type): + def __init__(cls, name, bases, dict): type.__init__(cls, name, bases, dict) if cls.name != 'env_module' and cls.name in CONFIGURATION[ diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index dfbd73b91f8..bf46e011b15 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -32,7 +32,8 @@ from spack.test.tally_plugin import Tally """Names of tests to be included in Spack's test suite""" -test_names = ['architecture', 'versions', 'url_parse', 'url_substitution', 'packages', 'stage', +test_names = ['architecture', 'versions', 'url_parse', 'url_substitution', + 'packages', 'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize', 'multimethod', 'install', 'package_sanity', 'config', 'directory_layout', 'pattern', 'python_version', 'git_fetch', @@ -40,7 +41,8 @@ 'cc', 'link_tree', 'spec_yaml', 'optional_deps', 'make_executable', 'configure_guess', 'lock', 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', - 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd', 'cmd.module'] + 'cmd.uninstall', 'cmd.test_install', + 'cmd.test_compiler_cmd', 'cmd.module'] def list_tests(): diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py index 52628f5b3b8..36a4a73fe64 100644 --- a/lib/spack/spack/test/cmd/module.py +++ b/lib/spack/spack/test/cmd/module.py @@ -31,9 +31,10 @@ class TestModule(spack.test.mock_database.MockDatabase): + def _get_module_files(self, args): return [ - modules.module_types[args.module_type](spec).file_name for spec in args.specs + modules.module_types[args.module_type](spec).file_name for spec in args.specs # NOQA: ignore=E501 ] def test_module_common_operations(self): diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py index 6af39c87d88..bc5e9d2ffef 100644 --- a/lib/spack/spack/util/pattern.py +++ b/lib/spack/spack/util/pattern.py @@ -28,42 +28,50 @@ def composite(interface=None, method_list=None, container=list): - """ - Returns a class decorator that patches a class adding all the methods it needs to be a composite for a given - interface. + """Returns a class decorator that patches a class adding all the methods + it needs to be a composite for a given interface. - :param interface: class exposing the interface to which the composite object must conform. Only non-private and - non-special methods will be taken into account + :param interface: class exposing the interface to which the composite + object must conform. Only non-private and non-special methods will be + taken into account :param method_list: names of methods that should be part of the composite - :param container: container for the composite object (default = list). Must fulfill the MutableSequence contract. - The composite class will expose the container API to manage object composition + :param container: container for the composite object (default = list). + Must fulfill the MutableSequence contract. The composite class will expose + the container API to manage object composition :return: class decorator """ - # Check if container fulfills the MutableSequence contract and raise an exception if it doesn't - # The patched class returned by the decorator will inherit from the container class to expose the - # interface needed to manage objects composition + # Check if container fulfills the MutableSequence contract and raise an + # exception if it doesn't. The patched class returned by the decorator will + # inherit from the container class to expose the interface needed to manage + # objects composition if not issubclass(container, collections.MutableSequence): raise TypeError("Container must fulfill the MutableSequence contract") - # Check if at least one of the 'interface' or the 'method_list' arguments are defined + # Check if at least one of the 'interface' or the 'method_list' arguments + # are defined if interface is None and method_list is None: - raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite") + raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite") # NOQA : ignore=E501 def cls_decorator(cls): - # Retrieve the base class of the composite. Inspect its methods and decide which ones will be overridden + # Retrieve the base class of the composite. Inspect its methods and + # decide which ones will be overridden def no_special_no_private(x): return inspect.ismethod(x) and not x.__name__.startswith('_') - # Patch the behavior of each of the methods in the previous list. This is done associating an instance of the - # descriptor below to any method that needs to be patched. + # Patch the behavior of each of the methods in the previous list. + # This is done associating an instance of the descriptor below to + # any method that needs to be patched. class IterateOver(object): + """Decorator used to patch methods in a composite. + + It iterates over all the items in the instance containing the + associated attribute and calls for each of them an attribute + with the same name """ - Decorator used to patch methods in a composite. It iterates over all the items in the instance containing the - associated attribute and calls for each of them an attribute with the same name - """ + def __init__(self, name, func=None): self.name = name self.func = func @@ -72,8 +80,9 @@ def __get__(self, instance, owner): def getter(*args, **kwargs): for item in instance: getattr(item, self.name)(*args, **kwargs) - # If we are using this descriptor to wrap a method from an interface, then we must conditionally - # use the `functools.wraps` decorator to set the appropriate fields. + # If we are using this descriptor to wrap a method from an + # interface, then we must conditionally use the + # `functools.wraps` decorator to set the appropriate fields if self.func is not None: getter = functools.wraps(self.func)(getter) return getter @@ -81,7 +90,8 @@ def getter(*args, **kwargs): dictionary_for_type_call = {} # Construct a dictionary with the methods explicitly passed as name if method_list is not None: - # python@2.7: method_list_dict = {name: IterateOver(name) for name in method_list} + # python@2.7: method_list_dict = {name: IterateOver(name) for name + # in method_list} method_list_dict = {} for name in method_list: method_list_dict[name] = IterateOver(name) @@ -89,28 +99,33 @@ def getter(*args, **kwargs): # Construct a dictionary with the methods inspected from the interface if interface is not None: ########## - # python@2.7: interface_methods = {name: method for name, method in inspect.getmembers(interface, predicate=no_special_no_private)} + # python@2.7: interface_methods = {name: method for name, method in + # inspect.getmembers(interface, predicate=no_special_no_private)} interface_methods = {} - for name, method in inspect.getmembers(interface, predicate=no_special_no_private): + for name, method in inspect.getmembers(interface, predicate=no_special_no_private): # NOQA: ignore=E501 interface_methods[name] = method ########## - # python@2.7: interface_methods_dict = {name: IterateOver(name, method) for name, method in interface_methods.iteritems()} + # python@2.7: interface_methods_dict = {name: IterateOver(name, + # method) for name, method in interface_methods.iteritems()} interface_methods_dict = {} for name, method in interface_methods.iteritems(): interface_methods_dict[name] = IterateOver(name, method) ########## dictionary_for_type_call.update(interface_methods_dict) - # Get the methods that are defined in the scope of the composite class and override any previous definition + # Get the methods that are defined in the scope of the composite + # class and override any previous definition ########## - # python@2.7: cls_method = {name: method for name, method in inspect.getmembers(cls, predicate=inspect.ismethod)} + # python@2.7: cls_method = {name: method for name, method in + # inspect.getmembers(cls, predicate=inspect.ismethod)} cls_method = {} - for name, method in inspect.getmembers(cls, predicate=inspect.ismethod): + for name, method in inspect.getmembers(cls, predicate=inspect.ismethod): # NOQA: ignore=E501 cls_method[name] = method ########## dictionary_for_type_call.update(cls_method) # Generate the new class on the fly and return it # FIXME : inherit from interface if we start to use ABC classes? - wrapper_class = type(cls.__name__, (cls, container), dictionary_for_type_call) + wrapper_class = type(cls.__name__, (cls, container), + dictionary_for_type_call) return wrapper_class return cls_decorator @@ -118,5 +133,6 @@ def getter(*args, **kwargs): class Bunch(object): """Carries a bunch of named attributes (from Alex Martelli bunch)""" + def __init__(self, **kwargs): self.__dict__.update(kwargs) From 55c4a676ad67c9ccaacbf5a4f315cc70b32ece6b Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 5 Jul 2016 14:30:48 +0200 Subject: [PATCH 017/126] gts : added package --- .../repos/builtin/packages/gts/package.py | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gts/package.py diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py new file mode 100644 index 00000000000..2b3d4dd4f81 --- /dev/null +++ b/var/spack/repos/builtin/packages/gts/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Gts(Package): + """GTS stands for the GNU Triangulated Surface Library. + + It is an Open Source Free Software Library intended to provide a set of + useful functions to deal with 3D surfaces meshed with interconnected + triangles. The source code is available free of charge under the Free + Software LGPL license. + + The code is written entirely in C with an object-oriented approach + based mostly on the design of GTK+. Careful attention is paid to + performance related issues as the initial goal of GTS is to provide a + simple and efficient library to scientists dealing with 3D computational + surface meshes. + """ + + homepage = "http://gts.sourceforge.net/index.html" + url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz" + + version('121130', '023ebb6b13b8707534182a3ef0d12908') + + depends_on('glib') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') From 379f23be02ea9213e726376c9f644c92668c7985 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 6 Jul 2016 17:51:46 +0200 Subject: [PATCH 018/126] swiftsim : fixed configuration for metis --- var/spack/repos/builtin/packages/swiftsim/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index 42e8fb466a0..f8bb91acd90 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -71,6 +71,7 @@ def install(self, spec, prefix): # Configure and install options = ['--prefix=%s' % prefix, '--enable-mpi' if '+mpi' in spec else '--disable-mpi', + '--with-metis={0}'.format(spec['metis'].prefix), '--enable-optimization'] configure(*options) make() From fb6d850637fd1399232a08f27d63da318eb474d2 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Thu, 7 Jul 2016 13:09:08 +0100 Subject: [PATCH 019/126] Add more python versions --- var/spack/repos/builtin/packages/python/package.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d0191335855..524f42633aa 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -38,9 +38,15 @@ class Python(Package): homepage = "http://www.python.org" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" + version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72') version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') - version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) + version('3.4.3', '4281ff86778db65892c05151d5de738d') + version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9') + version('3.2.6', '23815d82ae706e9b781ca65865353d39') + version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab') + version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True) + version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b') version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') From 8c1274bbbbc25f18bcfea4850bbf49db1b86ca47 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Thu, 7 Jul 2016 13:12:43 +0100 Subject: [PATCH 020/126] Fix Python configure arguments for ucs4 variant on Python 3.0 and above --- var/spack/repos/builtin/packages/python/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 524f42633aa..ce5377483dd 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -53,7 +53,7 @@ class Python(Package): extendable = True - variant('ucs4', default=False, description='Enable UCS4 unicode strings') + variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') depends_on("openssl") depends_on("bzip2") @@ -91,7 +91,10 @@ def install(self, spec, prefix): ] if '+ucs4' in spec: - config_args.append('--enable-unicode=ucs4') + if spec.satisfies('@:3.0'): + config_args.append('--enable-unicode=ucs4') + elif spec.satisfies('@3.0:3.2'): + config_args.append('--with-wide-unicode') if spec.satisfies('@3:'): config_args.append('--without-ensurepip') From 719b6bfffddb1e99606f5cfc71ec6b70e2ea08e7 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Thu, 7 Jul 2016 13:18:40 +0100 Subject: [PATCH 021/126] Modify range for ucs4 2.* configure arguments --- var/spack/repos/builtin/packages/python/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index ce5377483dd..735b8c90996 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -91,7 +91,7 @@ def install(self, spec, prefix): ] if '+ucs4' in spec: - if spec.satisfies('@:3.0'): + if spec.satisfies('@:2.7'): config_args.append('--enable-unicode=ucs4') elif spec.satisfies('@3.0:3.2'): config_args.append('--with-wide-unicode') From a2be05f24bd3c3e378dcdf4c336fb9c6c0058672 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Thu, 7 Jul 2016 14:00:37 +0100 Subject: [PATCH 022/126] Fix whitespace --- var/spack/repos/builtin/packages/python/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 735b8c90996..4ef9ec5b4f3 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -94,7 +94,7 @@ def install(self, spec, prefix): if spec.satisfies('@:2.7'): config_args.append('--enable-unicode=ucs4') elif spec.satisfies('@3.0:3.2'): - config_args.append('--with-wide-unicode') + config_args.append('--with-wide-unicode') if spec.satisfies('@3:'): config_args.append('--without-ensurepip') From 4c1b53660d019e1671a0dc22817276558089f618 Mon Sep 17 00:00:00 2001 From: Nicolas Richart Date: Thu, 7 Jul 2016 18:18:01 +0200 Subject: [PATCH 023/126] fixes #719 --- var/spack/repos/builtin/packages/py-numpy/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index e9672b7bb0b..8cf8c7ae0b3 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -63,6 +63,7 @@ def install(self, spec, prefix): f.write('[DEFAULT]\n') f.write('libraries=%s\n' % ','.join(libraries)) f.write('library_dirs=%s\n' % ':'.join(library_dirs)) + f.write('rpath=%s\n' % ':'.join(library_dirs)) python('setup.py', 'install', '--prefix=%s' % prefix) From d339f2af292a46401449395c81a87a37203b5061 Mon Sep 17 00:00:00 2001 From: Nicolas Richart Date: Thu, 7 Jul 2016 18:22:27 +0200 Subject: [PATCH 024/126] flake8 corrections --- var/spack/repos/builtin/packages/py-numpy/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 8cf8c7ae0b3..86118e682cf 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyNumpy(Package): """NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, @@ -38,7 +39,6 @@ class PyNumpy(Package): version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') version('1.9.1', '78842b73560ec378142665e712ae4ad9') - variant('blas', default=True) variant('lapack', default=True) @@ -66,4 +66,3 @@ def install(self, spec, prefix): f.write('rpath=%s\n' % ':'.join(library_dirs)) python('setup.py', 'install', '--prefix=%s' % prefix) - From 49e8e4b590e964a370c4c683113d0ba199c549ac Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Fri, 8 Jul 2016 13:47:25 +0100 Subject: [PATCH 025/126] Add comments explaining UCS4 and prevent variant being used on Python 3.3 and above --- var/spack/repos/builtin/packages/python/package.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 4ef9ec5b4f3..6018eeb6f8a 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -54,6 +54,13 @@ class Python(Package): extendable = True variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') + # From https://docs.python.org/2/c-api/unicode.html: Python's default + # builds use a 16-bit type for Py_UNICODE and store Unicode values + # internally as UCS2. It is also possible to build a UCS4 version of Python + # (most recent Linux distributions come with UCS4 builds of Python). These + # builds then use a 32-bit type for Py_UNICODE and store Unicode data + # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary + # compatible. depends_on("openssl") depends_on("bzip2") @@ -95,6 +102,9 @@ def install(self, spec, prefix): config_args.append('--enable-unicode=ucs4') elif spec.satisfies('@3.0:3.2'): config_args.append('--with-wide-unicode') + elif spec.satisfies('@3.3:'): + # https://docs.python.org/3.3/whatsnew/3.3.html + raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501 if spec.satisfies('@3:'): config_args.append('--without-ensurepip') From 7551e4c14f2f88c00f147684b01a72a69e3ecce5 Mon Sep 17 00:00:00 2001 From: Geoffrey Oxberry Date: Sun, 10 Jul 2016 18:02:51 -0700 Subject: [PATCH 026/126] cmake@3.6.0 Add CMake version 3.6.0. --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 7b2a125fe50..d7c8f646a0a 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -30,6 +30,7 @@ class Cmake(Package): homepage = 'https://www.cmake.org' url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' + version('3.6.0', 'aa40fbecf49d99c083415c2411d12db9') version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02') version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') From fbaff33f3f5cf9b3fdd7dfa95b965bd33b6d17fb Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Mon, 11 Jul 2016 09:44:20 -0700 Subject: [PATCH 027/126] Typo: verison -> version --- lib/spack/spack/cmd/setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py index 02e9bfd2811..04f3d663df5 100644 --- a/lib/spack/spack/cmd/setup.py +++ b/lib/spack/spack/cmd/setup.py @@ -44,7 +44,7 @@ def setup_parser(subparser): help="Display verbose build output while installing.") subparser.add_argument( 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. Must contain package AND verison.") + help="specs to use for install. Must contain package AND version.") def setup(self, args): From b7d9b58cc5de8a36d43cc082cac0e1ccb6e05f74 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Tue, 12 Jul 2016 19:54:44 +0200 Subject: [PATCH 028/126] Fix preferred providers. --- lib/spack/spack/preferred_packages.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index 48205841501..e873fa3c7ee 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -41,7 +41,7 @@ def _order_for_package(self, pkgname, component, second_key, test_all=True): pkglist.append('all') for pkg in pkglist: order = self.preferred.get(pkg, {}).get(component, {}) - if type(order) is dict: + if isinstance(order, dict) and second_key: order = order.get(second_key, {}) if not order: continue @@ -89,9 +89,9 @@ def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, # a and b are considered to match entries in the sorting list if they # satisfy the list component. def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key): - if not a or not a.concrete: + if not a or (not a.concrete and not second_key): return -1 - if not b or not b.concrete: + if not b or (not b.concrete and not second_key): return 1 specs = self._spec_for_pkgname(pkgname, component, second_key) a_index = None From 52ca215e2947f7fe5c5248ccbd5e4fa19c8536fd Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 13 Jul 2016 10:50:57 +0200 Subject: [PATCH 029/126] mkl: add provide blas/lapack --- .../repos/builtin/packages/mkl/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py index 454e78d29ca..889851c9530 100644 --- a/var/spack/repos/builtin/packages/mkl/package.py +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -18,6 +18,11 @@ class Mkl(IntelInstaller): version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34', url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd()) + # virtual dependency + provides('blas') + provides('lapack') + # TODO: MKL also provides implementation of Scalapack. + def install(self, spec, prefix): self.intel_prefix = os.path.join(prefix, "pkg") @@ -26,3 +31,21 @@ def install(self, spec, prefix): mkl_dir = os.path.join(self.intel_prefix, "mkl") for f in os.listdir(mkl_dir): os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f)) + + def setup_dependent_package(self, module, dspec): + # For now use Single Dynamic Library: + # To set the threading layer at run time, use the + # mkl_set_threading_layer function or set MKL_THREADING_LAYER + # variable to one of the following values: INTEL, SEQUENTIAL, PGI. + # To set interface layer at run time, use the mkl_set_interface_layer + # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64. + + # Otherwise one would need to specify several libraries + # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect + # different interface and threading layers. + + name = 'libmkl_rt.%s' % dso_suffix + libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib) + + self.spec.blas_shared_lib = join_path(libdir, name) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib From 0e2afedb7fa8286aeb019154b6a5f0085e78b155 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 13 Jul 2016 12:43:48 +0200 Subject: [PATCH 030/126] doc : fixes #1239 --- lib/spack/docs/packaging_guide.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 0f549e2957e..861a35c1544 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -2602,14 +2602,14 @@ Spack packages with variants similar to already-existing Spack packages should use the same name for their variants. Standard variant names are: -======= ======== ======================== -Name Default Description -------- -------- ------------------------ -shared True Build shared libraries -static Build static libraries -mpi Use MPI -python Build Python extension -------- -------- ------------------------ + ======= ======== ======================== + Name Default Description + ======= ======== ======================== + shared True Build shared libraries + static None Build static libraries + mpi None Use MPI + python None Build Python extension + ======= ======== ======================== If specified in this table, the corresponding default should be used when declaring a variant. From d09b0c95ec587cbb9ac45f6a2a106060dfb38643 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Jul 2016 16:26:55 -0500 Subject: [PATCH 031/126] Filter both makefiles to allow intel to build bzip2 --- var/spack/repos/builtin/packages/bzip2/package.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index 3b6d1d830ee..ea76911dee2 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -39,14 +39,17 @@ class Bzip2(Package): def patch(self): - mf = FileFilter('Makefile-libbz2_so') - mf.filter(r'^CC=gcc', 'CC=cc') + # bzip2 comes with two separate Makefiles for static and dynamic builds + # Tell both to use Spack's compiler wrapper instead of GCC + filter_file(r'^CC=gcc', 'CC=cc', 'Makefile') + filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so') # Below stuff patches the link line to use RPATHs on Mac OS X. if 'darwin' in self.spec.architecture: v = self.spec.version v1, v2, v3 = (v.up_to(i) for i in (1,2,3)) + mf = FileFilter('Makefile-libbz2_so') mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), string=True) @@ -59,8 +62,10 @@ def patch(self): def install(self, spec, prefix): + # Build the dynamic library first make('-f', 'Makefile-libbz2_so') - make('clean') + # Build the static library and everything else + make() make("install", "PREFIX=%s" % prefix) install('bzip2-shared', join_path(prefix.bin, 'bzip2')) From 3864da6300d3f7c99503b3787e2c09882c179a48 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Jul 2016 16:31:47 -0500 Subject: [PATCH 032/126] Flake8 --- .../repos/builtin/packages/bzip2/package.py | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index ea76911dee2..27303293d2e 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -24,59 +24,59 @@ ############################################################################## from spack import * + class Bzip2(Package): """bzip2 is a freely available, patent free high-quality data - compressor. It typically compresses files to within 10% to 15% - of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression - and six times faster at decompression. + compressor. It typically compresses files to within 10% to 15% + of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression + and six times faster at decompression.""" - """ homepage = "http://www.bzip.org" url = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz" version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b') - def patch(self): # bzip2 comes with two separate Makefiles for static and dynamic builds # Tell both to use Spack's compiler wrapper instead of GCC filter_file(r'^CC=gcc', 'CC=cc', 'Makefile') filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so') - # Below stuff patches the link line to use RPATHs on Mac OS X. + # Patch the link line to use RPATHs on macOS if 'darwin' in self.spec.architecture: v = self.spec.version - v1, v2, v3 = (v.up_to(i) for i in (1,2,3)) + v1, v2, v3 = (v.up_to(i) for i in (1, 2, 3)) + + kwargs = {'ignore_absent': False, 'backup': False, 'string': True} mf = FileFilter('Makefile-libbz2_so') - mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), - '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), string=True) + mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), # NOQA ignore=E501 + '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), **kwargs) # NOQA ignore=E501 - mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), - '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), string=True) + mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), # NOQA ignore=E501 + '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), **kwargs) # NOQA ignore=E501 mf.filter('rm -f libbz2.so.{0}'.format(v2), - 'rm -f libbz2.{0}.dylib'.format(v2), string=True) + 'rm -f libbz2.{0}.dylib'.format(v2), **kwargs) mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2), - 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), string=True) - + 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), **kwargs) # NOQA ignore=E501 def install(self, spec, prefix): # Build the dynamic library first make('-f', 'Makefile-libbz2_so') # Build the static library and everything else make() - make("install", "PREFIX=%s" % prefix) + make('install', 'PREFIX={0}'.format(prefix)) install('bzip2-shared', join_path(prefix.bin, 'bzip2')) - v1, v2, v3 = (self.spec.version.up_to(i) for i in (1,2,3)) + v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3)) if 'darwin' in self.spec.architecture: lib = 'libbz2.dylib' - lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3)) + lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 else: lib = 'libbz2.so' - lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3)) + lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 install(lib3, join_path(prefix.lib, lib3)) with working_dir(prefix.lib): From fcfe2618d50b39e8991685dc2f42f1495951da7e Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 13 Jul 2016 20:33:14 +0200 Subject: [PATCH 033/126] Improve shell integration. Enable sh emulation for Zsh and allow loading modules recursively. --- share/spack/setup-env.sh | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 8aa259cf159..c5245add5e5 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -57,6 +57,11 @@ ######################################################################## function spack { + # Zsh does not do word splitting by default, this enables it for this function only + if [ -n "$ZSH_VERSION" ]; then + emulate -L sh + fi + # save raw arguments into an array before butchering them args=( "$@" ) @@ -93,11 +98,18 @@ function spack { ;; "use"|"unuse"|"load"|"unload") # Shift any other args for use off before parsing spec. + _sp_subcommand_args="" _sp_module_args="" - if [[ "$1" =~ ^- ]]; then - _sp_module_args="$1"; shift - _sp_spec="$@" - fi + while [[ "$1" =~ ^- ]]; do + if [ "$1" = "-r" ]; then + _sp_subcommand_args="$_sp_subcommand_args $1" + else + _sp_module_args="$_sp_module_args $1" + fi + shift + done + + _sp_spec="$@" # Here the user has run use or unuse with a spec. Find a matching # spec using 'spack module find', then use the appropriate module @@ -105,19 +117,19 @@ function spack { # If spack module command comes back with an error, do nothing. case $_sp_subcommand in "use") - if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args dotkit $_sp_spec); then use $_sp_module_args $_sp_full_spec fi ;; "unuse") - if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args dotkit $_sp_spec); then unuse $_sp_module_args $_sp_full_spec fi ;; "load") - if _sp_full_spec=$(command spack $_sp_flags module find tcl $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args tcl $_sp_spec); then module load $_sp_module_args $_sp_full_spec fi ;; "unload") - if _sp_full_spec=$(command spack $_sp_flags module find tcl $_sp_spec); then + if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args tcl $_sp_spec); then module unload $_sp_module_args $_sp_full_spec fi ;; esac From 5ffc50732bdcfca325115e23d359612426f38854 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Wed, 13 Jul 2016 23:05:08 +0200 Subject: [PATCH 034/126] flake8 fixes --- lib/spack/spack/preferred_packages.py | 99 +++++++++++++++------------ 1 file changed, 56 insertions(+), 43 deletions(-) diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index e873fa3c7ee..1b94f03de7f 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -26,8 +26,10 @@ import spack from spack.version import * + class PreferredPackages(object): - _default_order = {'compiler' : [ 'gcc', 'intel', 'clang', 'pgi', 'xlc' ] } # Arbitrary, but consistent + # Arbitrary, but consistent + _default_order = {'compiler': ['gcc', 'intel', 'clang', 'pgi', 'xlc']} def __init__(self): self.preferred = spack.config.get_config('packages') @@ -35,7 +37,8 @@ def __init__(self): # Given a package name, sort component (e.g, version, compiler, ...), and # a second_key (used by providers), return the list - def _order_for_package(self, pkgname, component, second_key, test_all=True): + def _order_for_package(self, pkgname, component, second_key, + test_all=True): pkglist = [pkgname] if test_all: pkglist.append('all') @@ -48,11 +51,11 @@ def _order_for_package(self, pkgname, component, second_key, test_all=True): return [str(s).strip() for s in order] return [] - # A generic sorting function. Given a package name and sort # component, return less-than-0, 0, or greater-than-0 if # a is respectively less-than, equal to, or greater than b. - def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key): + def _component_compare(self, pkgname, component, a, b, + reverse_natural_compare, second_key): if a is None: return -1 if b is None: @@ -84,11 +87,11 @@ def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, else: return 0 - # A sorting function for specs. Similar to component_compare, but # a and b are considered to match entries in the sorting list if they # satisfy the list component. - def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key): + def _spec_compare(self, pkgname, component, a, b, + reverse_natural_compare, second_key): if not a or (not a.concrete and not second_key): return -1 if not b or (not b.concrete and not second_key): @@ -98,78 +101,88 @@ def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, secon b_index = None reverse = -1 if reverse_natural_compare else 1 for i, cspec in enumerate(specs): - if a_index == None and (cspec.satisfies(a) or a.satisfies(cspec)): + if a_index is None and (cspec.satisfies(a) or a.satisfies(cspec)): a_index = i if b_index: break - if b_index == None and (cspec.satisfies(b) or b.satisfies(cspec)): + if b_index is None and (cspec.satisfies(b) or b.satisfies(cspec)): b_index = i if a_index: break - if a_index != None and b_index == None: return -1 - elif a_index == None and b_index != None: return 1 - elif a_index != None and b_index == a_index: return -1 * cmp(a, b) - elif a_index != None and b_index != None and a_index != b_index: return cmp(a_index, b_index) - else: return cmp(a, b) * reverse - - + if a_index is not None and b_index is None: + return -1 + elif a_index is None and b_index is not None: + return 1 + elif a_index is not None and b_index == a_index: + return -1 * cmp(a, b) + elif (a_index is not None and b_index is not None and + a_index != b_index): + return cmp(a_index, b_index) + else: + return cmp(a, b) * reverse # Given a sort order specified by the pkgname/component/second_key, return # a list of CompilerSpecs, VersionLists, or Specs for that sorting list. def _spec_for_pkgname(self, pkgname, component, second_key): key = (pkgname, component, second_key) - if not key in self._spec_for_pkgname_cache: + if key not in self._spec_for_pkgname_cache: pkglist = self._order_for_package(pkgname, component, second_key) if not pkglist: if component in self._default_order: pkglist = self._default_order[component] if component == 'compiler': - self._spec_for_pkgname_cache[key] = [spack.spec.CompilerSpec(s) for s in pkglist] + self._spec_for_pkgname_cache[key] = \ + [spack.spec.CompilerSpec(s) for s in pkglist] elif component == 'version': - self._spec_for_pkgname_cache[key] = [VersionList(s) for s in pkglist] + self._spec_for_pkgname_cache[key] = \ + [VersionList(s) for s in pkglist] else: - self._spec_for_pkgname_cache[key] = [spack.spec.Spec(s) for s in pkglist] + self._spec_for_pkgname_cache[key] = \ + [spack.spec.Spec(s) for s in pkglist] return self._spec_for_pkgname_cache[key] - def provider_compare(self, pkgname, provider_str, a, b): - """Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or - greater-than b. A and b are possible implementations of provider_str. - One provider is less-than another if it is preferred over the other. - For example, provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would return -1 if - mvapich should be preferred over openmpi for scorep.""" - return self._spec_compare(pkgname, 'providers', a, b, False, provider_str) - + """Return less-than-0, 0, or greater than 0 if a is respecively + less-than, equal-to, or greater-than b. A and b are possible + implementations of provider_str. One provider is less-than another + if it is preferred over the other. For example, + provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would + return -1 if mvapich should be preferred over openmpi for scorep.""" + return self._spec_compare(pkgname, 'providers', a, b, False, + provider_str) def spec_has_preferred_provider(self, pkgname, provider_str): - """Return True iff the named package has a list of preferred provider""" - return bool(self._order_for_package(pkgname, 'providers', provider_str, False)) - + """Return True iff the named package has a list of preferred + providers""" + return bool(self._order_for_package(pkgname, 'providers', + provider_str, False)) def version_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if version a of pkgname is - respecively less-than, equal-to, or greater-than version b of pkgname. - One version is less-than another if it is preferred over the other.""" + respectively less-than, equal-to, or greater-than version b of + pkgname. One version is less-than another if it is preferred over + the other.""" return self._spec_compare(pkgname, 'version', a, b, True, None) - def variant_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if variant a of pkgname is - respecively less-than, equal-to, or greater-than variant b of pkgname. - One variant is less-than another if it is preferred over the other.""" + respectively less-than, equal-to, or greater-than variant b of + pkgname. One variant is less-than another if it is preferred over + the other.""" return self._component_compare(pkgname, 'variant', a, b, False, None) - def architecture_compare(self, pkgname, a, b): - """Return less-than-0, 0, or greater than 0 if architecture a of pkgname is - respecively less-than, equal-to, or greater-than architecture b of pkgname. - One architecture is less-than another if it is preferred over the other.""" - return self._component_compare(pkgname, 'architecture', a, b, False, None) - + """Return less-than-0, 0, or greater than 0 if architecture a of pkgname + is respectively less-than, equal-to, or greater-than architecture b + of pkgname. One architecture is less-than another if it is preferred + over the other.""" + return self._component_compare(pkgname, 'architecture', a, b, + False, None) def compiler_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if compiler a of pkgname is - respecively less-than, equal-to, or greater-than compiler b of pkgname. - One compiler is less-than another if it is preferred over the other.""" + respecively less-than, equal-to, or greater-than compiler b of + pkgname. One compiler is less-than another if it is preferred over + the other.""" return self._spec_compare(pkgname, 'compiler', a, b, False, None) From 668b4f1b2ce8e61457309d67b798e58ef481a08e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 13 Jul 2016 23:36:23 +0200 Subject: [PATCH 035/126] mkl: set MKLROOT --- var/spack/repos/builtin/packages/mkl/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py index 889851c9530..f1f07c90f5e 100644 --- a/var/spack/repos/builtin/packages/mkl/package.py +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -49,3 +49,10 @@ def setup_dependent_package(self, module, dspec): self.spec.blas_shared_lib = join_path(libdir, name) self.spec.lapack_shared_lib = self.spec.blas_shared_lib + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up MKLROOT for everyone using MKL package + spack_env.set('MKLROOT', self.prefix) + + def setup_environment(self, spack_env, env): + env.set('MKLROOT', self.prefix) From e052aaf44d5af53cdcb5e4afa3ed09eed14b38b1 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 14 Jul 2016 08:19:32 -0700 Subject: [PATCH 036/126] Minor typo fix the packages that depends on => the packages that depend on --- lib/spack/docs/basic_usage.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index dbad0a9f6d2..cde13e7417d 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -2,7 +2,7 @@ Basic usage ===================== - +p The ``spack`` command has many *subcommands*. You'll only need a small subset of them for typical usage. @@ -183,7 +183,7 @@ To uninstall a package and every package that depends on it, you may give the spack uninstall --dependents mpich -will display a list of all the packages that depends on `mpich` and, upon confirmation, +will display a list of all the packages that depend on `mpich` and, upon confirmation, will uninstall them in the right order. A line like From 3051c3d71d9d7bf0422d2b33a173e5db1ec42ab3 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 14 Jul 2016 08:31:07 -0700 Subject: [PATCH 037/126] Fix format of explanation of an example & question This list was not formatted correctly on [the ReadTheDocs site](http://software.llnl.gov/spack/basic_usage.html#specs-dependencies). I'm not a .rst expert, but I think that it was improperly indented. The example includes an `arch=...` string but *arch* is not listed in the valid compiler flag specifiers or architecture specifiers. Should it be, or is it considered an "optional variant specifier? --- lib/spack/docs/basic_usage.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index dbad0a9f6d2..44052ddbe89 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -543,11 +543,12 @@ More formally, a spec consists of the following pieces: * ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``, ``-qt``, or ``~qt``) for boolean variants * ``name=`` Optional variant specifiers that are not restricted to -boolean variants + boolean variants * ``name=`` Optional compiler flag specifiers. Valid flag names are -``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``. + ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``. * ``target= os=`` Optional architecture specifier -(``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``) + (``target=haswell os=CNL10``) +* ``^`` Dependency specs (``^callpath@1.1``) There are two things to notice here. The first is that specs are recursively defined. That is, each dependency after ``^`` is a spec From 3e718920d1fd981e732658ce1e36010e6e5c05fc Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 14 Jul 2016 09:40:47 -0700 Subject: [PATCH 038/126] Remove extraneous letter 'p' It got in there by mistake, now it's gone. --- lib/spack/docs/basic_usage.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index cde13e7417d..90ba1164e64 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -2,7 +2,7 @@ Basic usage ===================== -p + The ``spack`` command has many *subcommands*. You'll only need a small subset of them for typical usage. From 64d91943ec3773a539ef39be4e9ab5ab132df01a Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 14 Jul 2016 20:14:06 +0200 Subject: [PATCH 039/126] Support --dependencies for recursively loading modules. --- share/spack/setup-env.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index c5245add5e5..19206255db0 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -101,7 +101,7 @@ function spack { _sp_subcommand_args="" _sp_module_args="" while [[ "$1" =~ ^- ]]; do - if [ "$1" = "-r" ]; then + if [ "$1" = "-r" -o "$1" = "--dependencies" ]; then _sp_subcommand_args="$_sp_subcommand_args $1" else _sp_module_args="$_sp_module_args $1" From e275b567eb5b830897e726d90a0d0d56b080b705 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 19 Jan 2016 17:05:57 -0500 Subject: [PATCH 040/126] typos: fix some typos --- lib/spack/spack/package.py | 6 +++--- lib/spack/spack/spec.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 74008c4dd98..f44b2358909 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -644,10 +644,10 @@ def preorder_traversal(self, visited=None, **kwargs): for name in sorted(self.dependencies.keys()): spec = self.dependencies[name] - # currently, we do not descend into virtual dependencies, as this + # Currently, we do not descend into virtual dependencies, as this # makes doing a sensible traversal much harder. We just assume # that ANY of the virtual deps will work, which might not be true - # (due to conflicts or unsatisfiable specs). For now this is ok + # (due to conflicts or unsatisfiable specs). For now this is ok, # but we might want to reinvestigate if we start using a lot of # complicated virtual dependencies # TODO: reinvestigate this. @@ -1270,7 +1270,7 @@ def _sanity_check_extension(self): (self.name, self.extendee.name)) def do_activate(self, force=False): - """Called on an etension to invoke the extendee's activate method. + """Called on an extension to invoke the extendee's activate method. Commands should call this routine, and should not call activate() directly. diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 77bc57147d5..f55dad3c51d 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -1790,7 +1790,7 @@ def __getitem__(self, name): raise KeyError("No spec with name %s in %s" % (name, self)) def __contains__(self, spec): - """True if this spec satisfis the provided spec, or if any dependency + """True if this spec satisfies the provided spec, or if any dependency does. If the spec has no name, then we parse this one first. """ spec = self._autospec(spec) From b4682c8ca3a1a7b5898c0298cdc3bf2089652779 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 10 Mar 2016 09:44:58 -0500 Subject: [PATCH 041/126] directory_layout: fix error path when specs conflict --- lib/spack/spack/directory_layout.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index ee13e2dcbcb..a5e76043ada 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -285,7 +285,7 @@ def check_installed(self, spec): return path if spec.dag_hash() == installed_spec.dag_hash(): - raise SpecHashCollisionError(installed_hash, spec_hash) + raise SpecHashCollisionError(spec, installed_spec) else: raise InconsistentInstallDirectoryError( 'Spec file in %s does not match hash!' % spec_file_path) @@ -431,7 +431,7 @@ class SpecHashCollisionError(DirectoryLayoutError): def __init__(self, installed_spec, new_spec): super(SpecHashCollisionError, self).__init__( 'Specs %s and %s have the same SHA-1 prefix!' - % installed_spec, new_spec) + % (installed_spec, new_spec)) class RemoveFailedError(DirectoryLayoutError): From 6d2ec9baf7e91cde471cc9b542c8056bb7c65250 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 4 Feb 2016 14:30:23 -0500 Subject: [PATCH 042/126] test/stage: use os.path.realpath on the test paths When var/spack/stage is a symlink, the tests fail since realpath is used on the resulting path, but not the original path, so the string compare fails. Smarter path testing might be a better option. --- lib/spack/spack/test/stage.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index 6d8c3ac67c6..d3e3bf1383d 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -35,8 +35,8 @@ from spack.stage import Stage from spack.util.executable import which -test_files_dir = join_path(spack.stage_path, '.test') -test_tmp_path = join_path(test_files_dir, 'tmp') +test_files_dir = os.path.realpath(join_path(spack.stage_path, '.test')) +test_tmp_path = os.path.realpath(join_path(test_files_dir, 'tmp')) archive_dir = 'test-files' archive_name = archive_dir + '.tar.gz' From 1ae43b34058223d16ffe3ecd0c4bb6caf006197c Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 14:32:07 -0400 Subject: [PATCH 043/126] doxygen: add missing import --- var/spack/repos/builtin/packages/doxygen/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index b2e9582b5a9..b65eafb2cd9 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -24,6 +24,8 @@ ############################################################################## from spack import * +import sys + class Doxygen(Package): """Doxygen is the de facto standard tool for generating documentation From bdf82246f7569ea655544743eecb0d5ecf059626 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 4 Apr 2016 11:38:58 -0400 Subject: [PATCH 044/126] darwin: explicitly use the 'when=' kwarg --- var/spack/repos/builtin/packages/glib/package.py | 2 +- var/spack/repos/builtin/packages/numdiff/package.py | 2 +- var/spack/repos/builtin/packages/octave/package.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 342a61a6a1b..75602493ce2 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -39,7 +39,7 @@ class Glib(Package): depends_on("libffi") depends_on("zlib") depends_on("pkg-config") - depends_on('gettext', sys.platform == 'darwin') + depends_on('gettext', when=sys.platform == 'darwin') # The following patch is needed for gcc-6.1 patch('g_date_strftime.patch') diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index e15d60cb0b7..7e094370ac6 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -35,7 +35,7 @@ class Numdiff(Package): version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') - depends_on('gettext', sys.platform=='darwin') + depends_on('gettext', when=sys.platform=='darwin') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 6535f528eee..1e835512ca7 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -68,7 +68,7 @@ class Octave(Package): depends_on('blas') depends_on('lapack') # Octave does not configure with sed from darwin: - depends_on('sed', sys.platform == 'darwin') + depends_on('sed', when=sys.platform == 'darwin') depends_on('pcre') depends_on('pkg-config') From bae97d17d0adc6aac0083f2686c0121a3819fab3 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 17 Feb 2016 09:50:43 -0500 Subject: [PATCH 045/126] test: use file:// url for git repos --- lib/spack/spack/test/mock_repo.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py index a8098b8eecd..386af282e71 100644 --- a/lib/spack/spack/test/mock_repo.py +++ b/lib/spack/spack/test/mock_repo.py @@ -103,6 +103,8 @@ class MockGitRepo(MockVCSRepo): def __init__(self): super(MockGitRepo, self).__init__('mock-git-stage', 'mock-git-repo') + self.url = 'file://' + self.path + with working_dir(self.path): git('init') @@ -140,8 +142,6 @@ def __init__(self): self.r1 = self.rev_hash(self.branch) self.r1_file = self.branch_file - self.url = self.path - def rev_hash(self, rev): return git('rev-parse', rev, output=str).strip() From 45c675fe7ff69408e4f407a9c5eb8f92f746faf8 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 25 Jan 2016 10:26:35 -0500 Subject: [PATCH 046/126] spack: introduce dependency types deptypes: allow for different queries For things like Python modules, they are required for the build and runtime, but rather than adding a new parameter for what to query across the dependency DAG, just expose the recursive query parameter. --- lib/spack/docs/packaging_guide.rst | 25 ++ lib/spack/spack/__init__.py | 3 +- lib/spack/spack/build_environment.py | 14 +- lib/spack/spack/cmd/fetch.py | 2 +- lib/spack/spack/cmd/info.py | 14 +- lib/spack/spack/cmd/mirror.py | 2 +- lib/spack/spack/cmd/module.py | 2 +- lib/spack/spack/cmd/package-list.py | 14 +- lib/spack/spack/cmd/test-install.py | 7 +- lib/spack/spack/concretize.py | 10 +- lib/spack/spack/database.py | 22 +- lib/spack/spack/directives.py | 39 +- lib/spack/spack/graph.py | 10 +- lib/spack/spack/modules.py | 2 +- lib/spack/spack/package.py | 20 +- lib/spack/spack/spec.py | 348 +++++++++++++----- lib/spack/spack/test/cmd/test_install.py | 33 +- lib/spack/spack/test/concretize.py | 24 +- lib/spack/spack/test/mock_packages_test.py | 8 +- lib/spack/spack/test/spec_dag.py | 88 ++++- .../packages/cmake-client/package.py | 2 +- .../builtin.mock/packages/dtbuild1/package.py | 18 + .../builtin.mock/packages/dtbuild2/package.py | 13 + .../builtin.mock/packages/dtbuild3/package.py | 13 + .../builtin.mock/packages/dtlink1/package.py | 15 + .../builtin.mock/packages/dtlink2/package.py | 13 + .../builtin.mock/packages/dtlink3/package.py | 16 + .../builtin.mock/packages/dtlink4/package.py | 13 + .../builtin.mock/packages/dtlink5/package.py | 13 + .../builtin.mock/packages/dtrun1/package.py | 16 + .../builtin.mock/packages/dtrun2/package.py | 13 + .../builtin.mock/packages/dtrun3/package.py | 15 + .../builtin.mock/packages/dttop/package.py | 17 + .../builtin.mock/packages/dtuse/package.py | 15 + 34 files changed, 697 insertions(+), 182 deletions(-) create mode 100644 var/spack/repos/builtin.mock/packages/dtbuild1/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtbuild2/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtbuild3/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtlink1/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtlink2/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtlink3/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtlink4/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtlink5/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtrun1/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtrun2/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtrun3/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dttop/package.py create mode 100644 var/spack/repos/builtin.mock/packages/dtuse/package.py diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 0f549e2957e..a0d0feabbd3 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1286,6 +1286,31 @@ command line to find installed packages or to install packages with particular constraints, and package authors can use specs to describe relationships between packages. +Additionally, dependencies may be specified for specific use cases: + +.. code-block:: python + + depends_on("cmake", type="build") + depends_on("libelf", type=("build", "link")) + depends_on("python", type="run") + +The dependency types are: + + * **"build"**: made available during the project's build. The package will + be added to ``PATH``, the compiler include paths, and ``PYTHONPATH``. + Other projects which depend on this one will not have these modified + (building project X doesn't need project Y's build dependencies). + * **"link"**: the project is linked to by the project. The package will be + added to the current package's ``rpath``. + * **"run"**: the project is used by the project at runtime. The package will + be added to ``PATH`` and ``PYTHONPATH``. + +If not specified, ``type`` is assumed to be ``("build", "link")``. This is the +common case for compiled language usage. Also available are the aliases +``alldeps`` for all dependency types and ``nolink`` (``("build", "run")``) for +use by dependencies which are not expressed via a linker (e.g., Python or Lua +module loading). + .. _setup-dependent-environment: ``setup_dependent_environment()`` diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 20c9934704c..d67585aac49 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -177,10 +177,11 @@ # should live. This file is overloaded for spack core vs. for packages. # __all__ = ['Package', 'StagedPackage', 'CMakePackage', \ - 'Version', 'when', 'ver'] + 'Version', 'when', 'ver', 'alldeps', 'nolink'] from spack.package import Package, ExtensionConflictError from spack.package import StagedPackage, CMakePackage from spack.version import Version, ver +from spack.spec import DependencySpec, alldeps, nolink from spack.multimethod import when import llnl.util.filesystem diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index fe5186a7d7f..93fb0690f7f 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -254,7 +254,8 @@ def set_build_environment_variables(pkg, env, dirty=False): env.set_path(SPACK_ENV_PATH, env_paths) # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES - dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] + dep_prefixes = [d.prefix + for d in pkg.spec.traverse(root=False, deptype='build')] env.set_path(SPACK_DEPENDENCIES, dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) @@ -337,10 +338,6 @@ def set_module_variables_for_package(pkg, module): # Don't use which for this; we want to find it in the current dir. m.configure = Executable('./configure') - # TODO: shouldn't really use "which" here. Consider adding notion - # TODO: of build dependencies, as opposed to link dependencies. - # TODO: Currently, everything is a link dependency, but tools like - # TODO: this shouldn't be. m.cmake = Executable('cmake') m.ctest = Executable('ctest') @@ -388,9 +385,10 @@ def set_module_variables_for_package(pkg, module): def get_rpaths(pkg): """Get a list of all the rpaths for a package.""" rpaths = [pkg.prefix.lib, pkg.prefix.lib64] - rpaths.extend(d.prefix.lib for d in pkg.spec.dependencies.values() + deps = pkg.spec.dependencies(deptype='link') + rpaths.extend(d.prefix.lib for d in deps if os.path.isdir(d.prefix.lib)) - rpaths.extend(d.prefix.lib64 for d in pkg.spec.dependencies.values() + rpaths.extend(d.prefix.lib64 for d in deps if os.path.isdir(d.prefix.lib64)) # Second module is our compiler mod name. We use that to get rpaths from # module show output. @@ -449,7 +447,7 @@ def setup_package(pkg, dirty=False): load_external_modules(pkg) # traverse in postorder so package can use vars from its dependencies spec = pkg.spec - for dspec in pkg.spec.traverse(order='post', root=False): + for dspec in pkg.spec.traverse(order='post', root=False, deptype='build'): # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py index e40caaa2347..1afc51d9fae 100644 --- a/lib/spack/spack/cmd/fetch.py +++ b/lib/spack/spack/cmd/fetch.py @@ -51,7 +51,7 @@ def fetch(parser, args): for spec in specs: if args.missing or args.dependencies: to_fetch = set() - for s in spec.traverse(): + for s in spec.traverse(deptype_query=spack.alldeps): package = spack.repo.get(s) if args.missing and package.installed: continue diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py index 64d0d20e243..5774034062c 100644 --- a/lib/spack/spack/cmd/info.py +++ b/lib/spack/spack/cmd/info.py @@ -81,12 +81,14 @@ def print_text_info(pkg): print " " + fmt % (name, default, desc) - print - print "Dependencies:" - if pkg.dependencies: - colify(pkg.dependencies, indent=4) - else: - print " None" + for deptype in ('build', 'link', 'run'): + print + print "%s Dependencies:" % deptype.capitalize() + deps = pkg.dependencies(deptype) + if deps: + colify(deps, indent=4) + else: + print " None" print print "Virtual packages: " diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index d5f7abe212a..0cf682fc4fd 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -179,7 +179,7 @@ def mirror_create(args): new_specs = set() for spec in specs: spec.concretize() - for s in spec.traverse(): + for s in spec.traverse(deptype_query=spack.alldeps): new_specs.add(s) specs = list(new_specs) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 70da689b671..55826d133c2 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -87,7 +87,7 @@ def _find_modules(spec, modules_list): return if flags.recurse_dependencies: - for dep in spec.dependencies.values(): + for dep in spec.dependencies(): _find_modules(dep, modules_list) mod = module_types[mtype](spec) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index 6c5c4ae8c63..bc64c77eab4 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -80,11 +80,15 @@ def print_rst_package_list(): if pkg.versions: print "Versions:" print " " + ", ".join(str(v) for v in reversed(sorted(pkg.versions))) - if pkg.dependencies: - print "Dependencies" - print " " + ", ".join("`%s`_" % d if d != "mpi" else d - for d in pkg.dependencies) - print + + for deptype in ('build', 'link', 'run'): + deps = pkg.dependencies(deptype) + if deps: + print "%s Dependencies" % deptype.capitalize() + print " " + ", ".join("`%s`_" % d if d != "mpi" else d + for d in build_deps) + print + print "Description:" print pkg.format_doc(indent=2) print diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py index 45592a7dda4..14c06d136d5 100644 --- a/lib/spack/spack/cmd/test-install.py +++ b/lib/spack/spack/cmd/test-install.py @@ -133,7 +133,12 @@ def fetch_log(path): def failed_dependencies(spec): - return set(item for item in spec.dependencies.itervalues() if not spack.repo.get(item).installed) + def get_deps(deptype): + return set(item for item in spec.dependencies(deptype) + if not spack.repo.get(item).installed) + link_deps = get_deps('link') + run_deps = get_deps('run') + return link_deps.union(run_deps) def get_top_spec_or_die(args): diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index d9992a56805..386df08b2e5 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -103,7 +103,7 @@ def cmp_externals(a, b): usable.sort(cmp=cmp_externals) return usable - + # XXX(deptypes): Look here. def choose_virtual_or_external(self, spec): """Given a list of candidate virtual and external packages, try to find one that is most ABI compatible. @@ -394,8 +394,10 @@ def find_spec(spec, condition): """Searches the dag from spec in an intelligent order and looks for a spec that matches a condition""" # First search parents, then search children - dagiter = chain(spec.traverse(direction='parents', root=False), - spec.traverse(direction='children', root=False)) + deptype = ('build', 'link') + dagiter = chain( + spec.traverse(direction='parents', deptype=deptype, root=False), + spec.traverse(direction='children', deptype=deptype, root=False)) visited = set() for relative in dagiter: if condition(relative): @@ -403,7 +405,7 @@ def find_spec(spec, condition): visited.add(id(relative)) # Then search all other relatives in the DAG *except* spec - for relative in spec.root.traverse(): + for relative in spec.root.traverse(deptypes=spack.alldeps): if relative is spec: continue if id(relative) in visited: continue if condition(relative): diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index a4bbff3d5a0..c95abd74236 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -215,9 +215,14 @@ def _read_spec_from_yaml(self, hash_key, installs, parent_key=None): # Add dependencies from other records in the install DB to # form a full spec. if 'dependencies' in spec_dict[spec.name]: - for dep_hash in spec_dict[spec.name]['dependencies'].values(): + for dep in spec_dict[spec.name]['dependencies'].values(): + if type(dep) == tuple: + dep_hash, deptypes = dep + else: + dep_hash = dep + deptypes = spack.alldeps child = self._read_spec_from_yaml(dep_hash, installs, hash_key) - spec._add_dependency(child) + spec._add_dependency(child, deptypes) # Specs from the database need to be marked concrete because # they represent actual installations. @@ -334,7 +339,10 @@ def _check_ref_counts(self): counts = {} for key, rec in self._data.items(): counts.setdefault(key, 0) - for dep in rec.spec.dependencies.values(): + # XXX(deptype): This checks all dependencies, but build + # dependencies might be able to be dropped in the + # future. + for dep in rec.spec.dependencies(): dep_key = dep.dag_hash() counts.setdefault(dep_key, 0) counts[dep_key] += 1 @@ -406,7 +414,7 @@ def _add(self, spec, path, directory_layout=None, explicit=False): else: self._data[key] = InstallRecord(spec, path, True, explicit=explicit) - for dep in spec.dependencies.values(): + for dep in spec.dependencies(('link', 'run')): self._increment_ref_count(dep, directory_layout) def _increment_ref_count(self, spec, directory_layout=None): @@ -421,7 +429,7 @@ def _increment_ref_count(self, spec, directory_layout=None): self._data[key] = InstallRecord(spec.copy(), path, installed) - for dep in spec.dependencies.values(): + for dep in spec.dependencies('link'): self._increment_ref_count(dep) self._data[key].ref_count += 1 @@ -466,7 +474,7 @@ def _decrement_ref_count(self, spec): if rec.ref_count == 0 and not rec.installed: del self._data[key] - for dep in spec.dependencies.values(): + for dep in spec.dependencies('link'): self._decrement_ref_count(dep) def _remove(self, spec): @@ -480,7 +488,7 @@ def _remove(self, spec): return rec.spec del self._data[key] - for dep in rec.spec.dependencies.values(): + for dep in rec.spec.dependencies('link'): self._decrement_ref_count(dep) # Returns the concrete spec so we know it in the case where a diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py index ca8f21dc088..88d2aaf4728 100644 --- a/lib/spack/spack/directives.py +++ b/lib/spack/spack/directives.py @@ -171,7 +171,7 @@ def version(pkg, ver, checksum=None, **kwargs): pkg.versions[Version(ver)] = kwargs -def _depends_on(pkg, spec, when=None): +def _depends_on(pkg, spec, when=None, type=None): # If when is False do nothing if when is False: return @@ -180,10 +180,29 @@ def _depends_on(pkg, spec, when=None): when = pkg.name when_spec = parse_anonymous_spec(when, pkg.name) + if type is None: + # The default deptype is build and link because the common case is to + # build against a library which then turns into a runtime dependency + # due to the linker. + # XXX(deptype): Add 'run' to this? It's an uncommon dependency type, + # but is most backwards-compatible. + type = ('build', 'link') + + if isinstance(type, str): + type = (type,) + + for deptype in type: + if deptype not in spack.spec.alldeps: + raise UnknownDependencyTypeError('depends_on', pkg.name, deptype) + dep_spec = Spec(spec) if pkg.name == dep_spec.name: raise CircularReferenceError('depends_on', pkg.name) + pkg_deptypes = pkg._deptypes.setdefault(dep_spec.name, set()) + for deptype in type: + pkg_deptypes.add(deptype) + conditions = pkg.dependencies.setdefault(dep_spec.name, {}) if when_spec in conditions: conditions[when_spec].constrain(dep_spec, deps=False) @@ -191,13 +210,13 @@ def _depends_on(pkg, spec, when=None): conditions[when_spec] = dep_spec -@directive('dependencies') -def depends_on(pkg, spec, when=None): +@directive(('dependencies', '_deptypes')) +def depends_on(pkg, spec, when=None, type=None): """Creates a dict of deps with specs defining when they apply.""" - _depends_on(pkg, spec, when=when) + _depends_on(pkg, spec, when=when, type=type) -@directive(('extendees', 'dependencies')) +@directive(('extendees', 'dependencies', '_deptypes')) def extends(pkg, spec, **kwargs): """Same as depends_on, but dependency is symlinked into parent prefix. @@ -326,3 +345,13 @@ def __init__(self, directive, package): directive, "Package '%s' cannot pass itself to %s" % (package, directive)) self.package = package + + +class UnknownDependencyTypeError(DirectiveError): + """This is raised when a dependency is of an unknown type.""" + def __init__(self, directive, package, deptype): + super(UnknownDependencyTypeError, self).__init__( + directive, + "Package '%s' cannot depend on a package via %s." % + (package, deptype)) + self.package = package diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py index 22058d41d89..063e4647b60 100644 --- a/lib/spack/spack/graph.py +++ b/lib/spack/spack/graph.py @@ -80,12 +80,14 @@ def topological_sort(spec, **kwargs): """ reverse = kwargs.get('reverse', False) + # XXX(deptype): iterate over a certain kind of dependency. Maybe color + # edges based on the type of dependency? if not reverse: - parents = lambda s: s.dependents - children = lambda s: s.dependencies + parents = lambda s: s.dependents() + children = lambda s: s.dependencies() else: - parents = lambda s: s.dependencies - children = lambda s: s.dependents + parents = lambda s: s.dependencies() + children = lambda s: s.dependents() # Work on a copy so this is nondestructive. spec = spec.copy() diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index ce46047fa3f..a2e528d295a 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -120,7 +120,7 @@ def dependencies(spec, request='all'): return [] if request == 'direct': - return [xx for _, xx in spec.dependencies.items()] + return spec.dependencies() # FIXME : during module file creation nodes seem to be visited multiple # FIXME : times even if cover='nodes' is given. This work around permits diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index f44b2358909..78dfef58292 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -577,7 +577,7 @@ def extendee_spec(self): name = next(iter(self.extendees)) # If the extendee is in the spec's deps already, return that. - for dep in self.spec.traverse(): + for dep in self.spec.traverse(deptypes=('link', 'run')): if name == dep.name: return dep @@ -642,7 +642,8 @@ def preorder_traversal(self, visited=None, **kwargs): yield self for name in sorted(self.dependencies.keys()): - spec = self.dependencies[name] + dep_spec = self.get_dependency(name) + spec = dep_spec.spec # Currently, we do not descend into virtual dependencies, as this # makes doing a sensible traversal much harder. We just assume @@ -685,7 +686,9 @@ def installed_dependents(self): for spec in spack.installed_db.query(): if self.name == spec.name: continue - for dep in spec.traverse(): + # XXX(deptype): Should build dependencies not count here? + #for dep in spec.traverse(deptype=('run')): + for dep in spec.traverse(deptype=spack.alldeps): if self.spec == dep: dependents.append(spec) return dependents @@ -1089,7 +1092,7 @@ def check_paths(path_list, filetype, predicate): def do_install_dependencies(self, **kwargs): # Pass along paths of dependencies here - for dep in self.spec.dependencies.values(): + for dep in self.spec.dependencies(): dep.package.do_install(**kwargs) @property @@ -1282,7 +1285,7 @@ def do_activate(self, force=False): # Activate any package dependencies that are also extensions. if not force: - for spec in self.spec.traverse(root=False): + for spec in self.spec.traverse(root=False, deptype='run'): if spec.package.extends(self.extendee_spec): if not spec.package.activated: spec.package.do_activate(force=force) @@ -1328,7 +1331,7 @@ def do_deactivate(self, **kwargs): for name, aspec in activated.items(): if aspec == self.spec: continue - for dep in aspec.traverse(): + for dep in aspec.traverse(deptype='run'): if self.spec == dep: raise ActivationError( "Cannot deactivate %s because %s is activated and depends on it." # NOQA: ignore=E501 @@ -1414,9 +1417,10 @@ def fetch_remote_versions(self): def rpath(self): """Get the rpath this package links with, as a list of paths.""" rpaths = [self.prefix.lib, self.prefix.lib64] - rpaths.extend(d.prefix.lib for d in self.spec.traverse(root=False) + deps = self.spec.dependencies(deptype='link') + rpaths.extend(d.prefix.lib for d in deps if os.path.isdir(d.prefix.lib)) - rpaths.extend(d.prefix.lib64 for d in self.spec.traverse(root=False) + rpaths.extend(d.prefix.lib64 for d in deps if os.path.isdir(d.prefix.lib64)) return rpaths diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index f55dad3c51d..58fc139042f 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -155,6 +155,9 @@ every time we call str()""" _any_version = VersionList([':']) +alldeps = ('build', 'link', 'run') +nolink = ('build', 'run') + def index_specs(specs): """Take a list of specs and return a dict of lists. Dict is @@ -291,6 +294,27 @@ def __repr__(self): return str(self) +@key_ordering +class DependencySpec(object): + """ + Dependencies have conditions in which they apply. + + This stores both what is depended on and why it is a dependency. + """ + def __init__(self, spec, deptypes): + self.spec = spec + self.deptypes = deptypes + + def _cmp_key(self): + return self.spec + + def copy(self): + return DependencySpec(self.spec.copy(), self.deptype) + + def __str__(self): + return str(self.spec) + + @key_ordering class VariantSpec(object): @@ -440,11 +464,11 @@ class DependencyMap(HashableMap): The DependencyMap is keyed by name. """ @property def concrete(self): - return all(d.concrete for d in self.values()) + return all(d.spec.concrete for d in self.values()) def __str__(self): return ''.join( - ["^" + str(self[name]) for name in sorted(self.keys())]) + ["^" + str(self[name].spec) for name in sorted(self.keys())]) @key_ordering @@ -472,13 +496,13 @@ def __init__(self, spec_like, *dep_like, **kwargs): # writes directly into this Spec object. other = spec_list[0] self.name = other.name - self.dependents = other.dependents self.versions = other.versions self.architecture = other.architecture self.compiler = other.compiler self.compiler_flags = other.compiler_flags self.compiler_flags.spec = self - self.dependencies = other.dependencies + self._dependencies = other._dependencies + self._dependents = other._dependents self.variants = other.variants self.variants.spec = self self.namespace = other.namespace @@ -500,7 +524,49 @@ def __init__(self, spec_like, *dep_like, **kwargs): # Spec(a, b) will copy a but just add b as a dep. for dep in dep_like: spec = dep if isinstance(dep, Spec) else Spec(dep) - self._add_dependency(spec) + # XXX(deptype): default deptypes + self._add_dependency(spec, ('build', 'link')) + + def get_dependency(self, name): + dep = self._dependencies.get(name) + if dep is not None: + return dep + raise InvalidDependencyException( + self.name + " does not depend on " + comma_or(name)) + + def _deptype_norm(self, deptype): + if deptype is None: + return alldeps + # Force deptype to be a set object so that we can do set intersections. + if isinstance(deptype, str): + return (deptype,) + return deptype + + def _find_deps(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [dep.spec + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies(self, deptype=None): + return self._find_deps(self._dependencies, deptype) + + def dependents(self, deptype=None): + return self._find_deps(self._dependents, deptype) + + def _find_deps_dict(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [(dep.spec.name, dep) + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies_dict(self, deptype=None): + return dict(self._find_deps_dict(self._dependencies, deptype)) + + def dependents_dict(self, deptype=None): + return dict(self._find_deps_dict(self._dependents, deptype)) # # Private routines here are called by the parser when building a spec. @@ -609,13 +675,13 @@ def _set_target(self, value): if self.architecture.platform: self.architecture.target = self.architecture.platform.target(value) - def _add_dependency(self, spec): + def _add_dependency(self, spec, deptypes): """Called by the parser to add another spec as a dependency.""" - if spec.name in self.dependencies: + if spec.name in self._dependencies: raise DuplicateDependencyError( "Cannot depend on '%s' twice" % spec) - self.dependencies[spec.name] = spec - spec.dependents[self.name] = self + self._dependencies[spec.name] = DependencySpec(spec, deptypes) + spec._dependents[self.name] = DependencySpec(self, deptypes) # # Public interface @@ -632,15 +698,15 @@ def root(self): installed). This will throw an assertion error if that is not the case. """ - if not self.dependents: + if not self._dependents: return self # If the spec has multiple dependents, ensure that they all # lead to the same place. Spack shouldn't deal with any DAGs # with multiple roots, so something's wrong if we find one. - depiter = iter(self.dependents.values()) - first_root = next(depiter).root - assert(all(first_root is d.root for d in depiter)) + depiter = iter(self._dependents.values()) + first_root = next(depiter).spec.root + assert(all(first_root is d.spec.root for d in depiter)) return first_root @property @@ -687,10 +753,21 @@ def concrete(self): and self.architecture.concrete and self.compiler and self.compiler.concrete and self.compiler_flags.concrete - and self.dependencies.concrete) + and self._dependencies.concrete) return self._concrete - def traverse(self, visited=None, d=0, **kwargs): + def traverse(self, visited=None, deptype=None, **kwargs): + traversal = self.traverse_with_deptype(visited=visited, + deptype=deptype, + **kwargs) + if kwargs.get('depth', False): + return [(s[0], s[1].spec) for s in traversal] + else: + return [s.spec for s in traversal] + + def traverse_with_deptype(self, visited=None, d=0, deptype=None, + deptype_query=None, _self_deptype=None, + **kwargs): """Generic traversal of the DAG represented by this spec. This will yield each node in the spec. Options: @@ -742,6 +819,12 @@ def traverse(self, visited=None, d=0, **kwargs): direction = kwargs.get('direction', 'children') order = kwargs.get('order', 'pre') + if deptype is None: + deptype = alldeps + + if deptype_query is None: + deptype_query = ('link', 'run') + # Make sure kwargs have legal values; raise ValueError if not. def validate(name, val, allowed_values): if val not in allowed_values: @@ -759,30 +842,37 @@ def validate(name, val, allowed_values): if key in visited and cover == 'nodes': return - # Determine whether and what to yield for this node. + def return_val(res): + return (d, res) if depth else res + yield_me = yield_root or d > 0 - result = (d, self) if depth else self # Preorder traversal yields before successors if yield_me and order == 'pre': - yield result + yield return_val(DependencySpec(self, _self_deptype)) + + deps = self.dependencies_dict(deptype) # Edge traversal yields but skips children of visited nodes if not (key in visited and cover == 'edges'): # This code determines direction and yields the children/parents - successors = self.dependencies + successors = deps if direction == 'parents': - successors = self.dependents + successors = self.dependents_dict() visited.add(key) for name in sorted(successors): child = successors[name] - for elt in child.traverse(visited, d + 1, **kwargs): + children = child.spec.traverse_with_deptype( + visited, d=d + 1, deptype=deptype_query, + deptype_query=deptype_query, + _self_deptype=child.deptypes, **kwargs) + for elt in children: yield elt # Postorder traversal yields after successors if yield_me and order == 'post': - yield result + yield return_val(DependencySpec(self, _self_deptype)) @property def short_spec(self): @@ -807,6 +897,7 @@ def dag_hash(self, length=None): if self._hash: return self._hash[:length] else: + # XXX(deptype): ignore 'build' dependencies here yaml_text = yaml.dump( self.to_node_dict(), default_flow_style=True, width=sys.maxint) sha = hashlib.sha1(yaml_text) @@ -819,11 +910,13 @@ def to_node_dict(self): params = dict((name, v.value) for name, v in self.variants.items()) params.update(dict((name, value) for name, value in self.compiler_flags.items())) + deps = self.dependencies_dict(deptype=('link', 'run')) d = { - 'parameters' : params, - 'arch' : self.architecture, - 'dependencies' : dict((d, self.dependencies[d].dag_hash()) - for d in sorted(self.dependencies)) + 'parameters': params, + 'arch': self.architecture, + 'dependencies': dict((d, (deps[d].spec.dag_hash(), + deps[d].deptypes)) + for d in sorted(deps.keys())) } # Older concrete specs do not have a namespace. Omit for @@ -848,7 +941,7 @@ def to_node_dict(self): def to_yaml(self, stream=None): node_list = [] - for s in self.traverse(order='pre'): + for s in self.traverse(order='pre', deptype=('link', 'run')): node = s.to_node_dict() node[s.name]['hash'] = s.dag_hash() node_list.append(node) @@ -889,6 +982,11 @@ def from_node_dict(node): raise SpackRecordError( "Did not find a valid format for variants in YAML file") + # XXX(deptypes): why are dependencies not meant to be read here? + #for name, dep_info in node['dependencies'].items(): + # (dag_hash, deptypes) = dep_info + # spec._dependencies[name] = DependencySpec(dag_hash, deptypes) + return spec @staticmethod @@ -919,8 +1017,10 @@ def from_yaml(stream): for node in yfile['spec']: name = next(iter(node)) - for dep_name in node[name]['dependencies']: - deps[name].dependencies[dep_name] = deps[dep_name] + for dep_name, (dep, deptypes) in \ + node[name]['dependencies'].items(): + deps[name]._dependencies[dep_name] = \ + DependencySpec(deps[dep_name], deptypes) return spec def _concretize_helper(self, presets=None, visited=None): @@ -940,8 +1040,9 @@ def _concretize_helper(self, presets=None, visited=None): changed = False # Concretize deps first -- this is a bottom-up process. - for name in sorted(self.dependencies.keys()): - changed |= self.dependencies[name]._concretize_helper(presets, visited) + for name in sorted(self._dependencies.keys()): + changed |= self._dependencies[ + name].spec._concretize_helper(presets, visited) if self.name in presets: changed |= self.constrain(presets[self.name]) @@ -965,13 +1066,16 @@ def _concretize_helper(self, presets=None, visited=None): def _replace_with(self, concrete): """Replace this virtual spec with a concrete spec.""" assert(self.virtual) - for name, dependent in self.dependents.items(): + for name, dep_spec in self._dependents.items(): + dependent = dep_spec.spec + deptypes = dep_spec.deptypes + # remove self from all dependents. - del dependent.dependencies[self.name] + del dependent._dependencies[self.name] # add the replacement, unless it is already a dep of dependent. - if concrete.name not in dependent.dependencies: - dependent._add_dependency(concrete) + if concrete.name not in dependent._dependencies: + dependent._add_dependency(concrete, deptypes) def _replace_node(self, replacement): """Replace this spec with another. @@ -982,13 +1086,15 @@ def _replace_node(self, replacement): to be normalized. """ - for name, dependent in self.dependents.items(): - del dependent.dependencies[self.name] - dependent._add_dependency(replacement) + for name, dep_spec in self._dependents.items(): + dependent = dep_spec.spec + deptypes = dep_spec.deptypes + del dependent._dependencies[self.name] + dependent._add_dependency(replacement, deptypes) - for name, dep in self.dependencies.items(): - del dep.dependents[self.name] - del self.dependencies[dep.name] + for name, dep_spec in self._dependencies.items(): + del dep_spec.spec.dependents[self.name] + del self._dependencies[dep.name] def _expand_virtual_packages(self): """Find virtual packages in this spec, replace them with providers, @@ -1008,13 +1114,14 @@ def _expand_virtual_packages(self): a problem. """ # Make an index of stuff this spec already provides + # XXX(deptype): 'link' and 'run'? self_index = ProviderIndex(self.traverse(), restrict=True) changed = False done = False while not done: done = True - + # XXX(deptype): 'link' and 'run'? for spec in list(self.traverse()): replacement = None if spec.virtual: @@ -1054,10 +1161,10 @@ def _expand_virtual_packages(self): # If replacement is external then trim the dependencies if replacement.external or replacement.external_module: - if (spec.dependencies): + if (spec._dependencies): changed = True - spec.dependencies = DependencyMap() - replacement.dependencies = DependencyMap() + spec._dependencies = DependencyMap() + replacement._dependencies = DependencyMap() replacement.architecture = self.architecture # TODO: could this and the stuff in _dup be cleaned up? @@ -1068,7 +1175,7 @@ def feq(cfield, sfield): feq(replacement.versions, spec.versions) and feq(replacement.compiler, spec.compiler) and feq(replacement.architecture, spec.architecture) and - feq(replacement.dependencies, spec.dependencies) and + feq(replacement._dependencies, spec._dependencies) and feq(replacement.variants, spec.variants) and feq(replacement.external, spec.external) and feq(replacement.external_module, spec.external_module)): @@ -1146,7 +1253,7 @@ def _mark_concrete(self): Only for internal use -- client code should use "concretize" unless there is a need to force a spec to be concrete. """ - for s in self.traverse(): + for s in self.traverse(deptype_query=alldeps): s._normal = True s._concrete = True @@ -1159,6 +1266,13 @@ def concretized(self): return clone def flat_dependencies(self, **kwargs): + flat_deps = DependencyMap() + flat_deps_deptypes = self.flat_dependencies_with_deptype(**kwargs) + for name, depspec in flat_deps_deptypes.items(): + flat_deps[name] = depspec.spec + return flat_deps + + def flat_dependencies_with_deptype(self, **kwargs): """Return a DependencyMap containing all of this spec's dependencies with their constraints merged. @@ -1169,23 +1283,31 @@ def flat_dependencies(self, **kwargs): returns them. """ copy = kwargs.get('copy', True) + deptype_query = kwargs.get('deptype_query') flat_deps = DependencyMap() try: - for spec in self.traverse(root=False): + deptree = self.traverse_with_deptype(root=False, + deptype_query=deptype_query) + for depspec in deptree: + spec = depspec.spec + deptypes = depspec.deptypes + if spec.name not in flat_deps: if copy: - flat_deps[spec.name] = spec.copy(deps=False) + dep_spec = DependencySpec(spec.copy(deps=False), + deptypes) else: - flat_deps[spec.name] = spec + dep_spec = DependencySpec(spec, deptypes) + flat_deps[spec.name] = dep_spec else: - flat_deps[spec.name].constrain(spec) + flat_deps[spec.name].spec.constrain(spec) if not copy: - for dep in flat_deps.values(): - dep.dependencies.clear() - dep.dependents.clear() - self.dependencies.clear() + for depspec in flat_deps.values(): + depspec.spec._dependencies.clear() + depspec.spec._dependents.clear() + self._dependencies.clear() return flat_deps @@ -1200,17 +1322,11 @@ def index(self): """Return DependencyMap that points to all the dependencies in this spec.""" dm = DependencyMap() + # XXX(deptype): use a deptype kwarg. for spec in self.traverse(): dm[spec.name] = spec return dm - def flatten(self): - """Pull all dependencies up to the root (this spec). - Merge constraints for dependencies with the same name, and if they - conflict, throw an exception. """ - for dep in self.flat_dependencies(copy=False): - self._add_dependency(dep) - def _evaluate_dependency_conditions(self, name): """Evaluate all the conditions on a dependency with this name. @@ -1267,7 +1383,8 @@ def _find_provider(self, vdep, provider_index): elif required: raise UnsatisfiableProviderSpecError(required[0], vdep) - def _merge_dependency(self, dep, visited, spec_deps, provider_index): + def _merge_dependency(self, dep, deptypes, visited, spec_deps, + provider_index): """Merge the dependency into this spec. This is the core of normalize(). There are some basic steps: @@ -1294,7 +1411,9 @@ def _merge_dependency(self, dep, visited, spec_deps, provider_index): dep = provider else: index = ProviderIndex([dep], restrict=True) - for vspec in (v for v in spec_deps.values() if v.virtual): + for vspec in (v.spec + for v in spec_deps.values() + if v.spec.virtual): if index.providers_for(vspec): vspec._replace_with(dep) del spec_deps[vspec.name] @@ -1307,25 +1426,25 @@ def _merge_dependency(self, dep, visited, spec_deps, provider_index): # If the spec isn't already in the set of dependencies, clone # it from the package description. if dep.name not in spec_deps: - spec_deps[dep.name] = dep.copy() + spec_deps[dep.name] = DependencySpec(dep.copy(), deptypes) changed = True # Constrain package information with spec info try: - changed |= spec_deps[dep.name].constrain(dep) + changed |= spec_deps[dep.name].spec.constrain(dep) except UnsatisfiableSpecError, e: e.message = "Invalid spec: '%s'. " e.message += "Package %s requires %s %s, but spec asked for %s" - e.message %= (spec_deps[dep.name], dep.name, e.constraint_type, - e.required, e.provided) + e.message %= (spec_deps[dep.name].spec, dep.name, + e.constraint_type, e.required, e.provided) raise e # Add merged spec to my deps and recurse dependency = spec_deps[dep.name] - if dep.name not in self.dependencies: - self._add_dependency(dependency) + if dep.name not in self._dependencies: + self._add_dependency(dependency.spec, dependency.deptypes) - changed |= dependency._normalize_helper( + changed |= dependency.spec._normalize_helper( visited, spec_deps, provider_index) return changed @@ -1351,10 +1470,11 @@ def _normalize_helper(self, visited, spec_deps, provider_index): for dep_name in pkg.dependencies: # Do we depend on dep_name? If so pkg_dep is not None. pkg_dep = self._evaluate_dependency_conditions(dep_name) + deptypes = pkg._deptypes[dep_name] # If pkg_dep is a dependency, merge it. if pkg_dep: changed |= self._merge_dependency( - pkg_dep, visited, spec_deps, provider_index) + pkg_dep, deptypes, visited, spec_deps, provider_index) any_change |= changed return any_change @@ -1385,11 +1505,13 @@ def normalize(self, force=False): # Ensure first that all packages & compilers in the DAG exist. self.validate_names() # Get all the dependencies into one DependencyMap - spec_deps = self.flat_dependencies(copy=False) + spec_deps = self.flat_dependencies_with_deptype(copy=False, + deptype_query=alldeps) # Initialize index of virtual dependency providers if # concretize didn't pass us one already - provider_index = ProviderIndex(spec_deps.values(), restrict=True) + provider_index = ProviderIndex([s.spec for s in spec_deps.values()], + restrict=True) # traverse the package DAG and fill out dependencies according # to package files & their 'when' specs @@ -1510,7 +1632,7 @@ def _constrain_dependencies(self, other): """Apply constraints of other spec's dependencies to this spec.""" other = self._autospec(other) - if not self.dependencies or not other.dependencies: + if not self._dependencies or not other._dependencies: return False # TODO: might want more detail than this, e.g. specific deps @@ -1526,13 +1648,17 @@ def _constrain_dependencies(self, other): # Update with additional constraints from other spec for name in other.dep_difference(self): - self._add_dependency(other[name].copy()) + dep_spec_copy = other.get_dependency(name) + dep_copy = dep_spec_copy.spec + deptypes = dep_spec_copy.deptypes + self._add_dependency(dep_copy.copy(), deptypes) changed = True return changed def common_dependencies(self, other): """Return names of dependencies that self an other have in common.""" + # XXX(deptype): handle deptypes via deptype kwarg. common = set( s.name for s in self.traverse(root=False)) common.intersection_update( @@ -1657,13 +1783,14 @@ def satisfies_dependencies(self, other, strict=False): other = self._autospec(other) if strict: - if other.dependencies and not self.dependencies: + if other._dependencies and not self._dependencies: return False - if not all(dep in self.dependencies for dep in other.dependencies): + if not all(dep in self._dependencies + for dep in other._dependencies): return False - elif not self.dependencies or not other.dependencies: + elif not self._dependencies or not other._dependencies: # if either spec doesn't restrict dependencies then both are # compatible. return True @@ -1726,8 +1853,8 @@ def _dup(self, other, **kwargs): self.architecture = other.architecture self.compiler = other.compiler.copy() if other.compiler else None if kwargs.get('cleardeps', True): - self.dependents = DependencyMap() - self.dependencies = DependencyMap() + self._dependents = DependencyMap() + self._dependencies = DependencyMap() self.compiler_flags = other.compiler_flags.copy() self.variants = other.variants.copy() self.variants.spec = self @@ -1739,15 +1866,30 @@ def _dup(self, other, **kwargs): # If we copy dependencies, preserve DAG structure in the new spec if kwargs.get('deps', True): # This copies the deps from other using _dup(deps=False) - new_nodes = other.flat_dependencies() + # XXX(deptype): We can keep different instances of specs here iff + # it is only a 'build' dependency (from its parent). + # All other instances must be shared (due to symbol + # and PATH contention). These should probably search + # for any existing installation which can satisfy the + # build and latch onto that because if 3 things need + # the same build dependency and it is *not* + # available, we only want to build it once. + new_nodes = other.flat_dependencies(deptype_query=alldeps) new_nodes[self.name] = self - # Hook everything up properly here by traversing. - for spec in other.traverse(cover='nodes'): - parent = new_nodes[spec.name] - for child in spec.dependencies: - if child not in parent.dependencies: - parent._add_dependency(new_nodes[child]) + stack = [other] + while stack: + cur_spec = stack.pop(0) + new_spec = new_nodes[cur_spec.name] + + for depspec in cur_spec._dependencies.values(): + stack.append(depspec.spec) + + # XXX(deptype): add any new deptypes that may have appeared + # here. + if depspec.spec.name not in new_spec._dependencies: + new_spec._add_dependency( + new_nodes[depspec.spec.name], depspec.deptypes) # Since we preserved structure, we can copy _normal safely. self._normal = other._normal @@ -1814,13 +1956,13 @@ def _eq_dag(self, other, vs, vo): if self.ne_node(other): return False - if len(self.dependencies) != len(other.dependencies): + if len(self._dependencies) != len(other._dependencies): return False - ssorted = [self.dependencies[name] - for name in sorted(self.dependencies)] - osorted = [other.dependencies[name] - for name in sorted(other.dependencies)] + ssorted = [self._dependencies[name].spec + for name in sorted(self._dependencies)] + osorted = [other._dependencies[name].spec + for name in sorted(other._dependencies)] for s, o in zip(ssorted, osorted): visited_s = id(s) in vs @@ -1874,9 +2016,10 @@ def _cmp_key(self): 1. A tuple describing this node in the DAG. 2. The hash of each of this node's dependencies' cmp_keys. """ + dep_dict = self.dependencies_dict(deptype=('link', 'run')) return self._cmp_node() + ( - tuple(hash(self.dependencies[name]) - for name in sorted(self.dependencies)),) + tuple(hash(dep_dict[name]) + for name in sorted(dep_dict)),) def colorized(self): return colorize_spec(self) @@ -2081,8 +2224,8 @@ def __cmp__(self, other): self.architecture, other.architecture) #Dependency is not configurable - if self.dependencies != other.dependencies: - return -1 if self.dependencies < other.dependencies else 1 + if self._dependencies != other._dependencies: + return -1 if self._dependencies < other._dependencies else 1 #Equal specs return 0 @@ -2196,10 +2339,13 @@ def do_parse(self): specs.append(self.spec(None)) self.previous = None if self.accept(HASH): - specs[-1]._add_dependency(self.spec_by_hash()) + dep = self.spec_by_hash() else: self.expect(ID) - specs[-1]._add_dependency(self.spec(self.token.value)) + dep = self.spec(self.token.value) + # XXX(deptype): default deptypes + def_deptypes = ('build', 'link') + specs[-1]._add_dependency(dep, def_deptypes) else: # Attempt to construct an anonymous spec, but check that @@ -2263,8 +2409,8 @@ def spec(self, name, check_valid_token=False): spec.external = None spec.external_module = None spec.compiler_flags = FlagMap(spec) - spec.dependents = DependencyMap() - spec.dependencies = DependencyMap() + spec._dependents = DependencyMap() + spec._dependencies = DependencyMap() spec.namespace = spec_namespace spec._hash = None diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py index d17e013ed23..a94d3c8bba0 100644 --- a/lib/spack/spack/test/cmd/test_install.py +++ b/lib/spack/spack/test/cmd/test_install.py @@ -58,16 +58,39 @@ def mock_open(filename, mode): class MockSpec(object): def __init__(self, name, version, hashStr=None): - self.dependencies = {} + self._dependencies = {} self.name = name self.version = version self.hash = hashStr if hashStr else hash((name, version)) + def _deptype_norm(self, deptype): + if deptype is None: + return spack.alldeps + # Force deptype to be a tuple so that we can do set intersections. + if isinstance(deptype, str): + return (deptype,) + return deptype + + def _find_deps(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [dep.spec + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies(self, deptype=None): + return self._find_deps(self._dependencies, deptype) + + def dependents(self, deptype=None): + return self._find_deps(self._dependents, deptype) + def traverse(self, order=None): - for _, spec in self.dependencies.items(): - yield spec + for _, spec in self._dependencies.items(): + yield spec.spec yield self - #allDeps = itertools.chain.from_iterable(i.traverse() for i in self.dependencies.itervalues()) + #from_iterable = itertools.chain.from_iterable + #allDeps = from_iterable(i.traverse() + # for i in self.dependencies()) #return set(itertools.chain([self], allDeps)) def dag_hash(self): @@ -104,7 +127,7 @@ def mock_fetch_log(path): specX = MockSpec('X', "1.2.0") specY = MockSpec('Y', "2.3.8") -specX.dependencies['Y'] = specY +specX._dependencies['Y'] = spack.DependencySpec(specY, spack.alldeps) pkgX = MockPackage(specX, 'logX') pkgY = MockPackage(specY, 'logY') diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index ce02b08bc34..ae3ceecfc8d 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -197,32 +197,36 @@ def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self): def test_virtual_is_fully_expanded_for_callpath(self): # force dependence on fake "zmpi" by asking for MPI 10.0 spec = Spec('callpath ^mpi@10.0') - self.assertTrue('mpi' in spec.dependencies) + self.assertTrue('mpi' in spec._dependencies) self.assertFalse('fake' in spec) spec.concretize() - self.assertTrue('zmpi' in spec.dependencies) - self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue('zmpi' in spec._dependencies) + self.assertTrue(all('mpi' not in d._dependencies + for d in spec.traverse())) self.assertTrue('zmpi' in spec) self.assertTrue('mpi' in spec) - self.assertTrue('fake' in spec.dependencies['zmpi']) + self.assertTrue('fake' in spec._dependencies['zmpi'].spec) def test_virtual_is_fully_expanded_for_mpileaks(self): spec = Spec('mpileaks ^mpi@10.0') - self.assertTrue('mpi' in spec.dependencies) + self.assertTrue('mpi' in spec._dependencies) self.assertFalse('fake' in spec) spec.concretize() - self.assertTrue('zmpi' in spec.dependencies) - self.assertTrue('callpath' in spec.dependencies) - self.assertTrue('zmpi' in spec.dependencies['callpath'].dependencies) - self.assertTrue('fake' in spec.dependencies['callpath'].dependencies['zmpi'].dependencies) + self.assertTrue('zmpi' in spec._dependencies) + self.assertTrue('callpath' in spec._dependencies) + self.assertTrue('zmpi' in spec._dependencies['callpath']. + spec._dependencies) + self.assertTrue('fake' in spec._dependencies['callpath']. + spec._dependencies['zmpi']. + spec._dependencies) - self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue(all(not 'mpi' in d._dependencies for d in spec.traverse())) self.assertTrue('zmpi' in spec) self.assertTrue('mpi' in spec) diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py index c8b06cd7d70..9d96622a6e3 100644 --- a/lib/spack/spack/test/mock_packages_test.py +++ b/lib/spack/spack/test/mock_packages_test.py @@ -191,8 +191,7 @@ def initmock(self): # restore later. self.saved_deps = {} - - def set_pkg_dep(self, pkg_name, spec): + def set_pkg_dep(self, pkg_name, spec, deptypes=spack.alldeps): """Alters dependence information for a package. Adds a dependency on to pkg. @@ -206,7 +205,9 @@ def set_pkg_dep(self, pkg_name, spec): self.saved_deps[pkg_name] = (pkg, pkg.dependencies.copy()) # Change dep spec - pkg.dependencies[spec.name] = { Spec(pkg_name) : spec } + # XXX(deptype): handle deptypes. + pkg.dependencies[spec.name] = {Spec(pkg_name): spec} + pkg._deptypes[spec.name] = set(deptypes) def cleanmock(self): @@ -216,6 +217,7 @@ def cleanmock(self): shutil.rmtree(self.temp_config, ignore_errors=True) spack.config.clear_config_caches() + # XXX(deptype): handle deptypes. # Restore dependency changes that happened during the test for pkg_name, (pkg, deps) in self.saved_deps.items(): pkg.dependencies.clear() diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index c56c70b1fe4..972e79aa20f 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -148,10 +148,12 @@ def test_conflicting_spec_constraints(self): # Normalize then add conflicting constraints to the DAG (this is an # extremely unlikely scenario, but we test for it anyway) mpileaks.normalize() - mpileaks.dependencies['mpich'] = Spec('mpich@1.0') - mpileaks.dependencies['callpath'].dependencies['mpich'] = Spec('mpich@2.0') + mpileaks._dependencies['mpich'].spec = Spec('mpich@1.0') + mpileaks._dependencies['callpath']. \ + spec._dependencies['mpich'].spec = Spec('mpich@2.0') - self.assertRaises(spack.spec.InconsistentSpecError, mpileaks.flatten) + self.assertRaises(spack.spec.InconsistentSpecError, + lambda: mpileaks.flat_dependencies(copy=False)) def test_normalize_twice(self): @@ -197,15 +199,17 @@ def test_normalize_with_virtual_spec(self): def check_links(self, spec_to_check): for spec in spec_to_check.traverse(): - for dependent in spec.dependents.values(): + for dependent in spec.dependents(): self.assertTrue( - spec.name in dependent.dependencies, - "%s not in dependencies of %s" % (spec.name, dependent.name)) + spec.name in dependent.dependencies_dict(), + "%s not in dependencies of %s" % + (spec.name, dependent.name)) - for dependency in spec.dependencies.values(): + for dependency in spec.dependencies(): self.assertTrue( - spec.name in dependency.dependents, - "%s not in dependents of %s" % (spec.name, dependency.name)) + spec.name in dependency.dependents_dict(), + "%s not in dependents of %s" % + (spec.name, dependency.name)) def test_dependents_and_dependencies_are_correct(self): @@ -442,3 +446,69 @@ def test_copy_concretized(self): orig_ids = set(id(s) for s in orig.traverse()) copy_ids = set(id(s) for s in copy.traverse()) self.assertFalse(orig_ids.intersection(copy_ids)) + + """ + Here is the graph with deptypes labeled (assume all packages have a 'dt' + prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for + 'link', 'r' for 'run'). + + use -bl-> top + + top -b-> build1 + top -bl-> link1 + top -r-> run1 + + build1 -b-> build2 + build1 -bl-> link2 + build1 -r-> run2 + + link1 -bl-> link3 + + run1 -bl-> link5 + run1 -r-> run3 + + link3 -b-> build2 + link3 -bl-> link4 + + run3 -b-> build3 + """ + def test_deptype_traversal(self): + dag = Spec('dtuse') + dag.normalize() + + names = ['dtuse', 'dttop', 'dtlink1', 'dtlink3', 'dtlink4', + 'dtrun1', 'dtlink5', 'dtrun3'] + + traversal = dag.traverse() + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_with_builddeps(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtlink2', 'dtrun2', 'dtlink1', + 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', 'dtrun3'] + + traversal = dag.traverse() + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_full(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtbuild2', 'dtlink2', 'dtrun2', + 'dtlink1', 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', + 'dtrun3', 'dtbuild3'] + + traversal = dag.traverse(deptype_query=spack.alldeps) + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_pythonpath(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtrun2', 'dtlink1', 'dtrun1', + 'dtrun3'] + + traversal = dag.traverse(deptype=spack.nolink, deptype_query='run') + self.assertEqual([x.name for x in traversal], names) diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index 355689a2d24..c58430317ad 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -38,7 +38,7 @@ class CmakeClient(Package): version('1.0', '4cb3ff35b2472aae70f542116d616e63') - depends_on('cmake') + depends_on('cmake', type='build') def setup_environment(self, spack_env, run_env): diff --git a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py new file mode 100644 index 00000000000..7429b2a8ef5 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py @@ -0,0 +1,18 @@ +from spack import * + + +class Dtbuild1(Package): + """Package for use as a build tool for deptypes testing which has its own + deptree""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild2', type='build') + depends_on('dtlink2') + depends_on('dtrun2', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py new file mode 100644 index 00000000000..cf3bb82a10c --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtbuild2(Package): + """Simple package which acts as a build dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py new file mode 100644 index 00000000000..6ba7e69a411 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtbuild3(Package): + """Simple package which acts as a build dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink1/package.py b/var/spack/repos/builtin.mock/packages/dtlink1/package.py new file mode 100644 index 00000000000..2747dcf354e --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink1/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtlink1(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtlink3') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink2/package.py b/var/spack/repos/builtin.mock/packages/dtlink2/package.py new file mode 100644 index 00000000000..b80bad053f9 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink2(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink3/package.py b/var/spack/repos/builtin.mock/packages/dtlink3/package.py new file mode 100644 index 00000000000..bee8b4b8f8a --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink3/package.py @@ -0,0 +1,16 @@ +from spack import * + + +class Dtlink3(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild2', type='build') + depends_on('dtlink4') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink4/package.py b/var/spack/repos/builtin.mock/packages/dtlink4/package.py new file mode 100644 index 00000000000..3f05d5c0d66 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink4/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink4(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink4-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink5/package.py b/var/spack/repos/builtin.mock/packages/dtlink5/package.py new file mode 100644 index 00000000000..c8b1e97d379 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink5/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink5(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink5-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun1/package.py b/var/spack/repos/builtin.mock/packages/dtrun1/package.py new file mode 100644 index 00000000000..fb33b9b2f2d --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun1/package.py @@ -0,0 +1,16 @@ +from spack import * + + +class Dtrun1(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtlink5') + depends_on('dtrun3', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun2/package.py b/var/spack/repos/builtin.mock/packages/dtrun2/package.py new file mode 100644 index 00000000000..e5d4b5e0b4f --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtrun2(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun3/package.py b/var/spack/repos/builtin.mock/packages/dtrun3/package.py new file mode 100644 index 00000000000..70dacf45ff9 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun3/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtrun3(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild3', type='build') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dttop/package.py b/var/spack/repos/builtin.mock/packages/dttop/package.py new file mode 100644 index 00000000000..202a3b6883c --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dttop/package.py @@ -0,0 +1,17 @@ +from spack import * + + +class Dttop(Package): + """Package with a complicated dependency tree""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dttop-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild1', type='build') + depends_on('dtlink1') + depends_on('dtrun1', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtuse/package.py b/var/spack/repos/builtin.mock/packages/dtuse/package.py new file mode 100644 index 00000000000..bd7391cee8d --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtuse/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtuse(Package): + """Simple package which uses dttop""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtuse-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dttop') + + def install(self, spec, prefix): + pass From 6fd45520daa93ee6094eaf9df57e5b26d4d6d1bf Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 9 Mar 2016 10:46:56 -0500 Subject: [PATCH 047/126] deptypes: mark deptypes in packages --- .../builtin/packages/ImageMagick/package.py | 2 +- .../repos/builtin/packages/Mitos/package.py | 1 + .../builtin/packages/adept-utils/package.py | 1 + .../repos/builtin/packages/apex/package.py | 2 +- .../builtin/packages/arpack-ng/package.py | 8 +++---- .../builtin/packages/autoconf/package.py | 2 +- .../builtin/packages/automaded/package.py | 1 + .../repos/builtin/packages/bear/package.py | 2 +- .../repos/builtin/packages/bertini/package.py | 4 ++-- .../builtin/packages/binutils/package.py | 6 ++--- .../repos/builtin/packages/bison/package.py | 2 +- .../repos/builtin/packages/boxlib/package.py | 1 + .../repos/builtin/packages/c-blosc/package.py | 2 +- .../repos/builtin/packages/caliper/package.py | 1 + .../builtin/packages/callpath/package.py | 1 + .../repos/builtin/packages/cantera/package.py | 2 +- .../packages/cbtf-argonavis/package.py | 2 +- .../builtin/packages/cbtf-krell/package.py | 2 +- .../builtin/packages/cbtf-lanl/package.py | 2 +- .../repos/builtin/packages/cbtf/package.py | 2 +- .../repos/builtin/packages/cereal/package.py | 2 +- .../repos/builtin/packages/cgal/package.py | 2 +- .../builtin/packages/cleverleaf/package.py | 1 + .../repos/builtin/packages/cmake/package.py | 4 ++-- .../repos/builtin/packages/cmocka/package.py | 2 ++ .../repos/builtin/packages/cram/package.py | 1 + .../repos/builtin/packages/czmq/package.py | 8 +++---- .../repos/builtin/packages/dakota/package.py | 1 + .../builtin/packages/damselfly/package.py | 2 ++ .../repos/builtin/packages/dealii/package.py | 2 +- .../repos/builtin/packages/dia/package.py | 2 +- .../repos/builtin/packages/doxygen/package.py | 8 +++---- .../repos/builtin/packages/dyninst/package.py | 1 + .../repos/builtin/packages/eigen/package.py | 2 +- .../packages/environment-modules/package.py | 2 +- .../builtin/packages/exodusii/package.py | 4 +--- .../repos/builtin/packages/expat/package.py | 2 +- .../repos/builtin/packages/flex/package.py | 2 +- .../repos/builtin/packages/flux/package.py | 4 ++-- .../repos/builtin/packages/gdal/package.py | 2 +- .../repos/builtin/packages/gdb/package.py | 2 +- .../repos/builtin/packages/gflags/package.py | 2 ++ .../repos/builtin/packages/git/package.py | 2 +- .../repos/builtin/packages/glib/package.py | 2 +- .../repos/builtin/packages/glm/package.py | 4 ++-- .../repos/builtin/packages/global/package.py | 2 +- .../repos/builtin/packages/gmp/package.py | 2 +- .../repos/builtin/packages/gmsh/package.py | 2 +- .../repos/builtin/packages/go/package.py | 2 +- .../builtin/packages/googletest/package.py | 2 +- .../builtin/packages/graphlib/package.py | 2 ++ .../builtin/packages/graphviz/package.py | 2 +- .../repos/builtin/packages/gromacs/package.py | 1 + .../builtin/packages/hdf5-blosc/package.py | 2 +- .../builtin/packages/hoomd-blue/package.py | 6 ++--- .../repos/builtin/packages/ibmisc/package.py | 8 +++---- .../repos/builtin/packages/ipopt/package.py | 2 +- .../repos/builtin/packages/julia/package.py | 20 ++++++++-------- .../builtin/packages/launchmon/package.py | 6 ++--- .../repos/builtin/packages/libgd/package.py | 1 + .../builtin/packages/libjpeg-turbo/package.py | 4 ++-- .../repos/builtin/packages/libtool/package.py | 2 +- .../repos/builtin/packages/libuv/package.py | 6 ++--- .../repos/builtin/packages/libxcb/package.py | 4 ++-- .../builtin/packages/llvm-lld/package.py | 2 ++ .../repos/builtin/packages/llvm/package.py | 2 +- .../repos/builtin/packages/lmod/package.py | 4 ++-- .../repos/builtin/packages/mbedtls/package.py | 2 +- .../repos/builtin/packages/memaxes/package.py | 2 +- .../repos/builtin/packages/mesa/package.py | 4 ++-- .../repos/builtin/packages/metis/package.py | 2 +- .../repos/builtin/packages/mfem/package.py | 2 +- .../repos/builtin/packages/mpibash/package.py | 2 +- .../repos/builtin/packages/muster/package.py | 1 + .../builtin/packages/netcdf-cxx4/package.py | 2 +- .../repos/builtin/packages/netcdf/package.py | 2 +- .../builtin/packages/netlib-lapack/package.py | 2 +- .../packages/netlib-scalapack/package.py | 2 +- .../repos/builtin/packages/numdiff/package.py | 2 +- .../repos/builtin/packages/oce/package.py | 2 +- .../repos/builtin/packages/octave/package.py | 4 ++-- .../builtin/packages/ompt-openmp/package.py | 2 +- .../repos/builtin/packages/opencv/package.py | 3 ++- .../builtin/packages/openjpeg/package.py | 2 +- .../builtin/packages/openspeedshop/package.py | 2 +- .../repos/builtin/packages/p4est/package.py | 6 ++--- .../builtin/packages/paradiseo/package.py | 6 ++--- .../packages/parallel-netcdf/package.py | 2 +- .../builtin/packages/paraview/package.py | 5 ++-- .../builtin/packages/parmetis/package.py | 2 +- .../repos/builtin/packages/pidx/package.py | 1 + .../repos/builtin/packages/psi4/package.py | 4 ++-- .../builtin/packages/py-astroid/package.py | 8 +++---- .../builtin/packages/py-astropy/package.py | 18 +++++++------- .../builtin/packages/py-autopep8/package.py | 4 ++-- .../builtin/packages/py-basemap/package.py | 8 +++---- .../builtin/packages/py-biopython/package.py | 4 ++-- .../builtin/packages/py-blessings/package.py | 2 +- .../builtin/packages/py-bottleneck/package.py | 2 +- .../repos/builtin/packages/py-cffi/package.py | 4 ++-- .../builtin/packages/py-coverage/package.py | 2 +- .../builtin/packages/py-csvkit/package.py | 12 +++++----- .../repos/builtin/packages/py-dask/package.py | 2 +- .../builtin/packages/py-dateutil/package.py | 4 ++-- .../builtin/packages/py-decorator/package.py | 2 +- .../builtin/packages/py-emcee/package.py | 2 +- .../builtin/packages/py-flake8/package.py | 2 +- .../builtin/packages/py-funcsigs/package.py | 2 +- .../builtin/packages/py-genshi/package.py | 2 +- .../builtin/packages/py-gnuplot/package.py | 2 +- .../repos/builtin/packages/py-h5py/package.py | 8 +++---- .../builtin/packages/py-iminuit/package.py | 8 +++---- .../builtin/packages/py-ipython/package.py | 4 ++-- .../builtin/packages/py-jinja2/package.py | 6 ++--- .../builtin/packages/py-lockfile/package.py | 2 +- .../packages/py-logilab-common/package.py | 6 ++--- .../repos/builtin/packages/py-mako/package.py | 2 +- .../builtin/packages/py-markupsafe/package.py | 2 +- .../builtin/packages/py-matplotlib/package.py | 24 +++++++++---------- .../builtin/packages/py-mistune/package.py | 2 +- .../repos/builtin/packages/py-mock/package.py | 4 ++-- .../builtin/packages/py-mpi4py/package.py | 2 +- .../builtin/packages/py-mysqldb1/package.py | 2 +- .../builtin/packages/py-nestle/package.py | 4 ++-- .../builtin/packages/py-netcdf/package.py | 4 ++-- .../builtin/packages/py-networkx/package.py | 2 +- .../repos/builtin/packages/py-nose/package.py | 2 +- .../builtin/packages/py-numexpr/package.py | 2 +- .../builtin/packages/py-numpy/package.py | 2 +- .../builtin/packages/py-openpyxl/package.py | 4 ++-- .../builtin/packages/py-pandas/package.py | 12 +++++----- .../repos/builtin/packages/py-pbr/package.py | 2 +- .../repos/builtin/packages/py-pep8/package.py | 2 +- .../packages/py-periodictable/package.py | 4 ++-- .../builtin/packages/py-phonopy/package.py | 8 +++---- .../builtin/packages/py-pillow/package.py | 4 ++-- .../packages/py-prettytable/package.py | 2 +- .../builtin/packages/py-protobuf/package.py | 2 +- .../builtin/packages/py-py2neo/package.py | 2 +- .../builtin/packages/py-pycparser/package.py | 2 +- .../builtin/packages/py-pygments/package.py | 2 +- .../builtin/packages/py-pylint/package.py | 4 ++-- .../repos/builtin/packages/py-pyqt/package.py | 2 +- .../builtin/packages/py-pyside/package.py | 5 ++-- .../builtin/packages/py-pytables/package.py | 6 ++--- .../packages/py-python-daemon/package.py | 4 ++-- .../builtin/packages/py-restview/package.py | 4 ++-- .../repos/builtin/packages/py-rpy2/package.py | 2 +- .../packages/py-scikit-image/package.py | 12 +++++----- .../packages/py-scikit-learn/package.py | 6 ++--- .../builtin/packages/py-scipy/package.py | 4 ++-- .../builtin/packages/py-shiboken/package.py | 5 ++-- .../repos/builtin/packages/py-six/package.py | 2 +- .../builtin/packages/py-sncosmo/package.py | 14 +++++------ .../builtin/packages/py-storm/package.py | 2 +- .../builtin/packages/py-tappy/package.py | 2 +- .../builtin/packages/py-tuiview/package.py | 4 ++-- .../builtin/packages/py-twisted/package.py | 2 +- .../builtin/packages/py-unittest2/package.py | 2 +- .../packages/py-unittest2py3k/package.py | 2 +- .../builtin/packages/py-urwid/package.py | 2 +- .../builtin/packages/py-virtualenv/package.py | 2 +- .../builtin/packages/py-wcsaxes/package.py | 6 ++--- .../builtin/packages/py-wheel/package.py | 2 +- .../repos/builtin/packages/py-yapf/package.py | 2 +- .../repos/builtin/packages/qhull/package.py | 2 +- .../repos/builtin/packages/qt/package.py | 4 ++-- .../repos/builtin/packages/ravel/package.py | 3 +-- .../repos/builtin/packages/rose/package.py | 6 ++--- .../repos/builtin/packages/scotch/package.py | 4 ++-- .../repos/builtin/packages/serf/package.py | 2 +- .../repos/builtin/packages/spot/package.py | 2 +- .../repos/builtin/packages/stat/package.py | 2 +- .../builtin/packages/swiftsim/package.py | 8 +++---- .../repos/builtin/packages/task/package.py | 1 + .../repos/builtin/packages/taskd/package.py | 1 + .../repos/builtin/packages/tetgen/package.py | 4 +--- .../packages/the_platinum_searcher/package.py | 2 +- .../packages/the_silver_searcher/package.py | 2 +- .../repos/builtin/packages/thrift/package.py | 10 ++++---- .../builtin/packages/trilinos/package.py | 2 ++ .../repos/builtin/packages/vim/package.py | 2 +- .../repos/builtin/packages/vtk/package.py | 1 + 183 files changed, 329 insertions(+), 305 deletions(-) diff --git a/var/spack/repos/builtin/packages/ImageMagick/package.py b/var/spack/repos/builtin/packages/ImageMagick/package.py index f8173169e11..b0ccba10099 100644 --- a/var/spack/repos/builtin/packages/ImageMagick/package.py +++ b/var/spack/repos/builtin/packages/ImageMagick/package.py @@ -51,7 +51,7 @@ class Imagemagick(Package): url="http://sourceforge.net/projects/imagemagick/files/old-sources/6.x/6.8/ImageMagick-6.8.9-10.tar.gz/download") depends_on('jpeg') - depends_on('libtool') + depends_on('libtool', type='build') depends_on('libpng') depends_on('freetype') depends_on('fontconfig') diff --git a/var/spack/repos/builtin/packages/Mitos/package.py b/var/spack/repos/builtin/packages/Mitos/package.py index 83aca3dc6a0..d577a1b285f 100644 --- a/var/spack/repos/builtin/packages/Mitos/package.py +++ b/var/spack/repos/builtin/packages/Mitos/package.py @@ -41,6 +41,7 @@ class Mitos(Package): depends_on('dyninst@8.2.1:') depends_on('hwloc') depends_on('mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py index 7b6c3702aff..592681bb822 100644 --- a/var/spack/repos/builtin/packages/adept-utils/package.py +++ b/var/spack/repos/builtin/packages/adept-utils/package.py @@ -35,6 +35,7 @@ class AdeptUtils(Package): depends_on("boost") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(*std_cmake_args) diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py index 20cbd8e8c6c..59fbe50c93f 100644 --- a/var/spack/repos/builtin/packages/apex/package.py +++ b/var/spack/repos/builtin/packages/apex/package.py @@ -33,7 +33,7 @@ class Apex(Package): depends_on("binutils+libiberty") depends_on("boost@1.54:") - depends_on("cmake@2.8.12:") + depends_on('cmake@2.8.12:', type='build') depends_on("activeharmony@4.5:") depends_on("ompt-openmp") diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index d9021f80439..d5dc703c063 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -72,10 +72,10 @@ class ArpackNg(Package): depends_on('blas') depends_on('lapack') - depends_on('automake', when='@3.3.0') - depends_on('autoconf', when='@3.3.0') - depends_on('libtool@2.4.2:', when='@3.3.0') - depends_on('cmake@2.8.6:', when='@3.4.0:') + depends_on('automake', when='@3.3.0', type='build') + depends_on('autoconf', when='@3.3.0', type='build') + depends_on('libtool@2.4.2:', when='@3.3.0', type='build') + depends_on('cmake@2.8.6:', when='@3.4.0:', type='build') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 770ceed48b4..2de1c390db0 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -35,7 +35,7 @@ class Autoconf(Package): version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') version('2.62', '6c1f3b3734999035d77da5024aab4fbd') - depends_on('m4') + depends_on('m4', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py index fc65a04a066..2b4681778f0 100644 --- a/var/spack/repos/builtin/packages/automaded/package.py +++ b/var/spack/repos/builtin/packages/automaded/package.py @@ -44,6 +44,7 @@ class Automaded(Package): depends_on('mpi') depends_on('boost') depends_on('callpath') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake("-DSTATE_TRACKER_WITH_CALLPATH=ON", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py index 730a684ec57..a137fded088 100644 --- a/var/spack/repos/builtin/packages/bear/package.py +++ b/var/spack/repos/builtin/packages/bear/package.py @@ -31,7 +31,7 @@ class Bear(Package): version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011') - depends_on("cmake") + depends_on('cmake', type='build') depends_on("python") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py index 8d7da705e45..7dd17a062e5 100644 --- a/var/spack/repos/builtin/packages/bertini/package.py +++ b/var/spack/repos/builtin/packages/bertini/package.py @@ -37,8 +37,8 @@ class Bertini(Package): variant('mpi', default=True, description='Compile in parallel') - depends_on('flex') - depends_on('bison') + depends_on('flex', type='build') + depends_on('bison', type='build') depends_on('gmp') depends_on('mpfr') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 35d52128c3c..e329e6fd7a5 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -38,9 +38,9 @@ class Binutils(Package): version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') - depends_on('m4') - depends_on('flex') - depends_on('bison') + depends_on('m4', type='build') + depends_on('flex', type='build') + depends_on('bison', type='build') # Add a patch that creates binutils libiberty_pic.a which is preferred by # OpenSpeedShop and cbtf-krell diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index c5bc051c800..c7a125df15b 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -34,7 +34,7 @@ class Bison(Package): version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') - depends_on("m4") + depends_on("m4", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index ec7db6c08e5..216ae1ec122 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -35,6 +35,7 @@ class Boxlib(Package): version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git') depends_on('mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): args = std_cmake_args diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py index dee332be14c..49f98611268 100644 --- a/var/spack/repos/builtin/packages/c-blosc/package.py +++ b/var/spack/repos/builtin/packages/c-blosc/package.py @@ -38,7 +38,7 @@ class CBlosc(Package): version('1.8.1', 'd73d5be01359cf271e9386c90dcf5b05') version('1.8.0', '5b92ecb287695ba20cc33d30bf221c4f') - depends_on("cmake") + depends_on("cmake", type='build') depends_on("snappy") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py index a424c73859f..4a0fc54acc7 100644 --- a/var/spack/repos/builtin/packages/caliper/package.py +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -41,6 +41,7 @@ class Caliper(Package): depends_on('libunwind') depends_on('papi') depends_on('mpi', when='+mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('build', create=True): diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py index 2ad2dc60e4d..2f171fb9ce6 100644 --- a/var/spack/repos/builtin/packages/callpath/package.py +++ b/var/spack/repos/builtin/packages/callpath/package.py @@ -39,6 +39,7 @@ class Callpath(Package): depends_on("dyninst") depends_on("adept-utils") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): # TODO: offer options for the walker used. diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index e9e5da44868..646d106d88f 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -42,7 +42,7 @@ class Cantera(Package): variant('matlab', default=False, description='Build the Cantera Matlab toolbox') # Required dependencies - depends_on('scons') + depends_on('scons', type='build') # Recommended dependencies depends_on('blas', when='+lapack') diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 7ce90ce0db2..321d02b5568 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -53,7 +53,7 @@ class CbtfArgonavis(Package): version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git') - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") depends_on("papi") depends_on("mrnet@5.0.1:+lwthreads+krellpatch") diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index 7506f78146b..acb78a73951 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -64,7 +64,7 @@ class CbtfKrell(Package): variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") # Dependencies for cbtf-krell - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # For binutils service depends_on("binutils@2.24+krellpatch") diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py index fa7de3d4a37..5694535fccf 100644 --- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py +++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py @@ -53,7 +53,7 @@ class CbtfLanl(Package): version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl') - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # Dependencies for cbtf-krell depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py index 2231cf1d45b..017b897f3c6 100644 --- a/var/spack/repos/builtin/packages/cbtf/package.py +++ b/var/spack/repos/builtin/packages/cbtf/package.py @@ -57,7 +57,7 @@ class Cbtf(Package): variant('runtime', default=False, description="build only the runtime libraries and collectors.") - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index 80198fa2248..41dc9a274b8 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -40,7 +40,7 @@ class Cereal(Package): patch("Werror.patch") - depends_on("cmake @2.6.2:") + depends_on('cmake@2.6.2:', type='build') def install(self, spec, prefix): # Don't use -Werror diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index ea1b20e34ff..5c87978339e 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -46,7 +46,7 @@ class Cgal(Package): depends_on('mpfr') depends_on('gmp') depends_on('zlib') - depends_on('cmake') + depends_on('cmake', type='build') # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL) # FIXME : Optional third party libraries missing diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py index 6b54d1bf267..c258e89514a 100644 --- a/var/spack/repos/builtin/packages/cleverleaf/package.py +++ b/var/spack/repos/builtin/packages/cleverleaf/package.py @@ -40,6 +40,7 @@ class Cleverleaf(Package): depends_on("SAMRAI@3.8.0:") depends_on("hdf5+mpi") depends_on("boost") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(*std_cmake_args) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 7b2a125fe50..b39b0863966 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -47,8 +47,8 @@ class Cmake(Package): depends_on('ncurses', when='+ncurses') depends_on('openssl', when='+openssl') depends_on('qt', when='+qt') - depends_on('python@2.7.11:', when='+doc') - depends_on('py-sphinx', when='+doc') + depends_on('python@2.7.11:', when='+doc', type='build') + depends_on('py-sphinx', when='+doc', type='build') def url_for_version(self, version): """Handle CMake's version-based custom URLs.""" diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index 41f80d97615..aa2b3cc3bb2 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -32,6 +32,8 @@ class Cmocka(Package): version('1.0.1', 'ed861e501a21a92b2af63e466df2015e') parallel = False + depends_on('cmake', type='build') + def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake('..', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py index 7e055870872..283bc5adea3 100644 --- a/var/spack/repos/builtin/packages/cram/package.py +++ b/var/spack/repos/builtin/packages/cram/package.py @@ -33,6 +33,7 @@ class Cram(Package): extends('python') depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index d69f3e50093..a251a94470f 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -32,10 +32,10 @@ class Czmq(Package): version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz') - depends_on('libtool') - depends_on('automake') - depends_on('autoconf') - depends_on('pkg-config') + depends_on('libtool', type='build') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('pkg-config', type='build') depends_on('zeromq') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py index 3a8ddf28ef6..d0d22d97286 100644 --- a/var/spack/repos/builtin/packages/dakota/package.py +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -55,6 +55,7 @@ class Dakota(Package): depends_on('python') depends_on('boost') + depends_on('cmake', type='build') def url_for_version(self, version): return Dakota._url_str.format(version=version) diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py index 42fab63f98f..427997072c4 100644 --- a/var/spack/repos/builtin/packages/damselfly/package.py +++ b/var/spack/repos/builtin/packages/damselfly/package.py @@ -31,6 +31,8 @@ class Damselfly(Package): version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', git='https://github.com/llnl/damselfly.git', tag='v1.0') + depends_on('cmake', type='build') + def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index e7984466ba9..54604d351ff 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -60,7 +60,7 @@ class Dealii(Package): depends_on("boost@1.59.0:+thread+system+serialization+iostreams", when='~mpi') # NOQA: ignore=E501 depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi') # NOQA: ignore=E501 depends_on("bzip2") - depends_on("cmake") + depends_on("cmake", type='build') depends_on("lapack") depends_on("muparser") depends_on("suite-sparse") diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index 38742b7e7df..1685f0009f5 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -31,7 +31,7 @@ class Dia(Package): version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c') - depends_on('intltool') + depends_on('intltool', type='build') depends_on('gtkplus@2.6.0:') depends_on('cairo') #depends_on('libart') # optional dependency, not yet supported by spack. diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index b65eafb2cd9..267ba617565 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -43,12 +43,12 @@ class Doxygen(Package): # graphviz appears to be a run-time optional dependency variant('graphviz', default=True, description='Build with dot command support from Graphviz.') # NOQA: ignore=E501 - depends_on("cmake@2.8.12:") - depends_on("flex") - depends_on("bison") + depends_on("cmake@2.8.12:", type='build') + depends_on("flex", type='build') + depends_on("bison", type='build') # optional dependencies - depends_on("graphviz", when="+graphviz") + depends_on("graphviz", when="+graphviz", type='run') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py index 735936f087d..efe4de4abf1 100644 --- a/var/spack/repos/builtin/packages/dyninst/package.py +++ b/var/spack/repos/builtin/packages/dyninst/package.py @@ -43,6 +43,7 @@ class Dyninst(Package): depends_on("libelf") depends_on("libdwarf") depends_on("boost@1.42:") + depends_on('cmake', type='build') # new version uses cmake def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 9ff41076197..97343f499b1 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -47,7 +47,7 @@ class Eigen(Package): variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr') # TODO : dependency on googlehash, superlu, adolc missing - depends_on('cmake') + depends_on('cmake', type='build') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py index fe7a5ee4f64..5d5bb3be029 100644 --- a/var/spack/repos/builtin/packages/environment-modules/package.py +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -35,7 +35,7 @@ class EnvironmentModules(Package): version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb') # Dependencies: - depends_on('tcl') + depends_on('tcl', type=alldeps) def install(self, spec, prefix): tcl_spec = spec['tcl'] diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index 5e9227af46d..eb6c23afeb6 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -44,9 +44,7 @@ class Exodusii(Package): version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529') - # TODO: Make this a build dependency once build dependencies are supported - # (see: https://github.com/LLNL/spack/pull/378). - depends_on('cmake@2.8.7:') + depends_on('cmake@2.8.7:', type='build') depends_on('hdf5~shared~mpi') depends_on('netcdf~mpi') diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 51e827b2c52..2a9ac123f34 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -31,7 +31,7 @@ class Expat(Package): version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index b778538606a..800e4b9d96a 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -34,7 +34,7 @@ class Flex(Package): version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec') version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') - depends_on("bison") + depends_on("bison", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py index 2b972d63ae8..dec339a6aff 100644 --- a/var/spack/repos/builtin/packages/flux/package.py +++ b/var/spack/repos/builtin/packages/flux/package.py @@ -45,8 +45,8 @@ class Flux(Package): depends_on("py-cffi") # TODO: This provides a catalog, hacked with environment below for now - depends_on("docbook-xml") - depends_on("asciidoc") + depends_on("docbook-xml", type='build') + depends_on("asciidoc", type='build') def install(self, spec, prefix): # Bootstrap with autotools diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index caff06bdd6d..9ed83bc3be9 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -62,7 +62,7 @@ class Gdal(Package): depends_on("libpng") depends_on("zlib") depends_on("proj") - depends_on("py-numpy") + depends_on("py-numpy", type=nolink) parallel = False diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 58d8a545dbc..78ad4b307dc 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -41,7 +41,7 @@ class Gdb(Package): version('7.9', '8f8ced422fe462a00e0135a643544f17') version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc') - depends_on('texinfo') + depends_on('texinfo', type='build') def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py index 9f3552d53dc..47bbf369efd 100644 --- a/var/spack/repos/builtin/packages/gflags/package.py +++ b/var/spack/repos/builtin/packages/gflags/package.py @@ -37,6 +37,8 @@ class Gflags(Package): version('2.1.2', 'ac432de923f9de1e9780b5254884599f') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake("-DCMAKE_INSTALL_PREFIX=" + prefix, "-DBUILD_SHARED_LIBS=ON") diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 03e7d3e0312..4cbbaac3424 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -49,7 +49,7 @@ class Git(Package): depends_on("openssl") - depends_on("autoconf") + depends_on("autoconf", type='build') depends_on("curl") depends_on("expat") diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 75602493ce2..0a0a02f464e 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -38,7 +38,7 @@ class Glib(Package): depends_on("libffi") depends_on("zlib") - depends_on("pkg-config") + depends_on("pkg-config", type='build') depends_on('gettext', when=sys.platform == 'darwin') # The following patch is needed for gcc-6.1 diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index 0c9212f17d6..442c1cdf40a 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -35,8 +35,8 @@ class Glm(Package): url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') - - depends_on ("cmake") + + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py index c144d6660b2..f832834a280 100644 --- a/var/spack/repos/builtin/packages/global/package.py +++ b/var/spack/repos/builtin/packages/global/package.py @@ -34,7 +34,7 @@ class Global(Package): version('6.5', 'dfec818b4f53d91721e247cf7b218078') - depends_on('exuberant-ctags') + depends_on('exuberant-ctags', type=nolink) depends_on('ncurses') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index 39337884252..e2c2892f18c 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -35,7 +35,7 @@ class Gmp(Package): version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') version('6.0.0' , '6ef5869ae735db9995619135bd856b84') - depends_on("m4") + depends_on("m4", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 0951b86d57e..fe26cb3bf2d 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -53,7 +53,7 @@ class Gmsh(Package): depends_on('blas') depends_on('lapack') - depends_on('cmake@2.8:') + depends_on('cmake@2.8:', type='build') depends_on('gmp') depends_on('mpi', when='+mpi') # Assumes OpenGL with GLU is already provided by the system: diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 13b83517d17..ff2c2f67819 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -24,7 +24,7 @@ class Go(Package): # to-do, make non-c self-hosting compilers feasible without backflips # should be a dep on external go compiler - depends_on('go-bootstrap') + depends_on('go-bootstrap', type='build') depends_on('git') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index 9444253c8cb..1dc74fbcf4b 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -31,7 +31,7 @@ class Googletest(Package): version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4') - depends_on("cmake") + depends_on("cmake", type='build') def install(self, spec, prefix): which('cmake')('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py index f70f32cc8a1..087a322acc9 100644 --- a/var/spack/repos/builtin/packages/graphlib/package.py +++ b/var/spack/repos/builtin/packages/graphlib/package.py @@ -31,6 +31,8 @@ class Graphlib(Package): version('2.0.0', '43c6df84f1d38ba5a5dce0ae19371a70') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 2f99015ba26..e5898a6e590 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -44,7 +44,7 @@ class Graphviz(Package): depends_on("swig") depends_on("python") depends_on("ghostscript") - depends_on("pkg-config") + depends_on("pkg-config", type='build') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 1a50a424888..55eacc8d38d 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -50,6 +50,7 @@ class Gromacs(Package): depends_on('mpi', when='+mpi') depends_on('fftw') + depends_on('cmake', type='build') # TODO : add GPU support diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py index 50f380083cf..28b65711b0f 100644 --- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py +++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py @@ -53,7 +53,7 @@ class Hdf5Blosc(Package): depends_on("c-blosc") depends_on("hdf5") - depends_on("libtool") + depends_on("libtool", type='build') parallel = False diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index 90d5107e3be..060cd0b713d 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -45,12 +45,12 @@ class HoomdBlue(Package): variant('doc', default=True, description='Generate documentation') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) depends_on('boost+python') - depends_on('cmake') + depends_on('cmake', type='build') depends_on('mpi', when='+mpi') depends_on('cuda', when='+cuda') - depends_on('doxygen', when='+doc') + depends_on('doxygen', when='+doc', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 8e6cf429a7f..ed1e6c6cbf3 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -26,13 +26,13 @@ class Ibmisc(CMakePackage): depends_on('netcdf-cxx4', when='+netcdf') depends_on('udunits2', when='+udunits2') depends_on('googletest', when='+googletest') - depends_on('py-cython', when='+python') - depends_on('py-numpy', when='+python') + depends_on('py-cython', when='+python', type=nolink) + depends_on('py-numpy', when='+python', type=nolink) depends_on('boost', when='+boost') # Build dependencies - depends_on('cmake') - depends_on('doxygen') + depends_on('cmake', type='build') + depends_on('doxygen', type='build') def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index 47c5ca0c098..3bd21df89ea 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -38,7 +38,7 @@ class Ipopt(Package): depends_on("blas") depends_on("lapack") - depends_on("pkg-config") + depends_on("pkg-config", type='build') depends_on("mumps+double~mpi") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 99d138dcff9..536ce692364 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -44,16 +44,16 @@ class Julia(Package): patch('openblas.patch', when='@0.4:0.4.5') # Build-time dependencies: - # depends_on("awk") - # depends_on("m4") - # depends_on("pkg-config") + # depends_on("awk", type='build') + # depends_on("m4", type='build') + # depends_on("pkg-config", type='build') # Combined build-time and run-time dependencies: - depends_on("binutils") - depends_on("cmake @2.8:") - depends_on("git") - depends_on("openssl") - depends_on("python @2.7:2.999") + depends_on("binutils", type=nolink) + depends_on("cmake @2.8:", type=nolink) + depends_on("git", type=nolink) + depends_on("openssl", type=nolink) + depends_on("python @2.7:2.999", type=nolink) # I think that Julia requires the dependencies above, but it # builds fine (on my system) without these. We should enable them @@ -93,8 +93,8 @@ class Julia(Package): # USE_SYSTEM_LIBGIT2=0 # Run-time dependencies for Julia packages: - depends_on("hdf5") - depends_on("mpi") + depends_on("hdf5", type='run') + depends_on("mpi", type='run') def install(self, spec, prefix): # Explicitly setting CC, CXX, or FC breaks building libuv, one diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py index f2568100059..8aa6d727278 100644 --- a/var/spack/repos/builtin/packages/launchmon/package.py +++ b/var/spack/repos/builtin/packages/launchmon/package.py @@ -33,9 +33,9 @@ class Launchmon(Package): version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a') - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') def install(self, spec, prefix): configure( diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 5e4e420842b..938f4f6f3b7 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -40,6 +40,7 @@ class Libgd(Package): version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e') depends_on('libpng') + depends_on('cmake', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index 8615b2ed833..d1239ba0d98 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -35,8 +35,8 @@ class LibjpegTurbo(Package): version('1.3.1', '2c3a68129dac443a72815ff5bb374b05') # Can use either of these. - depends_on("yasm") - depends_on("nasm") + depends_on("yasm", type='build') + depends_on("nasm", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 0e410a50614..a0070d72d07 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -35,7 +35,7 @@ class Libtool(Package): version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e') version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50') - depends_on('m4') + depends_on('m4', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py index 63565c7aeab..0d29270b381 100644 --- a/var/spack/repos/builtin/packages/libuv/package.py +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -31,9 +31,9 @@ class Libuv(Package): version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool', type='build') def install(self, spec, prefix): bash = which("bash") diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index 746d4567e20..586eb970d8f 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -36,9 +36,9 @@ class Libxcb(Package): version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') version('1.11.1', '118623c15a96b08622603a71d8789bf3') - depends_on("python") + depends_on("python", type='build') depends_on("xcb-proto") - depends_on("pkg-config") + depends_on("pkg-config", type='build') depends_on("libpthread-stubs") depends_on('libxau') diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py index 073c2d1b9e3..127fe1204d2 100644 --- a/var/spack/repos/builtin/packages/llvm-lld/package.py +++ b/var/spack/repos/builtin/packages/llvm-lld/package.py @@ -34,6 +34,8 @@ class LlvmLld(Package): version('3.4', '3b6a17e58c8416c869c14dd37682f78e') + depends_on('cmake', type='build') + def install(self, spec, prefix): env['CXXFLAGS'] = self.compier.cxx11_flag diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 7a6ea7401ce..e79c123a7ea 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -51,7 +51,7 @@ class Llvm(Package): variant('all_targets', default=True, description="Build all supported targets, default targets ,NVPTX,AMDGPU,CppBackend") # Build dependency - depends_on('cmake @2.8.12.2:') + depends_on('cmake@2.8.12.2:', type='build') # Universal dependency depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 7d75866d52f..efa235f646a 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -42,8 +42,8 @@ class Lmod(Package): version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9') depends_on('lua@5.2:') - depends_on('lua-luaposix') - depends_on('lua-luafilesystem') + depends_on('lua-luaposix', type=nolink) + depends_on('lua-luafilesystem', type=nolink) parallel = False diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index ae34d256911..13c0ce768fe 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -37,7 +37,7 @@ class Mbedtls(Package): version('2.1.3' , '7eb4cf1dfa68578a2c8dbd0b6fa752dd') version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py index 135384e2f77..31672abaec0 100644 --- a/var/spack/repos/builtin/packages/memaxes/package.py +++ b/var/spack/repos/builtin/packages/memaxes/package.py @@ -32,7 +32,7 @@ class Memaxes(Package): version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5', url='https://github.com/llnl/MemAxes/archive/v0.5.tar.gz') - depends_on("cmake@2.8.9:") + depends_on('cmake@2.8.9:', type='build') depends_on("qt@5:") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index bd9c9eec4aa..3bad17b5cb0 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -44,8 +44,8 @@ class Mesa(Package): # mesa 10.x # depends_on("py-mako") - # depends_on("flex") - # depends_on("bison") + # depends_on("flex", type='build') + # depends_on("bison", type='build') # depends_on("dri2proto") # depends_on("libxcb") # depends_on("libxshmfence") diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index c4f2afaff25..2180f2cce2f 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -50,7 +50,7 @@ class Metis(Package): variant('idx64', default=False, description='Use int64_t as default index type') variant('real64', default=False, description='Use double precision floating point types') - depends_on('cmake@2.8:', when='@5:') # build-time dependency + depends_on('cmake@2.8:', when='@5:', type='build') patch('install_gklib_defs_rename.patch', when='@5:') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 1b4456380b4..e7a1d963889 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -62,7 +62,7 @@ class Mfem(Package): depends_on('blas', when='+suite-sparse') depends_on('lapack', when='+suite-sparse') depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:') - depends_on('cmake', when='^metis@5:') + depends_on('cmake', when='^metis@5:', type='build') def check_variants(self, spec): if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec): diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py index b328b98ecf7..e659663d901 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpibash/package.py @@ -36,7 +36,7 @@ class Mpibash(Package): patch('mpibash-4.3.patch', level=1, when='@4.3') # above patch modifies configure.ac - depends_on('autoconf') + depends_on('autoconf', type='build') # uses MPI_Exscan which is in MPI-1.2 and later depends_on('mpi@1.2:') diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py index 993f1472450..64b7324415f 100644 --- a/var/spack/repos/builtin/packages/muster/package.py +++ b/var/spack/repos/builtin/packages/muster/package.py @@ -39,6 +39,7 @@ class Muster(Package): depends_on("boost") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index f8af76429b8..0fb181a7b2e 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -34,7 +34,7 @@ class NetcdfCxx4(Package): version('4.2.1', 'd019853802092cf686254aaba165fc81') depends_on('netcdf') - depends_on("autoconf") + depends_on("autoconf", type='build') def install(self, spec, prefix): # Rebuild to prevent problems of inconsistency in git repo diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index c2256d5e9f9..063d38e4f94 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -39,7 +39,7 @@ class Netcdf(Package): variant('mpi', default=True, description='Enables MPI parallelism') variant('hdf4', default=False, description='Enable HDF4 support') - depends_on("m4") + depends_on("m4", type='build') depends_on("hdf", when='+hdf4') # Required for DAP support diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 47857eb713e..70015baf1c5 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -52,7 +52,7 @@ class NetlibLapack(Package): provides('blas', when='~external-blas') provides('lapack') - depends_on('cmake') + depends_on('cmake', type='build') depends_on('blas', when='+external-blas') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index f7fe26a42da..a8250a38de3 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -42,9 +42,9 @@ class NetlibScalapack(Package): provides('scalapack') - depends_on('cmake') depends_on('mpi') depends_on('lapack') + depends_on('cmake', when='@2.0.0:', type='build') def install(self, spec, prefix): options = [ diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index 7e094370ac6..97164165e01 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -35,7 +35,7 @@ class Numdiff(Package): version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') - depends_on('gettext', when=sys.platform=='darwin') + depends_on('gettext', when=sys.platform=='darwin', type='build') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 06b6b7cbb07..108c8f8a41c 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -42,7 +42,7 @@ class Oce(Package): variant('tbb', default=True, description='Build with Intel Threading Building Blocks') - depends_on('cmake@2.8:') + depends_on('cmake@2.8:', type='build') depends_on('tbb', when='+tbb') # There is a bug in OCE which appears with Clang (version?) or GCC 6.0 diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 1e835512ca7..aa521899e5c 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -68,9 +68,9 @@ class Octave(Package): depends_on('blas') depends_on('lapack') # Octave does not configure with sed from darwin: - depends_on('sed', when=sys.platform == 'darwin') + depends_on('sed', when=sys.platform == 'darwin', type='build') depends_on('pcre') - depends_on('pkg-config') + depends_on('pkg-config', type='build') # Strongly recommended dependencies depends_on('readline', when='+readline') diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py index e74dcf6c233..800c04ae0ea 100644 --- a/var/spack/repos/builtin/packages/ompt-openmp/package.py +++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py @@ -31,7 +31,7 @@ class OmptOpenmp(Package): version('0.1', '2334e6a84b52da41b27afd9831ed5370') - # depends_on("foo") + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir("runtime/build", create=True): diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index 989c66316c3..ff551d0b920 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -54,7 +54,8 @@ class Opencv(Package): depends_on('python') depends_on('py-numpy') - depends_on('eigen', when='+eigen') + depends_on('eigen', when='+eigen', type='build') + depends_on('cmake', type='build') # FIXME : GUI extensions missing # FIXME : CUDA extensions still missing diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index 1d00edb06d3..1bc5b04f6fc 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -43,7 +43,7 @@ class Openjpeg(Package): version('1.5.2', '545f98923430369a6b046ef3632ef95c') version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index c501ea063c3..4e2694a53c6 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -80,7 +80,7 @@ class Openspeedshop(Package): variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build depends_on("bison") depends_on("flex") diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index d0db4f7f207..4bbf0c13110 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -34,9 +34,9 @@ class P4est(Package): variant('tests', default=True, description='Run small tests') # build dependencies - depends_on('automake') - depends_on('autoconf') - depends_on('libtool@2.4.2:') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool@2.4.2:', type='build') # other dependencies depends_on('lua') # Needed for the submodule sc diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py index d6324b63e6c..97d36d94a49 100644 --- a/var/spack/repos/builtin/packages/paradiseo/package.py +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -48,13 +48,13 @@ class Paradiseo(Package): variant('gnuplot', default=False, description='Enable GnuPlot support') # Required dependencies - depends_on ("cmake") + depends_on ("cmake", type='build') # Optional dependencies depends_on ("mpi", when="+mpi") - depends_on ("doxygen", when='+doc') + depends_on ("doxygen", when='+doc', type='build') depends_on ("gnuplot", when='+gnuplot') - depends_on ("eigen", when='+edo') + depends_on ("eigen", when='+edo', type='build') depends_on ("boost~mpi", when='+edo~mpi') depends_on ("boost+mpi", when='+edo+mpi') diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index 59c44c8a4a2..deee46df8ff 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -39,7 +39,7 @@ class ParallelNetcdf(Package): variant('fortran', default=True, description='Build the Fortran Interface') variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)') - depends_on("m4") + depends_on("m4", type='build') depends_on("mpi") # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 711cbc98c9c..75f5272006e 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -43,12 +43,13 @@ class Paraview(Package): variant('opengl2', default=False, description='Enable OpenGL2 backend') depends_on('python@2:2.7', when='+python') - depends_on('py-numpy', when='+python') - depends_on('py-matplotlib', when='+python') + depends_on('py-numpy', when='+python', type='run') + depends_on('py-matplotlib', when='+python', type='run') depends_on('tcl', when='+tcl') depends_on('mpi', when='+mpi') depends_on('qt@:4', when='+qt') + depends_on('cmake', type='build') depends_on('bzip2') depends_on('freetype') #depends_on('hdf5+mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 9b36f273e4c..b2ceadc1283 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -42,7 +42,7 @@ class Parmetis(Package): variant('debug', default=False, description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - depends_on('cmake@2.8:') # build dependency + depends_on('cmake@2.8:', type='build') # build dependency depends_on('mpi') depends_on('metis@5:') diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py index d38dcd7b963..e7b18ce7a84 100644 --- a/var/spack/repos/builtin/packages/pidx/package.py +++ b/var/spack/repos/builtin/packages/pidx/package.py @@ -36,6 +36,7 @@ class Pidx(Package): version('1.0', git='https://github.com/sci-visus/PIDX.git', commit='6afa1cf71d1c41263296dc049c8fabaf73c296da') + depends_on('cmake', type='build') depends_on("mpi") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py index fc77ba74123..192dd86e0ef 100644 --- a/var/spack/repos/builtin/packages/psi4/package.py +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -41,8 +41,8 @@ class Psi4(Package): depends_on('lapack') depends_on('boost+chrono+filesystem+python+regex+serialization+system+timer+thread') depends_on('python') - depends_on('cmake') - depends_on('py-numpy') + depends_on('cmake', type='build') + depends_on('py-numpy', type=nolink) # Optional dependencies # TODO: add packages for these diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index 8ba6696b0c3..e1ea71fb671 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -37,9 +37,9 @@ class PyAstroid(Package): version('1.4.1', 'ed70bfed5e4b25be4292e7fe72da2c02') extends('python') - depends_on('py-logilab-common') - depends_on('py-setuptools') - depends_on('py-six') + depends_on('py-logilab-common', type=nolink) + depends_on('py-setuptools', type='build') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index a9962777dc0..25dce87e494 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -38,18 +38,18 @@ class PyAstropy(Package): # Required dependencies extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) # Optional dependencies - depends_on('py-h5py') - depends_on('py-beautifulsoup4') - depends_on('py-pyyaml') - depends_on('py-scipy') + depends_on('py-h5py', type=nolink) + depends_on('py-beautifulsoup4', type=nolink) + depends_on('py-pyyaml', type=nolink) + depends_on('py-scipy', type=nolink) depends_on('libxml2') - depends_on('py-matplotlib') - depends_on('py-pytz') - depends_on('py-scikit-image') - depends_on('py-pandas') + depends_on('py-matplotlib', type=nolink) + depends_on('py-pytz', type=nolink) + depends_on('py-scikit-image', type=nolink) + depends_on('py-pandas', type=nolink) # System dependencies depends_on('cfitsio') diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py index f2fd3cd683c..507664949b8 100644 --- a/var/spack/repos/builtin/packages/py-autopep8/package.py +++ b/var/spack/repos/builtin/packages/py-autopep8/package.py @@ -8,8 +8,8 @@ class PyAutopep8(Package): version('1.2.2', 'def3d023fc9dfd1b7113602e965ad8e1') extends('python') - depends_on('py-setuptools') - depends_on('py-pep8') + depends_on('py-setuptools', type='build') + depends_on('py-pep8', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py index 13f604bacd3..9c7f6454df4 100644 --- a/var/spack/repos/builtin/packages/py-basemap/package.py +++ b/var/spack/repos/builtin/packages/py-basemap/package.py @@ -35,10 +35,10 @@ class PyBasemap(Package): version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8') extends('python') - depends_on('py-setuptools') - depends_on('py-numpy') - depends_on('py-matplotlib+gui') - depends_on('pil') + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib+gui', type=nolink) + depends_on('pil', type=nolink) depends_on("geos") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py index 26f42e060b6..bcc889756ef 100644 --- a/var/spack/repos/builtin/packages/py-biopython/package.py +++ b/var/spack/repos/builtin/packages/py-biopython/package.py @@ -32,8 +32,8 @@ class PyBiopython(Package): version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67') extends('python') - depends_on('py-mx') - depends_on('py-numpy') + depends_on('py-mx', type=nolink) + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py index 05a1f5bcbbe..8d7a2343d11 100644 --- a/var/spack/repos/builtin/packages/py-blessings/package.py +++ b/var/spack/repos/builtin/packages/py-blessings/package.py @@ -31,7 +31,7 @@ class PyBlessings(Package): version('1.6', '4f552a8ebcd4982693c92571beb99394') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends("python") diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 1a186b219cb..2483fab85f1 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -32,7 +32,7 @@ class PyBottleneck(Package): version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index 58d0a81990e..e54d50fa506 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -33,8 +33,8 @@ class PyCffi(Package): version('1.1.2', 'ca6e6c45b45caa87aee9adc7c796eaea') extends('python') - depends_on('py-setuptools') - depends_on('py-pycparser') + depends_on('py-setuptools', type='build') + depends_on('py-pycparser', type=nolink) depends_on('libffi') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index 92a5bd00884..b7eaf58cd67 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -32,7 +32,7 @@ class PyCoverage(Package): version('4.0a6', '1bb4058062646148965bef0796b61efc') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index 7fe2f953f70..2deaa2f74e8 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -35,12 +35,12 @@ class PyCsvkit(Package): extends('python') - depends_on('py-dateutil') - depends_on('py-dbf') - depends_on('py-xlrd') - depends_on('py-SQLAlchemy') - depends_on('py-six') - depends_on('py-openpyxl') + depends_on('py-dateutil', type=nolink) + depends_on('py-dbf', type=nolink) + depends_on('py-xlrd', type=nolink) + depends_on('py-SQLAlchemy', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-openpyxl', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py index 831f86e81cf..b7dbab3d979 100644 --- a/var/spack/repos/builtin/packages/py-dask/package.py +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -33,7 +33,7 @@ class PyDask(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index eb8eb09e75d..dfd1e143d90 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -34,8 +34,8 @@ class PyDateutil(Package): version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') extends('python') - depends_on('py-setuptools') - depends_on('py-six') + depends_on('py-setuptools', type='build') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index 90a95cd0cb9..bd78f262f43 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -33,7 +33,7 @@ class PyDecorator(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py index d57ef4bd76c..397f737cb1d 100644 --- a/var/spack/repos/builtin/packages/py-emcee/package.py +++ b/var/spack/repos/builtin/packages/py-emcee/package.py @@ -35,7 +35,7 @@ class PyEmcee(Package): version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py index b261467d84d..2fabe03d663 100644 --- a/var/spack/repos/builtin/packages/py-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-flake8/package.py @@ -34,7 +34,7 @@ class PyFlake8(Package): version('2.5.4', 'a4585b3569b95c3f66acb8294a7f06ef') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py index 9d987b284e7..11ba639b85d 100644 --- a/var/spack/repos/builtin/packages/py-funcsigs/package.py +++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py @@ -34,7 +34,7 @@ class PyFuncsigs(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py index cba479a88f8..ea8d26c7966 100644 --- a/var/spack/repos/builtin/packages/py-genshi/package.py +++ b/var/spack/repos/builtin/packages/py-genshi/package.py @@ -36,7 +36,7 @@ class PyGenshi(Package): version('0.6', '604e8b23b4697655d36a69c2d8ef7187') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py index 3381c4a5ac3..b08b03d1f1c 100644 --- a/var/spack/repos/builtin/packages/py-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py @@ -32,7 +32,7 @@ class PyGnuplot(Package): version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index 67461babe71..c1950a91ac0 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -41,17 +41,17 @@ class PyH5py(Package): extends('python') # Build dependencies - depends_on('py-cython@0.19:') - depends_on('pkg-config') + depends_on('py-cython@0.19:', type='build') + depends_on('pkg-config', type='build') depends_on('hdf5@1.8.4:') depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') # Build and runtime dependencies - depends_on('py-numpy@1.6.1:') + depends_on('py-numpy@1.6.1:', type=nolink) # Runtime dependencies - depends_on('py-six') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'configure', diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py index 47751a702d1..d7446c06d47 100644 --- a/var/spack/repos/builtin/packages/py-iminuit/package.py +++ b/var/spack/repos/builtin/packages/py-iminuit/package.py @@ -35,12 +35,12 @@ class PyIminuit(Package): # Required dependencies extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') # Optional dependencies - depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-cython', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py index 7a94f90b386..b583609953c 100644 --- a/var/spack/repos/builtin/packages/py-ipython/package.py +++ b/var/spack/repos/builtin/packages/py-ipython/package.py @@ -33,8 +33,8 @@ class PyIpython(Package): version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f') extends('python') - depends_on('py-pygments') - depends_on('py-setuptools') + depends_on('py-pygments', type=nolink) + depends_on('py-setuptools', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index 48312d9baf6..57f26e3b904 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -43,8 +43,8 @@ class PyJinja2(Package): version('2.7', 'ec70433f325051dcedacbb2465028a35') extends("python") - depends_on("py-setuptools") - depends_on("py-markupsafe") + depends_on("py-setuptools", type='build') + depends_on("py-markupsafe", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py index 998b41abc65..38cc81b8953 100644 --- a/var/spack/repos/builtin/packages/py-lockfile/package.py +++ b/var/spack/repos/builtin/packages/py-lockfile/package.py @@ -41,7 +41,7 @@ class PyLockfile(Package): version('0.10.2', '1aa6175a6d57f082cd12e7ac6102ab15') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py index 8675c48e9a8..6dab4a40e4e 100644 --- a/var/spack/repos/builtin/packages/py-logilab-common/package.py +++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -34,8 +34,8 @@ class PyLogilabCommon(Package): version('1.2.0', 'f7b51351b7bfe052746fa04c03253c0b') extends("python") - depends_on("py-setuptools") - depends_on("py-six") + depends_on("py-setuptools", type='build') + depends_on("py-six", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py index a03ef4defb9..56741ec11f2 100644 --- a/var/spack/repos/builtin/packages/py-mako/package.py +++ b/var/spack/repos/builtin/packages/py-mako/package.py @@ -33,7 +33,7 @@ class PyMako(Package): version('1.0.1', '9f0aafd177b039ef67b90ea350497a54') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index 58c9f700665..ee396de7be6 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -44,7 +44,7 @@ class PyMarkupsafe(Package): version('0.19', '64b05361adb92c11839fc470e308c593') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 14f9716ae6b..d4f96706b3b 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -38,19 +38,19 @@ class PyMatplotlib(Package): extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') - depends_on('py-pyside', when='+gui') - depends_on('py-ipython', when='+ipython') - depends_on('py-pyparsing') - depends_on('py-six') - depends_on('py-dateutil') - depends_on('py-pytz') - depends_on('py-nose') - depends_on('py-numpy') - depends_on('py-mock') - depends_on('py-pbr') - depends_on('py-funcsigs') + depends_on('py-pyside', when='+gui', type=nolink) + depends_on('py-ipython', when='+ipython', type=nolink) + depends_on('py-pyparsing', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-dateutil', type=nolink) + depends_on('py-pytz', type=nolink) + depends_on('py-nose', type=nolink) + depends_on('py-numpy', type=nolink) + depends_on('py-mock', type=nolink) + depends_on('py-pbr', type=nolink) + depends_on('py-funcsigs', type=nolink) - depends_on('pkg-config') + depends_on('pkg-config', type='build') depends_on('freetype') depends_on('qt', when='+gui') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py index 9bcbb5a9270..399c10005ea 100644 --- a/var/spack/repos/builtin/packages/py-mistune/package.py +++ b/var/spack/repos/builtin/packages/py-mistune/package.py @@ -40,7 +40,7 @@ class PyMistune(Package): version('0.5', '997736554f1f95eea78c66ae339b5722') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index 0587131b886..f4c178de670 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -35,8 +35,8 @@ class PyMock(Package): version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb') extends('python') - depends_on('py-pbr') - depends_on('py-setuptools@17.1:') + depends_on('py-pbr', type=nolink) + depends_on('py-setuptools@17.1:', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index 2764b8b3c6e..a749e16779e 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -33,7 +33,7 @@ class PyMpi4py(Package): version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('mpi') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py index 9918ba3e64f..46b44f34dd5 100644 --- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py +++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py @@ -32,7 +32,7 @@ class PyMysqldb1(Package): version('1.2.5', '332c8f4955b6bc0c79ea15170bf7321b') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py index 16506e3eca0..81f9fe4d098 100644 --- a/var/spack/repos/builtin/packages/py-nestle/package.py +++ b/var/spack/repos/builtin/packages/py-nestle/package.py @@ -35,10 +35,10 @@ class PyNestle(Package): # Required dependencies extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) # Optional dependencies - depends_on('py-scipy') + depends_on('py-scipy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py index e3f857a0cea..9a354cb1c16 100644 --- a/var/spack/repos/builtin/packages/py-netcdf/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf/package.py @@ -32,8 +32,8 @@ class PyNetcdf(Package): version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af') extends('python') - depends_on('py-numpy') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-cython', type=nolink) depends_on('netcdf') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index 6bdb24e36e5..d5457176284 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -33,7 +33,7 @@ class PyNetworkx(Package): extends('python') - depends_on('py-decorator') + depends_on('py-decorator', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index abb2d500a2b..d15a1784d1e 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -37,7 +37,7 @@ class PyNose(Package): version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') extends('python', ignore=r'bin/nosetests.*$') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index d8bacd179ff..fd8d7dc0c6d 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -34,7 +34,7 @@ class PyNumexpr(Package): version('2.5', '84f66cced45ba3e30dcf77a937763aaa') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index e9672b7bb0b..273f5bfd8de 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -43,7 +43,7 @@ class PyNumpy(Package): variant('lapack', default=True) extends('python') - depends_on('py-nose') + depends_on('py-nose', type='build') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 30cb52348f5..624da58ff30 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -34,8 +34,8 @@ class PyOpenpyxl(Package): extends('python') - depends_on('py-jdcal') - depends_on('py-setuptools') + depends_on('py-jdcal', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 7f54fc5d761..8bd4227faf6 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -35,12 +35,12 @@ class PyPandas(Package): version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') extends('python') - depends_on('py-dateutil') - depends_on('py-numpy') - depends_on('py-setuptools') - depends_on('py-pytz') - depends_on('py-numexpr') - depends_on('py-bottleneck') + depends_on('py-dateutil', type=nolink) + depends_on('py-numpy', type=nolink) + depends_on('py-setuptools', type='build') + depends_on('py-pytz', type=nolink) + depends_on('py-numexpr', type=nolink) + depends_on('py-bottleneck', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index 336ea371440..8502b0b3642 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -34,7 +34,7 @@ class PyPbr(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py index 987783b3927..ffcc2b318c7 100644 --- a/var/spack/repos/builtin/packages/py-pep8/package.py +++ b/var/spack/repos/builtin/packages/py-pep8/package.py @@ -8,7 +8,7 @@ class PyPep8(Package): version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py index 7d8a6359792..608f4e16c16 100644 --- a/var/spack/repos/builtin/packages/py-periodictable/package.py +++ b/var/spack/repos/builtin/packages/py-periodictable/package.py @@ -33,8 +33,8 @@ class PyPeriodictable(Package): version('1.4.1', '7246b63cc0b6b1be6e86b6616f9e866e') - depends_on('py-numpy') - depends_on('py-pyparsing') + depends_on('py-numpy', type=nolink) + depends_on('py-pyparsing', type=nolink) extends('python') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py index 68774c90c2b..a3a4b7a9f7f 100644 --- a/var/spack/repos/builtin/packages/py-phonopy/package.py +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -33,10 +33,10 @@ class PyPhonopy(Package): version('1.10.0', '973ed1bcea46e21b9bf747aab9061ff6') extends('python') - depends_on('py-numpy') - depends_on('py-scipy') - depends_on('py-matplotlib') - depends_on('py-pyyaml') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-pyyaml', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--home=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 25cf412b316..13a09f63cfa 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -62,8 +62,8 @@ class PyPillow(Package): # Required dependencies extends('python') - depends_on('binutils') - depends_on('py-setuptools') + depends_on('binutils', type='build') + depends_on('py-setuptools', type='build') # Recommended dependencies depends_on('jpeg', when='+jpeg') diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py index e3edc7b706f..cf814733d49 100644 --- a/var/spack/repos/builtin/packages/py-prettytable/package.py +++ b/var/spack/repos/builtin/packages/py-prettytable/package.py @@ -38,7 +38,7 @@ class PyPrettytable(Package): version('0.7.2', 'a6b80afeef286ce66733d54a0296b13b') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py index da3a65c22ea..dd2b5651de7 100644 --- a/var/spack/repos/builtin/packages/py-protobuf/package.py +++ b/var/spack/repos/builtin/packages/py-protobuf/package.py @@ -44,7 +44,7 @@ class PyProtobuf(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index 9c6e2192647..02f37d8b784 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -38,7 +38,7 @@ class PyPy2neo(Package): version('2.0.5', '143b1f9c0aa22faf170c1b9f84c7343b') version('2.0.4', 'b3f7efd3344dc3f66db4eda11e5899f7') - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') extends("python") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index c33769c526f..9afba500779 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -33,7 +33,7 @@ class PyPycparser(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index fedf3d068dc..0ca15dd10dc 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -33,7 +33,7 @@ class PyPygments(Package): version('2.0.2', '238587a1370d62405edabd0794b3ec4a') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 66118e82282..7107b2987fd 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -34,8 +34,8 @@ class PyPylint(Package): version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44') extends('python') - depends_on('py-nose') - depends_on('py-setuptools') + depends_on('py-nose', type='build') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py index b090e256821..05fb7aa22cc 100644 --- a/var/spack/repos/builtin/packages/py-pyqt/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt/package.py @@ -34,7 +34,7 @@ class PyPyqt(Package): version('4.11.3', '997c3e443165a89a559e0d96b061bf70') extends('python') - depends_on('py-sip') + depends_on('py-sip', type=nolink) # TODO: allow qt5 when conditional deps are supported. # TODO: Fix version matching so that @4 works like @:4 diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index affee6c55a1..cd174ce6583 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -32,11 +32,10 @@ class PyPyside(Package): version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d') - # TODO: make build dependency - # depends_on("cmake") + depends_on('cmake', type='build') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('qt@:4') def patch(self): diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py index 47592fb3d1d..58ed067b218 100644 --- a/var/spack/repos/builtin/packages/py-pytables/package.py +++ b/var/spack/repos/builtin/packages/py-pytables/package.py @@ -34,9 +34,9 @@ class PyPytables(Package): extends('python') depends_on('hdf5') - depends_on('py-numpy') - depends_on('py-numexpr') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-numexpr', type=nolink) + depends_on('py-cython', type=nolink) def install(self, spec, prefix): env["HDF5_DIR"] = spec['hdf5'].prefix diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py index ae6393986d6..c2c7c4de4f8 100644 --- a/var/spack/repos/builtin/packages/py-python-daemon/package.py +++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py @@ -42,8 +42,8 @@ class PyPythonDaemon(Package): version('2.0.5', '73e7f49f525c51fa4a995aea4d80de41') extends("python") - depends_on("py-setuptools") - depends_on("py-lockfile") + depends_on("py-setuptools", type='build') + depends_on("py-lockfile", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py index 91b1db993ed..047214c58ec 100644 --- a/var/spack/repos/builtin/packages/py-restview/package.py +++ b/var/spack/repos/builtin/packages/py-restview/package.py @@ -34,8 +34,8 @@ class PyRestview(Package): version('2.6.1', 'ac8b70e15b8f1732d1733d674813666b') extends('python') - depends_on('py-docutils') - depends_on('py-pygments') + depends_on('py-docutils', type=nolink) + depends_on('py-pygments', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py index 03fd2b4a06f..8f4771f0eb5 100644 --- a/var/spack/repos/builtin/packages/py-rpy2/package.py +++ b/var/spack/repos/builtin/packages/py-rpy2/package.py @@ -33,7 +33,7 @@ class PyRpy2(Package): version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('R') diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 4c8fd0942a4..26c286e4be0 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -36,12 +36,12 @@ class PyScikitImage(Package): extends('python', ignore=r'bin/.*\.py$') - depends_on('py-dask') - depends_on('pil') - depends_on('py-networkx') - depends_on('py-six') - depends_on('py-scipy') - depends_on('py-matplotlib') + depends_on('py-dask', type=nolink) + depends_on('pil', type=nolink) + depends_on('py-networkx', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 7bb5853b191..1a6112bcf3e 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -35,9 +35,9 @@ class PyScikitLearn(Package): extends('python') - depends_on('py-setuptools') - depends_on('py-numpy') - depends_on('py-scipy') + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index f7c372b3459..ea3731cf1bb 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -34,8 +34,8 @@ class PyScipy(Package): version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') extends('python') - depends_on('py-nose') - depends_on('py-numpy+blas+lapack') + depends_on('py-nose', type='build') + depends_on('py-numpy+blas+lapack', type=nolink) def install(self, spec, prefix): if 'atlas' in spec: diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py index a2240c68a4c..27188e14172 100644 --- a/var/spack/repos/builtin/packages/py-shiboken/package.py +++ b/var/spack/repos/builtin/packages/py-shiboken/package.py @@ -32,11 +32,10 @@ class PyShiboken(Package): version('1.2.2', '345cfebda221f525842e079a6141e555') - # TODO: make build dependency - # depends_on("cmake") + depends_on('cmake', type='build') extends('python') - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') depends_on("libxml2") depends_on("qt@:4.8") diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 3efb3d43172..eb4846d5af8 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -33,7 +33,7 @@ class PySix(Package): version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py index 82ae2a2e69c..feb3856e8b8 100644 --- a/var/spack/repos/builtin/packages/py-sncosmo/package.py +++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py @@ -37,15 +37,15 @@ class PySncosmo(Package): # Required dependencies # py-sncosmo binaries are duplicates of those from py-astropy extends('python', ignore=r'bin/.*') - depends_on('py-numpy') - depends_on('py-scipy') - depends_on('py-astropy') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-astropy', type=nolink) # Recommended dependencies - depends_on('py-matplotlib') - depends_on('py-iminuit') - depends_on('py-emcee') - depends_on('py-nestle') + depends_on('py-matplotlib', type=nolink) + depends_on('py-iminuit', type=nolink) + depends_on('py-emcee', type=nolink) + depends_on('py-nestle', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py index 53af720c50e..0e972480f36 100644 --- a/var/spack/repos/builtin/packages/py-storm/package.py +++ b/var/spack/repos/builtin/packages/py-storm/package.py @@ -34,7 +34,7 @@ class PyStorm(Package): version('0.20', '8628503141f0f06c0749d607ac09b9c7') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py index a1026a9b4b4..b10244acddf 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tappy/package.py @@ -33,7 +33,7 @@ class PyTappy(Package): version('1.6', 'c8bdb93ad66e05f939905172a301bedf') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index 200a33a676c..56056ebad16 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -35,8 +35,8 @@ class PyTuiview(Package): version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') extends("python") - depends_on("py-pyqt") - depends_on("py-numpy") + depends_on("py-pyqt", type=nolink) + depends_on("py-numpy", type=nolink) depends_on("gdal") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py index 27db4adff42..2ce83cd24c0 100644 --- a/var/spack/repos/builtin/packages/py-twisted/package.py +++ b/var/spack/repos/builtin/packages/py-twisted/package.py @@ -32,7 +32,7 @@ class PyTwisted(Package): version('15.4.0', '5337ffb6aeeff3790981a2cd56db9655') version('15.3.0', 'b58e83da2f00b3352afad74d0c5c4599') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py index f669a500ec8..174ab0ca5f2 100644 --- a/var/spack/repos/builtin/packages/py-unittest2/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -35,7 +35,7 @@ class PyUnittest2(Package): version('1.1.0', 'f72dae5d44f091df36b6b513305ea000') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py index ca857395fbe..95e6dcbff0e 100644 --- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py @@ -36,7 +36,7 @@ class PyUnittest2py3k(Package): version('0.5.1', '8824ff92044310d9365f90d892bf0f09') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py index 0accc72df8a..48ba84e7bc8 100644 --- a/var/spack/repos/builtin/packages/py-urwid/package.py +++ b/var/spack/repos/builtin/packages/py-urwid/package.py @@ -31,7 +31,7 @@ class PyUrwid(Package): version('1.3.0', 'a989acd54f4ff1a554add464803a9175') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends("python") diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index d42cb96eb77..d6b33ae175a 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -35,7 +35,7 @@ class PyVirtualenv(Package): version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py index b0adbe36580..9588b879fa0 100644 --- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py +++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py @@ -35,9 +35,9 @@ class PyWcsaxes(Package): version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920') extends('python', ignore=r'bin/pbr') - depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-astropy') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-astropy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py index 68b6f3d6791..9e383a9a19f 100644 --- a/var/spack/repos/builtin/packages/py-wheel/package.py +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -33,7 +33,7 @@ class PyWheel(Package): version('0.26.0', '4cfc6e7e3dc7377d0164914623922a10') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py index 60f740c98dc..f7fe4037a13 100644 --- a/var/spack/repos/builtin/packages/py-yapf/package.py +++ b/var/spack/repos/builtin/packages/py-yapf/package.py @@ -33,7 +33,7 @@ class PyYapf(Package): version('0.2.1', '348ccf86cf2057872e4451b204fb914c') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index 280c9cc12c0..f7cbcc27365 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -45,7 +45,7 @@ class Qhull(Package): # https://github.com/qhull/qhull/pull/5 patch('qhull-iterator.patch', when='@1.0') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 0c91a5ce87c..f33e5c2d0e5 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -60,8 +60,8 @@ class Qt(Package): # Webkit # depends_on("gperf") - # depends_on("flex") - # depends_on("bison") + # depends_on("flex", type='build') + # depends_on("bison", type='build') # depends_on("ruby") # depends_on("icu4c") diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py index 763ec1b9a2e..96692ac7c14 100644 --- a/var/spack/repos/builtin/packages/ravel/package.py +++ b/var/spack/repos/builtin/packages/ravel/package.py @@ -33,8 +33,7 @@ class Ravel(Package): version('1.0.0', 'b25fece58331c2adfcce76c5036485c2') - # TODO: make this a build dependency - depends_on('cmake@2.8.9:') + depends_on('cmake@2.8.9:', type='build') depends_on('muster@1.0.1:') depends_on('otf') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index b8a65e8574b..bcd317eb8ff 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -40,9 +40,9 @@ class Rose(Package): patch('add_spack_compiler_recognition.patch') - depends_on("autoconf@2.69") - depends_on("automake@1.14") - depends_on("libtool@2.4") + depends_on("autoconf@2.69", type='build') + depends_on("automake@1.14", type='build') + depends_on("libtool@2.4", type='build') depends_on("boost@1.54.0") depends_on("jdk@8u25-linux-x64") diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 2f6e42c439a..c2bad20c2fe 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -45,8 +45,8 @@ class Scotch(Package): variant('shared', default=True, description='Build a shared version of the library') variant('metis', default=True, description='Build metis and parmetis wrapper libraries') - depends_on('flex') - depends_on('bison') + depends_on('flex', type='build') + depends_on('bison', type='build') depends_on('mpi', when='+mpi') depends_on('zlib', when='+compression') diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py index ff6fd2da9b0..ebca74a3ab8 100644 --- a/var/spack/repos/builtin/packages/serf/package.py +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -36,7 +36,7 @@ class Serf(Package): depends_on('apr') depends_on('apr-util') - depends_on('scons') + depends_on('scons', type='build') depends_on('expat') depends_on('openssl') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py index 59535dcc4cb..21bb6f03a70 100644 --- a/var/spack/repos/builtin/packages/spot/package.py +++ b/var/spack/repos/builtin/packages/spot/package.py @@ -32,7 +32,7 @@ class Spot(Package): version('1.99.3', 'd53adcb2d0fe7c69f45d4e595a58254e') - #depends_on("gcc@4.8:") + #depends_on("gcc@4.8:", type='build') depends_on("python@3.2:") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index 80d27e149f9..a03713397b6 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -39,7 +39,7 @@ class Stat(Package): depends_on('libdwarf') depends_on('dyninst') depends_on('graphlib') - depends_on('graphviz') + depends_on('graphviz', type=alldeps) depends_on('launchmon') depends_on('mrnet') diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index 42e8fb466a0..37862a73a9a 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -43,10 +43,10 @@ class Swiftsim(Package): variant('mpi', default=True, description='Enable distributed memory parallelism') # Build dependencies - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') - depends_on('m4') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') # link-time / run-time dependencies depends_on('mpi', when='+mpi') depends_on('metis') diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py index dc52c4f9f6f..8c3b412f48d 100644 --- a/var/spack/repos/builtin/packages/task/package.py +++ b/var/spack/repos/builtin/packages/task/package.py @@ -31,6 +31,7 @@ class Task(Package): version('2.4.4', '517450c4a23a5842df3e9905b38801b3') + depends_on('cmake', type='build') depends_on("gnutls") depends_on("libuuid") # depends_on("gcc@4.8:") diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py index 8a022b4fe98..1d7f9ed49ea 100644 --- a/var/spack/repos/builtin/packages/taskd/package.py +++ b/var/spack/repos/builtin/packages/taskd/package.py @@ -32,6 +32,7 @@ class Taskd(Package): version('1.1.0', 'ac855828c16f199bdbc45fbc227388d0') + depends_on('cmake', type='build') depends_on("libuuid") depends_on("gnutls") diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index c301a5b4e5b..97aa68be65a 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -38,9 +38,7 @@ class Tetgen(Package): version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18') version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') - # TODO: Make this a build dependency once build dependencies are supported - # (see: https://github.com/LLNL/spack/pull/378). - depends_on('cmake@2.8.7:', when='@1.5.0:') + depends_on('cmake@2.8.7:', when='@1.5.0:', type='build') def install(self, spec, prefix): make('tetgen', 'tetlib') diff --git a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py b/var/spack/repos/builtin/packages/the_platinum_searcher/package.py index 9c9a66cdefc..0d2c2918c4f 100644 --- a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_platinum_searcher/package.py @@ -12,7 +12,7 @@ class ThePlatinumSearcher(Package): version('head', go=package) - extends("go") + extends("go", deptypes='build') def install(self, spec, prefix): env = os.environ diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py index e289b6d7836..988619df304 100644 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py @@ -33,7 +33,7 @@ class TheSilverSearcher(Package): depends_on('pcre') depends_on('xz') - depends_on('pkg-config') + depends_on('pkg-config', type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 6d834c6321d..025ee2b8858 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -41,12 +41,12 @@ class Thrift(Package): variant('python', default=True, description="Build support for python") depends_on('jdk') - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') depends_on('boost@1.53:') - depends_on('bison') - depends_on('flex') + depends_on('bison', type='build') + depends_on('flex', type='build') depends_on('openssl') # Variant dependencies diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3a53ac5c01c..56499af8d99 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -68,6 +68,8 @@ class Trilinos(Package): variant('debug', default=False, description='Builds a debug version of the libraries') variant('boost', default=True, description='Compile with Boost') + depends_on('cmake', type='build') + # Everything should be compiled with -fpic depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index f66c20894bb..e0dfb648791 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -60,7 +60,7 @@ class Vim(Package): depends_on('ruby', when='+ruby') variant('cscope', default=False, description="build with cscope support") - depends_on('cscope', when='+cscope') + depends_on('cscope', when='+cscope', type='run') variant('gui', default=False, description="build with gui (gvim)") # virtual dependency? diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index d2296dbc266..5c196b5ea81 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -37,6 +37,7 @@ class Vtk(Package): version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') + depends_on('cmake', type='build') depends_on("qt") # VTK7 defaults to OpenGL2 rendering backend From 77965ce5bf601cd60e712430eddb99a843f58a3c Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 10 Mar 2016 09:44:25 -0500 Subject: [PATCH 048/126] py-matplotlib: require py-setuptools to build --- var/spack/repos/builtin/packages/py-matplotlib/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index d4f96706b3b..b5eb8a53c48 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -38,6 +38,7 @@ class PyMatplotlib(Package): extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') + depends_on('py-setuptools', type='build') depends_on('py-pyside', when='+gui', type=nolink) depends_on('py-ipython', when='+ipython', type=nolink) depends_on('py-pyparsing', type=nolink) From ac1701ae29f25fdc595ab585f22eb48b7c58eb0b Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 14:32:49 -0400 Subject: [PATCH 049/126] msgpack-c: add missing dependency on cmake --- var/spack/repos/builtin/packages/msgpack-c/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py index 925dceabed6..d42ac255d0e 100644 --- a/var/spack/repos/builtin/packages/msgpack-c/package.py +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -31,6 +31,8 @@ class MsgpackC(Package): version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake('.', *std_cmake_args) From 0ca1a481a3dd77110c3ab2be7b3125a0c559a953 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 23 Mar 2016 14:47:01 -0400 Subject: [PATCH 050/126] python: setup the dependent environment properly We want the run dependencies of all build and run dependencies of the current package. --- var/spack/repos/builtin/packages/python/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d0191335855..dafafabb05a 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -146,7 +146,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec): extension and any other python extensions it depends on.""" python_paths = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): python_paths.append(join_path(d.prefix, self.site_packages_dir)) From a82385cdae7e5f5538202c16fa1281dc6701764d Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 14:31:06 -0400 Subject: [PATCH 051/126] R: look only at run dependencies of build and run deps --- var/spack/repos/builtin/packages/R/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 07bb6b6b034..11c5909efaf 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -123,7 +123,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec): # Set R_LIBS to include the library dir for the # extension and any other R extensions it depends on. r_libs_path = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir)) From 39aef5fc00eb935595235a53ca3568c3e063c371 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Tue, 31 May 2016 14:32:35 -0400 Subject: [PATCH 052/126] lua: bring in run deps of build and run deps --- var/spack/repos/builtin/packages/lua/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 48c1c6a9199..ca0a481a83d 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -86,7 +86,7 @@ def append_paths(self, paths, cpaths, path): def setup_dependent_environment(self, spack_env, run_env, extension_spec): lua_paths = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptypes=nolink, deptype_query='run'): if d.package.extends(self.spec): lua_paths.append(os.path.join(d.prefix, self.lua_lib_dir)) lua_paths.append(os.path.join(d.prefix, self.lua_share_dir)) From d71a12438b527e76aa710cff0eb2b032160343cd Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 29 Jun 2016 15:05:57 -0400 Subject: [PATCH 053/126] cantera: use nolink for python module dependencies Unsure about this, but this is probably true. --- var/spack/repos/builtin/packages/cantera/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index 646d106d88f..8e4f23046b4 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -52,10 +52,10 @@ class Cantera(Package): # Python module dependencies extends('python', when='+python') - depends_on('py-numpy', when='+python') - depends_on('py-scipy', when='+python') - depends_on('py-cython', when='+python') - depends_on('py-3to2', when='+python') + depends_on('py-numpy', when='+python', type=nolink) + depends_on('py-scipy', when='+python', type=nolink) + depends_on('py-cython', when='+python', type=nolink) + depends_on('py-3to2', when='+python', type=nolink) # TODO: these "when" specs don't actually work # depends_on('py-unittest2', when='+python^python@2.6') # depends_on('py-unittest2py3k', when='+python^python@3.1') From a0584c78a8c1a93ad60f394f054907ecb3b371e7 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 29 Jun 2016 15:06:21 -0400 Subject: [PATCH 054/126] foam-extend, sundials: add cmake as a builddep The sundials doesn't use CMake directly, but it is referenced in the patch step. I suspect it calls CMake somewhere else in its build system. --- var/spack/repos/builtin/packages/foam-extend/package.py | 1 + var/spack/repos/builtin/packages/sundials/package.py | 1 + 2 files changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py index 4479fc9beef..0ff57658950 100644 --- a/var/spack/repos/builtin/packages/foam-extend/package.py +++ b/var/spack/repos/builtin/packages/foam-extend/package.py @@ -29,6 +29,7 @@ class FoamExtend(Package): depends_on('python') depends_on('flex@:2.5.99') depends_on('zlib') + depends_on('cmake', type='build') depends_on('scotch ~ metis', when='~ptscotch+scotch') depends_on('scotch ~ metis + mpi', when='+ptscotch') diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index c55198a8502..e52b90eb8ad 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -42,6 +42,7 @@ class Sundials(Package): variant('openmp', default=False, description='Enable OpenMP support') variant('pthread', default=True, description='Enable POSIX threads support') + depends_on('cmake', type='build') depends_on('mpi', when='+mpi') depends_on('blas', when='+lapack') depends_on('lapack', when='+lapack') From faa3d43d9c3269d0dba400463ca76f5d0911bf00 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 14 Jul 2016 16:33:38 -0400 Subject: [PATCH 055/126] package: mention the package that is no concrete --- lib/spack/spack/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 78dfef58292..7f53b461b29 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -911,7 +911,7 @@ def do_install(self, run_tests -- Runn tests within the package's install() """ if not self.spec.concrete: - raise ValueError("Can only install concrete packages.") + raise ValueError("Can only install concrete packages: %s." % self.spec.name) # No installation needed if package is external if self.spec.external: From 5d152edcafbe1b5c4a3937163b58c395b01d27c5 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 14 Jul 2016 16:33:48 -0400 Subject: [PATCH 056/126] spec: assign namespaces to the full dependency DAG --- lib/spack/spack/spec.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 58fc139042f..d3a5f66e57c 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -1223,7 +1223,7 @@ def concretize(self): changed = any(changes) force = True - for s in self.traverse(): + for s in self.traverse(deptype_query=alldeps): # After concretizing, assign namespaces to anything left. # Note that this doesn't count as a "change". The repository # configuration is constant throughout a spack run, and From b8e27997000c448d191121ef0f8b08ebca877ed0 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 14 Jul 2016 14:38:30 -0700 Subject: [PATCH 057/126] Add GNU Prolog package. --- .../builtin/packages/gnu-prolog/package.py | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gnu-prolog/package.py diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py new file mode 100644 index 00000000000..f497ed30019 --- /dev/null +++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class GnuProlog(Package): + """A free Prolog compiler with constraint solving over finite domains.""" + homepage = "http://www.gprolog.org/" + url = "http://www.gprolog.org/gprolog-1.4.4.tar.gz" + + version('1.4.4', '37009da471e5217ff637ad1c516448c8') + + parallel = False + + def install(self, spec, prefix): + with working_dir('src'): + configure('--with-install-dir=%s' % prefix, + '--without-links-dir') + make() + make('install') From 487ec2aff1e97f5f694cdbe5097f699bef324cf7 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Thu, 14 Jul 2016 19:04:30 -0700 Subject: [PATCH 058/126] added py-pydatalog package --- .../builtin/packages/py-pydatalog/package.py | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pydatalog/package.py diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py new file mode 100644 index 00000000000..efc9c9bbe81 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PyDatalog(Package): + """pyDatalog adds logic programming to Python.""" + homepage = 'https://pypi.python.org/pypi/pyDatalog/' + url = 'https://pypi.python.org/packages/09/0b/2670eb9c0027aacfb5b5024ca75e5fee2f1261180ab8797108ffc941158a/pyDatalog-0.17.1.zip' + + version('0.17.1', '6b2682301200068d208d6f2d01723939') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) From f3e95884572ee379b38b6b77516dc4fe6ad3d3fc Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 14 Jul 2016 23:15:54 -0700 Subject: [PATCH 059/126] Fix package name bug. --- var/spack/repos/builtin/packages/py-pydatalog/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py index efc9c9bbe81..da157d3679c 100644 --- a/var/spack/repos/builtin/packages/py-pydatalog/package.py +++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py @@ -25,7 +25,7 @@ from spack import * -class PyDatalog(Package): +class PyPydatalog(Package): """pyDatalog adds logic programming to Python.""" homepage = 'https://pypi.python.org/pypi/pyDatalog/' url = 'https://pypi.python.org/packages/09/0b/2670eb9c0027aacfb5b5024ca75e5fee2f1261180ab8797108ffc941158a/pyDatalog-0.17.1.zip' From b29b7595dda88831b7c0330b34df4c7b1e1c1734 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 15 Jul 2016 17:35:10 +0200 Subject: [PATCH 060/126] mkl: add info on interface and threading layers to the docstring --- var/spack/repos/builtin/packages/mkl/package.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py index f1f07c90f5e..6ea64f53133 100644 --- a/var/spack/repos/builtin/packages/mkl/package.py +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -9,7 +9,13 @@ class Mkl(IntelInstaller): Note: You will have to add the download file to a mirror so that Spack can find it. For instructions on how to set up a - mirror, see http://software.llnl.gov/spack/mirrors.html""" + mirror, see http://software.llnl.gov/spack/mirrors.html. + + To set the threading layer at run time set MKL_THREADING_LAYER + variable to one of the following values: INTEL, SEQUENTIAL, PGI. + To set interface layer at run time, use set the MKL_INTERFACE_LAYER + variable to LP64 or ILP64. + """ homepage = "https://software.intel.com/en-us/intel-mkl" From 5f1b6f000daef95f4797dde7c419e21439243c9b Mon Sep 17 00:00:00 2001 From: Mitchell Devlin Date: Thu, 14 Jul 2016 14:22:23 -0500 Subject: [PATCH 061/126] add HMMER package --- .../repos/builtin/packages/hmmer/package.py | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 var/spack/repos/builtin/packages/hmmer/package.py diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py new file mode 100644 index 00000000000..6a236e9fc91 --- /dev/null +++ b/var/spack/repos/builtin/packages/hmmer/package.py @@ -0,0 +1,76 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Hmmer(Package): + """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments. It implements methods using + probabilistic models called profile hidden Markov models (profile HMMs). + """ + homepage = 'http://www.hmmer.org' + url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz' + + version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f') + version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588') + version('2.4i', 'dab234c87e026ac1de942450750acd20') + version('2.3.2', '5f073340c0cf761288f961a73821228a') + version('2.3.1', 'c724413e5761c630892506698a4716e2') + + variant('mpi', default=True, description='Compile with MPI') + variant('gsl', default=False, description='Compile with GSL') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + def url_for_version(self, version): + base_url = 'http://eddylab.org/software' + + if version >= Version('3.0'): + return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + else: + return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + + def install(self, spec, prefix): + configure_args = [ + '--prefix={0}'.format(prefix) + ] + + if '+gsl' in self.spec: + configure_args.extend([ + '--with-gsl', + 'LIBS=-lgsl -lgslcblas' + ]) + + if '+mpi' in self.spec: + configure_args.append('--enable-mpi') + + configure(*configure_args) + make() + + if self.run_tests: + make('check') + + make('install') From 4663288b4947593c9e60b149cdf78544c22fe8ed Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 15 Jul 2016 13:00:48 -0400 Subject: [PATCH 062/126] Update to OpenMPI 2.0.0 --- var/spack/repos/builtin/packages/openmpi/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 15c8eefe964..1fa4f708114 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -63,6 +63,7 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674') version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') @@ -101,6 +102,7 @@ class Openmpi(Package): provides('mpi@:2.2', when='@1.6.5') provides('mpi@:3.0', when='@1.7.5:') + provides('mpi@:3.1', when='@2.0.0:') depends_on('hwloc') depends_on('sqlite', when='+sqlite3') @@ -169,7 +171,8 @@ def install(self, spec, prefix): '--with-psm2' if '+psm2' in spec else '--without-psm2', '--with-mxm' if '+mxm' in spec else '--without-mxm', # Other options - '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', # NOQA: ignore=E501 + ('--enable-mpi-thread-multiple' if '+thread_multiple' in spec + else '--disable-mpi-thread-multiple'), '--with-pmi' if '+pmi' in spec else '--without-pmi', '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3', '--enable-vt' if '+vt' in spec else '--disable-vt' From a4a2f179c712df806f12e0904d1d3eddcd54dfef Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 15 Jul 2016 12:11:41 -0500 Subject: [PATCH 063/126] Updates to run-flake8 test --- share/spack/qa/run-flake8 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/share/spack/qa/run-flake8 b/share/spack/qa/run-flake8 index 57534eb6e2d..595df417ecd 100755 --- a/share/spack/qa/run-flake8 +++ b/share/spack/qa/run-flake8 @@ -18,7 +18,7 @@ if [[ ! $flake8 ]]; then fi # Check if changed files are flake8 conformant [framework] -changed=$(git diff --name-only develop... | grep '.py$') +changed=$(git diff --name-only --find-renames develop... | grep '.py$') # Add approved style exemptions to the changed packages. for file in $changed; do @@ -26,6 +26,7 @@ for file in $changed; do cp "$file" "$file~" # Exempt lines with urls and descriptions from overlong line errors. + perl -i -pe 's/^(\s*homepage\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*url\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*version\(.*\).*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*variant\(.*\).*)$/\1 # NOQA: ignore=E501/' $file From 8c1cc44522b42bfb847c41522265eeee9511298d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 15 Jul 2016 16:43:25 -0500 Subject: [PATCH 064/126] Automatically add deptype to newly created packages --- lib/spack/spack/cmd/create.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index 18c748e483f..c9fa687b749 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -142,9 +142,9 @@ def __call__(self, stage): # Build dependencies and extensions dependenciesDict = { 'autotools': "# depends_on('foo')", - 'cmake': "depends_on('cmake')", - 'scons': "depends_on('scons')", - 'python': "extends('python')", + 'cmake': "depends_on('cmake', type='build')", + 'scons': "depends_on('scons', type='build')", + 'python': "extends('python', type=nolink)", 'R': "extends('R')", 'unknown': "# depends_on('foo')" } From 5a1ed51dcd374285028a4020678a5c2cf18da81b Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 15 Jul 2016 18:10:33 -0400 Subject: [PATCH 065/126] Correct indentation --- var/spack/repos/builtin/packages/openmpi/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 1fa4f708114..3fcf942f050 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -172,7 +172,7 @@ def install(self, spec, prefix): '--with-mxm' if '+mxm' in spec else '--without-mxm', # Other options ('--enable-mpi-thread-multiple' if '+thread_multiple' in spec - else '--disable-mpi-thread-multiple'), + else '--disable-mpi-thread-multiple'), '--with-pmi' if '+pmi' in spec else '--without-pmi', '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3', '--enable-vt' if '+vt' in spec else '--disable-vt' From 96e9dbca0828e0664c4c20d6223b94d8040fc1a6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 15 Jul 2016 22:41:01 +0200 Subject: [PATCH 066/126] suite-sparse: enable TBB and fix Blas/Lapack libs --- .../builtin/packages/suite-sparse/package.py | 29 ++++++++++--------- .../packages/suite-sparse/tbb_453.patch | 13 +++++++++ 2 files changed, 29 insertions(+), 13 deletions(-) create mode 100644 var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 2cc89b843f0..a71bfd8bd45 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -32,21 +32,20 @@ class SuiteSparse(Package): homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' - version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') version('4.5.3', '8ec57324585df3c6483ad7f556afccbd') + version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') - # FIXME: (see below) - # variant('tbb', default=True, description='Build with Intel TBB') + variant('tbb', default=True, description='Build with Intel TBB') depends_on('blas') depends_on('lapack') depends_on('metis@5.1.0', when='@4.5.1:') - # FIXME: # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng # flags does not seem to be used, which leads to linking errors on Linux. - # Try re-enabling in future versions. - # depends_on('tbb', when='+tbb') + depends_on('tbb', when='@4.5.3:+tbb') + + patch('tbb_453.patch', when='@4.5.3') def install(self, spec, prefix): # The build system of SuiteSparse is quite old-fashioned. @@ -73,20 +72,24 @@ def install(self, spec, prefix): ]) # Intel TBB in SuiteSparseQR - if '+tbb' in spec: + if 'tbb' in spec: make_args.extend([ 'SPQR_CONFIG=-DHAVE_TBB', 'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib, ]) - # BLAS arguments require path to libraries - # FIXME: (blas/lapack always provide libblas and liblapack as aliases) + # Make sure Spack's Blas/Lapack is used. Otherwise System's + # Blas/Lapack might be picked up. + blas = to_link_flags(spec['blas'].blas_shared_lib) + lapack = to_link_flags(spec['lapack'].lapack_shared_lib) if '@4.5.1' in spec: # adding -lstdc++ is clearly an ugly way to do this, but it follows # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk - make_args.extend([ - 'BLAS=-lblas -lstdc++', - 'LAPACK=-llapack' - ]) + blas += ' -lstdc++' + + make_args.extend([ + 'BLAS=%s' % blas, + 'LAPACK=%s' % lapack + ]) make('install', *make_args) diff --git a/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch b/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch new file mode 100644 index 00000000000..70241ed0174 --- /dev/null +++ b/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch @@ -0,0 +1,13 @@ +diff --git a/SPQR/Lib/Makefile b/SPQR/Lib/Makefile +index eaade58..d0de852 100644 +--- a/SPQR/Lib/Makefile ++++ b/SPQR/Lib/Makefile +@@ -13,7 +13,7 @@ ccode: all + include ../../SuiteSparse_config/SuiteSparse_config.mk + + # SPQR depends on CHOLMOD, AMD, COLAMD, LAPACK, the BLAS and SuiteSparse_config +-LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(LAPACK) $(BLAS) ++LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(TBB) $(LAPACK) $(BLAS) + + # compile and install in SuiteSparse/lib + library: From d61190c3fffc3597c49dc995590dc419b10aab73 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sat, 16 Jul 2016 00:48:04 +0200 Subject: [PATCH 067/126] Explicitly request zmpi in module blacklist test. --- lib/spack/spack/test/modules.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py index 6d2e3705bd4..b6d35154e33 100644 --- a/lib/spack/spack/test/modules.py +++ b/lib/spack/spack/test/modules.py @@ -266,7 +266,7 @@ def test_alter_environment(self): def test_blacklist(self): spack.modules.CONFIGURATION = configuration_blacklist - spec = spack.spec.Spec('mpileaks') + spec = spack.spec.Spec('mpileaks ^zmpi') content = self.get_modulefile_content(spec) self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1) self.assertEqual(len([x for x in content if 'module load ' in x]), 1) From 992250ddeab77a605c1e0c47363bd750949d59a5 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:24:05 +0200 Subject: [PATCH 068/126] add to_lib_name() to get library name from a path --- lib/spack/llnl/util/filesystem.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index e800c6717ad..adb6b8034e2 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -42,7 +42,7 @@ 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink', 'set_executable', 'copy_mode', 'unset_executable_mode', 'remove_dead_links', 'remove_linked_tree', 'find_library_path', - 'fix_darwin_install_name', 'to_link_flags'] + 'fix_darwin_install_name', 'to_link_flags', 'to_lib_name'] def filter_file(regex, repl, *filenames, **kwargs): @@ -430,6 +430,11 @@ def fix_darwin_install_name(path): subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 break +def to_lib_name(library): + """Transforms a path to the library /path/to/lib.xyz into + """ + # Assume libXYZ.suffix + return os.path.basename(library)[3:].split(".")[0] def to_link_flags(library): """Transforms a path to a into linking flags -L -l. @@ -438,8 +443,7 @@ def to_link_flags(library): A string of linking flags. """ dir = os.path.dirname(library) - # Assume libXYZ.suffix - name = os.path.basename(library)[3:].split(".")[0] + name = to_lib_name(library) res = '-L%s -l%s' % (dir, name) return res From 514c61b8fe923de7eb0c41205fdfaae48afb5cdf Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:28:31 +0200 Subject: [PATCH 069/126] hypre: don't hardcode blas/lapack/mpi; optionally run tests --- .../repos/builtin/packages/hypre/package.py | 39 ++++++++++++------- 1 file changed, 26 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index f87dae9f4ef..0941d07ebef 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -46,21 +46,26 @@ class Hypre(Package): depends_on("lapack") def install(self, spec, prefix): - blas_dir = spec['blas'].prefix - lapack_dir = spec['lapack'].prefix - mpi_dir = spec['mpi'].prefix - - os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc') - os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx') - os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77') - + os.environ['CC'] = spec['mpi'].mpicc + os.environ['CXX'] = spec['mpi'].mpicxx + os.environ['F77'] = spec['mpi'].mpif77 + # Since +shared does not build on macOS and also Atlas does not have + # a single static lib to build against, link against shared libs with + # a hope that --whole-archive linker option (or alike) was used + # to command the linker to include whole static libs' content into the + # shared lib + # Note: --with-(lapack|blas)_libs= needs space separated list of names configure_args = [ - "--prefix=%s" % prefix, - "--with-lapack-libs=lapack", - "--with-lapack-lib-dirs=%s/lib" % lapack_dir, - "--with-blas-libs=blas", - "--with-blas-lib-dirs=%s/lib" % blas_dir] + '--prefix=%s' % prefix, + '--with-lapack-libs=%s' % to_lib_name( + spec['lapack'].lapack_shared_lib), + '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix, + '--with-blas-libs=%s' % to_lib_name( + spec['blas'].blas_shared_lib), + '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix + ] + if '+shared' in self.spec: configure_args.append("--enable-shared") @@ -76,4 +81,12 @@ def install(self, spec, prefix): configure(*configure_args) make() + if self.run_tests: + make("check") + make("test") + Executable(join_path('test', 'ij'))() + sstruct = Executable(join_path('test', 'struct')) + sstruct() + sstruct('-in', 'test/sstruct.in.default', '-solver', '40', + '-rhsone') make("install") From 987fb137f97b8673efdcd126bef56bc6c8d06dc0 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:31:38 +0200 Subject: [PATCH 070/126] trilinos: don't hardcode blas/lapack names --- var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3a53ac5c01c..100e30169da 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -116,6 +116,7 @@ def install(self, spec, prefix): options.extend(std_cmake_args) mpi_bin = spec['mpi'].prefix.bin + # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names options.extend([ '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', @@ -129,10 +130,12 @@ def install(self, spec, prefix): '-DTPL_ENABLE_MPI:BOOL=ON', '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, '-DTPL_ENABLE_BLAS=ON', - '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names + '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name( + spec['blas'].blas_shared_lib), '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, '-DTPL_ENABLE_LAPACK=ON', - '-DLAPACK_LIBRARY_NAMES=lapack', + '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name( + spec['lapack'].lapack_shared_lib), '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', From 6175ce75596bf1abdedda3aaccb7bbed86453f0a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:37:38 +0200 Subject: [PATCH 071/126] netlib-scalapack: make sure Spack's Lapack is used --- .../repos/builtin/packages/netlib-scalapack/package.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index f7fe26a42da..cb2d8b44fc5 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -53,6 +53,15 @@ def install(self, spec, prefix): "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK) ] + # Make sure we use Spack's Lapack: + options.extend([ + '-DLAPACK_FOUND=true', + '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include, + '-DLAPACK_LIBRARIES=%s' % ( + spec['lapack'].lapack_shared_lib if '+shared' in spec else + spec['lapack'].lapack_static_lib), + ]) + if '+fpic' in spec: options.extend([ "-DCMAKE_C_FLAGS=-fPIC", From 0752eccfa5f865419f0ab4f3de06f5feea1aa422 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:38:42 +0200 Subject: [PATCH 072/126] mumps: don't hardcode blas name; remove unused depends_on(lapack) --- var/spack/repos/builtin/packages/mumps/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 92c45c9b95d..630c33562b5 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -50,7 +50,6 @@ class Mumps(Package): depends_on('metis@5:', when='+metis') depends_on('parmetis', when="+parmetis") depends_on('blas') - depends_on('lapack') depends_on('scalapack', when='+mpi') depends_on('mpi', when='+mpi') @@ -63,7 +62,9 @@ def write_makefile_inc(self): if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') - makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] + makefile_conf = ["LIBBLAS = %s" % to_link_flags( + self.spec['blas'].blas_shared_lib) + ] orderings = ['-Dpord'] @@ -189,7 +190,7 @@ def install(self, spec, prefix): install_tree('lib', prefix.lib) install_tree('include', prefix.include) - if '~mpi' in spec: + if '~mpi' in spec: lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' lib_suffix = lib_dsuffix if '+shared' in spec else '.a' install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) From 9ea4f80f154f264986dcadf9de4dd192b8dce037 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 07:58:51 +0200 Subject: [PATCH 073/126] flake8 fixes --- lib/spack/llnl/util/filesystem.py | 2 ++ var/spack/repos/builtin/packages/hypre/package.py | 6 ++++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index adb6b8034e2..6e4cd338fe5 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -430,12 +430,14 @@ def fix_darwin_install_name(path): subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 break + def to_lib_name(library): """Transforms a path to the library /path/to/lib.xyz into """ # Assume libXYZ.suffix return os.path.basename(library)[3:].split(".")[0] + def to_link_flags(library): """Transforms a path to a into linking flags -L -l. diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 0941d07ebef..65fef575599 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -23,7 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, sys +import os +import sys + class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -37,7 +39,7 @@ class Hypre(Package): version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') # hypre does not know how to build shared libraries on Darwin - variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") + variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)") # SuperluDist have conflicting headers with those in Hypre variant('internal-superlu', default=True, description="Use internal Superlu routines") From 561748a063f8dab8bb5542b8bfab0878ab0fff06 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 08:03:54 +0200 Subject: [PATCH 074/126] netlib-scalapack: flake8 fixes --- .../packages/netlib-scalapack/package.py | 21 ++++++++++++------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index cb2d8b44fc5..e91c0449656 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -25,8 +25,10 @@ from spack import * import sys + class NetlibScalapack(Package): - """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" + """ScaLAPACK is a library of high-performance linear algebra routines for + parallel distributed memory machines""" homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" @@ -48,10 +50,13 @@ class NetlibScalapack(Package): def install(self, spec, prefix): options = [ - "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'), - "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'), - "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK) - ] + "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else + 'OFF'), + "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else + 'ON'), + # forces scalapack to use find_package(LAPACK): + "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", + ] # Make sure we use Spack's Lapack: options.extend([ @@ -75,11 +80,10 @@ def install(self, spec, prefix): make() make("install") - # The shared libraries are not installed correctly on Darwin; correct this + # The shared libraries are not installed correctly on Darwin: if (sys.platform == 'darwin') and ('+shared' in spec): fix_darwin_install_name(prefix.lib) - def setup_dependent_package(self, module, dependent_spec): spec = self.spec lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' @@ -87,4 +91,5 @@ def setup_dependent_package(self, module, dependent_spec): spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib spec.cc_link = spec.fc_link - spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)] + spec.libraries = [join_path(spec.prefix.lib, + 'libscalapack%s' % lib_suffix)] From 1bd3a702c99ec41bbed510102769bba6984bbd30 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 16 Jul 2016 08:12:57 +0200 Subject: [PATCH 075/126] mumps: flake8 fixes --- .../repos/builtin/packages/mumps/package.py | 67 ++++++++++--------- 1 file changed, 37 insertions(+), 30 deletions(-) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 630c33562b5..b85a6d2b949 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -23,7 +23,10 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, sys, glob +import os +import sys +import glob + class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -44,7 +47,6 @@ class Mumps(Package): variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') variant('shared', default=True, description='Build shared libraries') - depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') depends_on('metis@5:', when='+metis') @@ -59,8 +61,8 @@ class Mumps(Package): # end before install # def patch(self): def write_makefile_inc(self): - if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: - raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') + if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: # NOQA: ignore=E501 + raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: ignore=E501 makefile_conf = ["LIBBLAS = %s" % to_link_flags( self.spec['blas'].blas_shared_lib) @@ -70,33 +72,41 @@ def write_makefile_inc(self): if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') - makefile_conf.extend( - ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, - "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, - join_lib, - join_lib.join(['esmumps', 'scotch', 'scotcherr']))]) + makefile_conf.extend([ + "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, + "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, + join_lib, + join_lib.join(['esmumps', + 'scotch', + 'scotcherr'])) + ]) + orderings.append('-Dscotch') if '+ptscotch' in self.spec: orderings.append('-Dptscotch') if '+parmetis' in self.spec and '+metis' in self.spec: - libname = 'parmetis' if '+parmetis' in self.spec else 'metis' - makefile_conf.extend( - ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, - "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) + makefile_conf.extend([ + "IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % ( + self.spec['parmetis'].prefix.lib, 'parmetis', + self.spec['metis'].prefix.lib, 'metis') + ]) orderings.append('-Dparmetis') elif '+metis' in self.spec: - makefile_conf.extend( - ["IMETIS = -I%s" % self.spec['metis'].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) + makefile_conf.extend([ + "IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis') + ]) orderings.append('-Dmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) # when building shared libs need -fPIC, otherwise - # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC + # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' + # can not be used when making a shared object; recompile with -fPIC fpic = '-fPIC' if '+shared' in self.spec else '' # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers @@ -105,7 +115,7 @@ def write_makefile_inc(self): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: ignore=E501 'OPTL = %s -O ' % fpic, 'OPTC = %s -O -DINTSIZE64' % fpic]) else: @@ -114,7 +124,6 @@ def write_makefile_inc(self): 'OPTL = %s -O ' % fpic, 'OPTC = %s -O ' % fpic]) - if '+mpi' in self.spec: makefile_conf.extend( ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), @@ -135,16 +144,17 @@ def write_makefile_inc(self): if '+shared' in self.spec: if sys.platform == 'darwin': - # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + # Building dylibs with mpif90 causes segfaults on 10.8 and + # 10.10. Use gfortran. (Homebrew) makefile_conf.extend([ 'LIBEXT=.dylib', - 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib), # NOQA: ignore=E501 'RANLIB=echo' ]) else: makefile_conf.extend([ 'LIBEXT=.so', - 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, # NOQA: ignore=E501 'RANLIB=echo' ]) else: @@ -154,9 +164,8 @@ def write_makefile_inc(self): 'RANLIB = ranlib' ]) - - makefile_inc_template = join_path(os.path.dirname(self.module.__file__), - 'Makefile.inc') + makefile_inc_template = join_path( + os.path.dirname(self.module.__file__), 'Makefile.inc') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) @@ -165,8 +174,6 @@ def write_makefile_inc(self): makefile_inc = '\n'.join(makefile_conf) fh.write(makefile_inc) - - def install(self, spec, prefix): make_libs = [] @@ -194,11 +201,11 @@ def install(self, spec, prefix): lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' lib_suffix = lib_dsuffix if '+shared' in spec else '.a' install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) - for f in glob.glob(join_path('libseq','*.h')): + for f in glob.glob(join_path('libseq', '*.h')): install(f, prefix.include) - # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI - # FIXME: use something like numdiff to compare blessed output with the current + # FIXME: extend the tests to mpirun -np 2 when build with MPI + # FIXME: use something like numdiff to compare output files with working_dir('examples'): if '+float' in spec: os.system('./ssimpletest < input_simpletest_real') From dc671ad0370fa87ca2e5f09b1da1d54a1bfa0700 Mon Sep 17 00:00:00 2001 From: alalazo Date: Sun, 17 Jul 2016 22:17:52 +0200 Subject: [PATCH 076/126] docs : substituted None with empty cell --- lib/spack/docs/packaging_guide.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 861a35c1544..a1bfe600596 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -2606,9 +2606,9 @@ variant names are: Name Default Description ======= ======== ======================== shared True Build shared libraries - static None Build static libraries - mpi None Use MPI - python None Build Python extension + static Build static libraries + mpi Use MPI + python Build Python extension ======= ======== ======================== If specified in this table, the corresponding default should be used From 2e4966c8544efbd41d737e4ba2e7d005af32bcbb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 18 Jul 2016 10:11:18 +0200 Subject: [PATCH 077/126] netlib-scalapack: use dso_suffix --- var/spack/repos/builtin/packages/netlib-scalapack/package.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index e91c0449656..a96b367be40 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -86,10 +86,9 @@ def install(self, spec, prefix): def setup_dependent_package(self, module, dependent_spec): spec = self.spec - lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' - lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + lib_suffix = dso_suffix if '+shared' in spec else 'a' spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib spec.cc_link = spec.fc_link spec.libraries = [join_path(spec.prefix.lib, - 'libscalapack%s' % lib_suffix)] + 'libscalapack.%s' % lib_suffix)] From cdc2ebee9018cc4cf067d73f269628901a8d4487 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 18 Jul 2016 01:11:24 -0700 Subject: [PATCH 078/126] Better error messages for `spack reindex`. --- lib/spack/spack/database.py | 7 ++++--- lib/spack/spack/directory_layout.py | 17 +++++++++++++---- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index c95abd74236..eabf740dbc1 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -646,6 +646,7 @@ def __init__(self, path, msg=''): class InvalidDatabaseVersionError(SpackError): def __init__(self, expected, found): super(InvalidDatabaseVersionError, self).__init__( - "Expected database version %s but found version %s." + \ - "Try running `spack reindex` to fix." % - (expected, found)) + "Expected database version %s but found version %s." + % (expected, found), + "`spack reindex` may fix this, or you may need a newer " + "Spack version.") diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index a5e76043ada..8150a6da2bb 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -34,6 +34,7 @@ import llnl.util.tty as tty from llnl.util.filesystem import join_path, mkdirp +import spack from spack.spec import Spec from spack.error import SpackError @@ -223,8 +224,14 @@ def write_spec(self, spec, path): def read_spec(self, path): """Read the contents of a file and parse them as a spec""" - with open(path) as f: - spec = Spec.from_yaml(f) + try: + with open(path) as f: + spec = Spec.from_yaml(f) + except Exception as e: + if spack.debug: + raise + raise SpecReadError( + 'Unable to read file: %s' % path, 'Cause: ' + str(e)) # Specs read from actual installations are always concrete spec._mark_concrete() @@ -456,10 +463,12 @@ def __init__(self, path): "Install path %s already exists!") +class SpecReadError(DirectoryLayoutError): + """Raised when directory layout can't read a spec.""" + + class InvalidExtensionSpecError(DirectoryLayoutError): """Raised when an extension file has a bad spec in it.""" - def __init__(self, message): - super(InvalidExtensionSpecError, self).__init__(message) class ExtensionAlreadyInstalledError(DirectoryLayoutError): From 73f10c9363e584708a39cf02758fc837dc02b8d3 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 15 Jul 2016 16:01:01 -0700 Subject: [PATCH 079/126] Fix broken `spack info` command after build dep merge. - Added a method to get dependencies of particular types from Package - Fixed info command. --- lib/spack/spack/cmd/info.py | 2 +- lib/spack/spack/package.py | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py index 5774034062c..f8b6ceab594 100644 --- a/lib/spack/spack/cmd/info.py +++ b/lib/spack/spack/cmd/info.py @@ -84,7 +84,7 @@ def print_text_info(pkg): for deptype in ('build', 'link', 'run'): print print "%s Dependencies:" % deptype.capitalize() - deps = pkg.dependencies(deptype) + deps = pkg.dependencies_of_type(deptype) if deps: colify(deps, indent=4) else: diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 7f53b461b29..3a7b61f7e63 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -565,6 +565,13 @@ def fetcher(self): def fetcher(self, f): self._fetcher = f + + def dependencies_of_type(self, *deptypes): + """Get subset of the dependencies with certain types.""" + return dict((name, conds) for name, conds in self.dependencies.items() + if any(d in self._deptypes[name] for d in deptypes)) + + @property def extendee_spec(self): """ From 192369dd2b495678e9c701f253eefd15d57fc7d1 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 17 Jul 2016 15:47:57 -0700 Subject: [PATCH 080/126] Fix #1265: Errors in spack reindex - Consolidated code to read spec.yaml and database index.yaml into one method (`read_yaml_dep_specs()`) in spec.py. - Code understands old hash format, tuple format, and dicts for dep specs, for backward compatibility. - Spec YAML now uses a dict with keys to represent dep specs (this is more future-proof). - Dep specs no longer contain !!py-tuple entries in YAML (only lists properly YAML-ize) - bump database version. --- lib/spack/spack/database.py | 14 ++--- lib/spack/spack/spec.py | 103 ++++++++++++++++++++++++------------ 2 files changed, 74 insertions(+), 43 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index eabf740dbc1..a30994b57c5 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -60,7 +60,7 @@ _db_dirname = '.spack-db' # DB version. This is stuck in the DB file to track changes in format. -_db_version = Version('0.9.1') +_db_version = Version('0.9.2') # Default timeout for spack database locks is 5 min. _db_lock_timeout = 60 @@ -215,14 +215,10 @@ def _read_spec_from_yaml(self, hash_key, installs, parent_key=None): # Add dependencies from other records in the install DB to # form a full spec. if 'dependencies' in spec_dict[spec.name]: - for dep in spec_dict[spec.name]['dependencies'].values(): - if type(dep) == tuple: - dep_hash, deptypes = dep - else: - dep_hash = dep - deptypes = spack.alldeps - child = self._read_spec_from_yaml(dep_hash, installs, hash_key) - spec._add_dependency(child, deptypes) + yaml_deps = spec_dict[spec.name]['dependencies'] + for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps): + child = self._read_spec_from_yaml(dhash, installs, hash_key) + spec._add_dependency(child, dtypes) # Specs from the database need to be marked concrete because # they represent actual installations. diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index d3a5f66e57c..7f765f80900 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -155,6 +155,7 @@ every time we call str()""" _any_version = VersionList([':']) +# Special types of dependencies. alldeps = ('build', 'link', 'run') nolink = ('build', 'run') @@ -296,10 +297,15 @@ def __repr__(self): @key_ordering class DependencySpec(object): - """ - Dependencies have conditions in which they apply. + """Dependencies can be one (or more) of several types: - This stores both what is depended on and why it is a dependency. + - build: needs to be in the PATH at build time. + - link: is linked to and added to compiler flags. + - run: needs to be in the PATH for the package to run. + + Fields: + - spec: the spack.spec.Spec description of a dependency. + - deptypes: strings representing the type of dependency this is. """ def __init__(self, spec, deptypes): self.spec = spec @@ -558,15 +564,15 @@ def dependents(self, deptype=None): def _find_deps_dict(self, where, deptype): deptype = self._deptype_norm(deptype) - return [(dep.spec.name, dep) - for dep in where.values() - if deptype and any(d in deptype for d in dep.deptypes)] + return dict((dep.spec.name, dep) + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)) def dependencies_dict(self, deptype=None): - return dict(self._find_deps_dict(self._dependencies, deptype)) + return self._find_deps_dict(self._dependencies, deptype) def dependents_dict(self, deptype=None): - return dict(self._find_deps_dict(self._dependents, deptype)) + return self._find_deps_dict(self._dependents, deptype) # # Private routines here are called by the parser when building a spec. @@ -914,9 +920,11 @@ def to_node_dict(self): d = { 'parameters': params, 'arch': self.architecture, - 'dependencies': dict((d, (deps[d].spec.dag_hash(), - deps[d].deptypes)) - for d in sorted(deps.keys())) + 'dependencies': dict( + (name, { + 'hash': dspec.spec.dag_hash(), + 'type': [str(s) for s in dspec.deptypes]}) + for name, dspec in deps.items()) } # Older concrete specs do not have a namespace. Omit for @@ -982,13 +990,35 @@ def from_node_dict(node): raise SpackRecordError( "Did not find a valid format for variants in YAML file") - # XXX(deptypes): why are dependencies not meant to be read here? - #for name, dep_info in node['dependencies'].items(): - # (dag_hash, deptypes) = dep_info - # spec._dependencies[name] = DependencySpec(dag_hash, deptypes) + # Don't read dependencies here; from_node_dict() is used by + # from_yaml() to read the root *and* each dependency spec. return spec + + @staticmethod + def read_yaml_dep_specs(dependency_dict): + """Read the DependencySpec portion of a YAML-formatted Spec. + + This needs to be backward-compatible with older spack spec + formats so that reindex will work on old specs/databases. + """ + for dep_name, elt in dependency_dict.items(): + if isinstance(elt, basestring): + # original format, elt is just the dependency hash. + dag_hash, deptypes = elt, ['build', 'link'] + elif isinstance(elt, tuple): + # original deptypes format: (used tuples, not future-proof) + dag_hash, deptypes = elt + elif isinstance(elt, dict): + # new format: elements of dependency spec are keyed. + dag_hash, deptypes = elt['hash'], elt['type'] + else: + raise SpecError("Couldn't parse dependency types in spec.") + + yield dep_name, dag_hash, list(deptypes) + + @staticmethod def from_yaml(stream): """Construct a spec from YAML. @@ -1000,27 +1030,30 @@ def from_yaml(stream): represent more than the DAG does. """ - deps = {} - spec = None - try: yfile = yaml.load(stream) except MarkedYAMLError, e: raise SpackYAMLError("error parsing YAML spec:", str(e)) - for node in yfile['spec']: - name = next(iter(node)) - dep = Spec.from_node_dict(node) - if not spec: - spec = dep - deps[dep.name] = dep + nodes = yfile['spec'] - for node in yfile['spec']: + # Read nodes out of list. Root spec is the first element; + # dependencies are the following elements. + dep_list = [Spec.from_node_dict(node) for node in nodes] + if not dep_list: + raise SpecError("YAML spec contains no nodes.") + deps = dict((spec.name, spec) for spec in dep_list) + spec = dep_list[0] + + for node in nodes: + # get dependency dict from the node. name = next(iter(node)) - for dep_name, (dep, deptypes) in \ - node[name]['dependencies'].items(): - deps[name]._dependencies[dep_name] = \ - DependencySpec(deps[dep_name], deptypes) + yaml_deps = node[name]['dependencies'] + for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps): + # Fill in dependencies by looking them up by name in deps dict + deps[name]._dependencies[dname] = DependencySpec( + deps[dname], set(dtypes)) + return spec def _concretize_helper(self, presets=None, visited=None): @@ -1505,13 +1538,13 @@ def normalize(self, force=False): # Ensure first that all packages & compilers in the DAG exist. self.validate_names() # Get all the dependencies into one DependencyMap - spec_deps = self.flat_dependencies_with_deptype(copy=False, - deptype_query=alldeps) + spec_deps = self.flat_dependencies_with_deptype( + copy=False, deptype_query=alldeps) # Initialize index of virtual dependency providers if # concretize didn't pass us one already - provider_index = ProviderIndex([s.spec for s in spec_deps.values()], - restrict=True) + provider_index = ProviderIndex( + [s.spec for s in spec_deps.values()], restrict=True) # traverse the package DAG and fill out dependencies according # to package files & their 'when' specs @@ -2244,12 +2277,14 @@ def tree(self, **kwargs): indent = kwargs.pop('indent', 0) fmt = kwargs.pop('format', '$_$@$%@+$+$=') prefix = kwargs.pop('prefix', None) + deptypes = kwargs.pop('deptypes', ('build', 'link')) check_kwargs(kwargs, self.tree) out = "" cur_id = 0 ids = {} - for d, node in self.traverse(order='pre', cover=cover, depth=True): + for d, node in self.traverse( + order='pre', cover=cover, depth=True, deptypes=deptypes): if prefix is not None: out += prefix(node) out += " " * indent From cddaba8add41bc93659070f1ffd18ffc9a0dabb0 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 18 Jul 2016 02:20:41 -0700 Subject: [PATCH 081/126] flake8 fixes. - package.py - spec.py - test/architecture.py --- lib/spack/spack/cmd/info.py | 5 +- lib/spack/spack/database.py | 4 +- lib/spack/spack/package.py | 118 ++++++++-------- lib/spack/spack/spec.py | 193 ++++++++++++++------------- lib/spack/spack/test/architecture.py | 64 ++++++--- 5 files changed, 214 insertions(+), 170 deletions(-) diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py index f8b6ceab594..498518057bf 100644 --- a/lib/spack/spack/cmd/info.py +++ b/lib/spack/spack/cmd/info.py @@ -29,9 +29,11 @@ description = "Get detailed information on a particular package" + def padder(str_list, extra=0): """Return a function to pad elements of a list.""" length = max(len(str(s)) for s in str_list) + extra + def pad(string): string = str(string) padding = max(0, length - len(string)) @@ -40,7 +42,8 @@ def pad(string): def setup_parser(subparser): - subparser.add_argument('name', metavar="PACKAGE", help="Name of package to get info for.") + subparser.add_argument( + 'name', metavar="PACKAGE", help="Name of package to get info for.") def print_text_info(pkg): diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index a30994b57c5..317b0d5784f 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -635,8 +635,8 @@ def _exit(self): class CorruptDatabaseError(SpackError): def __init__(self, path, msg=''): super(CorruptDatabaseError, self).__init__( - "Spack database is corrupt: %s. %s." + \ - "Try running `spack reindex` to fix." % (path, msg)) + "Spack database is corrupt: %s. %s." % (path, msg), + "Try running `spack reindex` to fix.") class InvalidDatabaseVersionError(SpackError): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 3a7b61f7e63..6a92c548fbf 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -37,7 +37,6 @@ import re import textwrap import time -import glob import string import llnl.util.tty as tty @@ -62,10 +61,10 @@ from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive from spack.util.environment import dump_environment -from spack.util.executable import ProcessError, Executable, which +from spack.util.executable import ProcessError, which from spack.version import * from spack import directory_layout -from urlparse import urlparse + """Allowed URL schemes for spack packages.""" _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"] @@ -410,7 +409,6 @@ def package_dir(self): """Return the directory where the package.py file lives.""" return os.path.dirname(self.module.__file__) - @property def global_license_dir(self): """Returns the directory where global license files for all @@ -565,13 +563,11 @@ def fetcher(self): def fetcher(self, f): self._fetcher = f - def dependencies_of_type(self, *deptypes): """Get subset of the dependencies with certain types.""" return dict((name, conds) for name, conds in self.dependencies.items() if any(d in self._deptypes[name] for d in deptypes)) - @property def extendee_spec(self): """ @@ -694,7 +690,7 @@ def installed_dependents(self): if self.name == spec.name: continue # XXX(deptype): Should build dependencies not count here? - #for dep in spec.traverse(deptype=('run')): + # for dep in spec.traverse(deptype=('run')): for dep in spec.traverse(deptype=spack.alldeps): if self.spec == dep: dependents.append(spec) @@ -706,13 +702,13 @@ def prefix(self): return self.spec.prefix @property - #TODO: Change this to architecture + # TODO: Change this to architecture def compiler(self): """Get the spack.compiler.Compiler object used to build this package""" if not self.spec.concrete: raise ValueError("Can only get a compiler for a concrete package.") return spack.compilers.compiler_for_spec(self.spec.compiler, - self.spec.architecture) + self.spec.architecture) def url_version(self, version): """ @@ -768,7 +764,6 @@ def do_fetch(self, mirror_only=False): self.stage.cache_local() - def do_stage(self, mirror_only=False): """Unpacks the fetched tarball, then changes into the expanded tarball directory.""" @@ -886,6 +881,7 @@ def _resource_stage(self, resource): return resource_stage_folder install_phases = set(['configure', 'build', 'install', 'provenance']) + def do_install(self, keep_prefix=False, keep_stage=False, @@ -897,7 +893,7 @@ def do_install(self, fake=False, explicit=False, dirty=False, - install_phases = install_phases): + install_phases=install_phases): """Called by commands to install a package and its dependencies. Package implementations should override install() to describe @@ -918,7 +914,8 @@ def do_install(self, run_tests -- Runn tests within the package's install() """ if not self.spec.concrete: - raise ValueError("Can only install concrete packages: %s." % self.spec.name) + raise ValueError("Can only install concrete packages: %s." + % self.spec.name) # No installation needed if package is external if self.spec.external: @@ -927,7 +924,8 @@ def do_install(self, return # Ensure package is not already installed - if 'install' in install_phases and spack.install_layout.check_installed(self.spec): + layout = spack.install_layout + if 'install' in install_phases and layout.check_installed(self.spec): tty.msg("%s is already installed in %s" % (self.name, self.prefix)) rec = spack.installed_db.get_record(self.spec) if (not rec.explicit) and explicit: @@ -1008,20 +1006,17 @@ def build_process(): if 'install' in self.install_phases: self.sanity_check_prefix() - # Copy provenance into the install directory on success if 'provenance' in self.install_phases: - log_install_path = spack.install_layout.build_log_path( - self.spec) - env_install_path = spack.install_layout.build_env_path( - self.spec) - packages_dir = spack.install_layout.build_packages_path( - self.spec) + log_install_path = layout.build_log_path(self.spec) + env_install_path = layout.build_env_path(self.spec) + packages_dir = layout.build_packages_path(self.spec) # Remove first if we're overwriting another build # (can happen with spack setup) try: - shutil.rmtree(packages_dir) # log_install_path and env_install_path are inside this + # log_install_path and env_install_path are here + shutil.rmtree(packages_dir) except: pass @@ -1048,7 +1043,7 @@ def build_process(): except directory_layout.InstallDirectoryAlreadyExistsError: if 'install' in install_phases: # Abort install if install directory exists. - # But do NOT remove it (you'd be overwriting someon else's stuff) + # But do NOT remove it (you'd be overwriting someone's data) tty.warn("Keeping existing install prefix in place.") raise else: @@ -1540,24 +1535,29 @@ def _hms(seconds): parts.append("%.2fs" % s) return ' '.join(parts) + class StagedPackage(Package): """A Package subclass where the install() is split up into stages.""" def install_setup(self): - """Creates an spack_setup.py script to configure the package later if we like.""" - raise InstallError("Package %s provides no install_setup() method!" % self.name) + """Creates a spack_setup.py script to configure the package later.""" + raise InstallError( + "Package %s provides no install_setup() method!" % self.name) def install_configure(self): """Runs the configure process.""" - raise InstallError("Package %s provides no install_configure() method!" % self.name) + raise InstallError( + "Package %s provides no install_configure() method!" % self.name) def install_build(self): """Runs the build process.""" - raise InstallError("Package %s provides no install_build() method!" % self.name) + raise InstallError( + "Package %s provides no install_build() method!" % self.name) def install_install(self): """Runs the install process.""" - raise InstallError("Package %s provides no install_install() method!" % self.name) + raise InstallError( + "Package %s provides no install_install() method!" % self.name) def install(self, spec, prefix): if 'setup' in self.install_phases: @@ -1574,9 +1574,10 @@ def install(self, spec, prefix): else: # Create a dummy file so the build doesn't fail. # That way, the module file will also be created. - with open(os.path.join(prefix, 'dummy'), 'w') as fout: + with open(os.path.join(prefix, 'dummy'), 'w'): pass + # stackoverflow.com/questions/12791997/how-do-you-do-a-simple-chmod-x-from-within-python def make_executable(path): mode = os.stat(path).st_mode @@ -1584,9 +1585,7 @@ def make_executable(path): os.chmod(path, mode) - class CMakePackage(StagedPackage): - def make_make(self): import multiprocessing # number of jobs spack will to build with. @@ -1600,37 +1599,41 @@ def make_make(self): return make def configure_args(self): - """Returns package-specific arguments to be provided to the configure command.""" + """Returns package-specific arguments to be provided to + the configure command. + """ return list() def configure_env(self): - """Returns package-specific environment under which the configure command should be run.""" + """Returns package-specific environment under which the + configure command should be run. + """ return dict() - def spack_transitive_include_path(self): + def transitive_inc_path(self): return ';'.join( os.path.join(dep, 'include') for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep) ) def install_setup(self): - cmd = [str(which('cmake'))] + \ - spack.build_environment.get_std_cmake_args(self) + \ - ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'], - '-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'], - '-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'], - '-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + \ - self.configure_args() + cmd = [str(which('cmake'))] + cmd += spack.build_environment.get_std_cmake_args(self) + cmd += ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'], + '-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'], + '-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'], + '-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + cmd += self.configure_args() - env = dict() - env['PATH'] = os.environ['PATH'] - env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path() - env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH'] + env = { + 'PATH': os.environ['PATH'], + 'SPACK_TRANSITIVE_INCLUDE_PATH': self.transitive_inc_path(), + 'CMAKE_PREFIX_PATH': os.environ['CMAKE_PREFIX_PATH'] + } setup_fname = 'spconfig.py' with open(setup_fname, 'w') as fout: - fout.write(\ -r"""#!%s + fout.write(r"""#!%s # import sys @@ -1638,7 +1641,7 @@ def install_setup(self): import subprocess def cmdlist(str): - return list(x.strip().replace("'",'') for x in str.split('\n') if x) + return list(x.strip().replace("'",'') for x in str.split('\n') if x) env = dict(os.environ) """ % sys.executable) @@ -1646,34 +1649,39 @@ def cmdlist(str): for name in env_vars: val = env[name] if string.find(name, 'PATH') < 0: - fout.write('env[%s] = %s\n' % (repr(name),repr(val))) + fout.write('env[%s] = %s\n' % (repr(name), repr(val))) else: if name == 'SPACK_TRANSITIVE_INCLUDE_PATH': sep = ';' else: sep = ':' - fout.write('env[%s] = "%s".join(cmdlist("""\n' % (repr(name),sep)) + fout.write('env[%s] = "%s".join(cmdlist("""\n' + % (repr(name), sep)) for part in string.split(val, sep): fout.write(' %s\n' % part) fout.write('"""))\n') - fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n") + fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = " + "env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n") fout.write('\ncmd = cmdlist("""\n') fout.write('%s\n' % cmd[0]) for arg in cmd[1:]: fout.write(' %s\n' % arg) fout.write('""") + sys.argv[1:]\n') - fout.write('\nproc = subprocess.Popen(cmd, env=env)\nproc.wait()\n') + fout.write('\nproc = subprocess.Popen(cmd, env=env)\n') + fout.write('proc.wait()\n') make_executable(setup_fname) - def install_configure(self): cmake = which('cmake') with working_dir(self.build_directory, create=True): - os.environ.update(self.configure_env()) - os.environ['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path() - options = self.configure_args() + spack.build_environment.get_std_cmake_args(self) + env = os.environ + env.update(self.configure_env()) + env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.transitive_inc_path() + + options = self.configure_args() + options += spack.build_environment.get_std_cmake_args(self) cmake(self.source_directory, *options) def install_build(self): diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 7f765f80900..e694f2b2da0 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -96,7 +96,6 @@ expansion when it is the first character in an id typed on the command line. """ import sys -import itertools import hashlib import base64 import imp @@ -116,8 +115,6 @@ import spack.error import spack.compilers as compilers -# TODO: move display_specs to some other location. -from spack.cmd.find import display_specs from spack.version import * from spack.util.string import * from spack.util.prefix import Prefix @@ -650,7 +647,8 @@ def _set_platform(self, value): mod = imp.load_source(mod_name, path) class_name = mod_to_class(value) if not hasattr(mod, class_name): - tty.die('No class %s defined in %s' % (class_name, mod_name)) + tty.die( + 'No class %s defined in %s' % (class_name, mod_name)) cls = getattr(mod, class_name) if not inspect.isclass(cls): tty.die('%s.%s is not a class' % (mod_name, class_name)) @@ -673,13 +671,15 @@ def _set_platform(self, value): def _set_os(self, value): """Called by the parser to set the architecture operating system""" - if self.architecture.platform: - self.architecture.platform_os = self.architecture.platform.operating_system(value) + arch = self.architecture + if arch.platform: + arch.platform_os = arch.platform.operating_system(value) def _set_target(self, value): """Called by the parser to set the architecture target""" - if self.architecture.platform: - self.architecture.target = self.architecture.platform.target(value) + arch = self.architecture + if arch.platform: + arch.target = arch.platform.target(value) def _add_dependency(self, spec, deptypes): """Called by the parser to add another spec as a dependency.""" @@ -694,8 +694,9 @@ def _add_dependency(self, spec, deptypes): # @property def fullname(self): - return (('%s.%s' % (self.namespace, self.name)) if self.namespace else - (self.name if self.name else '')) + return ( + ('%s.%s' % (self.namespace, self.name)) if self.namespace else + (self.name if self.name else '')) @property def root(self): @@ -751,15 +752,15 @@ def concrete(self): if self._concrete: return True - self._concrete = bool(not self.virtual - and self.namespace is not None - and self.versions.concrete - and self.variants.concrete - and self.architecture - and self.architecture.concrete - and self.compiler and self.compiler.concrete - and self.compiler_flags.concrete - and self._dependencies.concrete) + self._concrete = bool(not self.virtual and + self.namespace is not None and + self.versions.concrete and + self.variants.concrete and + self.architecture and + self.architecture.concrete and + self.compiler and self.compiler.concrete and + self.compiler_flags.concrete and + self._dependencies.concrete) return self._concrete def traverse(self, visited=None, deptype=None, **kwargs): @@ -870,9 +871,9 @@ def return_val(res): for name in sorted(successors): child = successors[name] children = child.spec.traverse_with_deptype( - visited, d=d + 1, deptype=deptype_query, - deptype_query=deptype_query, - _self_deptype=child.deptypes, **kwargs) + visited, d=d + 1, deptype=deptype_query, + deptype_query=deptype_query, + _self_deptype=child.deptypes, **kwargs) for elt in children: yield elt @@ -995,7 +996,6 @@ def from_node_dict(node): return spec - @staticmethod def read_yaml_dep_specs(dependency_dict): """Read the DependencySpec portion of a YAML-formatted Spec. @@ -1018,7 +1018,6 @@ def read_yaml_dep_specs(dependency_dict): yield dep_name, dag_hash, list(deptypes) - @staticmethod def from_yaml(stream): """Construct a spec from YAML. @@ -1204,14 +1203,16 @@ def _expand_virtual_packages(self): def feq(cfield, sfield): return (not cfield) or (cfield == sfield) - if replacement is spec or (feq(replacement.name, spec.name) and - feq(replacement.versions, spec.versions) and - feq(replacement.compiler, spec.compiler) and - feq(replacement.architecture, spec.architecture) and - feq(replacement._dependencies, spec._dependencies) and - feq(replacement.variants, spec.variants) and - feq(replacement.external, spec.external) and - feq(replacement.external_module, spec.external_module)): + if replacement is spec or ( + feq(replacement.name, spec.name) and + feq(replacement.versions, spec.versions) and + feq(replacement.compiler, spec.compiler) and + feq(replacement.architecture, spec.architecture) and + feq(replacement._dependencies, spec._dependencies) and + feq(replacement.variants, spec.variants) and + feq(replacement.external, spec.external) and + feq(replacement.external_module, + spec.external_module)): continue # Refine this spec to the candidate. This uses # replace_with AND dup so that it can work in @@ -1268,10 +1269,10 @@ def concretize(self): if s.namespace is None: s.namespace = spack.repo.repo_for_pkg(s.name).namespace - for s in self.traverse(root=False): if s.external_module: - compiler = spack.compilers.compiler_for_spec(s.compiler, s.architecture) + compiler = spack.compilers.compiler_for_spec( + s.compiler, s.architecture) for mod in compiler.modules: load_module(mod) @@ -1617,20 +1618,17 @@ def constrain(self, other, deps=True): other.variants[v]) # TODO: Check out the logic here - if self.architecture is not None and other.architecture is not None: - if self.architecture.platform is not None and other.architecture.platform is not None: - if self.architecture.platform != other.architecture.platform: - raise UnsatisfiableArchitectureSpecError(self.architecture, - other.architecture) - if self.architecture.platform_os is not None and other.architecture.platform_os is not None: - if self.architecture.platform_os != other.architecture.platform_os: - raise UnsatisfiableArchitectureSpecError(self.architecture, - other.architecture) - if self.architecture.target is not None and other.architecture.target is not None: - if self.architecture.target != other.architecture.target: - raise UnsatisfiableArchitectureSpecError(self.architecture, - other.architecture) - + sarch, oarch = self.architecture, other.architecture + if sarch is not None and oarch is not None: + if sarch.platform is not None and oarch.platform is not None: + if sarch.platform != oarch.platform: + raise UnsatisfiableArchitectureSpecError(sarch, oarch) + if sarch.platform_os is not None and oarch.platform_os is not None: + if sarch.platform_os != oarch.platform_os: + raise UnsatisfiableArchitectureSpecError(sarch, oarch) + if sarch.target is not None and oarch.target is not None: + if sarch.target != oarch.target: + raise UnsatisfiableArchitectureSpecError(sarch, oarch) changed = False if self.compiler is not None and other.compiler is not None: @@ -1645,15 +1643,16 @@ def constrain(self, other, deps=True): changed |= self.compiler_flags.constrain(other.compiler_flags) old = str(self.architecture) - if self.architecture is None or other.architecture is None: - self.architecture = self.architecture or other.architecture + sarch, oarch = self.architecture, other.architecture + if sarch is None or other.architecture is None: + self.architecture = sarch or oarch else: - if self.architecture.platform is None or other.architecture.platform is None: - self.architecture.platform = self.architecture.platform or other.architecture.platform - if self.architecture.platform_os is None or other.architecture.platform_os is None: - self.architecture.platform_os = self.architecture.platform_os or other.architecture.platform_os - if self.architecture.target is None or other.architecture.target is None: - self.architecture.target = self.architecture.target or other.architecture.target + if sarch.platform is None or oarch.platform is None: + self.architecture.platform = sarch.platform or oarch.platform + if sarch.platform_os is None or oarch.platform_os is None: + sarch.platform_os = sarch.platform_os or oarch.platform_os + if sarch.target is None or oarch.target is None: + sarch.target = sarch.target or oarch.target changed |= (str(self.architecture) != old) if deps: @@ -1784,15 +1783,25 @@ def satisfies(self, other, deps=True, strict=False): # Architecture satisfaction is currently just string equality. # If not strict, None means unconstrained. - if self.architecture and other.architecture: - if ((self.architecture.platform and other.architecture.platform and self.architecture.platform != other.architecture.platform) or - (self.architecture.platform_os and other.architecture.platform_os and self.architecture.platform_os != other.architecture.platform_os) or - (self.architecture.target and other.architecture.target and self.architecture.target != other.architecture.target)): + sarch, oarch = self.architecture, other.architecture + if sarch and oarch: + if ((sarch.platform and + oarch.platform and + sarch.platform != oarch.platform) or + + (sarch.platform_os and + oarch.platform_os and + sarch.platform_os != oarch.platform_os) or + + (sarch.target and + oarch.target and + sarch.target != oarch.target)): return False - elif strict and ((other.architecture and not self.architecture) or - (other.architecture.platform and not self.architecture.platform) or - (other.architecture.platform_os and not self.architecture.platform_os) or - (other.architecture.target and not self.architecture.target)): + + elif strict and ((oarch and not sarch) or + (oarch.platform and not sarch.platform) or + (oarch.platform_os and not sarch.platform_os) or + (oarch.target and not sarch.target)): return False if not self.compiler_flags.satisfies( @@ -1874,11 +1883,16 @@ def _dup(self, other, **kwargs): # We don't count dependencies as changes here changed = True if hasattr(self, 'name'): - changed = (self.name != other.name and self.versions != other.versions and \ - self.architecture != other.architecture and self.compiler != other.compiler and \ - self.variants != other.variants and self._normal != other._normal and \ - self.concrete != other.concrete and self.external != other.external and \ - self.external_module != other.external_module and self.compiler_flags != other.compiler_flags) + changed = (self.name != other.name and + self.versions != other.versions and + self.architecture != other.architecture and + self.compiler != other.compiler and + self.variants != other.variants and + self._normal != other._normal and + self.concrete != other.concrete and + self.external != other.external and + self.external_module != other.external_module and + self.compiler_flags != other.compiler_flags) # Local node attributes get copied first. self.name = other.name @@ -1922,7 +1936,7 @@ def _dup(self, other, **kwargs): # here. if depspec.spec.name not in new_spec._dependencies: new_spec._add_dependency( - new_nodes[depspec.spec.name], depspec.deptypes) + new_nodes[depspec.spec.name], depspec.deptypes) # Since we preserved structure, we can copy _normal safely. self._normal = other._normal @@ -2033,7 +2047,6 @@ def _cmp_node(self): self.compiler, self.compiler_flags) - def eq_node(self, other): """Equality with another spec, not including dependencies.""" return self._cmp_node() == other._cmp_node() @@ -2229,41 +2242,39 @@ def write(s, c): def dep_string(self): return ''.join("^" + dep.format() for dep in self.sorted_deps()) - def __cmp__(self, other): - #Package name sort order is not configurable, always goes alphabetical + # Package name sort order is not configurable, always goes alphabetical if self.name != other.name: return cmp(self.name, other.name) - #Package version is second in compare order + # Package version is second in compare order pkgname = self.name if self.versions != other.versions: - return spack.pkgsort.version_compare(pkgname, - self.versions, other.versions) + return spack.pkgsort.version_compare( + pkgname, self.versions, other.versions) - #Compiler is third + # Compiler is third if self.compiler != other.compiler: - return spack.pkgsort.compiler_compare(pkgname, - self.compiler, other.compiler) + return spack.pkgsort.compiler_compare( + pkgname, self.compiler, other.compiler) - #Variants + # Variants if self.variants != other.variants: - return spack.pkgsort.variant_compare(pkgname, - self.variants, other.variants) + return spack.pkgsort.variant_compare( + pkgname, self.variants, other.variants) - #Target + # Target if self.architecture != other.architecture: - return spack.pkgsort.architecture_compare(pkgname, - self.architecture, other.architecture) + return spack.pkgsort.architecture_compare( + pkgname, self.architecture, other.architecture) - #Dependency is not configurable + # Dependency is not configurable if self._dependencies != other._dependencies: return -1 if self._dependencies < other._dependencies else 1 - #Equal specs + # Equal specs return 0 - def __str__(self): return self.format() + self.dep_string() @@ -2338,8 +2349,8 @@ def __init__(self): # Lexer is always the same for every parser. _lexer = SpecLexer() -class SpecParser(spack.parse.Parser): +class SpecParser(spack.parse.Parser): def __init__(self): super(SpecParser, self).__init__(_lexer) self.previous = None @@ -2392,8 +2403,8 @@ def do_parse(self): except spack.parse.ParseError, e: raise SpecParseError(e) - - # If the spec has an os or a target and no platform, give it the default platform + # If the spec has an os or a target and no platform, give it + # the default platform for spec in specs: for s in spec.traverse(): if s.architecture.os_string or s.architecture.target_string: diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index ae3f08deed6..09bdb021af7 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -1,7 +1,31 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## """ Test checks if the architecture class is created correctly and also that the functions are looking for the correct architecture name """ -import unittest +import itertools import os import platform as py_platform import spack @@ -14,9 +38,8 @@ from spack.test.mock_packages_test import * -#class ArchitectureTest(unittest.TestCase): -class ArchitectureTest(MockPackagesTest): +class ArchitectureTest(MockPackagesTest): def setUp(self): super(ArchitectureTest, self).setUp() self.platform = spack.architecture.platform() @@ -36,24 +59,22 @@ def test_dict_functions_for_architecture(self): self.assertEqual(arch, new_arch) - self.assertTrue( isinstance(arch, spack.architecture.Arch) ) - self.assertTrue( isinstance(arch.platform, spack.architecture.Platform) ) - self.assertTrue( isinstance(arch.platform_os, - spack.architecture.OperatingSystem) ) - self.assertTrue( isinstance(arch.target, - spack.architecture.Target) ) - self.assertTrue( isinstance(new_arch, spack.architecture.Arch) ) - self.assertTrue( isinstance(new_arch.platform, - spack.architecture.Platform) ) - self.assertTrue( isinstance(new_arch.platform_os, - spack.architecture.OperatingSystem) ) - self.assertTrue( isinstance(new_arch.target, - spack.architecture.Target) ) - + self.assertTrue(isinstance(arch, spack.architecture.Arch)) + self.assertTrue(isinstance(arch.platform, spack.architecture.Platform)) + self.assertTrue(isinstance(arch.platform_os, + spack.architecture.OperatingSystem)) + self.assertTrue(isinstance(arch.target, + spack.architecture.Target)) + self.assertTrue(isinstance(new_arch, spack.architecture.Arch)) + self.assertTrue(isinstance(new_arch.platform, + spack.architecture.Platform)) + self.assertTrue(isinstance(new_arch.platform_os, + spack.architecture.OperatingSystem)) + self.assertTrue(isinstance(new_arch.target, + spack.architecture.Target)) def test_platform(self): output_platform_class = spack.architecture.platform() - my_arch_class = None if os.path.exists('/opt/cray/craype'): my_platform_class = CrayXc() elif os.path.exists('/bgsys'): @@ -91,7 +112,7 @@ def test_user_defaults(self): default_os = self.platform.operating_system("default_os") default_target = self.platform.target("default_target") - default_spec = Spec("libelf") # default is no args + default_spec = Spec("libelf") # default is no args default_spec.concretize() self.assertEqual(default_os, default_spec.architecture.platform_os) self.assertEqual(default_target, default_spec.architecture.target) @@ -107,10 +128,11 @@ def test_user_input_combination(self): combinations = itertools.product(os_list, target_list) results = [] for arch in combinations: - o,t = arch + o, t = arch spec = Spec("libelf os=%s target=%s" % (o, t)) spec.concretize() - results.append(spec.architecture.platform_os == self.platform.operating_system(o)) + results.append(spec.architecture.platform_os == + self.platform.operating_system(o)) results.append(spec.architecture.target == self.platform.target(t)) res = all(results) From 2b3ba850b31af879312bc1e7c8400c2725a5c038 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Mon, 18 Jul 2016 12:51:58 +0100 Subject: [PATCH 082/126] Fix spack package-list to correctly handle deptypes --- lib/spack/spack/cmd/package-list.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index bc64c77eab4..ffb656c4689 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -48,7 +48,8 @@ def rst_table(elts): def print_rst_package_list(): """Print out information on all packages in restructured text.""" - pkgs = sorted(spack.repo.all_packages(), key=lambda s:s.name.lower()) + pkgs = sorted(spack.repo.all_packages(), key=lambda s: s.name.lower()) + pkg_names = [p.name for p in pkgs] print ".. _package-list:" print @@ -62,7 +63,7 @@ def print_rst_package_list(): print "Spack currently has %d mainline packages:" % len(pkgs) print - print rst_table("`%s`_" % p.name for p in pkgs) + print rst_table("`%s`_" % p for p in pkg_names) print print "-----" @@ -79,14 +80,15 @@ def print_rst_package_list(): print if pkg.versions: print "Versions:" - print " " + ", ".join(str(v) for v in reversed(sorted(pkg.versions))) + print " " + ", ".join(str(v) for v in + reversed(sorted(pkg.versions))) - for deptype in ('build', 'link', 'run'): - deps = pkg.dependencies(deptype) + for deptype in spack.alldeps: + deps = pkg.dependencies_of_type(deptype) if deps: print "%s Dependencies" % deptype.capitalize() - print " " + ", ".join("`%s`_" % d if d != "mpi" else d - for d in build_deps) + print " " + ", ".join("%s_" % d if d in pkg_names + else d for d in deps) print print "Description:" From cc027148ebdafbc58f3ad86b384c38534357062a Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Mon, 18 Jul 2016 12:52:23 +0100 Subject: [PATCH 083/126] Flake8 fixes in cmd/package-list.py file --- lib/spack/spack/cmd/package-list.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index ffb656c4689..2d25ebc63ed 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -34,15 +34,15 @@ def github_url(pkg): """Link to a package file on github.""" - return ("https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" % - pkg.name) + url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" # NOQA: ignore=E501 + return (url % pkg.name) def rst_table(elts): """Print out a RST-style table.""" cols = StringIO() ncol, widths = colify(elts, output=cols, tty=True) - header = " ".join("=" * (w-1) for w in widths) + header = " ".join("=" * (w - 1) for w in widths) return "%s\n%s%s" % (header, cols.getvalue(), header) From e9f42c1a94f58e5fa916705f67716c26818a7eae Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 5 Jul 2016 10:21:15 -0500 Subject: [PATCH 084/126] Allow spack create to automatically detect octave build system --- lib/spack/spack/cmd/checksum.py | 2 +- lib/spack/spack/cmd/create.py | 145 +++++++++++++++++--------------- 2 files changed, 78 insertions(+), 69 deletions(-) diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py index 95bd4771ed6..9cdb0bd0125 100644 --- a/lib/spack/spack/cmd/checksum.py +++ b/lib/spack/spack/cmd/checksum.py @@ -59,7 +59,7 @@ def get_checksums(versions, urls, **kwargs): with Stage(url, keep=keep_stage) as stage: stage.fetch() if i == 0 and first_stage_function: - first_stage_function(stage) + first_stage_function(stage, url) hashes.append((version, spack.util.crypto.checksum(hashlib.md5, stage.archive_file))) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index c9fa687b749..009b2f308b6 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -103,6 +103,64 @@ def install(self, spec, prefix): ${install} """) +# Build dependencies and extensions +dependencies_dict = { + 'autotools': "# depends_on('foo')", + 'cmake': "depends_on('cmake')", + 'scons': "depends_on('scons')", + 'python': "extends('python')", + 'R': "extends('R')", + 'octave': "extends('octave')", + 'unknown': "# depends_on('foo')" +} + +# Default installation instructions +install_dict = { + 'autotools': """\ + # FIXME: Modify the configure line to suit your build system here. + configure('--prefix={0}'.format(prefix)) + + # FIXME: Add logic to build and install here. + make() + make('install')""", + + 'cmake': """\ + with working_dir('spack-build', create=True): + # FIXME: Modify the cmake line to suit your build system here. + cmake('..', *std_cmake_args) + + # FIXME: Add logic to build and install here. + make() + make('install')""", + + 'scons': """\ + # FIXME: Add logic to build and install here. + scons('prefix={0}'.format(prefix)) + scons('install')""", + + 'python': """\ + # FIXME: Add logic to build and install here. + python('setup.py', 'install', '--prefix={0}'.format(prefix))""", + + 'R': """\ + # FIXME: Add logic to build and install here. + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path)""", + + 'octave': """\ + # FIXME: Add logic to build and install here. + octave('--quiet', '--norc', + '--built-in-docstrings-file=/dev/null', + '--texi-macros-file=/dev/null', + '--eval', 'pkg prefix {0}; pkg install {1}'.format( + prefix, self.stage.archive_file))""", + + 'unknown': """\ + # FIXME: Unknown build system + make() + make('install')""" +} + def make_version_calls(ver_hash_tuples): """Adds a version() call to the package for each version found.""" @@ -133,60 +191,17 @@ def setup_parser(subparser): setup_parser.subparser = subparser -class ConfigureGuesser(object): - def __call__(self, stage): - """Try to guess the type of build system used by the project. - Set any necessary build dependencies or extensions. - Set the appropriate default installation instructions.""" +class BuildSystemGuesser(object): + def __call__(self, stage, url): + """Try to guess the type of build system used by a project based on + the contents of its archive or the URL it was downloaded from.""" - # Build dependencies and extensions - dependenciesDict = { - 'autotools': "# depends_on('foo')", - 'cmake': "depends_on('cmake', type='build')", - 'scons': "depends_on('scons', type='build')", - 'python': "extends('python', type=nolink)", - 'R': "extends('R')", - 'unknown': "# depends_on('foo')" - } - - # Default installation instructions - installDict = { - 'autotools': """\ - # FIXME: Modify the configure line to suit your build system here. - configure('--prefix={0}'.format(prefix)) - - # FIXME: Add logic to build and install here. - make() - make('install')""", - - 'cmake': """\ - with working_dir('spack-build', create=True): - # FIXME: Modify the cmake line to suit your build system here. - cmake('..', *std_cmake_args) - - # FIXME: Add logic to build and install here. - make() - make('install')""", - - 'scons': """\ - # FIXME: Add logic to build and install here. - scons('prefix={0}'.format(prefix)) - scons('install')""", - - 'python': """\ - # FIXME: Add logic to build and install here. - python('setup.py', 'install', '--prefix={0}'.format(prefix))""", - - 'R': """\ - # FIXME: Add logic to build and install here. - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path)""", - - 'unknown': """\ - # FIXME: Unknown build system - make() - make('install')""" - } + # Most octave extensions are hosted on Octave-Forge: + # http://octave.sourceforge.net/index.html + # They all have the same base URL. + if 'downloads.sourceforge.net/octave/' in url: + self.build_system = 'octave' + return # A list of clues that give us an idea of the build system a package # uses. If the regular expression matches a file contained in the @@ -224,12 +239,6 @@ def __call__(self, stage): self.build_system = build_system - # Set any necessary build dependencies or extensions. - self.dependencies = dependenciesDict[build_system] - - # Set the appropriate default installation instructions - self.install = installDict[build_system] - def guess_name_and_version(url, args): # Try to deduce name and version of the new package from the URL @@ -334,8 +343,8 @@ def create(parser, args): # Fetch tarballs (prompting user if necessary) versions, urls = fetch_tarballs(url, name, version) - # Try to guess what configure system is used. - guesser = ConfigureGuesser() + # Try to guess what build system is used. + guesser = BuildSystemGuesser() ver_hash_tuples = spack.cmd.checksum.get_checksums( versions, urls, first_stage_function=guesser, @@ -344,13 +353,13 @@ def create(parser, args): if not ver_hash_tuples: tty.die("Could not fetch any tarballs for %s" % name) - # Prepend 'py-' to python package names, by convention. + # Add prefix to package name if it is an extension. if guesser.build_system == 'python': - name = 'py-%s' % name - - # Prepend 'r-' to R package names, by convention. + name = 'py-{0}'.format(name) if guesser.build_system == 'R': - name = 'r-%s' % name + name = 'r-{0}'.format(name) + if guesser.build_system == 'octave': + name = 'octave-{0}'.format(name) # Create a directory for the new package. pkg_path = repo.filename_for_package_name(name) @@ -367,8 +376,8 @@ def create(parser, args): class_name=mod_to_class(name), url=url, versions=make_version_calls(ver_hash_tuples), - dependencies=guesser.dependencies, - install=guesser.install)) + dependencies=dependencies_dict[guesser.build_system], + install=install_dict[guesser.build_system])) # If everything checks out, go ahead and edit. spack.editor(pkg_path) From 199a8af7cc4e75e66cf53c3a2bb4c9b28aec64f1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 5 Jul 2016 10:39:40 -0500 Subject: [PATCH 085/126] Flake8 --- lib/spack/spack/cmd/checksum.py | 19 +++++++++++-------- lib/spack/spack/cmd/create.py | 2 +- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py index 9cdb0bd0125..aedb0fd99cc 100644 --- a/lib/spack/spack/cmd/checksum.py +++ b/lib/spack/spack/cmd/checksum.py @@ -42,7 +42,8 @@ def setup_parser(subparser): '--keep-stage', action='store_true', dest='keep_stage', help="Don't clean up staging area when command completes.") subparser.add_argument( - 'versions', nargs=argparse.REMAINDER, help='Versions to generate checksums for') + 'versions', nargs=argparse.REMAINDER, + help='Versions to generate checksums for') def get_checksums(versions, urls, **kwargs): @@ -61,8 +62,8 @@ def get_checksums(versions, urls, **kwargs): if i == 0 and first_stage_function: first_stage_function(stage, url) - hashes.append((version, - spack.util.crypto.checksum(hashlib.md5, stage.archive_file))) + hashes.append((version, spack.util.crypto.checksum( + hashlib.md5, stage.archive_file))) i += 1 except FailedDownloadError as e: tty.msg("Failed to fetch %s" % url) @@ -79,12 +80,12 @@ def checksum(parser, args): # If the user asked for specific versions, use those. if args.versions: versions = {} - for v in args.versions: - v = ver(v) - if not isinstance(v, Version): + for version in args.versions: + version = ver(version) + if not isinstance(version, Version): tty.die("Cannot generate checksums for version lists or " + "version ranges. Use unambiguous versions.") - versions[v] = pkg.url_for_version(v) + versions[version] = pkg.url_for_version(version) else: versions = pkg.fetch_remote_versions() if not versions: @@ -111,5 +112,7 @@ def checksum(parser, args): if not version_hashes: tty.die("Could not fetch any versions for %s" % pkg.name) - version_lines = [" version('%s', '%s')" % (v, h) for v, h in version_hashes] + version_lines = [ + " version('%s', '%s')" % (v, h) for v, h in version_hashes + ] tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index 009b2f308b6..2c440096d11 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -124,7 +124,7 @@ def install(self, spec, prefix): make() make('install')""", - 'cmake': """\ + 'cmake': """\ with working_dir('spack-build', create=True): # FIXME: Modify the cmake line to suit your build system here. cmake('..', *std_cmake_args) From 262ab401884a8b46992872b8c010fa844cb14271 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 5 Jul 2016 11:33:29 -0500 Subject: [PATCH 086/126] Update build_system_guess test with new class name --- lib/spack/spack/test/__init__.py | 2 +- ...nfigure_guess.py => build_system_guess.py} | 26 ++++++++++++------- 2 files changed, 17 insertions(+), 11 deletions(-) rename lib/spack/spack/test/{configure_guess.py => build_system_guess.py} (88%) diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index fb91f247214..19bc1d89d37 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -38,7 +38,7 @@ 'directory_layout', 'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml', 'optional_deps', - 'make_executable', 'configure_guess', 'lock', 'database', + 'make_executable', 'build_system_guess', 'lock', 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd'] diff --git a/lib/spack/spack/test/configure_guess.py b/lib/spack/spack/test/build_system_guess.py similarity index 88% rename from lib/spack/spack/test/configure_guess.py rename to lib/spack/spack/test/build_system_guess.py index bad3673e7ad..80b867a528e 100644 --- a/lib/spack/spack/test/configure_guess.py +++ b/lib/spack/spack/test/build_system_guess.py @@ -28,14 +28,14 @@ import unittest from llnl.util.filesystem import * -from spack.cmd.create import ConfigureGuesser +from spack.cmd.create import BuildSystemGuesser from spack.stage import Stage from spack.test.mock_packages_test import * from spack.util.executable import which class InstallTest(unittest.TestCase): - """Tests the configure guesser in spack create""" + """Tests the build system guesser in spack create""" def setUp(self): self.tar = which('tar') @@ -60,15 +60,11 @@ def check_archive(self, filename, system): with Stage(url) as stage: stage.fetch() - guesser = ConfigureGuesser() - guesser(stage) + guesser = BuildSystemGuesser() + guesser(stage, url) self.assertEqual(system, guesser.build_system) - def test_python(self): - self.check_archive('setup.py', 'python') - - def test_autotools(self): self.check_archive('configure', 'autotools') @@ -77,7 +73,17 @@ def test_cmake(self): self.check_archive('CMakeLists.txt', 'cmake') + def test_scons(self): + self.check_archive('SConstruct', 'scons') + + + def test_python(self): + self.check_archive('setup.py', 'python') + + + def test_R(self): + self.check_archive('NAMESPACE', 'R') + + def test_unknown(self): self.check_archive('foobar', 'unknown') - - From 89c9bec81ec3afa96ba25dd6aea9727abc8a8f0f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 5 Jul 2016 11:36:07 -0500 Subject: [PATCH 087/126] Flake8 --- lib/spack/spack/test/__init__.py | 19 ++++++++++--------- lib/spack/spack/test/build_system_guess.py | 8 -------- 2 files changed, 10 insertions(+), 17 deletions(-) diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index 19bc1d89d37..9f7da46a1a3 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -32,15 +32,16 @@ from spack.test.tally_plugin import Tally """Names of tests to be included in Spack's test suite""" -test_names = ['architecture', 'versions', 'url_parse', 'url_substitution', 'packages', 'stage', - 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize', - 'multimethod', 'install', 'package_sanity', 'config', - 'directory_layout', 'pattern', 'python_version', 'git_fetch', - 'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate', - 'cc', 'link_tree', 'spec_yaml', 'optional_deps', - 'make_executable', 'build_system_guess', 'lock', 'database', - 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', - 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd'] +test_names = [ + 'architecture', 'versions', 'url_parse', 'url_substitution', 'packages', + 'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize', + 'multimethod', 'install', 'package_sanity', 'config', 'directory_layout', + 'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch', + 'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml', + 'optional_deps', 'make_executable', 'build_system_guess', 'lock', + 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', + 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd' +] def list_tests(): diff --git a/lib/spack/spack/test/build_system_guess.py b/lib/spack/spack/test/build_system_guess.py index 80b867a528e..e728a47cf44 100644 --- a/lib/spack/spack/test/build_system_guess.py +++ b/lib/spack/spack/test/build_system_guess.py @@ -44,12 +44,10 @@ def setUp(self): os.chdir(self.tmpdir) self.stage = None - def tearDown(self): shutil.rmtree(self.tmpdir, ignore_errors=True) os.chdir(self.orig_dir) - def check_archive(self, filename, system): mkdirp('archive') touch(join_path('archive', filename)) @@ -64,26 +62,20 @@ def check_archive(self, filename, system): guesser(stage, url) self.assertEqual(system, guesser.build_system) - def test_autotools(self): self.check_archive('configure', 'autotools') - def test_cmake(self): self.check_archive('CMakeLists.txt', 'cmake') - def test_scons(self): self.check_archive('SConstruct', 'scons') - def test_python(self): self.check_archive('setup.py', 'python') - def test_R(self): self.check_archive('NAMESPACE', 'R') - def test_unknown(self): self.check_archive('foobar', 'unknown') From 583232ea521c24158a9e537520a5eb434b08a74c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Jul 2016 11:38:13 -0500 Subject: [PATCH 088/126] Build Python with Tkinter support --- .../repos/builtin/packages/python/package.py | 42 ++++++++++++++++--- .../repos/builtin/packages/tcl/package.py | 6 +++ .../repos/builtin/packages/tk/package.py | 6 +++ 3 files changed, 48 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 516b5c6cfe6..bbb1e9c13ad 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -53,6 +53,7 @@ class Python(Package): extendable = True + variant('tk', default=False, description='Provide support for Tkinter') variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') # From https://docs.python.org/2/c-api/unicode.html: Python's default # builds use a 16-bit type for Py_UNICODE and store Unicode values @@ -68,6 +69,8 @@ class Python(Package): depends_on("ncurses") depends_on("sqlite") depends_on("zlib") + depends_on("tk", when="+tk") + depends_on("tcl", when="+tk") def install(self, spec, prefix): # Need this to allow python build to find the Python installation. @@ -77,24 +80,32 @@ def install(self, spec, prefix): # Rest of install is pretty standard except setup.py needs to # be able to read the CPPFLAGS and LDFLAGS as it scans for the # library and headers to build - cppflags = ' -I'.join([ + include_dirs = [ spec['openssl'].prefix.include, spec['bzip2'].prefix.include, spec['readline'].prefix.include, spec['ncurses'].prefix.include, spec['sqlite'].prefix.include, spec['zlib'].prefix.include - ]) + ] - ldflags = ' -L'.join([ + library_dirs = [ spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib, spec['readline'].prefix.lib, spec['ncurses'].prefix.lib, spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib - ]) + ] + + if '+tk' in spec: + include_dirs.extend([ + spec['tk'].prefix.include, spec['tcl'].prefix.include + ]) + library_dirs.extend([ + spec['tk'].prefix.lib, spec['tcl'].prefix.lib + ]) config_args = [ "--prefix={0}".format(prefix), "--with-threads", "--enable-shared", - "CPPFLAGS=-I{0}".format(cppflags), - "LDFLAGS=-L{0}".format(ldflags) + "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)), + "LDFLAGS=-L{0}".format(" -L".join(library_dirs)) ] if '+ucs4' in spec: @@ -116,6 +127,25 @@ def install(self, spec, prefix): self.filter_compilers(spec, prefix) + # TODO: Once better testing support is integrated, add the following tests + # https://wiki.python.org/moin/TkInter + # + # if '+tk' in spec: + # env['TK_LIBRARY'] = join_path(spec['tk'].prefix.lib, + # 'tk{0}'.format(spec['tk'].version.up_to(2))) + # env['TCL_LIBRARY'] = join_path(spec['tcl'].prefix.lib, + # 'tcl{0}'.format(spec['tcl'].version.up_to(2))) + # + # $ python + # >>> import _tkinter + # + # if spec.satisfies('@3:') + # >>> import tkinter + # >>> tkinter._test() + # else: + # >>> import Tkinter + # >>> Tkinter._test() + def filter_compilers(self, spec, prefix): """Run after install to tell the configuration files and Makefiles to use the compilers that Spack built the package with. diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index a4d8b515bb1..4a957fd9de2 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -44,6 +44,12 @@ def url_for_version(self, version): depends_on('zlib') + def setup_environment(self, spack_env, env): + # When using Tkinter from within spack provided python+tk, python + # will not be able to find Tcl/Tk unless TCL_LIBRARY is set. + env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format( + self.spec.version.up_to(2)))) + def install(self, spec, prefix): with working_dir('unix'): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 330e1c77f56..097cd411f18 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -40,6 +40,12 @@ def url_for_version(self, version): depends_on("tcl") + def setup_environment(self, spack_env, env): + # When using Tkinter from within spack provided python+tk, python + # will not be able to find Tcl/Tk unless TK_LIBRARY is set. + env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format( + self.spec.version.up_to(2)))) + def install(self, spec, prefix): with working_dir('unix'): configure("--prefix=%s" % prefix, From ea425a101a698705609698771c0542d2be70987e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Jul 2016 11:44:24 -0500 Subject: [PATCH 089/126] Flake8 and new tk version --- var/spack/repos/builtin/packages/tcl/package.py | 10 ++++++---- var/spack/repos/builtin/packages/tk/package.py | 13 ++++++++----- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index 4a957fd9de2..ef922314d8f 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Tcl(Package): """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide @@ -34,9 +35,6 @@ class Tcl(Package): extensible.""" homepage = "http://www.tcl.tk" - def url_for_version(self, version): - return 'http://prdownloads.sourceforge.net/tcl/tcl%s-src.tar.gz' % version - version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326') version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304') version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f') @@ -44,6 +42,10 @@ def url_for_version(self, version): depends_on('zlib') + def url_for_version(self, version): + base_url = 'http://prdownloads.sourceforge.net/tcl' + return '{0}/tcl{1}-src.tar.gz'.format(base_url, version) + def setup_environment(self, spack_env, env): # When using Tkinter from within spack provided python+tk, python # will not be able to find Tcl/Tk unless TCL_LIBRARY is set. @@ -52,6 +54,6 @@ def setup_environment(self, spack_env, env): def install(self, spec, prefix): with working_dir('unix'): - configure("--prefix=%s" % prefix) + configure("--prefix={0}".format(prefix)) make() make("install") diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 097cd411f18..894d3af6cc9 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Tk(Package): """Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional @@ -33,13 +34,15 @@ class Tk(Package): and more.""" homepage = "http://www.tcl.tk" - def url_for_version(self, version): - return "http://prdownloads.sourceforge.net/tcl/tk%s-src.tar.gz" % version - + version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4') version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221') depends_on("tcl") + def url_for_version(self, version): + base_url = "http://prdownloads.sourceforge.net/tcl" + return "{0}/tk{1}-src.tar.gz".format(base_url, version) + def setup_environment(self, spack_env, env): # When using Tkinter from within spack provided python+tk, python # will not be able to find Tcl/Tk unless TK_LIBRARY is set. @@ -48,7 +51,7 @@ def setup_environment(self, spack_env, env): def install(self, spec, prefix): with working_dir('unix'): - configure("--prefix=%s" % prefix, - "--with-tcl=%s" % spec['tcl'].prefix.lib) + configure("--prefix={0}".format(prefix), + "--with-tcl={0}".format(spec['tcl'].prefix.lib)) make() make("install") From a46138dea94cdcddd91f83aaedb7388a0e53f7e4 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Mon, 18 Jul 2016 13:59:58 +0100 Subject: [PATCH 090/126] More flake8 fixes for package-list --- lib/spack/spack/cmd/package-list.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index 2d25ebc63ed..a27502d30e6 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -22,10 +22,8 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import re import cgi from StringIO import StringIO -import llnl.util.tty as tty from llnl.util.tty.colify import * import spack From 2b4d2b8748669ad5a2c45d2024d265f12071c441 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 18 Jul 2016 11:39:26 -0400 Subject: [PATCH 091/126] gitignore: don't require opt to be a directory I use a symlink to make it easy to swap out. --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 040df3eafd2..bfc6172a4e7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,7 @@ /var/spack/stage /var/spack/cache *.pyc -/opt/ +/opt *~ .DS_Store .idea From 19df1ea79d5539986652de84782856bcc7a84037 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Mon, 18 Jul 2016 17:53:26 +0200 Subject: [PATCH 092/126] flake8 fix --- lib/spack/spack/test/modules.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py index b6d35154e33..135cd028e3d 100644 --- a/lib/spack/spack/test/modules.py +++ b/lib/spack/spack/test/modules.py @@ -27,7 +27,6 @@ import StringIO import spack.modules -import unittest from spack.test.mock_packages_test import MockPackagesTest FILE_REGISTRY = collections.defaultdict(StringIO.StringIO) From 49cd6f6269267b5388b3dcc31ec2cafc58567e80 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 18 Jul 2016 16:01:48 -0400 Subject: [PATCH 093/126] py-numpy: Add py-setuptools dependencies Closes #1281. --- var/spack/repos/builtin/packages/py-numpy/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 6bc11a5e484..15adcbc2aca 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -44,6 +44,7 @@ class PyNumpy(Package): extends('python') depends_on('py-nose', type='build') + depends_on('py-setuptools') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') From 67fade5b1e128e7bb08ef4709da5e15a22d10ee6 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 18 Jul 2016 17:08:56 -0400 Subject: [PATCH 094/126] Declare dependency of "py-h5py +mpi" on "py-mpi4py" --- var/spack/repos/builtin/packages/py-h5py/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index c1950a91ac0..f96cb9b4cd1 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -46,6 +46,7 @@ class PyH5py(Package): depends_on('hdf5@1.8.4:') depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') + depends_on('py-mpi4py', when='+mpi') # Build and runtime dependencies depends_on('py-numpy@1.6.1:', type=nolink) From 607813d5ce6dbd5063f9a0ac6d90aea8b307da3f Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 18 Jul 2016 14:13:14 -0700 Subject: [PATCH 095/126] setuptools is a build dependency in numpy. --- var/spack/repos/builtin/packages/py-numpy/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 15adcbc2aca..2febdac6589 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -44,7 +44,7 @@ class PyNumpy(Package): extends('python') depends_on('py-nose', type='build') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') From 46ee4a3a5360010e77f77f201ffd5e4289516cc4 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Mon, 18 Jul 2016 14:25:17 -0700 Subject: [PATCH 096/126] Using cc -craype-verbose to get cray platform type --- lib/spack/spack/platforms/cray_xc.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index e710303e23a..8dc575bb716 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -2,6 +2,7 @@ from spack.architecture import Platform, Target from spack.operating_systems.linux_distro import LinuxDistro from spack.operating_systems.cnl import Cnl +from spack.util.executable import which class CrayXc(Platform): priority = 20 @@ -42,5 +43,11 @@ def __init__(self): @classmethod def detect(self): - return os.path.exists('/opt/cray/craype') + if os.path.exists('/cray_home'): + cc_verbose = which('cc') + cc_verbose.add_default_arg('-craype-verbose') + text = cc_verbose(output=str, error=str, ignore_errors=True).split() + if '-D__CRAYXC' in text: + return True + return False From 02340062b4d435ee97cec857f25122b8f2e3c990 Mon Sep 17 00:00:00 2001 From: mwilliammyers Date: Mon, 18 Jul 2016 16:17:07 -0600 Subject: [PATCH 097/126] package - jasper - Add new jasper package --- .../fix_alpha_channel_assert_fail.patch | 25 ++++++++ .../repos/builtin/packages/jasper/package.py | 63 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch create mode 100644 var/spack/repos/builtin/packages/jasper/package.py diff --git a/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch b/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch new file mode 100644 index 00000000000..cbf79ff9719 --- /dev/null +++ b/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch @@ -0,0 +1,25 @@ +diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c +index fa72a0e..1f4845f 100644 +--- a/src/libjasper/jpc/jpc_dec.c ++++ b/src/libjasper/jpc/jpc_dec.c +@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile) + /* Apply an inverse intercomponent transform if necessary. */ + switch (tile->cp->mctid) { + case JPC_MCT_RCT: +- assert(dec->numcomps == 3); ++ if (dec->numcomps != 3 && dec->numcomps != 4) { ++ jas_eprintf("bad number of components (%d)\n", dec->numcomps); ++ return -1; ++ } + jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data, + tile->tcomps[2].data); + break; + case JPC_MCT_ICT: +- assert(dec->numcomps == 3); ++ if (dec->numcomps != 3 && dec->numcomps != 4) { ++ jas_eprintf("bad number of components (%d)\n", dec->numcomps); ++ return -1; ++ } + jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data, + tile->tcomps[2].data); + break; diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py new file mode 100644 index 00000000000..f450c7d155f --- /dev/null +++ b/var/spack/repos/builtin/packages/jasper/package.py @@ -0,0 +1,63 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Jasper(Package): + """Library for manipulating JPEG-2000 images""" + + homepage = "https://www.ece.uvic.ca/~frodo/jasper/" + url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip" + + version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754') + + variant('shared', default=True, + description='Builds shared versions of the libraries') + variant('debug', default=False, + description='Builds debug versions of the libraries') + + depends_on('libjpeg-turbo') + + # Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails + # when certain JPEG-2000 files with an alpha channel are processed + # see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786 + patch('fix_alpha_channel_assert_fail.patch') + + def install(self, spec, prefix): + configure_options = [ + '--prefix={0}'.format(prefix), + '--mandir={0}'.format(spec.prefix.man), + ] + + if '+shared' in spec: + configure_options.append('--enable-shared') + + if '+debug' not in spec: + configure_options.append('--disable-debug') + + configure(*configure_options) + + make() + make('install') From 218fc602fad2caf88b5e71c640b1569e5ab408da Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Mon, 18 Jul 2016 15:43:21 -0700 Subject: [PATCH 098/126] Let packages call use_cray_compilers() in install to get , etc set to cray names --- lib/spack/env/cc | 4 ++-- lib/spack/env/craype/CC | 1 + lib/spack/env/craype/cc | 1 + lib/spack/env/craype/ftn | 1 + lib/spack/spack/package.py | 7 +++++++ 5 files changed, 12 insertions(+), 2 deletions(-) create mode 120000 lib/spack/env/craype/CC create mode 120000 lib/spack/env/craype/cc create mode 120000 lib/spack/env/craype/ftn diff --git a/lib/spack/env/cc b/lib/spack/env/cc index bf98b4c3540..c6bb50d261a 100755 --- a/lib/spack/env/cc +++ b/lib/spack/env/cc @@ -110,13 +110,13 @@ case "$command" in comp="CXX" lang_flags=CXX ;; - f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor) + ftn|f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor) command="$SPACK_FC" language="Fortran 90" comp="FC" lang_flags=F ;; - f77|gfortran|ifort|pgfortran|xlf|nagfor) + f77|gfortran|ifort|pgfortran|xlf|nagfor|ftn) command="$SPACK_F77" language="Fortran 77" comp="F77" diff --git a/lib/spack/env/craype/CC b/lib/spack/env/craype/CC new file mode 120000 index 00000000000..82c2b8e90a3 --- /dev/null +++ b/lib/spack/env/craype/CC @@ -0,0 +1 @@ +../cc \ No newline at end of file diff --git a/lib/spack/env/craype/cc b/lib/spack/env/craype/cc new file mode 120000 index 00000000000..82c2b8e90a3 --- /dev/null +++ b/lib/spack/env/craype/cc @@ -0,0 +1 @@ +../cc \ No newline at end of file diff --git a/lib/spack/env/craype/ftn b/lib/spack/env/craype/ftn new file mode 120000 index 00000000000..82c2b8e90a3 --- /dev/null +++ b/lib/spack/env/craype/ftn @@ -0,0 +1 @@ +../cc \ No newline at end of file diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 6a92c548fbf..c916bfaaa28 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1439,6 +1439,13 @@ def install_dependency_symlinks(pkg, spec, prefix): flatten_dependencies(spec, prefix) +def use_cray_compiler_names(): + """Compiler names for builds that rely on cray compiler names.""" + os.environ['CC'] = 'cc' + os.environ['CXX'] = 'CC' + os.environ['FC'] = 'ftn' + os.environ['F77'] = 'ftn' + def flatten_dependencies(spec, flat_dir): """Make each dependency of spec present in dir via symlink.""" for dep in spec.traverse(root=False): From 94df1b801a70b72f86e4a4a30c5bfeb018a8c5d2 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 18 Jul 2016 20:11:32 -0400 Subject: [PATCH 099/126] Update NetCDF to version 4.4.1 This version supports HDF5 1.10 in a backward-compatible manner. --- var/spack/repos/builtin/packages/netcdf/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 063d38e4f94..13d6bc69440 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -33,6 +33,7 @@ class Netcdf(Package): homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz" + version('4.4.1', '7843e35b661c99e1d49e60791d5072d8') version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') From 4dec06e4f48044977acf484b95532b6f682ad960 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 18 Jul 2016 20:14:44 -0400 Subject: [PATCH 100/126] Make HDF5 1.10 the default version Apply this only after NetCDF 4.4.1 is supported. --- var/spack/repos/builtin/packages/hdf5/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 51a5823aa5c..d169940c863 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -40,7 +40,7 @@ class Hdf5(Package): version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295') version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') - version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True) + version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') From 71684cb07128bebdbabaaa695ef05f98ed9cd49f Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 18 Jul 2016 23:04:20 -0400 Subject: [PATCH 101/126] Flex requires m4 --- var/spack/repos/builtin/packages/flex/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index 800e4b9d96a..9b173bb0dd6 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -35,6 +35,7 @@ class Flex(Package): version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') depends_on("bison", type='build') + depends_on("m4", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) From 25e765baae6f98141cb7896bbcbb840607a4842f Mon Sep 17 00:00:00 2001 From: "Robert D. French" Date: Tue, 19 Jul 2016 10:15:00 -0700 Subject: [PATCH 102/126] Download Adios from Github Get adios from github, not NCCS Use correct hash, thanks Ben --- var/spack/repos/builtin/packages/adios/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 9e0452ba6f1..59e0a451a90 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -12,9 +12,9 @@ class Adios(Package): """ homepage = "http://www.olcf.ornl.gov/center-projects/adios/" - url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz" + url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz" - version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76') + version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678') # Lots of setting up here for this package # module swap PrgEnv-intel PrgEnv-$COMP From afa4cdc2d876fa9d4743813f7961661875430df1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 19 Jul 2016 12:33:04 -0500 Subject: [PATCH 103/126] Updates to Armadillo package --- var/spack/repos/builtin/packages/armadillo/package.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index b3e5994e305..5043a6a2123 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -33,11 +33,13 @@ class Armadillo(Package): homepage = "http://arma.sourceforge.net/" url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2') version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') variant('hdf5', default=False, description='Include HDF5 support') - depends_on('arpack') + depends_on('cmake@2.8:', type='build') + depends_on('arpack-ng') # old arpack causes undefined symbols depends_on('blas') depends_on('lapack') depends_on('superlu@5.2:') @@ -46,8 +48,8 @@ class Armadillo(Package): def install(self, spec, prefix): cmake_args = [ # ARPACK support - '-DARPACK_LIBRARY={0}/libarpack.a'.format( - spec['arpack'].prefix.lib), + '-DARPACK_LIBRARY={0}/libarpack.so'.format( + spec['arpack-ng'].prefix.lib), # BLAS support '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib), # LAPACK support From 8034536054b4fcd94809bde379ecc5e2d6a61647 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 19 Jul 2016 12:37:34 -0500 Subject: [PATCH 104/126] Fix shared object suffix for macOS --- var/spack/repos/builtin/packages/armadillo/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index 5043a6a2123..4356f60aca2 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -48,8 +48,8 @@ class Armadillo(Package): def install(self, spec, prefix): cmake_args = [ # ARPACK support - '-DARPACK_LIBRARY={0}/libarpack.so'.format( - spec['arpack-ng'].prefix.lib), + '-DARPACK_LIBRARY={0}/libarpack.{1}'.format( + spec['arpack-ng'].prefix.lib, dso_suffix), # BLAS support '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib), # LAPACK support From 1c9cf668a1c56a7259d988f263cdab89e7234890 Mon Sep 17 00:00:00 2001 From: "Robert D. French" Date: Tue, 19 Jul 2016 10:06:36 -0700 Subject: [PATCH 105/126] Silver Search 0.32 is out PEP8 Love + Re-adding v0.30.0 --- .../repos/builtin/packages/the_silver_searcher/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py index 988619df304..c98e964efa6 100644 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py @@ -24,11 +24,13 @@ ############################################################################## from spack import * + class TheSilverSearcher(Package): """Fast recursive grep alternative""" homepage = "http://geoff.greer.fm/ag/" - url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.30.0.tar.gz" + url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz" + version('0.32.0', '3fdfd5836924246073d5344257a06823') version('0.30.0', '95e2e7859fab1156c835aff7413481db') depends_on('pcre') From 1315753e704615a37cde4e3a6b342cd253bfd95b Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 18 Jul 2016 14:23:29 -0400 Subject: [PATCH 106/126] deptypes: support special deptypes by string --- lib/spack/docs/packaging_guide.rst | 6 +++--- lib/spack/spack/directives.py | 2 +- lib/spack/spack/spec.py | 7 ++++++- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 6bafaecc7db..70def5c39a0 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1307,9 +1307,9 @@ The dependency types are: If not specified, ``type`` is assumed to be ``("build", "link")``. This is the common case for compiled language usage. Also available are the aliases -``alldeps`` for all dependency types and ``nolink`` (``("build", "run")``) for -use by dependencies which are not expressed via a linker (e.g., Python or Lua -module loading). +``"alldeps"`` for all dependency types and ``"nolink"`` (``("build", "run")``) +for use by dependencies which are not expressed via a linker (e.g., Python or +Lua module loading). .. _setup-dependent-environment: diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py index 88d2aaf4728..e92dd6fb679 100644 --- a/lib/spack/spack/directives.py +++ b/lib/spack/spack/directives.py @@ -189,7 +189,7 @@ def _depends_on(pkg, spec, when=None, type=None): type = ('build', 'link') if isinstance(type, str): - type = (type,) + type = spack.spec.special_types.get(type, (type,)) for deptype in type: if deptype not in spack.spec.alldeps: diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index e694f2b2da0..8bdae0445e6 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -155,6 +155,10 @@ # Special types of dependencies. alldeps = ('build', 'link', 'run') nolink = ('build', 'run') +special_types = { + 'alldeps': alldeps, + 'nolink': nolink, +} def index_specs(specs): @@ -542,7 +546,8 @@ def _deptype_norm(self, deptype): return alldeps # Force deptype to be a set object so that we can do set intersections. if isinstance(deptype, str): - return (deptype,) + # Support special deptypes. + return special_types.get(deptype, (deptype,)) return deptype def _find_deps(self, where, deptype): From dd7bd4f320651411a1125268310b2b1f590ad213 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 19 Jul 2016 14:59:04 -0700 Subject: [PATCH 107/126] Make frontend OS on Cray machines a proper linux distro. --- lib/spack/spack/platforms/cray_xc.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index 8dc575bb716..0f6599ab30d 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -10,9 +10,8 @@ class CrayXc(Platform): back_end = 'ivybridge' default = 'ivybridge' - front_os = "SuSE11" back_os = "CNL10" - default_os = "CNL10" + default_os = "CNL10" def __init__(self): ''' Since cori doesn't have ivybridge as a front end it's better @@ -33,12 +32,15 @@ def __init__(self): # Could switch to use modules and fe targets for front end # Currently using compilers by path for front end. self.add_target('sandybridge', Target('sandybridge')) - self.add_target('ivybridge', + self.add_target('ivybridge', Target('ivybridge', 'craype-ivybridge')) - self.add_target('haswell', - Target('haswell','craype-haswell')) + self.add_target('haswell', + Target('haswell','craype-haswell')) - self.add_operating_system('SuSE11', LinuxDistro()) + # Front end of the cray platform is a linux distro. + linux_dist = LinuxDistro() + self.front_os = str(linux_dist) + self.add_operating_system(str(linux_dist), linux_dist) self.add_operating_system('CNL10', Cnl()) @classmethod @@ -50,4 +52,3 @@ def detect(self): if '-D__CRAYXC' in text: return True return False - From 6b0fb476ab917e68370b61cf77eff8fdedb79e09 Mon Sep 17 00:00:00 2001 From: "Robert D. French" Date: Tue, 19 Jul 2016 15:57:55 -0700 Subject: [PATCH 108/126] Draft CDO --- .../repos/builtin/packages/cdo/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cdo/package.py diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py new file mode 100644 index 00000000000..09c4fde4558 --- /dev/null +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Cdo(Package): + """CDO is a collection of command line Operators to manipulate and analyse + Climate and NWP model Data. """ + + # FIXME: Add a proper url for your package's homepage here. + homepage = "https://code.zmaw.de/projects/cdo" + url = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz" + + version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2') + + # FIXME: Add additional dependencies if required. + depends_on('netcdf') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') From 26480f14f901da087efbac263835c8767eaea23a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 19 Jul 2016 17:10:17 -0700 Subject: [PATCH 109/126] Add "default" configuration scope. - Default scope is versioned with spack and can be overridden by site or user config. - Default scope provides sensible default concretization preferences for all of Spack. - per-platform concretization scope can be added later (to force a particular MPI on, e.g., Cray systems) --- .gitignore | 2 +- etc/spack/{ => defaults}/modules.yaml | 15 ++++++++++++--- etc/spack/defaults/packages.yaml | 21 +++++++++++++++++++++ etc/spack/defaults/repos.yaml | 14 ++++++++++++++ etc/spack/repos.yaml | 8 -------- lib/spack/spack/config.py | 9 ++++++++- 6 files changed, 56 insertions(+), 13 deletions(-) rename etc/spack/{ => defaults}/modules.yaml (53%) create mode 100644 etc/spack/defaults/packages.yaml create mode 100644 etc/spack/defaults/repos.yaml delete mode 100644 etc/spack/repos.yaml diff --git a/.gitignore b/.gitignore index bfc6172a4e7..1d4d24aa522 100644 --- a/.gitignore +++ b/.gitignore @@ -5,7 +5,7 @@ *~ .DS_Store .idea -/etc/spack/* +/etc/spack/*.yaml /etc/spackconfig /share/spack/dotkit /share/spack/modules diff --git a/etc/spack/modules.yaml b/etc/spack/defaults/modules.yaml similarity index 53% rename from etc/spack/modules.yaml rename to etc/spack/defaults/modules.yaml index 9ae54a2d098..8864a76547a 100644 --- a/etc/spack/modules.yaml +++ b/etc/spack/defaults/modules.yaml @@ -1,8 +1,17 @@ # ------------------------------------------------------------------------- -# This is the default spack module files generation configuration. +# This is the default configuration for Spack's module file generation. # -# Changes to this file will affect all users of this spack install, -# although users can override these settings in their ~/.spack/modules.yaml. +# Settings here are versioned with Spack and are intended to provide +# sensible defaults out of the box. Spack maintainers should edit this +# file to keep it current. +# +# Users can override these settings by editing the following files. +# +# Per-spack-instance settings (overrides defaults): +# $SPACK_ROOT/etc/spack/modules.yaml +# +# Per-user settings (overrides default and site settings): +# ~/.spack/modules.yaml # ------------------------------------------------------------------------- modules: enable: diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml new file mode 100644 index 00000000000..83f9eb7ece1 --- /dev/null +++ b/etc/spack/defaults/packages.yaml @@ -0,0 +1,21 @@ +# ------------------------------------------------------------------------- +# This file controls default concretization preferences for Spack. +# +# Settings here are versioned with Spack and are intended to provide +# sensible defaults out of the box. Spack maintainers should edit this +# file to keep it current. +# +# Users can override these settings by editing the following files. +# +# Per-spack-instance settings (overrides defaults): +# $SPACK_ROOT/etc/spack/packages.yaml +# +# Per-user settings (overrides default and site settings): +# ~/.spack/packages.yaml +# ------------------------------------------------------------------------- +packages: + all: + providers: + mpi: [openmpi, mpich] + blas: [openblas] + lapack: [openblas] diff --git a/etc/spack/defaults/repos.yaml b/etc/spack/defaults/repos.yaml new file mode 100644 index 00000000000..f3e00653eb1 --- /dev/null +++ b/etc/spack/defaults/repos.yaml @@ -0,0 +1,14 @@ +# ------------------------------------------------------------------------- +# This is the default spack repository configuration. It includes the +# builtin spack package repository. +# +# Users can override these settings by editing the following files. +# +# Per-spack-instance settings (overrides defaults): +# $SPACK_ROOT/etc/spack/repos.yaml +# +# Per-user settings (overrides default and site settings): +# ~/.spack/repos.yaml +# ------------------------------------------------------------------------- +repos: + - $spack/var/spack/repos/builtin diff --git a/etc/spack/repos.yaml b/etc/spack/repos.yaml deleted file mode 100644 index 2d4ff54ce6d..00000000000 --- a/etc/spack/repos.yaml +++ /dev/null @@ -1,8 +0,0 @@ -# ------------------------------------------------------------------------- -# This is the default spack repository configuration. -# -# Changes to this file will affect all users of this spack install, -# although users can override these settings in their ~/.spack/repos.yaml. -# ------------------------------------------------------------------------- -repos: - - $spack/var/spack/repos/builtin diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index 3a66e9f2a60..8b5e96f97d1 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -497,8 +497,15 @@ def clear(self): """Empty cached config information.""" self.sections = {} +"""Default configuration scope is the lowest-level scope. These are + versioned with Spack and can be overridden by sites or users.""" +ConfigScope('defaults', os.path.join(spack.etc_path, 'spack', 'defaults')) -ConfigScope('site', os.path.join(spack.etc_path, 'spack')), +"""Site configuration is per spack instance, for sites or projects. + No site-level configs should be checked into spack by default.""" +ConfigScope('site', os.path.join(spack.etc_path, 'spack')) + +"""User configuration can override both spack defaults and site config.""" ConfigScope('user', os.path.expanduser('~/.spack')) From 83330d2b59d925b2e57b63081461a759a5e92b11 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 20 Jul 2016 08:50:32 -0500 Subject: [PATCH 110/126] Re-ignore licenses directory --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 1d4d24aa522..960b5b0035b 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ *~ .DS_Store .idea +/etc/spack/licenses /etc/spack/*.yaml /etc/spackconfig /share/spack/dotkit From 69e36c98219cdf3eda9de44c4205c4de0f212fd9 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Wed, 20 Jul 2016 11:25:46 -0400 Subject: [PATCH 111/126] Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10 --- var/spack/repos/builtin/packages/netcdf/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 13d6bc69440..ad4ee596402 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -48,8 +48,10 @@ class Netcdf(Package): # Required for NetCDF-4 support depends_on("zlib") - depends_on("hdf5+mpi", when='+mpi') - depends_on("hdf5~mpi", when='~mpi') + depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi') + depends_on('hdf5+mpi', when='@4.4.1:+mpi') + depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi') + depends_on('hdf5~mpi', when='@4.4.1:~mpi') def install(self, spec, prefix): # Environment variables From 4434f482c08c90011ba489b65ce7f75be35fb5bb Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 20 Jul 2016 09:48:54 -0700 Subject: [PATCH 112/126] remove FIXMEs --- var/spack/repos/builtin/packages/cdo/package.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py index 09c4fde4558..7400c3a56c3 100644 --- a/var/spack/repos/builtin/packages/cdo/package.py +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -29,13 +29,11 @@ class Cdo(Package): """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. """ - # FIXME: Add a proper url for your package's homepage here. homepage = "https://code.zmaw.de/projects/cdo" url = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz" version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2') - # FIXME: Add additional dependencies if required. depends_on('netcdf') def install(self, spec, prefix): From 4c506b36c5e6762ce08b616fa32a6064f7766ad3 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 10:25:07 -0700 Subject: [PATCH 113/126] Improved cray_xc detection --- lib/spack/spack/platforms/cray_xc.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index 0f6599ab30d..24aa614e864 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -45,10 +45,10 @@ def __init__(self): @classmethod def detect(self): - if os.path.exists('/cray_home'): - cc_verbose = which('cc') - cc_verbose.add_default_arg('-craype-verbose') - text = cc_verbose(output=str, error=str, ignore_errors=True).split() + try: + cc_verbose = which('ftn') + text = cc_verbose('-craype-verbose', output=str, error=str, ignore_errors=True).split() if '-D__CRAYXC' in text: return True - return False + finally: + return False From 26d1ddc176ac52ff76893432755de54cab3cecfc Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 10:28:38 -0700 Subject: [PATCH 114/126] Improved cray_xc detection bug fix --- lib/spack/spack/platforms/cray_xc.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index 24aa614e864..8bc03874de9 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -50,5 +50,7 @@ def detect(self): text = cc_verbose('-craype-verbose', output=str, error=str, ignore_errors=True).split() if '-D__CRAYXC' in text: return True - finally: + else: + return False + except: return False From 0d18f7249c38fdf8c452acd39533b09d13031583 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 10:50:18 -0700 Subject: [PATCH 115/126] fixed flake errors --- lib/spack/spack/platforms/cray_xc.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index 8bc03874de9..fd16f7d9baf 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -4,6 +4,7 @@ from spack.operating_systems.cnl import Cnl from spack.util.executable import which + class CrayXc(Platform): priority = 20 front_end = 'sandybridge' @@ -35,7 +36,7 @@ def __init__(self): self.add_target('ivybridge', Target('ivybridge', 'craype-ivybridge')) self.add_target('haswell', - Target('haswell','craype-haswell')) + Target('haswell', 'craype-haswell')) # Front end of the cray platform is a linux distro. linux_dist = LinuxDistro() @@ -47,7 +48,9 @@ def __init__(self): def detect(self): try: cc_verbose = which('ftn') - text = cc_verbose('-craype-verbose', output=str, error=str, ignore_errors=True).split() + text = cc_verbose('-craype-verbose', + output=str, error=str, + ignore_errors=True).split() if '-D__CRAYXC' in text: return True else: From 106147716ac73180ce80e693ea276612d36b2215 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 11:00:56 -0700 Subject: [PATCH 116/126] fixed flake errors --- lib/spack/spack/platforms/cray_xc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index fd16f7d9baf..e3c7761a945 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -48,8 +48,8 @@ def __init__(self): def detect(self): try: cc_verbose = which('ftn') - text = cc_verbose('-craype-verbose', - output=str, error=str, + text = cc_verbose('-craype-verbose', + output=str, error=str, ignore_errors=True).split() if '-D__CRAYXC' in text: return True From f4fb9a07718068fb96e22a43be6066daada92d10 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 11:35:13 -0700 Subject: [PATCH 117/126] Set default link type to dynamic on cray. Includes hooks for platform-based environment changes --- lib/spack/spack/architecture.py | 6 ++++++ lib/spack/spack/build_environment.py | 6 ++++++ lib/spack/spack/platforms/cray_xc.py | 7 +++++++ 3 files changed, 19 insertions(+) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index a7cda2bf681..2701fa9a0c5 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -190,6 +190,12 @@ def operating_system(self, name): return self.operating_sys.get(name, None) + @classmethod + def setup_platform_environment(self, env): + """ Subclass can override this method if it requires any + platform-specific build environment modifications. + """ + pass @classmethod def detect(self): diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 93fb0690f7f..4e799eeea17 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -248,6 +248,11 @@ def set_build_environment_variables(pkg, env, dirty=False): ci = join_path(item, 'case-insensitive') if os.path.isdir(ci): env_paths.append(ci) + +# for item in pkg.spec.platform.env_paths: +# env_paths.append(item) + # TODO: move platform-specific knowledge to platform. + # (join_path(spack.build_env_path, 'cray')) for item in reversed(env_paths): env.prepend_path('PATH', item) @@ -444,6 +449,7 @@ def setup_package(pkg, dirty=False): set_compiler_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env, dirty) + pkg.spec.architecture.platform.setup_platform_environment(spack_env) load_external_modules(pkg) # traverse in postorder so package can use vars from its dependencies spec = pkg.spec diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index e3c7761a945..aee375ac897 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -44,6 +44,13 @@ def __init__(self): self.add_operating_system(str(linux_dist), linux_dist) self.add_operating_system('CNL10', Cnl()) + @classmethod + def setup_platform_environment(self, env): + """ Change the linker to default dynamic to be more + similar to linux/standard linker behavior + """ + env.set('CRAYPE_LINK_TYPE', 'dynamic') + @classmethod def detect(self): try: From 7db41700623f33a4266c8265e45b511bc1aed24a Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 11:36:47 -0700 Subject: [PATCH 118/126] removed commented-out code --- lib/spack/spack/build_environment.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 4e799eeea17..8e40e9883dc 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -249,11 +249,6 @@ def set_build_environment_variables(pkg, env, dirty=False): if os.path.isdir(ci): env_paths.append(ci) -# for item in pkg.spec.platform.env_paths: -# env_paths.append(item) - # TODO: move platform-specific knowledge to platform. - # (join_path(spack.build_env_path, 'cray')) - for item in reversed(env_paths): env.prepend_path('PATH', item) env.set_path(SPACK_ENV_PATH, env_paths) From 412618d53108d6417c88c62d85377f69f8bf1829 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 11:52:16 -0700 Subject: [PATCH 119/126] fixed flake errors --- lib/spack/spack/architecture.py | 13 ++++--------- lib/spack/spack/build_environment.py | 2 +- 2 files changed, 5 insertions(+), 10 deletions(-) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index 2701fa9a0c5..6c3c478f91e 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -76,7 +76,6 @@ will be responsible for compiler detection. """ import os -import imp import inspect from llnl.util.lang import memoized, list_modules, key_ordering @@ -206,15 +205,12 @@ def detect(self): """ raise NotImplementedError() - def __repr__(self): return self.__str__() - def __str__(self): return self.name - def _cmp_key(self): t_keys = ''.join(str(t._cmp_key()) for t in sorted(self.targets.values())) @@ -285,7 +281,7 @@ def find_compilers(self, *paths): # ensure all the version calls we made are cached in the parent # process, as well. This speeds up Spack a lot. - clist = reduce(lambda x, y: x+y, compiler_lists) + clist = reduce(lambda x, y: x + y, compiler_lists) return clist def find_compiler(self, cmp_cls, *path): @@ -326,7 +322,7 @@ def find_compiler(self, cmp_cls, *path): # prefer the one with more compilers. prev_paths = [prev.cc, prev.cxx, prev.f77, prev.fc] - newcount = len([p for p in paths if p is not None]) + newcount = len([p for p in paths if p is not None]) prevcount = len([p for p in prev_paths if p is not None]) # Don't add if it's not an improvement over prev compiler. @@ -343,6 +339,7 @@ def to_dict(self): d['version'] = self.version return d + @key_ordering class Arch(object): """Architecture is now a class to help with setting attributes. @@ -383,11 +380,9 @@ def __str__(self): else: return '' - def __contains__(self, string): return string in str(self) - def _cmp_key(self): if isinstance(self.platform, Platform): platform = self.platform.name @@ -430,7 +425,7 @@ def _operating_system_from_dict(os_name, plat=None): if isinstance(os_name, dict): name = os_name['name'] version = os_name['version'] - return plat.operating_system(name+version) + return plat.operating_system(name + version) else: return plat.operating_system(os_name) diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 8e40e9883dc..fbcba08367b 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -248,7 +248,7 @@ def set_build_environment_variables(pkg, env, dirty=False): ci = join_path(item, 'case-insensitive') if os.path.isdir(ci): env_paths.append(ci) - + for item in reversed(env_paths): env.prepend_path('PATH', item) env.set_path(SPACK_ENV_PATH, env_paths) From 6983c1d30d6e4f93ee8d8a0df87e3c9ea8cde103 Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 12:04:00 -0700 Subject: [PATCH 120/126] Documented linker default --- lib/spack/docs/basic_usage.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 50a161a1750..948092047bd 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -1866,6 +1866,10 @@ to call the Cray compiler wrappers during build time. For more on compiler configuration, check out :ref:`compiler-config`. +Spack sets the default Cray link type to dynamic, to better match other +other platforms. Individual packages can enable static linking (which is the +default outside of Spack on cray systems) using the -static flag. + Setting defaults and using Cray modules ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From c9f4e8ce5aac7fbcc1934606c1a330cdb5e7a36c Mon Sep 17 00:00:00 2001 From: mwilliammyers Date: Wed, 20 Jul 2016 13:13:47 -0600 Subject: [PATCH 121/126] ilmbase : Add new IlmBase package --- .../repos/builtin/packages/ilmbase/package.py | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ilmbase/package.py diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py new file mode 100644 index 00000000000..873c830623f --- /dev/null +++ b/var/spack/repos/builtin/packages/ilmbase/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Ilmbase(Package): + """OpenEXR ILM Base libraries (high dynamic-range image file format)""" + + homepage = "http://www.openexr.com/" + url = "http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.2.0.tar.gz" + + version('2.2.0', 'b540db502c5fa42078249f43d18a4652') + version('2.1.0', 'af1115f4d759c574ce84efcde9845d29') + version('2.0.1', '74c0d0d2873960bd0dc1993f8e03f0ae') + version('1.0.2', '26c133ee8ca48e1196fbfb3ffe292ab4') + version('0.9.0', '4df45f8116cb7a013b286caf6da30a2e') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make('install') From eda1176ba7d70327ca847d6b17afa02f8cca0d5b Mon Sep 17 00:00:00 2001 From: Gregory Becker Date: Wed, 20 Jul 2016 12:26:31 -0700 Subject: [PATCH 122/126] added package as argument to setup_platform_environment --- lib/spack/spack/architecture.py | 2 +- lib/spack/spack/build_environment.py | 2 +- lib/spack/spack/platforms/cray_xc.py | 5 ++++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index 6c3c478f91e..974505ee3a0 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -190,7 +190,7 @@ def operating_system(self, name): return self.operating_sys.get(name, None) @classmethod - def setup_platform_environment(self, env): + def setup_platform_environment(self, pkg, env): """ Subclass can override this method if it requires any platform-specific build environment modifications. """ diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index fbcba08367b..5affd3c7c56 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -444,7 +444,7 @@ def setup_package(pkg, dirty=False): set_compiler_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env, dirty) - pkg.spec.architecture.platform.setup_platform_environment(spack_env) + pkg.spec.architecture.platform.setup_platform_environment(pkg, spack_env) load_external_modules(pkg) # traverse in postorder so package can use vars from its dependencies spec = pkg.spec diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py index aee375ac897..2b065d5bbd1 100644 --- a/lib/spack/spack/platforms/cray_xc.py +++ b/lib/spack/spack/platforms/cray_xc.py @@ -45,11 +45,14 @@ def __init__(self): self.add_operating_system('CNL10', Cnl()) @classmethod - def setup_platform_environment(self, env): + def setup_platform_environment(self, pkg, env): """ Change the linker to default dynamic to be more similar to linux/standard linker behavior """ env.set('CRAYPE_LINK_TYPE', 'dynamic') + cray_wrapper_names = join_path(spack.build_env_path, 'cray') + if os.path.isdir(cray_wrapper_names): + env.prepend_path('PATH', cray_wrapper_names) @classmethod def detect(self): From 24c14ff7a84af509c1592ab44419e2d7cb3cd6e6 Mon Sep 17 00:00:00 2001 From: Samuel Knight Date: Wed, 20 Jul 2016 16:38:47 +0000 Subject: [PATCH 123/126] Added gnu packages datamash, parallel, and screen --- .../builtin/packages/datamash/package.py | 45 ++++++++++++++ .../builtin/packages/parallel/package.py | 45 ++++++++++++++ .../repos/builtin/packages/screen/package.py | 59 +++++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 var/spack/repos/builtin/packages/datamash/package.py create mode 100644 var/spack/repos/builtin/packages/parallel/package.py create mode 100644 var/spack/repos/builtin/packages/screen/package.py diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py new file mode 100644 index 00000000000..ef30c50ebe1 --- /dev/null +++ b/var/spack/repos/builtin/packages/datamash/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Datamash(Package): + """ + GNU datamash is a command-line program which performs basic numeric, + textual and statistical operations on input textual data files. + """ + + homepage = "https://www.gnu.org/software/datamash/" + url = "http://ftp.gnu.org/gnu/datamash/datamash-1.0.5.tar.gz" + + version('1.1.0', '79a6affca08107a095e97e4237fc8775') + version('1.0.7', '9f317bab07454032ba9c068e7f17b04b') + version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b') + version('1.0.5', '9a29549dc7feca49fdc5fab696614e11') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py new file mode 100644 index 00000000000..2306dace554 --- /dev/null +++ b/var/spack/repos/builtin/packages/parallel/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Parallel(Package): + """ + GNU parallel is a shell tool for executing jobs in parallel using + one or more computers. A job can be a single command or a small + script that has to be run for each of the lines in the input. + """ + + homepage = "http://www.gnu.org/software/parallel/" + url = "http://ftp.gnu.org/gnu/parallel/parallel-20160422.tar.bz2" + + version('20160422', '24621f684130472694333709bd4454cb') + version('20160322', '4e81e0d36902ab4c4e969ee6f35e6e57') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py new file mode 100644 index 00000000000..17335603e6f --- /dev/null +++ b/var/spack/repos/builtin/packages/screen/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Screen(Package): + """ + Screen is a full-screen window manager that multiplexes a physical + terminal between several processes, typically interactive shells. + """ + + homepage = "https://www.gnu.org/software/screen/" + url = "http://ftp.gnu.org/gnu/screen/screen-4.3.1.tar.gz" + + version('4.3.1', '5bb3b0ff2674e29378c31ad3411170ad') + version('4.3.0', 'f76d28eadc4caaf6cdff00685ae6ad46') + version('4.2.1', '419a0594e2b25039239af8b90eda7d92') + version('4.2.0', 'e5199156a8ac863bbf92495a7638b612') + version('4.0.3', '8506fd205028a96c741e4037de6e3c42') + version('4.0.2', 'ed68ea9b43d9fba0972cb017a24940a1') + version('3.9.15', '0dff6fdc3fbbceabf25a43710fbfe75f') + version('3.9.11', '19572f92404995e7b2dea8117204dd67') + version('3.9.10', 'bbe271715d1dee038b3cd72d6d2f05fb') + version('3.9.9', '9a8b1d6c7438c64b884c4f7d7662afdc') + version('3.9.8', '8ddfebe32c2d45410ce89ea9779bb1cf') + version('3.9.4', '7de72cd18f7adcdf993ecc6764d0478a') + version('3.7.6', '9a353b828d79c3c143109265cae663a7') + version('3.7.4', 'c5ab40b068968075e41e25607dfce543') + version('3.7.2', '2d6db5de7fb0cf849cc5a6f94203f029') + version('3.7.1', '27cdd29318446561ef7c966041cbd2c9') + + depends_on('ncurses') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") From f9137f606f68392cca56bd19810c3c86addbae7a Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 20 Jul 2016 15:37:31 -0500 Subject: [PATCH 124/126] Set environment variables This commit adds `setup_environment` to export the libraries and headers. Fixes #1314. --- var/spack/repos/builtin/packages/R/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 11c5909efaf..5e7c8492f6c 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -136,6 +136,14 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec): run_env.prepend_path('R_LIBS', os.path.join( extension_spec.prefix, self.r_lib_dir)) + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'rlib', 'R', 'include')) + def setup_dependent_package(self, module, ext_spec): """Called before R modules' install() methods. In most cases, extensions will only need to have one line: From e973adf84b9c431e95f792d24c5b15941780017e Mon Sep 17 00:00:00 2001 From: mwilliammyers Date: Wed, 20 Jul 2016 14:49:03 -0600 Subject: [PATCH 125/126] openexr : Add new package --- .../repos/builtin/packages/openexr/package.py | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 var/spack/repos/builtin/packages/openexr/package.py diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py new file mode 100644 index 00000000000..3619bd063ca --- /dev/null +++ b/var/spack/repos/builtin/packages/openexr/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Openexr(Package): + """OpenEXR Graphics Tools (high dynamic-range image file format)""" + + homepage = "http://www.openexr.com/" + url = "https://savannah.nongnu.org/download/openexr/openexr-2.2.0.tar.gz" + + version('2.2.0', 'b64e931c82aa3790329c21418373db4e') + version('2.1.0', '33735d37d2ee01c6d8fbd0df94fb8b43') + version('2.0.1', '4387e6050d2faa65dd5215618ff2ddce') + version('1.7.0', '27113284f7d26a58f853c346e0851d7a') + version('1.6.1', '11951f164f9c872b183df75e66de145a') + version('1.5.0', '55342d2256ab3ae99da16f16b2e12ce9') + version('1.4.0a', 'd0a4b9a930c766fa51561b05fb204afe') + version('1.3.2', '1522fe69135016c52eb88fc7d8514409') + + variant('debug', default=False, + description='Builds a debug version of the libraries') + + depends_on('pkg-config', type='build') + depends_on('ilmbase') + + def install(self, spec, prefix): + configure_options = ['--prefix={0}'.format(prefix)] + if '+debug' not in spec: + configure_options.append('--disable-debug') + configure(*configure_options) + make('install') From 0c75174ec323757400e9095e1cb9fa66e557a723 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 20 Jul 2016 15:56:20 -0500 Subject: [PATCH 126/126] Fix indent/flake8 error. --- var/spack/repos/builtin/packages/R/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 5e7c8492f6c..ad06c2ca48f 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -138,11 +138,11 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec): def setup_environment(self, spack_env, run_env): run_env.prepend_path('LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) + join_path(self.prefix, 'rlib', 'R', 'lib')) run_env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) + join_path(self.prefix, 'rlib', 'R', 'lib')) run_env.prepend_path('CPATH', - join_path(self.prefix, 'rlib', 'R', 'include')) + join_path(self.prefix, 'rlib', 'R', 'include')) def setup_dependent_package(self, module, ext_spec): """Called before R modules' install() methods. In most cases,