Bump version number to v0.17.2

Ubuntu patched git v2.25.1 with a security fix that also
introduced a breaking change, so v2.25.1 behaves like
v2.35.2 with respect to the use cases in CVE-2022-24765

.github/workflows/bootstrap.yml

@@ -59,6 +59,14 @@ jobs:
               bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
               make patch unzip xz-utils python3 python3-dev tree \
               cmake bison
+      - name: Work around CVE-2022-24765
+        run: |
+          # Apparently Ubuntu patched git v2.25.1 with a security patch that introduces 
+          # a breaking behavior. See:
+          # - https://github.blog/2022-04-12-git-security-vulnerability-announced/
+          # - https://github.com/actions/checkout/issues/760
+          # - http://changelogs.ubuntu.com/changelogs/pool/main/g/git/git_2.25.1-1ubuntu3.3/changelog
+          git config --global --add safe.directory /__w/spack/spack
       - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       - name: Setup repo and non-root user
         run: |
@@ -171,7 +179,15 @@ jobs:
           apt-get install -y \
               bzip2 curl file g++ gcc patchelf gfortran git gzip \
               make patch unzip xz-utils python3 python3-dev tree
-      - uses: actions/checkout@v2
+      - name: Work around CVE-2022-24765
+        run: |
+          # Apparently Ubuntu patched git v2.25.1 with a security patch that introduces 
+          # a breaking behavior. See:
+          # - https://github.blog/2022-04-12-git-security-vulnerability-announced/
+          # - https://github.com/actions/checkout/issues/760
+          # - http://changelogs.ubuntu.com/changelogs/pool/main/g/git/git_2.25.1-1ubuntu3.3/changelog
+          git config --global --add safe.directory /__w/spack/spack
+      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -200,7 +216,15 @@ jobs:
               bzip2 curl file g++ gcc patchelf gfortran git gzip \
               make patch unzip xz-utils python3 python3-dev tree \
               gawk
-      - uses: actions/checkout@v2
+      - name: Work around CVE-2022-24765
+        run: |
+          # Apparently Ubuntu patched git v2.25.1 with a security patch that introduces 
+          # a breaking behavior. See:
+          # - https://github.blog/2022-04-12-git-security-vulnerability-announced/
+          # - https://github.com/actions/checkout/issues/760
+          # - http://changelogs.ubuntu.com/changelogs/pool/main/g/git/git_2.25.1-1ubuntu3.3/changelog
+          git config --global --add safe.directory /__w/spack/spack
+      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -225,7 +249,7 @@ jobs:
           brew install tree
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh
@@ -241,7 +265,7 @@ jobs:
           brew install gawk tree
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh

.github/workflows/setup_git.sh

@@ -1,9 +1,8 @@
-#!/usr/bin/env sh
+#!/bin/bash -e
 git config --global user.email "spack@example.com"
 git config --global user.name "Test User"
-# With fetch-depth: 0 we have a remote develop
+
-# but not a local branch. Don't do this on develop
+# create a local pr base branch
-if [ "$(git branch --show-current)" != "develop" ]
+if [[ -n $GITHUB_BASE_REF ]]; then
-then
+    git fetch origin "${GITHUB_BASE_REF}:${GITHUB_BASE_REF}"
-  git branch develop origin/develop
 fi

.github/workflows/unit_tests.yaml

@@ -211,6 +211,7 @@ jobs:
           git clone "${{ github.server_url }}/${{ github.repository }}.git" && cd spack
           git fetch origin "${{ github.ref }}:test-branch"
           git checkout test-branch
+          . .github/workflows/setup_git.sh
           bin/spack unit-test -x
     - name: Run unit tests (only package tests)
       if: ${{ needs.changes.outputs.with_coverage == 'false' }}
@@ -223,6 +224,7 @@ jobs:
           git clone "${{ github.server_url }}/${{ github.repository }}.git" && cd spack
           git fetch origin "${{ github.ref }}:test-branch"
           git checkout test-branch
+          . .github/workflows/setup_git.sh
           bin/spack unit-test -x -m "not maybeslow" -k "package_sanity"
 
   # Test RHEL8 UBI with platform Python. This job is run

CHANGELOG.md

@@ -1,3 +1,44 @@
+# v0.17.2 (2022-04-13)
+
+### Spack bugfixes
+* Fix --reuse with upstreams set in an environment (#29680)
+* config add: fix parsing of validator error to infer type from oneOf (#29475)
+* Fix spack -C command_line_scope used in conjunction with other flags (#28418)
+* Use Spec.constrain to construct spec lists for stacks (#28783)
+* Fix bug occurring when searching for inherited patches in packages (#29574)
+* Fixed a few bugs when manipulating symlinks (#28318, #29515, #29636)
+* Fixed a few minor bugs affecting command prompt, terminal title and argument completion (#28279, #28278, #28939, #29405, #29070, #29402)
+* Fixed a few bugs affecting the spack ci command (#29518, #29419)
+* Fix handling of Intel compiler environment (#29439)
+* Fix a few edge cases when reindexing the DB (#28764)
+* Remove "Known issues" from documentation (#29664) 
+* Other miscellaneous bugfixes (0b72e070583fc5bcd016f5adc8a84c99f2b7805f, #28403, #29261)
+
+# v0.17.1 (2021-12-23)
+
+### Spack Bugfixes
+* Allow locks to work under high contention (#27846)
+* Improve errors messages from clingo (#27707 #27970)
+* Respect package permissions for sbang (#25764)
+* Fix --enable-locks behavior (#24675)
+* Fix log-format reporter ignoring install errors (#25961)
+* Fix overloaded argparse keys (#27379)
+* Allow style commands to run with targets other than "develop" (#27472)
+* Log lock messages to debug level, instead of verbose level (#27408)
+* Handle invalid unicode while logging (#21447)
+* spack audit: fix API calls to variants (#27713)
+* Provide meaningful message for empty environment installs (#28031)
+* Added opensuse leap containers to spack containerize (#27837)
+* Revert "patches: make re-applied patches idempotent" (#27625)
+* MANPATH can use system defaults (#21682)
+* Add "setdefault" subcommand to `spack module tcl` (#14686)
+* Regenerate views when specs already installed (#28113)
+
+### Package bugfixes
+* Fix external package detection for OpenMPI (#27255)
+* Update the UPC++ package to 2021.9.0 (#26996)
+* Added py-vermin v1.3.2 (#28072)
+
 # v0.17.0 (2021-11-05)
 
 `v0.17.0` is a major feature release.

lib/spack/docs/containers.rst

@@ -129,6 +129,9 @@ are currently supported are summarized in the table below:
    * - CentOS 7
      - ``centos:7``
      - ``spack/centos7``
+   * - openSUSE Leap
+     - ``opensuse/leap``
+     - ``spack/leap15``
 
 All the images are tagged with the corresponding release of Spack:
 

lib/spack/docs/index.rst

@@ -56,7 +56,6 @@ or refer to the full manual below.
    basic_usage
    workflows
    Tutorial: Spack 101 <https://spack-tutorial.readthedocs.io>
-   known_issues
 
 .. toctree::
    :maxdepth: 2

lib/spack/docs/known_issues.rst

@@ -1,77 +0,0 @@
-.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-   Spack Project Developers. See the top-level COPYRIGHT file for details.
-
-   SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-============
-Known Issues
-============
-
-This is a list of known bugs in Spack. It provides ways of getting around these
-problems if you encounter them.
-
----------------------------------------------------
-Variants are not properly forwarded to dependencies
----------------------------------------------------
-
-**Status:** Expected to be fixed by Spack's new concretizer
-
-Sometimes, a variant of a package can also affect how its dependencies are
-built. For example, in order to build MPI support for a package, it may
-require that its dependencies are also built with MPI support. In the
-``package.py``, this looks like:
-
-.. code-block:: python
-
-   depends_on('hdf5~mpi', when='~mpi')
-   depends_on('hdf5+mpi', when='+mpi')
-
-Spack handles this situation properly for *immediate* dependencies, and
-builds ``hdf5`` with the same variant you used for the package that
-depends on it. However, for *indirect* dependencies (dependencies of
-dependencies), Spack does not backtrack up the DAG far enough to handle
-this. Users commonly run into this situation when trying to build R with
-X11 support:
-
-.. code-block:: console
-
-   $ spack install r+X
-   ...
-   ==> Error: Invalid spec: 'cairo@1.14.8%gcc@6.2.1+X arch=linux-fedora25-x86_64 ^bzip2@1.0.6%gcc@6.2.1+shared arch=linux-fedora25-x86_64 ^font-util@1.3.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^fontconfig@2.12.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^freetype@2.7.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^gettext@0.19.8.1%gcc@6.2.1+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-fedora25-x86_64 ^glib@2.53.1%gcc@6.2.1~libmount arch=linux-fedora25-x86_64 ^inputproto@2.3.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^kbproto@1.0.7%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libffi@3.2.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpng@1.6.29%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpthread-stubs@0.4%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libx11@1.6.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxau@1.0.8%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxcb@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxdmcp@1.1.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxext@1.3.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxml2@2.9.4%gcc@6.2.1~python arch=linux-fedora25-x86_64 ^libxrender@0.9.10%gcc@6.2.1 arch=linux-fedora25-x86_64 ^ncurses@6.0%gcc@6.2.1~symlinks arch=linux-fedora25-x86_64 ^openssl@1.0.2k%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pcre@8.40%gcc@6.2.1+utf arch=linux-fedora25-x86_64 ^pixman@0.34.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pkg-config@0.29.2%gcc@6.2.1+internal_glib arch=linux-fedora25-x86_64 ^python@2.7.13%gcc@6.2.1+shared~tk~ucs4 arch=linux-fedora25-x86_64 ^readline@7.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^renderproto@0.11.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^sqlite@3.18.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^tar^util-macros@1.19.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xcb-proto@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xextproto@7.3.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xproto@7.0.31%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xtrans@1.3.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xz@5.2.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^zlib@1.2.11%gcc@6.2.1+pic+shared arch=linux-fedora25-x86_64'.
-   Package cairo requires variant ~X, but spec asked for +X
-
-A workaround is to explicitly activate the variants of dependencies as well:
-
-.. code-block:: console
-
-   $ spack install r+X ^cairo+X ^pango+X
-
-See https://github.com/spack/spack/issues/267 and
-https://github.com/spack/spack/issues/2546 for further details.
-
------------------------------------------------
-depends_on cannot handle recursive dependencies
------------------------------------------------
-
-**Status:** Not yet a work in progress
-
-Although ``depends_on`` can handle any aspect of Spack's spec syntax,
-it currently cannot handle recursive dependencies. If the ``^`` sigil
-appears in a ``depends_on`` statement, the concretizer will hang.
-For example, something like:
-
-.. code-block:: python
-
-   depends_on('mfem+cuda ^hypre+cuda', when='+cuda')
-
-
-should be rewritten as:
-
-.. code-block:: python
-
-   depends_on('mfem+cuda', when='+cuda')
-   depends_on('hypre+cuda', when='+cuda')
-
-
-See https://github.com/spack/spack/issues/17660 and
-https://github.com/spack/spack/issues/11160 for more details.

lib/spack/docs/packaging_guide.rst

@@ -2943,7 +2943,7 @@ The package base class, usually specialized for a given build system, determines
 actual set of entities available for overriding.
 The classes that are currently provided by Spack are:
 
-+-------------------------=--------------------------------+----------------------------------+
++----------------------------------------------------------+----------------------------------+
 |     **Base Class**                                       |           **Purpose**            |
 +==========================================================+==================================+
 | :class:`~spack.package.Package`                          | General base class not           |

lib/spack/llnl/util/filesystem.py

@@ -141,7 +141,7 @@ def filter_file(regex, repl, *filenames, **kwargs):
             file.
     """
     string = kwargs.get('string', False)
-    backup = kwargs.get('backup', True)
+    backup = kwargs.get('backup', False)
     ignore_absent = kwargs.get('ignore_absent', False)
     stop_at = kwargs.get('stop_at', None)
 

lib/spack/llnl/util/tty/log.py

@@ -780,7 +780,12 @@ def _writer_daemon(stdin_multiprocess_fd, read_multiprocess_fd, write_fd, echo,
                     try:
                         while line_count < 100:
                             # Handle output from the calling process.
-                            line = _retry(in_pipe.readline)()
+                            try:
+                                line = _retry(in_pipe.readline)()
+                            except UnicodeDecodeError:
+                                # installs like --test=root gpgme produce non-UTF8 logs
+                                line = '<line lost: output was not encoded as UTF-8>\n'
+
                             if not line:
                                 return
                             line_count += 1

lib/spack/spack/__init__.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 #: major, minor, patch version for Spack, in a tuple
-spack_version_info = (0, 17, 0)
+spack_version_info = (0, 17, 2)
 
 #: String containing Spack version joined with .'s
 spack_version = '.'.join(str(v) for v in spack_version_info)

lib/spack/spack/audit.py

@@ -389,9 +389,8 @@ def _unknown_variants_in_dependencies(pkgs, error_cls):
                 dependency_variants = dependency_edge.spec.variants
                 for name, value in dependency_variants.items():
                     try:
-                        dependency_pkg.variants[name].validate_or_raise(
+                        v, _ = dependency_pkg.variants[name]
-                            value, pkg=dependency_pkg
+                        v.validate_or_raise(value, pkg=dependency_pkg)
-                        )
                     except Exception as e:
                         summary = (pkg_name + ": wrong variant used for a "
                                    "dependency in a 'depends_on' directive")
@@ -419,7 +418,8 @@ def _analyze_variants_in_directive(pkg, constraint, directive, error_cls):
     errors = []
     for name, v in constraint.variants.items():
         try:
-            pkg.variants[name].validate_or_raise(v, pkg=pkg)
+            variant, _ = pkg.variants[name]
+            variant.validate_or_raise(v, pkg=pkg)
         except variant_exceptions as e:
             summary = pkg.name + ': wrong variant in "{0}" directive'
             summary = summary.format(directive)

lib/spack/spack/build_systems/intel.py

@@ -685,9 +685,9 @@ def openmp_libs(self):
             # packages.yaml), specificially to provide the 'iomp5' libs.
 
         elif '%gcc' in self.spec:
-            gcc = Executable(self.compiler.cc)
+            with self.compiler.compiler_environment():
-            omp_lib_path = gcc(
+                omp_lib_path = Executable(self.compiler.cc)(
-                '--print-file-name', 'libgomp.%s' % dso_suffix, output=str)
+                    '--print-file-name', 'libgomp.%s' % dso_suffix, output=str)
             omp_libs = LibraryList(omp_lib_path.strip())
 
         if len(omp_libs) < 1:
@@ -728,8 +728,9 @@ def tbb_libs(self):
 
         # TODO: clang(?)
         gcc = self._gcc_executable     # must be gcc, not self.compiler.cc
-        cxx_lib_path = gcc(
+        with self.compiler.compiler_environment():
-            '--print-file-name', 'libstdc++.%s' % dso_suffix, output=str)
+            cxx_lib_path = gcc(
+                '--print-file-name', 'libstdc++.%s' % dso_suffix, output=str)
 
         libs = tbb_lib + LibraryList(cxx_lib_path.rstrip())
         debug_print(libs)
@@ -739,8 +740,9 @@ def tbb_libs(self):
     def _tbb_abi(self):
         '''Select the ABI needed for linking TBB'''
         gcc = self._gcc_executable
-        matches = re.search(r'(gcc|LLVM).* ([0-9]+\.[0-9]+\.[0-9]+).*',
+        with self.compiler.compiler_environment():
-                            gcc('--version', output=str), re.I | re.M)
+            matches = re.search(r'(gcc|LLVM).* ([0-9]+\.[0-9]+\.[0-9]+).*',
+                                gcc('--version', output=str), re.I | re.M)
         abi = ''
         if sys.platform == 'darwin':
             pass

lib/spack/spack/ci.py

@@ -1551,7 +1551,7 @@ def setup_spack_repro_version(repro_dir, checkout_commit, merge_commit=None):
 
     # Next attempt to clone your local spack repo into the repro dir
     with fs.working_dir(repro_dir):
-        clone_out = git("clone", spack_git_path,
+        clone_out = git("clone", spack_git_path, "spack",
                         output=str, error=os.devnull,
                         fail_on_error=False)
 

lib/spack/spack/cmd/ci.py

@@ -362,8 +362,10 @@ def ci_rebuild(args):
     # Write information about spack into an artifact in the repro dir
     spack_info = spack_ci.get_spack_info()
     spack_info_file = os.path.join(repro_dir, 'spack_info.txt')
-    with open(spack_info_file, 'w') as fd:
+    with open(spack_info_file, 'wb') as fd:
-        fd.write('\n{0}\n'.format(spack_info))
+        fd.write(b'\n')
+        fd.write(spack_info.encode('utf8'))
+        fd.write(b'\n')
 
     # If we decided there should be a temporary storage mechanism, add that
     # mirror now so it's used when we check for a full hash match already

lib/spack/spack/cmd/commands.py

@@ -117,7 +117,7 @@ def format(self, cmd):
     'virtual': '_providers',
     'namespace': '_repos',
     'hash': '_all_resource_hashes',
-    'pytest': '_tests',
+    'pytest': '_unit_tests',
 }
 
 

lib/spack/spack/cmd/env.py

@@ -411,8 +411,6 @@ def env_status(args):
 #
 def env_loads_setup_parser(subparser):
     """list modules for an installed environment '(see spack module loads)'"""
-    subparser.add_argument(
-        'env', nargs='?', help='name of env to generate loads file for')
     subparser.add_argument(
         '-n', '--module-set-name', default='default',
         help='module set for which to generate load operations')
@@ -448,19 +446,19 @@ def env_loads(args):
 def env_update_setup_parser(subparser):
     """update environments to the latest format"""
     subparser.add_argument(
-        metavar='env', dest='env',
+        metavar='env', dest='update_env',
         help='name or directory of the environment to activate'
     )
     spack.cmd.common.arguments.add_common_arguments(subparser, ['yes_to_all'])
 
 
 def env_update(args):
-    manifest_file = ev.manifest_file(args.env)
+    manifest_file = ev.manifest_file(args.update_env)
     backup_file = manifest_file + ".bkp"
     needs_update = not ev.is_latest_format(manifest_file)
 
     if not needs_update:
-        tty.msg('No update needed for the environment "{0}"'.format(args.env))
+        tty.msg('No update needed for the environment "{0}"'.format(args.update_env))
         return
 
     proceed = True
@@ -470,7 +468,7 @@ def env_update(args):
                'Spack that are older than this version may not be able to '
                'read it. Spack stores backups of the updated environment '
                'which can be retrieved with "spack env revert"')
-        tty.msg(msg.format(args.env))
+        tty.msg(msg.format(args.update_env))
         proceed = tty.get_yes_or_no('Do you want to proceed?', default=False)
 
     if not proceed:
@@ -478,20 +476,20 @@ def env_update(args):
 
     ev.update_yaml(manifest_file, backup_file=backup_file)
     msg = 'Environment "{0}" has been updated [backup={1}]'
-    tty.msg(msg.format(args.env, backup_file))
+    tty.msg(msg.format(args.update_env, backup_file))
 
 
 def env_revert_setup_parser(subparser):
     """restore environments to their state before update"""
     subparser.add_argument(
-        metavar='env', dest='env',
+        metavar='env', dest='revert_env',
         help='name or directory of the environment to activate'
     )
     spack.cmd.common.arguments.add_common_arguments(subparser, ['yes_to_all'])
 
 
 def env_revert(args):
-    manifest_file = ev.manifest_file(args.env)
+    manifest_file = ev.manifest_file(args.revert_env)
     backup_file = manifest_file + ".bkp"
 
     # Check that both the spack.yaml and the backup exist, the inform user

lib/spack/spack/cmd/install.py

@@ -38,7 +38,7 @@ def update_kwargs_from_args(args, kwargs):
         'keep_stage': args.keep_stage,
         'restage': not args.dont_restage,
         'install_source': args.install_source,
-        'verbose': args.verbose,
+        'verbose': args.verbose or args.install_verbose,
         'fake': args.fake,
         'dirty': args.dirty,
         'use_cache': args.use_cache,
@@ -130,7 +130,7 @@ def setup_parser(subparser):
         help="install source files in prefix")
     arguments.add_common_arguments(subparser, ['no_checksum', 'deprecated'])
     subparser.add_argument(
-        '-v', '--verbose', action='store_true',
+        '-v', '--verbose', action='store_true', dest='install_verbose',
         help="display verbose build output while installing")
     subparser.add_argument(
         '--fake', action='store_true',
@@ -285,6 +285,8 @@ def install_specs(cli_args, kwargs, specs):
 
 
 def install(parser, args, **kwargs):
+    # TODO: unify args.verbose?
+    tty.set_verbose(args.verbose or args.install_verbose)
 
     if args.help_cdash:
         parser = argparse.ArgumentParser(
@@ -346,17 +348,22 @@ def get_tests(specs):
                     env.write(regenerate=False)
 
             specs = env.all_specs()
-            if not args.log_file and not reporter.filename:
+            if specs:
-                reporter.filename = default_log_file(specs[0])
+                if not args.log_file and not reporter.filename:
-            reporter.specs = specs
+                    reporter.filename = default_log_file(specs[0])
+                reporter.specs = specs
 
-            # Tell the monitor about the specs
+                # Tell the monitor about the specs
-            if args.use_monitor and specs:
+                if args.use_monitor and specs:
-                monitor.new_configuration(specs)
+                    monitor.new_configuration(specs)
 
-            tty.msg("Installing environment {0}".format(env.name))
+                tty.msg("Installing environment {0}".format(env.name))
-            with reporter('build'):
+                with reporter('build'):
-                env.install_all(**kwargs)
+                    env.install_all(**kwargs)
+
+            else:
+                msg = '{0} environment has no specs to install'.format(env.name)
+                tty.msg(msg)
 
             tty.debug("Regenerating environment views for {0}"
                       .format(env.name))

lib/spack/spack/cmd/modules/lmod.py

@@ -4,12 +4,11 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import functools
-import os
-
-import llnl.util.filesystem
 
 import spack.cmd.common.arguments
 import spack.cmd.modules
+import spack.config
+import spack.modules.lmod
 
 
 def add_command(parser, command_dict):
@@ -41,12 +40,19 @@ def setdefault(module_type, specs, args):
     # https://lmod.readthedocs.io/en/latest/060_locating.html#marking-a-version-as-default
     #
     spack.cmd.modules.one_spec_or_raise(specs)
-    writer = spack.modules.module_types['lmod'](
+    spec = specs[0]
-        specs[0], args.module_set_name)
+    data = {
-
+        'modules': {
-    module_folder = os.path.dirname(writer.layout.filename)
+            args.module_set_name: {
-    module_basename = os.path.basename(writer.layout.filename)
+                'lmod': {
-    with llnl.util.filesystem.working_dir(module_folder):
+                    'defaults': [str(spec)]
-        if os.path.exists('default') and os.path.islink('default'):
+                }
-            os.remove('default')
+            }
-        os.symlink(module_basename, 'default')
+        }
+    }
+    # Need to clear the cache if a SpackCommand is called during scripting
+    spack.modules.lmod.configuration_registry = {}
+    scope = spack.config.InternalConfigScope('lmod-setdefault', data)
+    with spack.config.override(scope):
+        writer = spack.modules.module_types['lmod'](spec, args.module_set_name)
+        writer.update_module_defaults()

lib/spack/spack/cmd/modules/tcl.py

@@ -2,18 +2,52 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 import functools
 
+import spack.cmd.common.arguments
 import spack.cmd.modules
+import spack.config
+import spack.modules.tcl
 
 
 def add_command(parser, command_dict):
     tcl_parser = parser.add_parser(
         'tcl', help='manipulate non-hierarchical module files'
     )
-    spack.cmd.modules.setup_parser(tcl_parser)
+    sp = spack.cmd.modules.setup_parser(tcl_parser)
+
+    # Set default module file for a package
+    setdefault_parser = sp.add_parser(
+        'setdefault', help='set the default module file for a package'
+    )
+    spack.cmd.common.arguments.add_common_arguments(
+        setdefault_parser, ['constraint']
+    )
+
+    callbacks = dict(spack.cmd.modules.callbacks.items())
+    callbacks['setdefault'] = setdefault
 
     command_dict['tcl'] = functools.partial(
-        spack.cmd.modules.modules_cmd, module_type='tcl'
+        spack.cmd.modules.modules_cmd, module_type='tcl', callbacks=callbacks
     )
+
+
+def setdefault(module_type, specs, args):
+    """Set the default module file, when multiple are present"""
+    # Currently, accepts only a single matching spec
+    spack.cmd.modules.one_spec_or_raise(specs)
+    spec = specs[0]
+    data = {
+        'modules': {
+            args.module_set_name: {
+                'tcl': {
+                    'defaults': [str(spec)]
+                }
+            }
+        }
+    }
+    spack.modules.tcl.configuration_registry = {}
+    scope = spack.config.InternalConfigScope('tcl-setdefault', data)
+    with spack.config.override(scope):
+        writer = spack.modules.module_types['tcl'](spec, args.module_set_name)
+        writer.update_module_defaults()

lib/spack/spack/cmd/python.py

@@ -23,7 +23,7 @@
 
 def setup_parser(subparser):
     subparser.add_argument(
-        '-V', '--version', action='store_true',
+        '-V', '--version', action='store_true', dest='python_version',
         help='print the Python version number and exit')
     subparser.add_argument(
         '-c', dest='python_command', help='command to execute')
@@ -42,7 +42,7 @@ def setup_parser(subparser):
 
 
 def python(parser, args, unknown_args):
-    if args.version:
+    if args.python_version:
         print('Python', platform.python_version())
         return
 

lib/spack/spack/cmd/repo.py

@@ -6,6 +6,7 @@
 from __future__ import print_function
 
 import os
+import sys
 
 import llnl.util.tty as tty
 
@@ -142,9 +143,10 @@ def repo_list(args):
         except spack.repo.RepoError:
             continue
 
-    msg = "%d package repositor" % len(repos)
+    if sys.stdout.isatty():
-    msg += "y." if len(repos) == 1 else "ies."
+        msg = "%d package repositor" % len(repos)
-    tty.msg(msg)
+        msg += "y." if len(repos) == 1 else "ies."
+        tty.msg(msg)
 
     if not repos:
         return

lib/spack/spack/compiler.py

@@ -325,7 +325,7 @@ def accessible_exe(exe):
 
         # setup environment before verifying in case we have executable names
         # instead of absolute paths
-        with self._compiler_environment():
+        with self.compiler_environment():
             missing = [cmp for cmp in (self.cc, self.cxx, self.f77, self.fc)
                        if cmp and not accessible_exe(cmp)]
             if missing:
@@ -407,7 +407,7 @@ def _get_compiler_link_paths(self, paths):
                     compiler_exe.add_default_arg(flag)
 
             output = ''
-            with self._compiler_environment():
+            with self.compiler_environment():
                 output = str(compiler_exe(
                     self.verbose_flag, fin, '-o', fout,
                     output=str, error=str))  # str for py2
@@ -523,7 +523,7 @@ def get_real_version(self):
         modifications) to enable the compiler to run properly on any platform.
         """
         cc = spack.util.executable.Executable(self.cc)
-        with self._compiler_environment():
+        with self.compiler_environment():
             output = cc(self.version_argument,
                         output=str, error=str,
                         ignore_errors=tuple(self.ignore_version_errors))
@@ -597,7 +597,7 @@ def __str__(self):
                 str(self.operating_system)))))
 
     @contextlib.contextmanager
-    def _compiler_environment(self):
+    def compiler_environment(self):
         # store environment to replace later
         backup_env = os.environ.copy()
 

lib/spack/spack/concretize.py

@@ -685,7 +685,7 @@ def find_spec(spec, condition, default=None):
         visited.add(id(relative))
 
     # Then search all other relatives in the DAG *except* spec
-    for relative in spec.root.traverse(deptypes=all):
+    for relative in spec.root.traverse(deptype='all'):
         if relative is spec:
             continue
         if id(relative) in visited:

lib/spack/spack/config.py

@@ -1090,11 +1090,11 @@ def get_valid_type(path):
         jsonschema_error = e.validation_error
         if jsonschema_error.validator == 'type':
             return types[jsonschema_error.validator_value]()
-        elif jsonschema_error.validator == 'anyOf':
+        elif jsonschema_error.validator in ('anyOf', 'oneOf'):
             for subschema in jsonschema_error.validator_value:
-                anyof_type = subschema.get('type')
+                schema_type = subschema.get('type')
-                if anyof_type is not None:
+                if schema_type is not None:
-                    return types[anyof_type]()
+                    return types[schema_type]()
     else:
         return type(None)
     raise ConfigError("Cannot determine valid type for path '%s'." % path)

lib/spack/spack/container/images.json

@@ -28,6 +28,19 @@
         "develop": "latest"
       }
     },
+    "opensuse/leap:15": {
+      "bootstrap": {
+        "template": "container/leap-15.dockerfile"
+      },
+      "os_package_manager": "zypper",
+      "build": "spack/leap15",
+      "build_tags": {
+        "develop": "latest"
+      },
+      "final": {
+        "image": "opensuse/leap:latest"
+      }
+    },
     "nvidia/cuda:11.2.1": {
       "bootstrap": {
         "template": "container/cuda_11_2_1.dockerfile",
@@ -85,6 +98,11 @@
       "update": "yum update -y && amazon-linux-extras install epel -y",
       "install": "yum install -y",
       "clean": "rm -rf /var/cache/yum  && yum clean all"
+    },
+    "zypper": {
+      "update": "zypper update -y",
+      "install": "zypper install -y",
+      "clean": "rm -rf /var/cache/zypp  && zypper clean -a"
     }
   }
 }

lib/spack/spack/database.py

@@ -937,22 +937,15 @@ def _construct_from_directory_layout(self, directory_layout, old_data):
                 tty.debug(
                     'RECONSTRUCTING FROM OLD DB: {0}'.format(entry.spec))
                 try:
-                    layout = spack.store.layout
+                    layout = None if entry.spec.external else spack.store.layout
-                    if entry.spec.external:
+                    kwargs = {
-                        layout = None
+                        'spec': entry.spec,
-                        install_check = True
+                        'directory_layout': layout,
-                    else:
+                        'explicit': entry.explicit,
-                        install_check = layout.check_installed(entry.spec)
+                        'installation_time': entry.installation_time  # noqa: E501
-
+                    }
-                    if install_check:
+                    self._add(**kwargs)
-                        kwargs = {
+                    processed_specs.add(entry.spec)
-                            'spec': entry.spec,
-                            'directory_layout': layout,
-                            'explicit': entry.explicit,
-                            'installation_time': entry.installation_time  # noqa: E501
-                        }
-                        self._add(**kwargs)
-                        processed_specs.add(entry.spec)
                 except Exception as e:
                     # Something went wrong, so the spec was not restored
                     # from old data
@@ -1096,24 +1089,28 @@ def _add(
                 }
                 self._add(dep, directory_layout, **extra_args)
 
-        if key not in self._data:
+        # Make sure the directory layout agrees whether the spec is installed
-            installed = bool(spec.external)
+        if not spec.external and directory_layout:
-            path = None
+            path = directory_layout.path_for_spec(spec)
-            if not spec.external and directory_layout:
+            installed = False
-                path = directory_layout.path_for_spec(spec)
+            try:
-                if path in self._installed_prefixes:
+                directory_layout.ensure_installed(spec)
-                    raise Exception("Install prefix collision.")
+                installed = True
-                try:
-                    directory_layout.check_installed(spec)
-                    installed = True
-                except DirectoryLayoutError as e:
-                    tty.warn(
-                        'Dependency missing: may be deprecated or corrupted:',
-                        path, str(e))
                 self._installed_prefixes.add(path)
-            elif spec.external_path:
+            except DirectoryLayoutError as e:
-                path = spec.external_path
+                msg = ("{0} is being {1} in the database with prefix {2}, "
+                       "but this directory does not contain an installation of "
+                       "the spec, due to: {3}")
+                action = "updated" if key in self._data else "registered"
+                tty.warn(msg.format(spec.short_spec, action, path, str(e)))
+        elif spec.external_path:
+            path = spec.external_path
+            installed = True
+        else:
+            path = None
+            installed = True
 
+        if key not in self._data:
             # Create a new install record with no deps initially.
             new_spec = spec.copy(deps=False)
             extra_args = {
@@ -1141,9 +1138,8 @@ def _add(
             new_spec._full_hash = spec._full_hash
 
         else:
-            # If it is already there, mark it as installed and update
+            # It is already in the database
-            # installation time
+            self._data[key].installed = installed
-            self._data[key].installed = True
             self._data[key].installation_time = _now()
 
         self._data[key].explicit = explicit
@@ -1210,7 +1206,7 @@ def _remove(self, spec):
 
         # This install prefix is now free for other specs to use, even if the
         # spec is only marked uninstalled.
-        if not rec.spec.external:
+        if not rec.spec.external and rec.installed:
             self._installed_prefixes.remove(rec.path)
 
         if rec.ref_count > 0:

lib/spack/spack/directory_layout.py

@@ -233,13 +233,20 @@ def create_install_directory(self, spec):
 
         self.write_spec(spec, self.spec_file_path(spec))
 
-    def check_installed(self, spec):
+    def ensure_installed(self, spec):
+        """
+        Throws DirectoryLayoutError if:
+        1. spec prefix does not exist
+        2. spec prefix does not contain a spec file
+        3. the spec file does not correspond to the spec
+        """
         _check_concrete(spec)
         path = self.path_for_spec(spec)
         spec_file_path = self.spec_file_path(spec)
 
         if not os.path.isdir(path):
-            return None
+            raise InconsistentInstallDirectoryError(
+                "Install prefix {0} does not exist.".format(path))
 
         if not os.path.isfile(spec_file_path):
             raise InconsistentInstallDirectoryError(
@@ -248,7 +255,7 @@ def check_installed(self, spec):
 
         installed_spec = self.read_spec(spec_file_path)
         if installed_spec == spec:
-            return path
+            return
 
         # DAG hashes currently do not include build dependencies.
         #
@@ -261,7 +268,7 @@ def check_installed(self, spec):
             # may be installed. This means for example that for two instances
             # that differ only in CMake version used to build, only one will
             # be installed.
-            return path
+            return
 
         if spec.dag_hash() == installed_spec.dag_hash():
             raise SpecHashCollisionError(spec, installed_spec)

lib/spack/spack/environment/environment.py

@@ -144,10 +144,12 @@ def activate(env, use_env_repo=False):
 
     # Check if we need to reinitialize the store due to pushing the configuration
     # below.
-    store_before_pushing = spack.config.get('config:install_tree')
+    install_tree_before = spack.config.get('config:install_tree')
+    upstreams_before = spack.config.get('upstreams')
     prepare_config_scope(env)
-    store_after_pushing = spack.config.get('config:install_tree')
+    install_tree_after = spack.config.get('config:install_tree')
-    if store_before_pushing != store_after_pushing:
+    upstreams_after = spack.config.get('upstreams')
+    if install_tree_before != install_tree_after or upstreams_before != upstreams_after:
         # Hack to store the state of the store before activation
         env.store_token = spack.store.reinitialize()
 
@@ -489,8 +491,14 @@ def regenerate(self, all_specs, roots):
                 raise SpackEnvironmentViewError(msg)
             os.rename(tmp_symlink_name, self.root)
 
-            # remove old_root
+            # Remove the old root when it's in the same folder as the new root. This
-            if old_root and os.path.exists(old_root):
+            # guards against removal of an arbitrary path when the original symlink in
+            # self.root was not created by the environment, but by the user.
+            if (
+                old_root and
+                os.path.exists(old_root) and
+                os.path.samefile(os.path.dirname(new_root), os.path.dirname(old_root))
+            ):
                 try:
                     shutil.rmtree(old_root)
                 except (IOError, OSError) as e:
@@ -1500,10 +1508,8 @@ def install_specs(self, specs=None, **install_args):
 
         if not specs_to_install:
             tty.msg('All of the packages are already installed')
-            return
+        else:
-
+            tty.debug('Processing {0} uninstalled specs'.format(len(specs_to_install)))
-        tty.debug('Processing {0} uninstalled specs'.format(
-            len(specs_to_install)))
 
         install_args['overwrite'] = install_args.get(
             'overwrite', []) + self._get_overwrite_specs()

lib/spack/spack/environment/shell.py

@@ -39,7 +39,7 @@ def activate_header(env, shell, prompt=None):
         #
     else:
         if 'color' in os.getenv('TERM', '') and prompt:
-            prompt = colorize('@G{%s} ' % prompt, color=True)
+            prompt = colorize('@G{%s}' % prompt, color=True)
 
         cmds += 'export SPACK_ENV=%s;\n' % env.path
         cmds += "alias despacktivate='spack env deactivate';\n"
@@ -73,7 +73,7 @@ def deactivate_header(shell):
         cmds += 'if [ ! -z ${SPACK_ENV+x} ]; then\n'
         cmds += 'unset SPACK_ENV; export SPACK_ENV;\n'
         cmds += 'fi;\n'
-        cmds += 'unalias despacktivate;\n'
+        cmds += 'alias despacktivate > /dev/null 2>&1 && unalias despacktivate;\n'
         cmds += 'if [ ! -z ${SPACK_OLD_PS1+x} ]; then\n'
         cmds += '    if [ "$SPACK_OLD_PS1" = \'$$$$\' ]; then\n'
         cmds += '        unset PS1; export PS1;\n'

lib/spack/spack/error.py

@@ -123,18 +123,11 @@ class UnsatisfiableSpecError(SpecError):
     For original concretizer, provide the requirement that was violated when
     raising.
     """
-    def __init__(self, provided, required=None, constraint_type=None, conflicts=None):
+    def __init__(self, provided, required, constraint_type):
-        # required is only set by the original concretizer.
+        # This is only the entrypoint for old concretizer errors
-        # clingo concretizer handles error messages differently.
+        super(UnsatisfiableSpecError, self).__init__(
-        if required is not None:
+            "%s does not satisfy %s" % (provided, required))
-            assert not conflicts  # can't mix formats
+
-            super(UnsatisfiableSpecError, self).__init__(
-                "%s does not satisfy %s" % (provided, required))
-        else:
-            indented = ['  %s\n' % conflict for conflict in conflicts]
-            conflict_msg = ''.join(indented)
-            msg = '%s is unsatisfiable, conflicts are:\n%s' % (provided, conflict_msg)
-            super(UnsatisfiableSpecError, self).__init__(msg)
         self.provided = provided
         self.required = required
         self.constraint_type = constraint_type

lib/spack/spack/hooks/sbang.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import filecmp
+import grp
 import os
 import re
 import shutil
@@ -14,7 +15,9 @@
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 
+import spack.package_prefs
 import spack.paths
+import spack.spec
 import spack.store
 
 #: OS-imposed character limit for shebang line: 127 for Linux; 511 for Mac.
@@ -187,11 +190,47 @@ def install_sbang():
             spack.paths.sbang_script, sbang_path):
         return
 
-    # make $install_tree/bin and copy in a new version of sbang if needed
+    # make $install_tree/bin
     sbang_bin_dir = os.path.dirname(sbang_path)
     fs.mkdirp(sbang_bin_dir)
-    fs.install(spack.paths.sbang_script, sbang_path)
+
-    fs.set_install_permissions(sbang_bin_dir)
+    # get permissions for bin dir from configuration files
+    group_name = spack.package_prefs.get_package_group(spack.spec.Spec("all"))
+    config_mode = spack.package_prefs.get_package_dir_permissions(
+        spack.spec.Spec("all")
+    )
+
+    if group_name:
+        os.chmod(sbang_bin_dir, config_mode)   # Use package directory permissions
+    else:
+        fs.set_install_permissions(sbang_bin_dir)
+
+    # set group on sbang_bin_dir if not already set (only if set in configuration)
+    if group_name and grp.getgrgid(os.stat(sbang_bin_dir).st_gid).gr_name != group_name:
+        os.chown(
+            sbang_bin_dir,
+            os.stat(sbang_bin_dir).st_uid,
+            grp.getgrnam(group_name).gr_gid
+        )
+
+    # copy over the fresh copy of `sbang`
+    sbang_tmp_path = os.path.join(
+        os.path.dirname(sbang_path),
+        ".%s.tmp" % os.path.basename(sbang_path),
+    )
+    shutil.copy(spack.paths.sbang_script, sbang_tmp_path)
+
+    # set permissions on `sbang` (including group if set in configuration)
+    os.chmod(sbang_tmp_path, config_mode)
+    if group_name:
+        os.chown(
+            sbang_tmp_path,
+            os.stat(sbang_tmp_path).st_uid,
+            grp.getgrnam(group_name).gr_gid
+        )
+
+    # Finally, move the new `sbang` into place atomically
+    os.rename(sbang_tmp_path, sbang_path)
 
 
 def post_install(spec):

lib/spack/spack/installer.py

@@ -632,9 +632,14 @@ def __init__(self, pkg_count):
         # Counters used for showing status information in the terminal title
         self.pkg_num = 0
         self.pkg_count = pkg_count
+        self.pkg_ids = set()
 
-    def next_pkg(self):
+    def next_pkg(self, pkg):
-        self.pkg_num += 1
+        pkg_id = package_id(pkg)
+
+        if pkg_id not in self.pkg_ids:
+            self.pkg_num += 1
+            self.pkg_ids.add(pkg_id)
 
     def set(self, text):
         if not spack.config.get('config:terminal_title', False):
@@ -794,10 +799,10 @@ def _check_deps_status(self, request):
                     .format(dep_id, action)
                 raise InstallError(err.format(request.pkg_id, msg))
 
-            # Attempt to get a write lock to ensure another process does not
+            # Attempt to get a read lock to ensure another process does not
             # uninstall the dependency while the requested spec is being
             # installed
-            ltype, lock = self._ensure_locked('write', dep_pkg)
+            ltype, lock = self._ensure_locked('read', dep_pkg)
             if lock is None:
                 msg = '{0} is write locked by another process'.format(dep_id)
                 raise InstallError(err.format(request.pkg_id, msg))
@@ -816,6 +821,8 @@ def _check_deps_status(self, request):
                 tty.debug('Flagging {0} as installed per the database'
                           .format(dep_id))
                 self._flag_installed(dep_pkg)
+            else:
+                lock.release_read()
 
     def _prepare_for_install(self, task):
         """
@@ -1022,12 +1029,12 @@ def _ensure_locked(self, lock_type, pkg):
                 tty.debug(msg.format('Upgrading to', desc, pkg_id, timeout))
                 op = 'upgrade to'
                 lock.upgrade_read_to_write(timeout)
-            tty.verbose('{0} is now {1} locked'.format(pkg_id, lock_type))
+            tty.debug('{0} is now {1} locked'.format(pkg_id, lock_type))
 
         except (lk.LockDowngradeError, lk.LockTimeoutError) as exc:
             tty.debug(err.format(op, desc, pkg_id, exc.__class__.__name__,
                                  str(exc)))
-            lock = None
+            return (lock_type, None)
 
         except (Exception, KeyboardInterrupt, SystemExit) as exc:
             tty.error(err.format(op, desc, pkg_id, exc.__class__.__name__,
@@ -1254,7 +1261,7 @@ def _push_task(self, task):
         # Remove any associated build task since its sequence will change
         self._remove_task(task.pkg_id)
         desc = 'Queueing' if task.attempts == 0 else 'Requeueing'
-        tty.verbose(msg.format(desc, task.pkg_id, task.status))
+        tty.debug(msg.format(desc, task.pkg_id, task.status))
 
         # Now add the new task to the queue with a new sequence number to
         # ensure it is the last entry popped with the same priority.  This
@@ -1276,7 +1283,7 @@ def _release_lock(self, pkg_id):
             ltype, lock = self.locks[pkg_id]
             if lock is not None:
                 try:
-                    tty.verbose(msg.format(ltype, pkg_id))
+                    tty.debug(msg.format(ltype, pkg_id))
                     if ltype == 'read':
                         lock.release_read()
                     else:
@@ -1296,8 +1303,8 @@ def _remove_task(self, pkg_id):
             pkg_id (str): identifier for the package to be removed
         """
         if pkg_id in self.build_tasks:
-            tty.verbose('Removing build task for {0} from list'
+            tty.debug('Removing build task for {0} from list'
-                        .format(pkg_id))
+                      .format(pkg_id))
             task = self.build_tasks.pop(pkg_id)
             task.status = STATUS_REMOVED
             return task
@@ -1328,8 +1335,7 @@ def _setup_install_dir(self, pkg):
             pkg (spack.package.Package): the package to be built and installed
         """
         if not os.path.exists(pkg.spec.prefix):
-            tty.verbose('Creating the installation directory {0}'
+            tty.debug('Creating the installation directory {0}'.format(pkg.spec.prefix))
-                        .format(pkg.spec.prefix))
             spack.store.layout.create_install_directory(pkg.spec)
         else:
             # Set the proper group for the prefix
@@ -1381,8 +1387,8 @@ def _update_failed(self, task, mark=False, exc=None):
                 self._update_failed(dep_task, mark)
                 self._remove_task(dep_id)
             else:
-                tty.verbose('No build task for {0} to skip since {1} failed'
+                tty.debug('No build task for {0} to skip since {1} failed'
-                            .format(dep_id, pkg_id))
+                          .format(dep_id, pkg_id))
 
     def _update_installed(self, task):
         """
@@ -1499,8 +1505,6 @@ def install(self):
         term_title = TermTitle(len(self.build_pq))
 
         while self.build_pq:
-            term_title.next_pkg()
-
             task = self._pop_task()
             if task is None:
                 continue
@@ -1510,8 +1514,9 @@ def install(self):
             keep_prefix = install_args.get('keep_prefix')
 
             pkg, pkg_id, spec = task.pkg, task.pkg_id, task.pkg.spec
+            term_title.next_pkg(pkg)
             term_title.set('Processing {0}'.format(pkg.name))
-            tty.verbose('Processing {0}: task={1}'.format(pkg_id, task))
+            tty.debug('Processing {0}: task={1}'.format(pkg_id, task))
             # Ensure that the current spec has NO uninstalled dependencies,
             # which is assumed to be reflected directly in its priority.
             #
@@ -1627,6 +1632,7 @@ def install(self):
             # established by the other process -- failed, installed, or
             # uninstalled -- on the next pass.
             if ltype == 'read':
+                lock.release_read()
                 self._requeue_task(task)
                 continue
 

lib/spack/spack/main.py

@@ -41,6 +41,7 @@
 import spack.paths
 import spack.platforms
 import spack.repo
+import spack.solver.asp
 import spack.spec
 import spack.store
 import spack.util.debug
@@ -380,6 +381,13 @@ def make_argument_parser(**kwargs):
     # stat names in groups of 7, for nice wrapping.
     stat_lines = list(zip(*(iter(stat_names),) * 7))
 
+    # help message for --show-cores
+    show_cores_help = 'provide additional information on concretization failures\n'
+    show_cores_help += 'off (default): show only the violated rule\n'
+    show_cores_help += 'full: show raw unsat cores from clingo\n'
+    show_cores_help += 'minimized: show subset-minimal unsat cores '
+    show_cores_help += '(Warning: this may take hours for some specs)'
+
     parser.add_argument(
         '-h', '--help',
         dest='help', action='store_const', const='short', default=None,
@@ -403,6 +411,9 @@ def make_argument_parser(**kwargs):
         '-d', '--debug', action='count', default=0,
         help="write out debug messages "
              "(more d's for more verbosity: -d, -dd, -ddd, etc.)")
+    parser.add_argument(
+        '--show-cores', choices=["off", "full", "minimized"], default="off",
+        help=show_cores_help)
     parser.add_argument(
         '--timestamp', action='store_true',
         help="Add a timestamp to tty output")
@@ -486,13 +497,21 @@ def setup_main_options(args):
         spack.config.set('config:debug', True, scope='command_line')
         spack.util.environment.tracing_enabled = True
 
+    if args.show_cores != "off":
+        # minimize_cores defaults to true, turn it off if we're showing full core
+        # but don't want to wait to minimize it.
+        spack.solver.asp.full_cores = True
+        if args.show_cores == 'full':
+            spack.solver.asp.minimize_cores = False
+
     if args.timestamp:
         tty.set_timestamp(True)
 
     # override lock configuration if passed on command line
     if args.locks is not None:
-        spack.util.lock.check_lock_safety(spack.paths.prefix)
+        if args.locks is False:
-        spack.config.set('config:locks', False, scope='command_line')
+            spack.util.lock.check_lock_safety(spack.paths.prefix)
+        spack.config.set('config:locks', args.locks, scope='command_line')
 
     if args.mock:
         rp = spack.repo.RepoPath(spack.paths.mock_packages_path)
@@ -800,13 +819,13 @@ def _main(argv=None):
     # scopes, then environment configuration here.
     # ------------------------------------------------------------------------
 
-    # ensure options on spack command come before everything
-    setup_main_options(args)
-
     # make spack.config aware of any command line configuration scopes
     if args.config_scopes:
         spack.config.command_line_scopes = args.config_scopes
 
+    # ensure options on spack command come before everything
+    setup_main_options(args)
+
     # activate an environment if one was specified on the command line
     env_format_error = None
     if not args.no_env:

lib/spack/spack/modules/common.py

@@ -906,6 +906,9 @@ def write(self, overwrite=False):
             fp.set_permissions_by_spec(self.layout.filename, self.spec)
 
         # Symlink defaults if needed
+        self.update_module_defaults()
+
+    def update_module_defaults(self):
         if any(self.spec.satisfies(default) for default in self.conf.defaults):
             # This spec matches a default, it needs to be symlinked to default
             # Symlink to a tmp location first and move, so that existing

lib/spack/spack/package.py

@@ -373,6 +373,21 @@ def fullname(self):
         """Name of this package, including the namespace"""
         return '%s.%s' % (self.namespace, self.name)
 
+    @property
+    def fullnames(self):
+        """
+        Fullnames for this package and any packages from which it inherits.
+        """
+        fullnames = []
+        for cls in inspect.getmro(self):
+            namespace = getattr(cls, 'namespace', None)
+            if namespace:
+                fullnames.append('%s.%s' % (namespace, self.name))
+            if namespace == 'builtin':
+                # builtin packages cannot inherit from other repos
+                break
+        return fullnames
+
     @property
     def name(self):
         """The name of this package.
@@ -450,7 +465,7 @@ def view_file_conflicts(self, view, merge_map):
         Alternative implementations may allow some of the files to exist in
         the view (in this case they would be omitted from the results).
         """
-        return set(dst for dst in merge_map.values() if os.path.exists(dst))
+        return set(dst for dst in merge_map.values() if os.path.lexists(dst))
 
     def add_files_to_view(self, view, merge_map):
         """Given a map of package files to destination paths in the view, add
@@ -459,7 +474,7 @@ def add_files_to_view(self, view, merge_map):
         linked into the view already include the file.
         """
         for src, dst in merge_map.items():
-            if not os.path.exists(dst):
+            if not os.path.lexists(dst):
                 view.link(src, dst, spec=self.spec)
 
     def remove_files_from_view(self, view, merge_map):
@@ -863,6 +878,10 @@ def fullname(self):
         """Name of this package, including namespace: namespace.name."""
         return type(self).fullname
 
+    @property
+    def fullnames(self):
+        return type(self).fullnames
+
     @property
     def name(self):
         """Name of this package (the module without parent modules)."""
@@ -1182,7 +1201,7 @@ 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(deptypes=('link', 'run')):
+        for dep in self.spec.traverse(deptype=('link', 'run')):
             if name == dep.name:
                 return dep
 

lib/spack/spack/patch.py

@@ -7,7 +7,6 @@
 import inspect
 import os
 import os.path
-import sys
 
 import llnl.util.filesystem
 import llnl.util.lang
@@ -26,12 +25,6 @@
 def apply_patch(stage, patch_path, level=1, working_dir='.'):
     """Apply the patch at patch_path to code in the stage.
 
-    Spack runs ``patch`` with ``-N`` so that it does not reject already-applied
-    patches.  This is useful for develop specs, so that the build does not fail
-    due to repeated application of patches, and for easing requirements on patch
-    specifications in packages -- packages won't stop working when patches we
-    previously had to apply land in upstream.
-
     Args:
         stage (spack.stage.Stage): stage with code that will be patched
         patch_path (str): filesystem location for the patch to apply
@@ -41,31 +34,10 @@ def apply_patch(stage, patch_path, level=1, working_dir='.'):
     """
     patch = which("patch", required=True)
     with llnl.util.filesystem.working_dir(stage.source_path):
-        output = patch(
+        patch('-s',
-            '-N',               # don't reject already-applied patches
+              '-p', str(level),
-            '-p', str(level),   # patch level (directory depth)
+              '-i', patch_path,
-            '-i', patch_path,   # input source is the patch file
+              '-d', working_dir)
-            '-d', working_dir,  # patch chdir's to here before patching
-            output=str,
-            fail_on_error=False,
-        )
-
-        if patch.returncode != 0:
-            # `patch` returns 1 both:
-            #   a) when an error applying a patch, and
-            #   b) when -N is supplied and the patch has already been applied
-            #
-            # It returns > 1 if there's something more serious wrong.
-            #
-            # So, the best we can do is to look for return code 1, look for output
-            # indicating that the patch was already applied, and ignore the error
-            # if we see it. Most implementations (BSD and GNU) seem to have the
-            # same messages, so we expect these checks to be reliable.
-            if patch.returncode > 1 or not any(
-                    s in output for s in ("Skipping patch", "ignored")
-            ):
-                sys.stderr.write(output)
-                raise patch.error
 
 
 class Patch(object):
@@ -376,8 +348,12 @@ def patch_for_package(self, sha256, pkg):
                 "Couldn't find patch for package %s with sha256: %s"
                 % (pkg.fullname, sha256))
 
-        patch_dict = sha_index.get(pkg.fullname)
+        # Find patches for this class or any class it inherits from
-        if not patch_dict:
+        for fullname in pkg.fullnames:
+            patch_dict = sha_index.get(fullname)
+            if patch_dict:
+                break
+        else:
             raise NoSuchPatchError(
                 "Couldn't find patch for package %s with sha256: %s"
                 % (pkg.fullname, sha256))

lib/spack/spack/report.py

@@ -151,6 +151,22 @@ def wrapper(instance, *args, **kwargs):
                     'installed_from_binary_cache': False
                 }
 
+                # Append the package to the correct spec report. In some
+                # cases it may happen that a spec that is asked to be
+                # installed explicitly will also be installed as a
+                # dependency of another spec. In this case append to both
+                # spec reports.
+                for s in llnl.util.lang.dedupe([pkg.spec.root, pkg.spec]):
+                    name = name_fmt.format(s.name, s.dag_hash(length=7))
+                    try:
+                        item = next((
+                            x for x in self.specs
+                            if x['name'] == name
+                        ))
+                        item['packages'].append(package)
+                    except StopIteration:
+                        pass
+
                 start_time = time.time()
                 value = None
                 try:
@@ -170,6 +186,7 @@ def wrapper(instance, *args, **kwargs):
                     package['stdout'] = fetch_log(pkg, do_fn, self.dir)
                     package['stdout'] += package['message']
                     package['exception'] = e.traceback
+                    raise
 
                 except (Exception, BaseException) as e:
                     # Everything else is an error (the installation
@@ -178,26 +195,11 @@ def wrapper(instance, *args, **kwargs):
                     package['stdout'] = fetch_log(pkg, do_fn, self.dir)
                     package['message'] = str(e) or 'Unknown error'
                     package['exception'] = traceback.format_exc()
+                    raise
 
                 finally:
                     package['elapsed_time'] = time.time() - start_time
 
-                # Append the package to the correct spec report. In some
-                # cases it may happen that a spec that is asked to be
-                # installed explicitly will also be installed as a
-                # dependency of another spec. In this case append to both
-                # spec reports.
-                for s in llnl.util.lang.dedupe([pkg.spec.root, pkg.spec]):
-                    name = name_fmt.format(s.name, s.dag_hash(length=7))
-                    try:
-                        item = next((
-                            x for x in self.specs
-                            if x['name'] == name
-                        ))
-                        item['packages'].append(package)
-                    except StopIteration:
-                        pass
-
                 return value
 
             return wrapper

lib/spack/spack/reporters/cdash.py

@@ -62,7 +62,6 @@ class CDash(Reporter):
 
     def __init__(self, args):
         Reporter.__init__(self, args)
-        tty.set_verbose(args.verbose)
         self.success = True
         self.template_dir = os.path.join('reports', 'cdash')
         self.cdash_upload_url = args.cdash_upload_url

lib/spack/spack/solver/asp.py

@@ -59,6 +59,14 @@
 parse_files = None
 
 
+#: whether we should write ASP unsat cores quickly in debug mode when the cores
+#: may be very large or take the time (sometimes hours) to minimize them
+minimize_cores = True
+
+#: whether we should include all facts in the unsat cores or only error messages
+full_cores = False
+
+
 # backward compatibility functions for clingo ASTs
 def ast_getter(*names):
     def getter(node):
@@ -366,6 +374,19 @@ def format_minimal_cores(self):
             string_list.extend(self.format_core(core))
         return string_list
 
+    def format_cores(self):
+        """List of facts for each core
+
+        Separate cores are separated by an empty line
+        Cores are not minimized
+        """
+        string_list = []
+        for core in self.cores:
+            if string_list:
+                string_list.append('\n')
+            string_list.extend(self.format_core(core))
+        return string_list
+
     def raise_if_unsat(self):
         """
         Raise an appropriate error if the result is unsatisfiable.
@@ -379,9 +400,13 @@ def raise_if_unsat(self):
         constraints = self.abstract_specs
         if len(constraints) == 1:
             constraints = constraints[0]
-        conflicts = self.format_minimal_cores()
 
-        raise spack.error.UnsatisfiableSpecError(constraints, conflicts=conflicts)
+        if minimize_cores:
+            conflicts = self.format_minimal_cores()
+        else:
+            conflicts = self.format_cores()
+
+        raise UnsatisfiableSpecError(constraints, conflicts=conflicts)
 
     @property
     def specs(self):
@@ -496,7 +521,11 @@ def fact(self, head, assumption=False):
         self.out.write("%s.\n" % str(symbol))
 
         atom = self.backend.add_atom(symbol)
-        choice = self.cores and assumption
+
+        # with `--show-cores=full or --show-cores=minimized, make all facts
+        # choices/assumptions, otherwise only if assumption=True
+        choice = self.cores and (full_cores or assumption)
+
         self.backend.add_rule([atom], [], choice=choice)
         if choice:
             self.assumptions.append(atom)
@@ -2024,3 +2053,33 @@ def solve(specs, dump=(), models=0, timers=False, stats=False, tests=False,
     return driver.solve(
         setup, specs, dump, models, timers, stats, tests, reuse
     )
+
+
+class UnsatisfiableSpecError(spack.error.UnsatisfiableSpecError):
+    """
+    Subclass for new constructor signature for new concretizer
+    """
+    def __init__(self, provided, conflicts):
+        indented = ['  %s\n' % conflict for conflict in conflicts]
+        conflict_msg = ''.join(indented)
+        issue = 'conflicts' if full_cores else 'errors'
+        msg = '%s is unsatisfiable, %s are:\n%s' % (provided, issue, conflict_msg)
+
+        newline_indent = '\n    '
+        if not full_cores:
+            msg += newline_indent + 'To see full clingo unsat cores, '
+            msg += 're-run with `spack --show-cores=full`'
+        if not minimize_cores or not full_cores:
+            # not solver.minimalize_cores and not solver.full_cores impossible
+            msg += newline_indent + 'For full, subset-minimal unsat cores, '
+            msg += 're-run with `spack --show-cores=minimized'
+            msg += newline_indent
+            msg += 'Warning: This may take (up to) hours for some specs'
+
+        super(spack.error.UnsatisfiableSpecError, self).__init__(msg)
+
+        self.provided = provided
+
+        # Add attribute expected of the superclass interface
+        self.required = None
+        self.constraint_type = None

lib/spack/spack/spec.py

@@ -3159,6 +3159,15 @@ def constrain(self, other, deps=True):
                     raise UnsatisfiableArchitectureSpecError(sarch, oarch)
 
         changed = False
+
+        if not self.name and other.name:
+            self.name = other.name
+            changed = True
+
+        if not self.namespace and other.namespace:
+            self.namespace = other.namespace
+            changed = True
+
         if self.compiler is not None and other.compiler is not None:
             changed |= self.compiler.constrain(other.compiler)
         elif self.compiler is None:
@@ -4259,7 +4268,7 @@ def tree(self, **kwargs):
 
         out = ""
         for d, dep_spec in self.traverse_edges(
-                order='pre', cover=cover, depth=True, deptypes=deptypes):
+                order='pre', cover=cover, depth=True, deptype=deptypes):
             node = dep_spec.spec
 
             if prefix is not None:

lib/spack/spack/spec_list.py

@@ -11,19 +11,6 @@
 from spack.spec import Spec
 
 
-def spec_ordering_key(s):
-    if s.startswith('^'):
-        return 5
-    elif s.startswith('/'):
-        return 4
-    elif s.startswith('%'):
-        return 3
-    elif any(s.startswith(c) for c in '~-+@') or '=' in s:
-        return 2
-    else:
-        return 1
-
-
 class SpecList(object):
 
     def __init__(self, name='specs', yaml_list=None, reference=None):
@@ -177,30 +164,36 @@ def __getitem__(self, key):
         return self.specs[key]
 
 
-def _expand_matrix_constraints(object, specify=True):
+def _expand_matrix_constraints(matrix_config):
-    # recurse so we can handle nexted matrices
+    # recurse so we can handle nested matrices
     expanded_rows = []
-    for row in object['matrix']:
+    for row in matrix_config['matrix']:
         new_row = []
         for r in row:
             if isinstance(r, dict):
+                # Flatten the nested matrix into a single row of constraints
                 new_row.extend(
-                    [[' '.join(c)]
+                    [[' '.join([str(c) for c in expanded_constraint_list])]
-                     for c in _expand_matrix_constraints(r, specify=False)])
+                     for expanded_constraint_list in _expand_matrix_constraints(r)]
+                )
             else:
                 new_row.append([r])
         expanded_rows.append(new_row)
 
-    excludes = object.get('exclude', [])  # only compute once
+    excludes = matrix_config.get('exclude', [])  # only compute once
-    sigil = object.get('sigil', '')
+    sigil = matrix_config.get('sigil', '')
 
     results = []
     for combo in itertools.product(*expanded_rows):
         # Construct a combined spec to test against excludes
-        flat_combo = [constraint for list in combo for constraint in list]
+        flat_combo = [constraint for constraint_list in combo
-        ordered_combo = sorted(flat_combo, key=spec_ordering_key)
+                      for constraint in constraint_list]
+        flat_combo = [Spec(x) for x in flat_combo]
+
+        test_spec = flat_combo[0].copy()
+        for constraint in flat_combo[1:]:
+            test_spec.constrain(constraint)
 
-        test_spec = Spec(' '.join(ordered_combo))
         # Abstract variants don't have normal satisfaction semantics
         # Convert all variants to concrete types.
         # This method is best effort, so all existing variants will be
@@ -214,14 +207,12 @@ def _expand_matrix_constraints(object, specify=True):
         if any(test_spec.satisfies(x) for x in excludes):
             continue
 
-        if sigil:  # add sigil if necessary
+        if sigil:
-            ordered_combo[0] = sigil + ordered_combo[0]
+            flat_combo[0] = Spec(sigil + str(flat_combo[0]))
 
         # Add to list of constraints
-        if specify:
+        results.append(flat_combo)
-            results.append([Spec(x) for x in ordered_combo])
+
-        else:
-            results.append(ordered_combo)
     return results
 
 

lib/spack/spack/stage.py

@@ -533,7 +533,7 @@ def steal_source(self, dest):
         for entry in hidden_entries + entries:
             if os.path.isdir(entry):
                 d = os.path.join(dest, os.path.basename(entry))
-                shutil.copytree(entry, d)
+                shutil.copytree(entry, d, symlinks=True)
             else:
                 shutil.copy2(entry, dest)
 
@@ -694,8 +694,8 @@ def _add_to_root_stage(self):
             source_path = os.path.join(self.source_path, key)
 
             if not os.path.exists(destination_path):
-                tty.info('Moving resource stage\n\tsource : '
+                tty.info('Moving resource stage\n\tsource: '
-                         '{stage}\n\tdestination : {destination}'.format(
+                         '{stage}\n\tdestination: {destination}'.format(
                              stage=source_path, destination=destination_path
                          ))
 

lib/spack/spack/test/cmd/config.py

@@ -239,6 +239,12 @@ def test_config_add_ordered_dict(mutable_empty_config):
 """
 
 
+def test_config_add_interpret_oneof(mutable_empty_config):
+    # Regression test for a bug that would raise a validation error
+    config('add', 'packages:all:target:[x86_64]')
+    config('add', 'packages:all:variants:~shared')
+
+
 def test_config_add_invalid_fails(mutable_empty_config):
     config('add', 'packages:all:variants:+debug')
     with pytest.raises(

lib/spack/spack/test/cmd/env.py

@@ -868,7 +868,7 @@ def test_env_loads(install_mockery, mock_fetch):
         install('--fake')
 
     with ev.read('test'):
-        env('loads', 'test')
+        env('loads')
 
     e = ev.read('test')
 
@@ -2693,3 +2693,14 @@ def test_activate_temp(monkeypatch, tmpdir):
                           if ev.spack_env_var in line)
     assert str(tmpdir) in active_env_var
     assert ev.is_env_dir(str(tmpdir))
+
+
+def test_env_view_fail_if_symlink_points_elsewhere(tmpdir, install_mockery, mock_fetch):
+    view = str(tmpdir.join('view'))
+    # Put a symlink to an actual directory in view
+    non_view_dir = str(tmpdir.mkdir('dont-delete-me'))
+    os.symlink(non_view_dir, view)
+    with ev.create('env', with_view=view):
+        add('libelf')
+        install('--fake')
+    assert os.path.isdir(non_view_dir)

lib/spack/spack/test/cmd/install.py

@@ -393,9 +393,14 @@ def test_junit_output_with_failures(tmpdir, exc_typename, msg):
             '--log-format=junit', '--log-file=test.xml',
             'raiser',
             'exc_type={0}'.format(exc_typename),
-            'msg="{0}"'.format(msg)
+            'msg="{0}"'.format(msg),
+            fail_on_error=False,
         )
 
+    assert isinstance(install.error, spack.build_environment.ChildError)
+    assert install.error.name == exc_typename
+    assert install.error.pkg.name == 'raiser'
+
     files = tmpdir.listdir()
     filename = tmpdir.join('test.xml')
     assert filename in files
@@ -407,18 +412,22 @@ def test_junit_output_with_failures(tmpdir, exc_typename, msg):
     assert 'failures="1"' in content
     assert 'errors="0"' in content
 
+    # Nothing should have succeeded
+    assert 'tests="0"' not in content
+    assert 'failures="0"' not in content
+
     # We want to have both stdout and stderr
     assert '<system-out>' in content
     assert msg in content
 
 
 @pytest.mark.disable_clean_stage_check
-@pytest.mark.parametrize('exc_typename,msg', [
+@pytest.mark.parametrize('exc_typename,expected_exc,msg', [
-    ('RuntimeError', 'something weird happened'),
+    ('RuntimeError', spack.installer.InstallError, 'something weird happened'),
-    ('KeyboardInterrupt', 'Ctrl-C strikes again')
+    ('KeyboardInterrupt', KeyboardInterrupt, 'Ctrl-C strikes again')
 ])
 def test_junit_output_with_errors(
-        exc_typename, msg,
+        exc_typename, expected_exc, msg,
         mock_packages, mock_archive, mock_fetch, install_mockery,
         config, tmpdir, monkeypatch):
 
@@ -429,11 +438,11 @@ def just_throw(*args, **kwargs):
     monkeypatch.setattr(spack.installer.PackageInstaller, '_install_task',
                         just_throw)
 
-    # TODO: Why does junit output capture appear to swallow the exception
-    # TODO: as evidenced by the two failing packages getting tagged as
-    # TODO: installed?
     with tmpdir.as_cwd():
-        install('--log-format=junit', '--log-file=test.xml', 'libdwarf')
+        install('--log-format=junit', '--log-file=test.xml', 'libdwarf',
+                fail_on_error=False)
+
+    assert isinstance(install.error, expected_exc)
 
     files = tmpdir.listdir()
     filename = tmpdir.join('test.xml')
@@ -441,10 +450,14 @@ def just_throw(*args, **kwargs):
 
     content = filename.open().read()
 
-    # Count failures and errors correctly: libdwarf _and_ libelf
+    # Only libelf error is reported (through libdwarf root spec). libdwarf
-    assert 'tests="2"' in content
+    # install is skipped and it is not an error.
+    assert 'tests="1"' in content
     assert 'failures="0"' in content
-    assert 'errors="2"' in content
+    assert 'errors="1"' in content
+
+    # Nothing should have succeeded
+    assert 'errors="0"' not in content
 
     # We want to have both stdout and stderr
     assert '<system-out>' in content
@@ -877,7 +890,7 @@ def test_install_help_cdash(capsys):
 
 
 @pytest.mark.disable_clean_stage_check
-def test_cdash_auth_token(tmpdir, install_mockery, capfd):
+def test_cdash_auth_token(tmpdir, mock_fetch, install_mockery, capfd):
     # capfd interferes with Spack's capturing
     with tmpdir.as_cwd():
         with capfd.disabled():
@@ -1086,3 +1099,15 @@ def test_install_env_with_tests_root(tmpdir, mock_packages, mock_fetch,
         add('depb')
         install('--test', 'root')
         assert not os.path.exists(test_dep.prefix)
+
+
+def test_install_empty_env(tmpdir, mock_packages, mock_fetch,
+                           install_mockery, mutable_mock_env_path):
+    env_name = 'empty'
+    env('create', env_name)
+    with ev.read(env_name):
+        out = install(fail_on_error=False)
+
+    assert env_name in out
+    assert 'environment' in out
+    assert 'no specs to install' in out

lib/spack/spack/test/cmd/load.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import re
 
 import pytest
 
@@ -16,6 +17,24 @@
 location = SpackCommand('location')
 
 
+def test_manpath_trailing_colon(install_mockery, mock_fetch, mock_archive,
+                                mock_packages, working_env):
+    """Test that the commands generated by load add the MANPATH prefix
+    inspections. Also test that Spack correctly preserves the default/existing
+    manpath search path via a trailing colon"""
+    install('mpileaks')
+
+    sh_out = load('--sh', '--only', 'package', 'mpileaks')
+    lines = sh_out.split('\n')
+    assert any(re.match(r'export MANPATH=.*:;', ln) for ln in lines)
+
+    os.environ['MANPATH'] = '/tmp/man:'
+
+    sh_out = load('--sh', '--only', 'package', 'mpileaks')
+    lines = sh_out.split('\n')
+    assert any(re.match(r'export MANPATH=.*:/tmp/man:;', ln) for ln in lines)
+
+
 def test_load(install_mockery, mock_fetch, mock_archive, mock_packages):
     """Test that the commands generated by load add the specified prefix
     inspections. Also test that Spack records loaded specs by hash in the

lib/spack/spack/test/cmd/module.py

@@ -178,10 +178,18 @@ def test_loads_recursive_blacklisted(database, module_configuration):
 
 @pytest.mark.db
 def test_setdefault_command(
-        mutable_database, module_configuration
+        mutable_database, mutable_config
 ):
-    module_configuration('autoload_direct')
+    data = {
-
+        'default': {
+            'enable': ['lmod'],
+            'lmod': {
+                'core_compilers': ['clang@3.3'],
+                'hierarchy': ['mpi']
+            }
+        }
+    }
+    spack.config.set('modules', data)
     # Install two different versions of a package
     other_spec, preferred = 'a@1.0', 'a@2.0'
 

lib/spack/spack/test/cmd/style.py

@@ -24,8 +24,19 @@
 
 style = spack.main.SpackCommand("style")
 
+
+def has_develop_branch():
+    git = which('git')
+    if not git:
+        return False
+    git("show-ref", "--verify", "--quiet",
+        "refs/heads/develop", fail_on_error=False)
+    return git.returncode == 0
+
+
 # spack style requires git to run -- skip the tests if it's not there
-pytestmark = pytest.mark.skipif(not which('git'), reason='requires git')
+pytestmark = pytest.mark.skipif(not has_develop_branch(),
+                                reason='requires git with develop branch')
 
 # The style tools have requirements to use newer Python versions.  We simplify by
 # requiring Python 3.6 or higher to run spack style.

lib/spack/spack/test/cmd/test.py

@@ -133,7 +133,8 @@ def test_junit_output_with_failures(tmpdir, mock_test_stage, pkg_name, msgs):
     with tmpdir.as_cwd():
         spack_test('run',
                    '--log-format=junit', '--log-file=test.xml',
-                   pkg_name)
+                   pkg_name,
+                   fail_on_error=False)
 
     files = tmpdir.listdir()
     filename = tmpdir.join('test.xml')
@@ -160,7 +161,8 @@ def test_cdash_output_test_error(
         spack_test('run',
                    '--log-format=cdash',
                    '--log-file=cdash_reports',
-                   'test-error')
+                   'test-error',
+                   fail_on_error=False)
         report_dir = tmpdir.join('cdash_reports')
         print(tmpdir.listdir())
         assert report_dir in tmpdir.listdir()

lib/spack/spack/test/concretize.py

@@ -557,6 +557,19 @@ def test_conflicts_in_spec(self, conflict_spec):
         with pytest.raises(spack.error.SpackError):
             s.concretize()
 
+    def test_conflicts_show_cores(self, conflict_spec, monkeypatch):
+        if spack.config.get('config:concretizer') == 'original':
+            pytest.skip('Testing debug statements specific to new concretizer')
+
+        monkeypatch.setattr(spack.solver.asp, 'full_cores', True)
+        monkeypatch.setattr(spack.solver.asp, 'minimize_cores', False)
+
+        s = Spec(conflict_spec)
+        with pytest.raises(spack.error.SpackError) as e:
+            s.concretize()
+
+        assert "conflict_trigger(" in e.value.message
+
     def test_conflict_in_all_directives_true(self):
         s = Spec('when-directives-true')
         with pytest.raises(spack.error.SpackError):

lib/spack/spack/test/conftest.py

@@ -876,8 +876,8 @@ def __init__(self, root):
     def path_for_spec(self, spec):
         return '/'.join([self.root, spec.name + '-' + spec.dag_hash()])
 
-    def check_installed(self, spec):
+    def ensure_installed(self, spec):
-        return True
+        pass
 
 
 @pytest.fixture()

lib/spack/spack/test/database.py

@@ -11,6 +11,7 @@
 import functools
 import json
 import os
+import shutil
 
 import pytest
 
@@ -909,3 +910,51 @@ def test_database_works_with_empty_dir(tmpdir):
         db.query()
     # Check that reading an empty directory didn't create a new index.json
     assert not os.path.exists(db._index_path)
+
+
+def test_reindex_removed_prefix_is_not_installed(mutable_database, mock_store, capfd):
+    """When a prefix of a dependency is removed and the database is reindexed,
+    the spec should still be added through the dependent, but should be listed as
+    not installed."""
+
+    # Remove libelf from the filesystem
+    prefix = mutable_database.query_one('libelf').prefix
+    assert prefix.startswith(str(mock_store))
+    shutil.rmtree(prefix)
+
+    # Reindex should pick up libelf as a dependency of libdwarf
+    spack.store.store.reindex()
+
+    # Reindexing should warn about libelf not being found on the filesystem
+    err = capfd.readouterr()[1]
+    assert 'this directory does not contain an installation of the spec' in err
+
+    # And we should still have libelf in the database, but not installed.
+    assert not mutable_database.query_one('libelf', installed=True)
+    assert mutable_database.query_one('libelf', installed=False)
+
+
+def test_reindex_when_all_prefixes_are_removed(mutable_database, mock_store):
+    # Remove all non-external installations from the filesystem
+    for spec in spack.store.db.query_local():
+        if not spec.external:
+            assert spec.prefix.startswith(str(mock_store))
+            shutil.rmtree(spec.prefix)
+
+    # Make sure we have some explicitly installed specs
+    num = len(mutable_database.query_local(installed=True, explicit=True))
+    assert num > 0
+
+    # Reindex uses the current index to repopulate itself
+    spack.store.store.reindex()
+
+    # Make sure all explicit specs are still there, but are now uninstalled.
+    specs = mutable_database.query_local(installed=False, explicit=True)
+    assert len(specs) == num
+
+    # And make sure they can be removed from the database (covers the case where
+    # `ref_count == 0 and not installed`, which hits some obscure branches.
+    for s in specs:
+        mutable_database.remove(s)
+
+    assert len(mutable_database.query_local(installed=False, explicit=True)) == 0

lib/spack/spack/test/package_sanity.py

@@ -206,8 +206,12 @@ def test_prs_update_old_api():
     """Ensures that every package modified in a PR doesn't contain
     deprecated calls to any method.
     """
+    ref = os.getenv("GITHUB_BASE_REF")
+    if not ref:
+        pytest.skip("No base ref found")
+
     changed_package_files = [
-        x for x in style.changed_files() if style.is_package(x)
+        x for x in style.changed_files(base=ref) if style.is_package(x)
     ]
     failing = []
     for file in changed_package_files:

lib/spack/spack/test/patch.py

@@ -15,9 +15,8 @@
 import spack.paths
 import spack.repo
 import spack.util.compression
-import spack.util.crypto
 from spack.spec import Spec
-from spack.stage import DIYStage, Stage
+from spack.stage import Stage
 from spack.util.executable import Executable
 
 # various sha256 sums (using variables for legibility)
@@ -34,43 +33,6 @@
 url2_archive_sha256 = 'abcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcdabcd'
 
 
-# some simple files for patch tests
-file_to_patch = """\
-first line
-second line
-"""
-
-patch_file = """\
-diff a/foo.txt b/foo-expected.txt
---- a/foo.txt
-+++ b/foo-expected.txt
-@@ -1,2 +1,3 @@
-+zeroth line
- first line
--second line
-+third line
-"""
-
-expected_patch_result = """\
-zeroth line
-first line
-third line
-"""
-
-file_patch_cant_apply_to = """\
-this file
-is completely different
-from anything in the files
-or patch above
-"""
-
-
-def write_file(filename, contents):
-    """Helper function for setting up tests."""
-    with open(filename, 'w') as f:
-        f.write(contents)
-
-
 @pytest.fixture()
 def mock_patch_stage(tmpdir_factory, monkeypatch):
     # Don't disrupt the spack install directory with tests.
@@ -105,9 +67,19 @@ def test_url_patch(mock_patch_stage, filename, sha256, archive_sha256):
 
         mkdirp(stage.source_path)
         with working_dir(stage.source_path):
-            write_file("foo.txt", file_to_patch)
+            # write a file to be patched
-            write_file("foo-expected.txt", expected_patch_result)
+            with open('foo.txt', 'w') as f:
-
+                f.write("""\
+first line
+second line
+""")
+            # write the expected result of patching.
+            with open('foo-expected.txt', 'w') as f:
+                f.write("""\
+zeroth line
+first line
+third line
+""")
         # apply the patch and compare files
         patch.fetch()
         patch.apply(stage)
@@ -117,47 +89,6 @@ def test_url_patch(mock_patch_stage, filename, sha256, archive_sha256):
             assert filecmp.cmp('foo.txt', 'foo-expected.txt')
 
 
-def test_apply_patch_twice(mock_patch_stage, tmpdir):
-    """Ensure that patch doesn't fail if applied twice."""
-
-    stage = DIYStage(str(tmpdir))
-    with tmpdir.as_cwd():
-        write_file("foo.txt", file_to_patch)
-        write_file("foo-expected.txt", expected_patch_result)
-        write_file("foo.patch", patch_file)
-
-    FakePackage = collections.namedtuple(
-        'FakePackage', ['name', 'namespace', 'fullname'])
-    fake_pkg = FakePackage('fake-package', 'test', 'fake-package')
-
-    def make_patch(filename):
-        path = os.path.realpath(str(tmpdir.join(filename)))
-        url = 'file://' + path
-        sha256 = spack.util.crypto.checksum("sha256", path)
-        return spack.patch.UrlPatch(fake_pkg, url, sha256=sha256)
-
-    # apply the first time
-    patch = make_patch('foo.patch')
-    patch.fetch()
-
-    patch.apply(stage)
-    with working_dir(stage.source_path):
-        assert filecmp.cmp('foo.txt', 'foo-expected.txt')
-
-    # ensure apply() is idempotent
-    patch.apply(stage)
-    with working_dir(stage.source_path):
-        assert filecmp.cmp('foo.txt', 'foo-expected.txt')
-
-    # now write a file that can't be patched
-    with working_dir(stage.source_path):
-        write_file("foo.txt", file_patch_cant_apply_to)
-
-    # this application should fail with a real error
-    with pytest.raises(spack.util.executable.ProcessError):
-        patch.apply(stage)
-
-
 def test_patch_in_spec(mock_packages, config):
     """Test whether patches in a package appear in the spec."""
     spec = Spec('patch')

lib/spack/spack/test/sbang.py

@@ -7,6 +7,7 @@
 Test that Spack's shebang filtering works correctly.
 """
 import filecmp
+import grp
 import os
 import shutil
 import stat
@@ -19,6 +20,7 @@
 import spack.hooks.sbang as sbang
 import spack.paths
 import spack.store
+import spack.util.spack_yaml as syaml
 from spack.util.executable import which
 
 too_long = sbang.system_shebang_limit + 1
@@ -256,7 +258,34 @@ def test_shebang_handles_non_writable_files(script_dir, sbang_line):
     assert oct(not_writable_mode) == oct(st.st_mode)
 
 
-def check_sbang_installation():
+@pytest.fixture(scope='function')
+def configure_group_perms():
+    conf = syaml.load_config("""\
+all:
+  permissions:
+    read: world
+    write: group
+    group: {0}
+""".format(grp.getgrgid(os.getegid()).gr_name))
+    spack.config.set('packages', conf, scope='user')
+
+    yield
+
+
+@pytest.fixture(scope='function')
+def configure_user_perms():
+    conf = syaml.load_config("""\
+all:
+  permissions:
+    read: world
+    write: user
+""")
+    spack.config.set('packages', conf, scope='user')
+
+    yield
+
+
+def check_sbang_installation(group=False):
     sbang_path = sbang.sbang_install_path()
     sbang_bin_dir = os.path.dirname(sbang_path)
     assert sbang_path.startswith(spack.store.store.unpadded_root)
@@ -264,14 +293,22 @@ def check_sbang_installation():
     assert os.path.exists(sbang_path)
     assert fs.is_exe(sbang_path)
 
-    status = os.stat(sbang_path)
-    assert (status.st_mode & 0o777) == 0o755
-
     status = os.stat(sbang_bin_dir)
-    assert (status.st_mode & 0o777) == 0o755
+    mode = (status.st_mode & 0o777)
+    if group:
+        assert mode == 0o775, 'Unexpected {0}'.format(oct(mode))
+    else:
+        assert mode == 0o755, 'Unexpected {0}'.format(oct(mode))
+
+    status = os.stat(sbang_path)
+    mode = (status.st_mode & 0o777)
+    if group:
+        assert mode == 0o775, 'Unexpected {0}'.format(oct(mode))
+    else:
+        assert mode == 0o755, 'Unexpected {0}'.format(oct(mode))
 
 
-def test_install_sbang(install_mockery):
+def run_test_install_sbang(group):
     sbang_path = sbang.sbang_install_path()
     sbang_bin_dir = os.path.dirname(sbang_path)
 
@@ -279,7 +316,7 @@ def test_install_sbang(install_mockery):
     assert not os.path.exists(sbang_bin_dir)
 
     sbang.install_sbang()
-    check_sbang_installation()
+    check_sbang_installation(group)
 
     # put an invalid file in for sbang
     fs.mkdirp(sbang_bin_dir)
@@ -287,11 +324,19 @@ def test_install_sbang(install_mockery):
         f.write("foo")
 
     sbang.install_sbang()
-    check_sbang_installation()
+    check_sbang_installation(group)
 
     # install again and make sure sbang is still fine
     sbang.install_sbang()
-    check_sbang_installation()
+    check_sbang_installation(group)
+
+
+def test_install_group_sbang(install_mockery, configure_group_perms):
+    run_test_install_sbang(True)
+
+
+def test_install_user_sbang(install_mockery, configure_user_perms):
+    run_test_install_sbang(False)
 
 
 def test_install_sbang_too_long(tmpdir):

lib/spack/spack/test/spec_dag.py

@@ -974,7 +974,6 @@ def test_canonical_deptype(self):
             canonical_deptype(('foo',))
 
     def test_invalid_literal_spec(self):
-
         # Can't give type 'build' to a top-level spec
         with pytest.raises(spack.spec.SpecParseError):
             Spec.from_literal({'foo:build': None})
@@ -982,3 +981,11 @@ def test_invalid_literal_spec(self):
         # Can't use more than one ':' separator
         with pytest.raises(KeyError):
             Spec.from_literal({'foo': {'bar:build:link': None}})
+
+    def test_spec_tree_respect_deptypes(self):
+        # Version-test-root uses version-test-pkg as a build dependency
+        s = Spec('version-test-root').concretized()
+        out = s.tree(deptypes='all')
+        assert 'version-test-pkg' in out
+        out = s.tree(deptypes=('link', 'run'))
+        assert 'version-test-pkg' not in out

lib/spack/spack/test/spec_list.py

@@ -45,24 +45,34 @@ def test_spec_list_expansions(self):
         assert speclist.specs_as_constraints == self.default_constraints
         assert speclist.specs == self.default_specs
 
-    def test_spec_list_constraint_ordering(self):
+    @pytest.mark.regression('28749')
-        specs = [{'matrix': [
+    @pytest.mark.parametrize('specs,expected', [
+        # Constraints are ordered randomly
+        ([{'matrix': [
             ['^zmpi'],
             ['%gcc@4.5.0'],
             ['hypre', 'libelf'],
             ['~shared'],
             ['cflags=-O3', 'cflags="-g -O0"'],
             ['^foo']
-        ]}]
+        ]}], [
-
+            'hypre cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi',
+            'hypre cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
+            'libelf cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi',
+            'libelf cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
+        ]),
+        # A constraint affects both the root and a dependency
+        ([{'matrix': [
+            ['gromacs'],
+            ['%gcc'],
+            ['+plumed ^plumed%gcc']
+        ]}], [
+            'gromacs+plumed%gcc ^plumed%gcc'
+        ])
+    ])
+    def test_spec_list_constraint_ordering(self, specs, expected):
         speclist = SpecList('specs', specs)
-
+        expected_specs = [Spec(x) for x in expected]
-        expected_specs = [
-            Spec('hypre cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi'),
-            Spec('hypre cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi'),
-            Spec('libelf cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi'),
-            Spec('libelf cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi'),
-        ]
         assert speclist.specs == expected_specs
 
     def test_spec_list_add(self):

lib/spack/spack/test/spec_semantics.py

@@ -1228,3 +1228,15 @@ def test_merge_abstract_anonymous_specs(specs, expected):
     specs = [Spec(x) for x in specs]
     result = spack.spec.merge_abstract_anonymous_specs(*specs)
     assert result == Spec(expected)
+
+
+@pytest.mark.parametrize('anonymous,named,expected', [
+    ('+plumed', 'gromacs', 'gromacs+plumed'),
+    ('+plumed ^plumed%gcc', 'gromacs', 'gromacs+plumed ^plumed%gcc'),
+    ('+plumed', 'builtin.gromacs', 'builtin.gromacs+plumed')
+])
+def test_merge_anonymous_spec_with_named_spec(anonymous, named, expected):
+    s = Spec(anonymous)
+    changed = s.constrain(named)
+    assert changed
+    assert s == Spec(expected)

lib/spack/spack/test/util/environment.py

@@ -22,6 +22,8 @@ def prepare_environment_for_tests():
 def test_is_system_path():
     assert(envutil.is_system_path('/usr/bin'))
     assert(not envutil.is_system_path('/nonsense_path/bin'))
+    assert(not envutil.is_system_path(''))
+    assert(not envutil.is_system_path(None))
 
 
 test_paths = ['/usr/bin',

lib/spack/spack/test/versions.py

@@ -630,6 +630,14 @@ def test_version_wrong_idx_type():
         v['0:']
 
 
+@pytest.mark.regression('29170')
+def test_version_range_satisfies_means_nonempty_intersection():
+    x = VersionRange('3.7.0', '3')
+    y = VersionRange('3.6.0', '3.6.0')
+    assert not x.satisfies(y)
+    assert not y.satisfies(x)
+
+
 @pytest.mark.regression('26482')
 def test_version_list_with_range_included_in_concrete_version_interpreted_as_range():
     # Note: this test only tests whether we can construct a version list of a range

lib/spack/spack/util/crypto.py

@@ -92,11 +92,6 @@ def checksum(hashlib_algo, filename, **kwargs):
     """Returns a hex digest of the filename generated using an
        algorithm from hashlib.
     """
-    if isinstance(hashlib_algo, str):
-        if hashlib_algo not in hashes:
-            raise ValueError("Invalid hash algorithm: ", hashlib_algo)
-        hashlib_algo = hash_fun_for_algo(hashlib_algo)
-
     block_size = kwargs.get('block_size', 2**20)
     hasher = hashlib_algo()
     with open(filename, 'rb') as file:

lib/spack/spack/util/environment.py

@@ -59,7 +59,7 @@ def is_system_path(path):
     Returns:
         True or False
     """
-    return os.path.normpath(path) in system_dirs
+    return path and os.path.normpath(path) in system_dirs
 
 
 def filter_system_paths(paths):
@@ -611,7 +611,6 @@ def apply_modifications(self, env=None):
     def shell_modifications(self, shell='sh', explicit=False, env=None):
         """Return shell code to apply the modifications and clears the list."""
         modifications = self.group_by_name()
-        new_env = os.environ.copy()
 
         if env is None:
             env = os.environ
@@ -622,6 +621,9 @@ def shell_modifications(self, shell='sh', explicit=False, env=None):
             for x in actions:
                 x.execute(new_env)
 
+        if 'MANPATH' in new_env and not new_env.get('MANPATH').endswith(':'):
+            new_env['MANPATH'] += ':'
+
         cmds = ''
 
         for name in sorted(set(modifications)):

lib/spack/spack/util/executable.py

@@ -27,7 +27,6 @@ def __init__(self, name):
         from spack.util.environment import EnvironmentModifications  # no cycle
         self.default_envmod = EnvironmentModifications()
         self.returncode = None
-        self.error = None  # saved ProcessError when fail_on_error
 
         if not self.exe:
             raise ProcessError("Cannot construct executable for '%s'" % name)
@@ -91,8 +90,7 @@ def __call__(self, *args, **kwargs):
                 the environment (neither requires nor precludes env)
             fail_on_error (bool): Raise an exception if the subprocess returns
                 an error. Default is True. The return code is available as
-                ``exe.returncode``, and a saved ``ProcessError`` that would
+                ``exe.returncode``
-                have been raised is in ``exe.error``.
             ignore_errors (int or list): A list of error codes to ignore.
                 If these codes are returned, this process will not raise
                 an exception even if ``fail_on_error`` is set to ``True``
@@ -215,7 +213,7 @@ def streamify(arg, mode):
                         sys.stderr.write(errstr)
 
             rc = self.returncode = proc.returncode
-            if rc != 0:
+            if fail_on_error and rc != 0 and (rc not in ignore_errors):
                 long_msg = cmd_line_string
                 if result:
                     # If the output is not captured in the result, it will have
@@ -224,11 +222,8 @@ def streamify(arg, mode):
                     # stdout/stderr (e.g. if 'output' is not specified)
                     long_msg += '\n' + result
 
-                self.error = ProcessError(
+                raise ProcessError('Command exited with status %d:' %
-                    'Command exited with status %d:' % proc.returncode, long_msg
+                                   proc.returncode, long_msg)
-                )
-                if fail_on_error and (rc not in ignore_errors):
-                    raise self.error
 
             return result
 
@@ -237,15 +232,10 @@ def streamify(arg, mode):
                 '%s: %s' % (self.exe[0], e.strerror), 'Command: ' + cmd_line_string)
 
         except subprocess.CalledProcessError as e:
-            self.error = ProcessError(
-                str(e),
-                '\nExit status %d when invoking command: %s' % (
-                    proc.returncode,
-                    cmd_line_string,
-                ),
-            )
             if fail_on_error:
-                raise self.error
+                raise ProcessError(
+                    str(e), '\nExit status %d when invoking command: %s' %
+                    (proc.returncode, cmd_line_string))
 
         finally:
             if close_ostream:

lib/spack/spack/version.py

@@ -586,35 +586,23 @@ def __contains__(self, other):
 
     @coerced
     def satisfies(self, other):
-        """A VersionRange satisfies another if some version in this range
-        would satisfy some version in the other range.  To do this it must
-        either:
-
-        a) Overlap with the other range
-        b) The start of this range satisfies the end of the other range.
-
-        This is essentially the same as overlaps(), but overlaps assumes
-        that its arguments are specific.  That is, 4.7 is interpreted as
-        4.7.0.0.0.0... .  This function assumes that 4.7 would be satisfied
-        by 4.7.3.5, etc.
-
-        Rationale:
-
-        If a user asks for gcc@4.5:4.7, and a package is only compatible with
-        gcc@4.7.3:4.8, then that package should be able to build under the
-        constraints.  Just using overlaps() would not work here.
-
-        Note that we don't need to check whether the end of this range
-        would satisfy the start of the other range, because overlaps()
-        already covers that case.
-
-        Note further that overlaps() is a symmetric operation, while
-        satisfies() is not.
         """
-        return (self.overlaps(other) or
+        x.satisfies(y) in general means that x and y have a
-                # if either self.start or other.end are None, then this can't
+        non-zero intersection. For VersionRange this means they overlap.
-                # satisfy, or overlaps() would've taken care of it.
+
-                self.start and other.end and self.start.satisfies(other.end))
+        `satisfies` is a commutative binary operator, meaning that
+        x.satisfies(y) if and only if y.satisfies(x).
+
+        Note: in some cases we have the keyword x.satisfies(y, strict=True)
+        to mean strict set inclusion, which is not commutative. However, this
+        lacks in VersionRange for unknown reasons.
+
+        Examples
+        - 1:3 satisfies 2:4, as their intersection is 2:3.
+        - 1:2 does not satisfy 3:4, as their intersection is empty.
+        - 4.5:4.7 satisfies 4.7.2:4.8, as their intersection is 4.7.2:4.7
+        """
+        return self.overlaps(other)
 
     @coerced
     def overlaps(self, other):

share/spack/bash/spack-completion.in

@@ -123,7 +123,7 @@ _bash_completion_spack() {
     # If the cursor is in the middle of the line, like:
     #     `spack -d [] install`
     # COMP_WORDS will not contain the empty character, so we have to add it.
-    if [[ "${COMP_LINE:$COMP_POINT:1}" == " " ]]
+    if [[ "${COMP_LINE:$COMP_POINT-1:1}" == " " ]]
     then
         cur=""
     fi
@@ -208,10 +208,10 @@ _repos() {
     SPACK_COMPREPLY="$SPACK_REPOS"
 }
 
-_tests() {
+_unit_tests() {
     if [[ -z "${SPACK_TESTS:-}" ]]
     then
-        SPACK_TESTS="$(spack test -l)"
+        SPACK_TESTS="$(spack unit-test -l)"
     fi
     SPACK_COMPREPLY="$SPACK_TESTS"
 }

share/spack/docker/leap-15.dockerfile

@@ -2,7 +2,7 @@ FROM opensuse/leap:15.3
 MAINTAINER Christian Goll <cgoll@suse.com>
 
 ENV DOCKERFILE_BASE=opensuse          \
-    DOCKERFILE_DISTRO=opensuse_leap   \
+    DOCKERFILE_DISTRO=leap   \
     DOCKERFILE_DISTRO_VERSION=15.3    \
     SPACK_ROOT=/opt/spack      \
     DEBIAN_FRONTEND=noninteractive    \
@@ -11,10 +11,21 @@ ENV DOCKERFILE_BASE=opensuse          \
 
 RUN zypper ref && \
     zypper up -y && \
-    zypper in -y python3-base python3-boto3 \
+    zypper in -y \
-    xz gzip tar bzip2 curl patch patchelf file \
+    bzip2\
-    gcc-c++ gcc-fortran make cmake automake && \
+    curl\
-    zypper clean
+    file\
+    gcc-c++\
+    gcc-fortran\
+    make\
+    gzip\
+    patch\
+    patchelf\
+    python3-base \
+    python3-boto3\
+    tar\
+    xz\
+&&  zypper clean
 
 # clean up manpages
 RUN	rm -rf /var/cache/zypp/*  \

share/spack/qa/completion-test.sh

@@ -70,6 +70,16 @@ _test_debug_functions() {
         emulate -L sh
     fi
 
+    # Test whether `spack install --verb[] spec` completes to `spack install --verbose spec`
+    COMP_LINE='spack install --verb spec'
+    COMP_POINT=20
+    COMP_WORDS=(spack install --verb spec)
+    COMP_CWORD=2
+    COMP_KEY=9
+    COMP_TYPE=64
+    _bash_completion_spack
+    contains "--verbose" echo "${COMPREPLY[@]}"
+
     # This is a particularly tricky case that involves the following situation:
     #     `spack -d [] install `
     # Here, [] represents the cursor, which is in the middle of the line.

share/spack/qa/run-style-tests

@@ -14,15 +14,17 @@
 # Usage:
 #     run-flake8-tests
 #
-. "$(dirname $0)/setup.sh"
+. "$(dirname "$0")/setup.sh"
 
-BASE=""
+args=()
-if [ -n "$GITHUB_BASE_REF" ]; then
+if [[ -n $GITHUB_BASE_REF ]]; then
-    BASE="--base ${GITHUB_BASE_REF}"
+    args+=("--base" "${GITHUB_BASE_REF}")
+else
+    args+=("--base" "${GITHUB_REF_NAME}")
 fi
 
 # verify that the code style is correct
-spack style --root-relative $BASE
+spack style --root-relative "${args[@]}"
 
 # verify that the license headers are present
 spack license verify

share/spack/spack-completion.bash

@@ -123,7 +123,7 @@ _bash_completion_spack() {
     # If the cursor is in the middle of the line, like:
     #     `spack -d [] install`
     # COMP_WORDS will not contain the empty character, so we have to add it.
-    if [[ "${COMP_LINE:$COMP_POINT:1}" == " " ]]
+    if [[ "${COMP_LINE:$COMP_POINT-1:1}" == " " ]]
     then
         cur=""
     fi
@@ -208,10 +208,10 @@ _repos() {
     SPACK_COMPREPLY="$SPACK_REPOS"
 }
 
-_tests() {
+_unit_tests() {
     if [[ -z "${SPACK_TESTS:-}" ]]
     then
-        SPACK_TESTS="$(spack test -l)"
+        SPACK_TESTS="$(spack unit-test -l)"
     fi
     SPACK_COMPREPLY="$SPACK_TESTS"
 }
@@ -335,7 +335,7 @@ _spacktivate() {
 _spack() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -H --all-help --color -c --config -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
+        SPACK_COMPREPLY="-h --help -H --all-help --color -c --config -C --config-scope -d --debug --show-cores --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
     else
         SPACK_COMPREPLY="activate add analyze arch audit blame bootstrap build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config containerize create deactivate debug dependencies dependents deprecate dev-build develop diff docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mark mirror module monitor patch pkg providers pydoc python reindex remove rm repo resource restage solve spec stage style tags test test-env tutorial undevelop uninstall unit-test unload url verify versions view"
     fi
@@ -969,12 +969,7 @@ _spack_env_st() {
 }
 
 _spack_env_loads() {
-    if $list_options
+    SPACK_COMPREPLY="-h --help -n --module-set-name -m --module-type --input-only -p --prefix -x --exclude -r --dependencies"
-    then
-        SPACK_COMPREPLY="-h --help -n --module-set-name -m --module-type --input-only -p --prefix -x --exclude -r --dependencies"
-    else
-        _environments
-    fi
 }
 
 _spack_env_view() {
@@ -1387,7 +1382,7 @@ _spack_module_tcl() {
     then
         SPACK_COMPREPLY="-h --help -n --name"
     else
-        SPACK_COMPREPLY="refresh find rm loads"
+        SPACK_COMPREPLY="refresh find rm loads setdefault"
     fi
 }
 
@@ -1427,6 +1422,15 @@ _spack_module_tcl_loads() {
     fi
 }
 
+_spack_module_tcl_setdefault() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help"
+    else
+        _installed_packages
+    fi
+}
+
 _spack_monitor() {
     SPACK_COMPREPLY="-h --help --monitor --monitor-save-local --monitor-no-auth --monitor-tags --monitor-keep-going --monitor-host --monitor-prefix"
 }
@@ -1776,7 +1780,7 @@ _spack_unit_test() {
     then
         SPACK_COMPREPLY="-h --help -H --pytest-help -l --list -L --list-long -N --list-names --extension -s -k --showlocals"
     else
-        _tests
+        _unit_tests
     fi
 }
 

share/spack/templates/container/leap-15.dockerfile

@@ -0,0 +1,21 @@
+{% extends "container/bootstrap-base.dockerfile" %}
+{% block install_os_packages %}
+RUN zypper ref && \
+    zypper up -y && \
+    zypper in -y \
+    bzip2\
+    curl\
+    file\
+    gcc-c++\
+    gcc-fortran\
+    make\
+    git\
+    gzip\
+    patch\
+    patchelf\
+    python3-base \
+    python3-boto3\
+    tar\
+    xz\
+&&  zypper clean
+{% endblock %}

var/spack/repos/builtin.mock/packages/mpileaks/package.py

@@ -28,6 +28,7 @@ class Mpileaks(Package):
 
     def install(self, spec, prefix):
         touch(prefix.mpileaks)
+        mkdirp(prefix.man)
 
     def setup_environment(self, senv, renv):
         renv.set('FOOBAR', self.name)

var/spack/repos/builtin/packages/elfutils/package.py

@@ -22,6 +22,7 @@ class Elfutils(AutotoolsPackage, SourcewarePackage):
     list_url = "https://sourceware.org/elfutils/ftp"
     list_depth = 1
 
+    version('0.186', sha256='7f6fb9149b1673d38d9178a0d3e0fb8a1ec4f53a9f4c2ff89469609879641177')
     version('0.185', sha256='dc8d3e74ab209465e7f568e1b3bb9a5a142f8656e2b57d10049a73da2ae6b5a6')
     version('0.184', sha256='87e7d1d7f0333815dd1f62135d047a4dc4082068f361452f357997c11360644b')
     version('0.183', sha256='c3637c208d309d58714a51e61e63f1958808fead882e9b607506a29e5474f2c5')

var/spack/repos/builtin/packages/openloops/get-process-list.py

@@ -8,7 +8,7 @@ def error(self, message):
         pass
 
     def __init__(self):
-        super().__init__()
+        super(HTMLParser, self).__init__()
         self.state = 0
         self.processes = []
 

var/spack/repos/builtin/packages/openmpi/package.py

@@ -1058,7 +1058,7 @@ def is_enabled(text):
 # This code gets all the fabric names from the variants list
 # Idea taken from the AutotoolsPackage source.
 def get_options_from_variant(self, name):
-    values = self.variants[name].values
+    values = self.variants[name][0].values
     if getattr(values, 'feature_values', None):
         values = values.feature_values
     return values

var/spack/repos/builtin/packages/py-charm4py/package.py

@@ -66,7 +66,7 @@ def setup_build_environment(self, env):
 
     def install_args(self, spec, prefix):
         # Have the parent class version set prefix
-        args = super().install_args(spec, prefix)
+        args = super(PythonPackage, self).install_args(spec, prefix)
         if '+mpi' in spec:
             args.append('--mpi')
         return args

var/spack/repos/builtin/packages/py-pandas/package.py

@@ -91,7 +91,7 @@ class PyPandas(PythonPackage):
 
     @property
     def import_modules(self):
-        modules = super().import_modules
+        modules = super(PyPandas, self).import_modules()
 
         ignored_imports = ["pandas.tests", "pandas.plotting._matplotlib"]
 

var/spack/repos/builtin/packages/py-vermin/package.py

@@ -8,10 +8,11 @@ class PyVermin(PythonPackage):
     """Concurrently detect the minimum Python versions needed to run code."""
 
     homepage = "https://github.com/netromdk/vermin"
-    url      = "https://github.com/netromdk/vermin/archive/v1.3.1.tar.gz"
+    url      = "https://github.com/netromdk/vermin/archive/v1.3.2.tar.gz"
 
     maintainers = ['netromdk']
 
+    version('1.3.2', sha256='2818eaea24c5be5dae1f374ddb2377e9cfaad04d0a3372ad129cffc46cec5404')
     version('1.3.1', sha256='ddcdaad5a708a483af192075f5d2eaaaf3aa4661b5101ddafa40d7837eeb5368')
     version('1.3.0', sha256='adf2b6ea34c01c3a81fc4fa78c2e5fa6c8dd6d35327a8e5a4caeeaef7ec21668')
     version('1.2.2', sha256='d0343b2a78d7e4de67dfd2d882eeaf8b241db724f7e67f83bdd4111edb97f1e2')

var/spack/repos/builtin/packages/upcxx/package.py

@@ -3,11 +3,18 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack import *
 
 
+def is_CrayXC():
+    return (spack.platforms.host().name == 'cray') and \
+           (os.environ.get('CRAYPE_NETWORK_TARGET') == "aries")
+
+
 def cross_detect():
-    if spack.platforms.host().name == 'cray':
+    if is_CrayXC():
         if which('srun'):
             return 'cray-aries-slurm'
         if which('aprun'):
@@ -24,6 +31,7 @@ class Upcxx(Package):
 
     homepage = "https://upcxx.lbl.gov"
     maintainers = ['bonachea']
+    url = "https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-2021.3.0.tar.gz"
     git = 'https://bitbucket.org/berkeleylab/upcxx.git'
 
     tags = ['e4s']
@@ -31,13 +39,15 @@ class Upcxx(Package):
     version('develop', branch='develop')
     version('master',  branch='master')
 
+    version('2021.9.0', sha256='9299e17602bcc8c05542cdc339897a9c2dba5b5c3838d6ef2df7a02250f42177')
     version('2021.3.0', sha256='3433714cd4162ffd8aad9a727c12dbf1c207b7d6664879fc41259a4b351595b7')
     version('2020.11.0', sha256='f6f212760a485a9f346ca11bb4751e7095bbe748b8e5b2389ff9238e9e321317',
             url='https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-2020.11.0-memory_kinds_prototype.tar.gz')
     version('2020.10.0', sha256='623e074b512bf8cad770a04040272e1cc660d2749760398b311f9bcc9d381a37')
+    version('2020.3.2', sha256='978adc315d21089c739d5efda764b77fc9a2a7c5860f169fe5cd2ca1d840620f')
     version('2020.3.0', sha256='01be35bef4c0cfd24e9b3d50c88866521b9cac3ad4cbb5b1fc97aea55078810f')
-    version('2019.9.0', sha256='7d67ccbeeefb59de9f403acc719f52127a30801a2c2b9774a1df03f850f8f1d4')
+    # Do NOT add older versions here.
-    version('2019.3.2', sha256='dcb0b337c05a0feb2ed5386f5da6c60342412b49cab10f282f461e74411018ad')
+    # UPC++ releases over 2 years old are not supported.
 
     variant('mpi', default=False,
             description='Enables MPI-based spawners and mpi-conduit')
@@ -48,8 +58,8 @@ class Upcxx(Package):
     variant('cross', default=cross_detect(),
             description="UPC++ cross-compile target (autodetect by default)")
 
-    conflicts('cross=none', when='platform=cray',
+    conflicts('cross=none', when=is_CrayXC(),
-              msg='cross=none is unacceptable on Cray.' +
+              msg='cross=none is unacceptable on Cray XC.' +
                   'Please specify an appropriate "cross" value')
 
     # UPC++ always relies on GASNet-EX.
@@ -61,47 +71,15 @@ class Upcxx(Package):
 
     depends_on('mpi', when='+mpi')
     depends_on('cuda', when='+cuda')
-    # Require Python2 2.7.5+ up to v2019.9.0
+    depends_on('python@2.7.5:', type=("build", "run"))
-    depends_on('python@2.7.5:2',
-               type=("build", "run"), when='@:2019.9.0')
-    # v2020.3.0 and later also permit Python3
-    depends_on('python@2.7.5:', type=("build", "run"), when='@2020.3.0:')
 
     # All flags should be passed to the build-env in autoconf-like vars
     flag_handler = env_flags
 
-    def url_for_version(self, version):
-        if version > Version('2019.3.2'):
-            url = "https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-{0}.tar.gz"
-        else:
-            url = "https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-{0}-offline.tar.gz"
-        return url.format(version)
-
-    def setup_build_environment(self, env):
-        # ensure we use the correct python
-        env.set('UPCXX_PYTHON', self.spec['python'].command.path)
-
-        if '+mpi' in self.spec:
-            env.set('GASNET_CONFIGURE_ARGS',
-                    '--enable-mpi --enable-mpi-compat')
-        else:
-            env.set('GASNET_CONFIGURE_ARGS', '--without-mpicc')
-
-        if 'cross=none' not in self.spec:
-            env.set('CROSS', self.spec.variants['cross'].value)
-
-        if '+cuda' in self.spec:
-            env.set('UPCXX_CUDA', '1')
-            env.set('UPCXX_CUDA_NVCC', self.spec['cuda'].prefix.bin.nvcc)
-
     def setup_run_environment(self, env):
-        # ensure we use the correct python
-        env.set('UPCXX_PYTHON', self.spec['python'].command.path)
-
         env.set('UPCXX_INSTALL', self.prefix)
         env.set('UPCXX', self.prefix.bin.upcxx)
-        if 'platform=cray' in self.spec:
+        if is_CrayXC():
-            env.set('UPCXX_GASNET_CONDUIT', 'aries')
             env.set('UPCXX_NETWORK', 'aries')
 
     def setup_dependent_package(self, module, dep_spec):
@@ -110,97 +88,91 @@ def setup_dependent_package(self, module, dep_spec):
     def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('UPCXX_INSTALL', self.prefix)
         env.set('UPCXX', self.prefix.bin.upcxx)
-        if 'platform=cray' in self.spec:
+        if is_CrayXC():
-            env.set('UPCXX_GASNET_CONDUIT', 'aries')
             env.set('UPCXX_NETWORK', 'aries')
 
     def install(self, spec, prefix):
+        env = os.environ
         # UPC++ follows autoconf naming convention for LDLIBS, which is 'LIBS'
         if (env.get('LDLIBS')):
             env['LIBS'] = env['LDLIBS']
 
-        if spec.version <= Version('2019.9.0'):
+        options = ["--prefix=%s" % prefix]
-            env['CC'] = self.compiler.cc
+
-            if '+mpi' in self.spec:
+        if 'cross=none' in spec:
-                if 'platform=cray' in self.spec:
+            options.append('--without-cross')
-                    env['GASNET_CONFIGURE_ARGS'] += \
-                        " --with-mpicc=" + self.compiler.cc
-                else:
-                    env['CXX'] = spec['mpi'].mpicxx
-            else:
-                env['CXX'] = self.compiler.cxx
-            if '+gasnet' in self.spec:
-                env['GASNET'] = spec['gasnet'].prefix.src
-            installsh = Executable("./install")
-            installsh(prefix)
         else:
-            if 'platform=cray' in self.spec:
+            options.append('--with-cross=' + spec.variants['cross'].value)
-                # Spack loads the cray-libsci module incorrectly on ALCF theta,
-                # breaking the Cray compiler wrappers
-                # cray-libsci is irrelevant to our build, so disable it
-                for var in ['PE_PKGCONFIG_PRODUCTS', 'PE_PKGCONFIG_LIBS']:
-                    env[var] = ":".join(
-                        filter(lambda x: "libsci" not in x.lower(),
-                               env[var].split(":")))
-                # Undo spack compiler wrappers:
-                # the C/C++ compilers must work post-install
-                # hack above no longer works after the fix to UPC++ issue #287
-                real_cc = join_path(env['CRAYPE_DIR'], 'bin', 'cc')
-                real_cxx = join_path(env['CRAYPE_DIR'], 'bin', 'CC')
-                # workaround a bug in the UPC++ installer: (issue #346)
-                env['GASNET_CONFIGURE_ARGS'] += \
-                    " --with-cc=" + real_cc + " --with-cxx=" + real_cxx
-                if '+mpi' in self.spec:
-                    env['GASNET_CONFIGURE_ARGS'] += " --with-mpicc=" + real_cc
-            else:
-                real_cc = self.compiler.cc
-                real_cxx = self.compiler.cxx
-                if '+mpi' in self.spec:
-                    real_cxx = spec['mpi'].mpicxx
 
-            env['CC'] = real_cc
+        if is_CrayXC():
-            env['CXX'] = real_cxx
+            # Spack loads the cray-libsci module incorrectly on ALCF theta,
+            # breaking the Cray compiler wrappers
+            # cray-libsci is irrelevant to our build, so disable it
+            for var in ['PE_PKGCONFIG_PRODUCTS', 'PE_PKGCONFIG_LIBS']:
+                env[var] = ":".join(
+                    filter(lambda x: "libsci" not in x.lower(),
+                           env[var].split(":")))
+            # Undo spack compiler wrappers:
+            # the C/C++ compilers must work post-install
+            real_cc = join_path(env['CRAYPE_DIR'], 'bin', 'cc')
+            real_cxx = join_path(env['CRAYPE_DIR'], 'bin', 'CC')
+            # workaround a bug in the UPC++ installer: (issue #346)
+            if (env.get('GASNET_CONFIGURE_ARGS') is None):
+                env['GASNET_CONFIGURE_ARGS'] = ''
+            env['GASNET_CONFIGURE_ARGS'] += \
+                " --with-cc=" + real_cc + " --with-cxx=" + real_cxx
+            if '+mpi' in spec:
+                env['GASNET_CONFIGURE_ARGS'] += " --with-mpicc=" + real_cc
+        else:
+            real_cc = self.compiler.cc
+            real_cxx = self.compiler.cxx
+            if '+mpi' in spec:
+                real_cxx = spec['mpi'].mpicxx
 
-            options = ["--prefix=%s" % prefix]
+        options.append('--with-cc=' + real_cc)
+        options.append('--with-cxx=' + real_cxx)
 
-            if '+gasnet' in self.spec:
+        if '+gasnet' in spec:
-                options.append('--with-gasnet=' + spec['gasnet'].prefix.src)
+            options.append('--with-gasnet=' + spec['gasnet'].prefix.src)
 
-            configure(*options)
+        options.append('--with-python=' + spec['python'].command.path)
 
-            make()
+        if '+mpi' in spec:
+            options.append('--enable-mpi')
+            options.append('--enable-mpi-compat')
+        else:
+            options.append('--without-mpicc')
 
-            make('install')
+        if '+cuda' in spec:
+            options.append('--with-cuda')
+            options.append('--with-nvcc=' + spec['cuda'].prefix.bin.nvcc)
+
+        configure(*options)
+
+        make()
+
+        make('install')
 
         install_tree('example', prefix.example)
 
     @run_after('install')
     @on_package_attributes(run_tests=True)
     def test_install(self):
-        if self.spec.version <= Version('2019.9.0'):
+        # enable testing of unofficial conduits (mpi)
-            spack.main.send_warning_to_tty(
+        test_networks = 'NETWORKS=$(CONDUITS)'
-                "run_tests not supported in UPC++ version " +
+        # build hello world against installed tree in all configurations
-                self.spec.version.string + " -- SKIPPED")
+        make('test_install', test_networks)
-        else:
+        make('tests-clean')  # cleanup
-            # enable testing of unofficial conduits (mpi)
+        # build all tests for all networks in debug mode
-            test_networks = 'NETWORKS=$(CONDUITS)'
+        make('tests', test_networks)
-            # build hello world against installed tree in all configurations
+        if 'cross=none' in self.spec:
-            make('test_install', test_networks)
+            make('run-tests', 'NETWORKS=smp')  # runs tests for smp backend
-            make('tests-clean')  # cleanup
+        make('tests-clean')  # cleanup
-            # build all tests for all networks in debug mode
-            make('tests', test_networks)
-            if 'cross=none' in self.spec:
-                make('run-tests', 'NETWORKS=smp')  # runs tests for smp backend
-            make('tests-clean')  # cleanup
 
     def test(self):
-        if self.spec.version <= Version('2019.9.0'):
+        # run post-install smoke test:
-            spack.main.send_warning_to_tty(
+        test_install = join_path(self.prefix.bin, 'test-upcxx-install.sh')
-                "post-install tests not supported in UPC++ version " +
+        self.run_test(test_install, expected=['SUCCESS'], status=0,
-                self.spec.version.string + " -- SKIPPED")
+                      installed=True,
-        else:   # run post-install smoke test:
+                      purpose='Checking UPC++ compile+link ' +
-            test_install = join_path(self.prefix.bin, 'test-upcxx-install.sh')
+                              'for all installed backends')
-            self.run_test(test_install, expected=['SUCCESS'], status=0,
-                          installed=True,
-                          purpose='Checking UPC++ compile+link ' +
-                                  'for all installed backends')