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Merge pull request #670 from epfl-scitas/uninstall_improved

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enhancement : recursive uninstallation of dependent packages
This commit is contained in:
Todd Gamblin 2016-04-04 10:04:14 -07:00
commit a6c1cfe037
7 changed files with 290 additions and 143 deletions
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42
lib/spack/docs/basic_usage.rst
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@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
``spack uninstall`` ``spack uninstall``
~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~
To uninstall a package, type ``spack uninstall <package>``. This will To uninstall a package, type ``spack uninstall <package>``. This will ask the user for
completely remove the directory in which the package was installed. confirmation, and in case will completely remove the directory in which the package was installed.
.. code-block:: sh .. code-block:: sh
spack uninstall mpich spack uninstall mpich
If there are still installed packages that depend on the package to be If there are still installed packages that depend on the package to be
uninstalled, spack will refuse to uninstall it. You can override this uninstalled, spack will refuse to uninstall it.
behavior with ``spack uninstall -f <package>``, but you risk breaking
other installed packages. In general, it is safer to remove dependent
packages *before* removing their dependencies.
A line like ``spack uninstall mpich`` may be ambiguous, if multiple To uninstall a package and every package that depends on it, you may give the
``mpich`` configurations are installed. For example, if both `--dependents` option.
.. code-block:: sh
spack uninstall --dependents mpich
will display a list of all the packages that depends on `mpich` and, upon confirmation,
will uninstall them in the right order.
A line like
.. code-block:: sh
spack uninstall mpich
may be ambiguous, if multiple ``mpich`` configurations are installed. For example, if both
``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer ``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
to either one. Because it cannot determine which one to uninstall, to either one. Because it cannot determine which one to uninstall,
Spack will ask you to provide a version number to remove the Spack will ask you either to provide a version number to remove the
ambiguity. As an example, ``spack uninstall mpich@3.1`` is ambiguity or use the ``--all`` option to uninstall all of the matching packages.
unambiguous in this scenario.
You may force uninstall a package with the `--force` option
.. code-block:: sh
spack uninstall --force mpich
but you risk breaking other installed packages. In general, it is safer to remove dependent
packages *before* removing their dependencies or use the `--dependents` option.
Seeing installed packages Seeing installed packages

187
lib/spack/spack/cmd/uninstall.py
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@ -23,19 +23,33 @@
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
from __future__ import print_function from __future__ import print_function
import sys
import argparse import argparse
import llnl.util.tty as tty import llnl.util.tty as tty
from llnl.util.tty.colify import colify
import spack import spack
import spack.cmd import spack.cmd
import spack.repository import spack.repository
from spack.cmd.find import display_specs from spack.cmd.find import display_specs
from spack.package import PackageStillNeededError
description="Remove an installed package" description = "Remove an installed package"
error_message = """You can either:
a) Use a more specific spec, or
b) use spack uninstall -a to uninstall ALL matching specs.
"""
def ask_for_confirmation(message):
while True:
tty.msg(message + '[y/n]')
choice = raw_input().lower()
if choice == 'y':
break
elif choice == 'n':
raise SystemExit('Operation aborted')
tty.warn('Please reply either "y" or "n"')
def setup_parser(subparser): def setup_parser(subparser):
subparser.add_argument( subparser.add_argument(
@ -47,7 +61,98 @@ def setup_parser(subparser):
"supplied spec. i.e., if you say uninstall libelf, ALL versions of " + "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
"libelf are uninstalled. This is both useful and dangerous, like rm -r.") "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
subparser.add_argument( subparser.add_argument(
'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall") '-d', '--dependents', action='store_true', dest='dependents',
help='Also uninstall any packages that depend on the ones given via command line.'
)
subparser.add_argument(
'-y', '--yes-to-all', action='store_true', dest='yes_to_all',
help='Assume "yes" is the answer to every confirmation asked to the user.'
)
subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
def concretize_specs(specs, allow_multiple_matches=False, force=False):
"""
Returns a list of specs matching the non necessarily concretized specs given from cli
Args:
specs: list of specs to be matched against installed packages
allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
Return:
list of specs
"""
specs_from_cli = [] # List of specs that match expressions given via command line
has_errors = False
for spec in specs:
matching = spack.installed_db.query(spec)
# For each spec provided, make sure it refers to only one package.
# Fail and ask user to be unambiguous if it doesn't
if not allow_multiple_matches and len(matching) > 1:
tty.error("%s matches multiple packages:" % spec)
print()
display_specs(matching, long=True)
print()
has_errors = True
# No installed package matches the query
if len(matching) == 0 and not force:
tty.error("%s does not match any installed packages." % spec)
has_errors = True
specs_from_cli.extend(matching)
if has_errors:
tty.die(error_message)
return specs_from_cli
def installed_dependents(specs):
"""
Returns a dictionary that maps a spec with a list of its installed dependents
Args:
specs: list of specs to be checked for dependents
Returns:
dictionary of installed dependents
"""
dependents = {}
for item in specs:
lst = [x for x in item.package.installed_dependents if x not in specs]
if lst:
lst = list(set(lst))
dependents[item] = lst
return dependents
def do_uninstall(specs, force):
"""
Uninstalls all the specs in a list.
Args:
specs: list of specs to be uninstalled
force: force uninstallation (boolean)
"""
packages = []
for item in specs:
try:
# should work if package is known to spack
packages.append(item.package)
except spack.repository.UnknownPackageError as e:
# The package.py file has gone away -- but still
# want to uninstall.
spack.Package(item).do_uninstall(force=True)
# Sort packages to be uninstalled by the number of installed dependents
# This ensures we do things in the right order
def num_installed_deps(pkg):
return len(pkg.installed_dependents)
packages.sort(key=num_installed_deps)
for item in packages:
item.do_uninstall(force=force)
def uninstall(parser, args): def uninstall(parser, args):
@ -56,50 +161,34 @@ def uninstall(parser, args):
with spack.installed_db.write_transaction(): with spack.installed_db.write_transaction():
specs = spack.cmd.parse_specs(args.packages) specs = spack.cmd.parse_specs(args.packages)
# Gets the list of installed specs that match the ones give via cli
uninstall_list = concretize_specs(specs, args.all, args.force) # takes care of '-a' is given in the cli
dependent_list = installed_dependents(uninstall_list) # takes care of '-d'
# For each spec provided, make sure it refers to only one package. # Process dependent_list and update uninstall_list
# Fail and ask user to be unambiguous if it doesn't has_error = False
pkgs = [] if dependent_list and not args.dependents and not args.force:
for spec in specs: for spec, lst in dependent_list.items():
matching_specs = spack.installed_db.query(spec) tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
if not args.all and len(matching_specs) > 1:
tty.error("%s matches multiple packages:" % spec)
print()
display_specs(matching_specs, long=True)
print()
print("You can either:")
print(" a) Use a more specific spec, or")
print(" b) use spack uninstall -a to uninstall ALL matching specs.")
sys.exit(1)
if len(matching_specs) == 0:
if args.force: continue
tty.die("%s does not match any installed packages." % spec)
for s in matching_specs:
try:
# should work if package is known to spack
pkgs.append(s.package)
except spack.repository.UnknownPackageError as e:
# The package.py file has gone away -- but still
# want to uninstall.
spack.Package(s).do_uninstall(force=True)
# Sort packages to be uninstalled by the number of installed dependents
# This ensures we do things in the right order
def num_installed_deps(pkg):
return len(pkg.installed_dependents)
pkgs.sort(key=num_installed_deps)
# Uninstall packages in order now.
for pkg in pkgs:
try:
pkg.do_uninstall(force=args.force)
except PackageStillNeededError as e:
tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
print('') print('')
print("The following packages depend on it:") print("The following packages depend on it:")
display_specs(e.dependents, long=True) display_specs(lst, long=True)
print('') print('')
print("You can use spack uninstall -f to force this action.") has_error = True
sys.exit(1) elif args.dependents:
for key, lst in dependent_list.items():
uninstall_list.extend(lst)
uninstall_list = list(set(uninstall_list))
if has_error:
tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
if not args.yes_to_all:
tty.msg("The following packages will be uninstalled : ")
print('')
display_specs(uninstall_list, long=True)
print('')
ask_for_confirmation('Do you want to proceed ? ')
# Uninstall everything on the list
do_uninstall(uninstall_list, args.force)

3
lib/spack/spack/test/__init__.py
View File

@ -67,7 +67,8 @@
'namespace_trie', 'namespace_trie',
'yaml', 'yaml',
'sbang', 'sbang',
'environment'] 'environment',
'cmd.uninstall']
def list_tests(): def list_tests():

0
lib/spack/spack/test/cmd/__init__.py Normal file
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37
lib/spack/spack/test/cmd/uninstall.py Normal file
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@ -0,0 +1,37 @@
import spack.test.mock_database
from spack.cmd.uninstall import uninstall
class MockArgs(object):
def __init__(self, packages, all=False, force=False, dependents=False):
self.packages = packages
self.all = all
self.force = force
self.dependents = dependents
self.yes_to_all = True
class TestUninstall(spack.test.mock_database.MockDatabase):
def test_uninstall(self):
parser = None
# Multiple matches
args = MockArgs(['mpileaks'])
self.assertRaises(SystemExit, uninstall, parser, args)
# Installed dependents
args = MockArgs(['libelf'])
self.assertRaises(SystemExit, uninstall, parser, args)
# Recursive uninstall
args = MockArgs(['callpath'], all=True, dependents=True)
uninstall(parser, args)
all_specs = spack.install_layout.all_specs()
self.assertEqual(len(all_specs), 7)
# query specs with multiple configurations
mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
self.assertEqual(len(mpileaks_specs), 0)
self.assertEqual(len(callpath_specs), 0)
self.assertEqual(len(mpi_specs), 3)

82
lib/spack/spack/test/database.py
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@ -28,16 +28,12 @@
""" """
import os.path import os.path
import multiprocessing import multiprocessing
import shutil
import tempfile
import spack import spack
from llnl.util.filesystem import join_path from llnl.util.filesystem import join_path
from llnl.util.lock import * from llnl.util.lock import *
from llnl.util.tty.colify import colify from llnl.util.tty.colify import colify
from spack.database import Database from spack.test.mock_database import MockDatabase
from spack.directory_layout import YamlDirectoryLayout
from spack.test.mock_packages_test import *
def _print_ref_counts(): def _print_ref_counts():
@ -75,80 +71,7 @@ def add_rec(spec):
colify(recs, cols=3) colify(recs, cols=3)
class DatabaseTest(MockPackagesTest): class DatabaseTest(MockDatabase):
def _mock_install(self, spec):
s = Spec(spec)
s.concretize()
pkg = spack.repo.get(s)
pkg.do_install(fake=True)
def _mock_remove(self, spec):
specs = spack.installed_db.query(spec)
assert(len(specs) == 1)
spec = specs[0]
spec.package.do_uninstall(spec)
def setUp(self):
super(DatabaseTest, self).setUp()
#
# TODO: make the mockup below easier.
#
# Make a fake install directory
self.install_path = tempfile.mkdtemp()
self.spack_install_path = spack.install_path
spack.install_path = self.install_path
self.install_layout = YamlDirectoryLayout(self.install_path)
self.spack_install_layout = spack.install_layout
spack.install_layout = self.install_layout
# Make fake database and fake install directory.
self.installed_db = Database(self.install_path)
self.spack_installed_db = spack.installed_db
spack.installed_db = self.installed_db
# make a mock database with some packages installed note that
# the ref count for dyninst here will be 3, as it's recycled
# across each install.
#
# Here is what the mock DB looks like:
#
# o mpileaks o mpileaks' o mpileaks''
# |\ |\ |\
# | o callpath | o callpath' | o callpath''
# |/| |/| |/|
# o | mpich o | mpich2 o | zmpi
# | | o | fake
# | | |
# | |______________/
# | .____________/
# |/
# o dyninst
# |\
# | o libdwarf
# |/
# o libelf
#
# Transaction used to avoid repeated writes.
with spack.installed_db.write_transaction():
self._mock_install('mpileaks ^mpich')
self._mock_install('mpileaks ^mpich2')
self._mock_install('mpileaks ^zmpi')
def tearDown(self):
super(DatabaseTest, self).tearDown()
shutil.rmtree(self.install_path)
spack.install_path = self.spack_install_path
spack.install_layout = self.spack_install_layout
spack.installed_db = self.spack_installed_db
def test_005_db_exists(self): def test_005_db_exists(self):
"""Make sure db cache file exists after creating.""" """Make sure db cache file exists after creating."""
index_file = join_path(self.install_path, '.spack-db', 'index.yaml') index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@ -157,7 +80,6 @@ def test_005_db_exists(self):
self.assertTrue(os.path.exists(index_file)) self.assertTrue(os.path.exists(index_file))
self.assertTrue(os.path.exists(lock_file)) self.assertTrue(os.path.exists(lock_file))
def test_010_all_install_sanity(self): def test_010_all_install_sanity(self):
"""Ensure that the install layout reflects what we think it does.""" """Ensure that the install layout reflects what we think it does."""
all_specs = spack.install_layout.all_specs() all_specs = spack.install_layout.all_specs()

78
lib/spack/spack/test/mock_database.py Normal file
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@ -0,0 +1,78 @@
import shutil
import tempfile
import spack
from spack.spec import Spec
from spack.database import Database
from spack.directory_layout import YamlDirectoryLayout
from spack.test.mock_packages_test import MockPackagesTest
class MockDatabase(MockPackagesTest):
def _mock_install(self, spec):
s = Spec(spec)
s.concretize()
pkg = spack.repo.get(s)
pkg.do_install(fake=True)
def _mock_remove(self, spec):
specs = spack.installed_db.query(spec)
assert(len(specs) == 1)
spec = specs[0]
spec.package.do_uninstall(spec)
def setUp(self):
super(MockDatabase, self).setUp()
#
# TODO: make the mockup below easier.
#
# Make a fake install directory
self.install_path = tempfile.mkdtemp()
self.spack_install_path = spack.install_path
spack.install_path = self.install_path
self.install_layout = YamlDirectoryLayout(self.install_path)
self.spack_install_layout = spack.install_layout
spack.install_layout = self.install_layout
# Make fake database and fake install directory.
self.installed_db = Database(self.install_path)
self.spack_installed_db = spack.installed_db
spack.installed_db = self.installed_db
# make a mock database with some packages installed note that
# the ref count for dyninst here will be 3, as it's recycled
# across each install.
#
# Here is what the mock DB looks like:
#
# o mpileaks o mpileaks' o mpileaks''
# |\ |\ |\
# | o callpath | o callpath' | o callpath''
# |/| |/| |/|
# o | mpich o | mpich2 o | zmpi
# | | o | fake
# | | |
# | |______________/
# | .____________/
# |/
# o dyninst
# |\
# | o libdwarf
# |/
# o libelf
#
# Transaction used to avoid repeated writes.
with spack.installed_db.write_transaction():
self._mock_install('mpileaks ^mpich')
self._mock_install('mpileaks ^mpich2')
self._mock_install('mpileaks ^zmpi')
def tearDown(self):
super(MockDatabase, self).tearDown()
shutil.rmtree(self.install_path)
spack.install_path = self.spack_install_path
spack.install_layout = self.spack_install_layout
spack.installed_db = self.spack_installed_db