def install(args, parser, command='install'):
"""
mamba install, mamba update, and mamba create
"""
context.validate_configuration()
check_non_admin()
newenv = bool(command == 'create')
isupdate = bool(command == 'update')
isinstall = bool(command == 'install')
if newenv:
ensure_name_or_prefix(args, command)
prefix = context.target_prefix
if newenv:
check_prefix(prefix, json=context.json)
if context.force_32bit and prefix == context.root_prefix:
raise CondaValueError("cannot use CONDA_FORCE_32BIT=1 in base env")
if isupdate and not (args.file or args.packages
or context.update_modifier == UpdateModifier.UPDATE_ALL):
raise CondaValueError("""no package names supplied
# If you want to update to a newer version of Anaconda, type:
#
# $ conda update --prefix %s anaconda
""" % prefix)
if not newenv:
if isdir(prefix):
delete_trash(prefix)
if not isfile(join(prefix, 'conda-meta', 'history')):
if paths_equal(prefix, context.conda_prefix):
raise NoBaseEnvironmentError()
else:
if not path_is_clean(prefix):
raise DirectoryNotACondaEnvironmentError(prefix)
else:
# fall-through expected under normal operation
pass
else:
if args.mkdir:
try:
mkdir_p(prefix)
except EnvironmentError as e:
raise CondaOSError("Could not create directory: %s" % prefix, caused_by=e)
else:
raise EnvironmentLocationNotFound(prefix)
# context.__init__(argparse_args=args)
prepend = not args.override_channels
prefix = context.target_prefix
index_args = {
'use_cache': args.use_index_cache,
'channel_urls': context.channels,
'unknown': args.unknown,
'prepend': not args.override_channels,
'use_local': args.use_local
}
args_packages = [s.strip('"\'') for s in args.packages]
if newenv and not args.no_default_packages:
# Override defaults if they are specified at the command line
# TODO: rework in 4.4 branch using MatchSpec
args_packages_names = [pkg.replace(' ', '=').split('=', 1)[0] for pkg in args_packages]
for default_pkg in context.create_default_packages:
default_pkg_name = default_pkg.replace(' ', '=').split('=', 1)[0]
if default_pkg_name not in args_packages_names:
args_packages.append(default_pkg)
num_cp = sum(s.endswith('.tar.bz2') for s in args_packages)
if num_cp:
if num_cp == len(args_packages):
explicit(args_packages, prefix, verbose=not context.quiet)
return
else:
raise CondaValueError("cannot mix specifications with conda package"
" filenames")
index = get_index(channel_urls=index_args['channel_urls'],
prepend=index_args['prepend'], platform=None,
use_local=index_args['use_local'], use_cache=index_args['use_cache'],
unknown=index_args['unknown'], prefix=prefix)
channel_json = []
for x in index:
# add priority here
if x.channel.name in index_args['channel_urls']:
priority = len(index_args['channel_urls']) - index_args['channel_urls'].index(x.channel.name)
else:
priority = 0
channel_json.append((str(x.channel), x.cache_path_json, priority))
installed_pkg_recs, output = get_installed_packages(prefix, show_channel_urls=True)
installed_json_f = tempfile.NamedTemporaryFile('w', delete=False)
installed_json_f.write(json_dump(output))
installed_json_f.flush()
specs = []
if args.file:
for fpath in args.file:
try:
specs.extend(specs_from_url(fpath, json=context.json))
except Unicode:
raise CondaError("Error reading file, file should be a text file containing"
" packages \nconda create --help for details")
if '@EXPLICIT' in specs:
explicit(specs, prefix, verbose=not context.quiet, index_args=index_args)
return
specs.extend(specs_from_args(args_packages, json=context.json))
if isinstall and args.revision:
get_revision(args.revision, json=context.json)
elif isinstall and not (args.file or args_packages):
raise CondaValueError("too few arguments, "
"must supply command line package specs or --file")
# for 'conda update', make sure the requested specs actually exist in the prefix
# and that they are name-only specs
if isupdate and context.update_modifier == UpdateModifier.UPDATE_ALL:
print("Currently, mamba can only update explicit packages! (e.g. mamba update numpy python ...)")
exit()
if isupdate and context.update_modifier != UpdateModifier.UPDATE_ALL:
prefix_data = PrefixData(prefix)
for spec in specs:
spec = MatchSpec(spec)
if not spec.is_name_only_spec:
raise CondaError("Invalid spec for 'conda update': %s\n"
"Use 'conda install' instead." % spec)
if not prefix_data.get(spec.name, None):
raise PackageNotInstalledError(prefix, spec.name)
if newenv and args.clone:
if args.packages:
raise TooManyArgumentsError(0, len(args.packages), list(args.packages),
'did not expect any arguments for --clone')
clone(args.clone, prefix, json=context.json, quiet=context.quiet, index_args=index_args)
touch_nonadmin(prefix)
print_activate(args.name if args.name else prefix)
return
specs = [MatchSpec(s) for s in specs]
mamba_solve_specs = [s.conda_build_form() for s in specs]
print("\n\nLooking for: {}\n\n".format(mamba_solve_specs))
strict_priority = (context.channel_priority == ChannelPriority.STRICT)
if strict_priority:
raise Exception("Cannot use strict priority with mamba!")
to_link, to_unlink = api.solve(channel_json, installed_json_f.name, mamba_solve_specs, isupdate, strict_priority)
to_link_records, to_unlink_records = [], []
final_precs = IndexedSet(PrefixData(prefix).iter_records())
def get_channel(c):
for x in index:
if str(x.channel) == c:
return x
for c, pkg in to_unlink:
for i_rec in installed_pkg_recs:
if i_rec.fn == pkg:
final_precs.remove(i_rec)
to_unlink_records.append(i_rec)
break
else:
print("No package record found!")
for c, pkg, jsn_s in to_link:
sdir = get_channel(c)
rec = to_package_record_from_subjson(sdir, pkg, jsn_s)
final_precs.add(rec)
to_link_records.append(rec)
unlink_precs, link_precs = diff_for_unlink_link_precs(prefix,
final_precs=IndexedSet(PrefixGraph(final_precs).graph),
specs_to_add=specs,
force_reinstall=context.force_reinstall)
pref_setup = PrefixSetup(
target_prefix = prefix,
unlink_precs = unlink_precs,
link_precs = link_precs,
remove_specs = [],
update_specs = specs
)
conda_transaction = UnlinkLinkTransaction(pref_setup)
handle_txn(conda_transaction, prefix, args, newenv)
try:
installed_json_f.close()
os.unlink(installed_json_f.name)
except:
pass
def execute(args, parser):
from .common import (confirm_yn, ensure_override_channels_requires_channel,
ensure_use_local, specs_from_args, stdout_json)
from ..base.context import context
from ..common.compat import iteritems, iterkeys
from ..core.index import get_index
from ..exceptions import CondaEnvironmentError, CondaValueError
from ..gateways.disk.delete import delete_trash
from ..resolve import MatchSpec
from ..core.envs_manager import EnvsDirectory
from ..core.linked_data import linked_data
from ..gateways.disk.delete import rm_rf
from ..instructions import PREFIX
from ..plan import (add_unlink)
if not (args.all or args.package_names):
raise CondaValueError('no package names supplied,\n'
' try "conda remove -h" for more details')
prefix = context.target_prefix
if args.all and prefix == context.default_prefix:
msg = "cannot remove current environment. deactivate and run conda remove again"
raise CondaEnvironmentError(msg)
if args.all and not isdir(prefix):
# full environment removal was requested, but environment doesn't exist anyway
return 0
if not EnvsDirectory.is_conda_environment(prefix):
from ..exceptions import EnvironmentLocationNotFound
raise EnvironmentLocationNotFound(prefix)
ensure_use_local(args)
ensure_override_channels_requires_channel(args)
if not args.features and args.all:
index = linked_data(prefix)
index = {dist: info for dist, info in iteritems(index)}
else:
index = get_index(channel_urls=context.channels,
prepend=not args.override_channels,
use_local=args.use_local,
use_cache=args.use_index_cache,
prefix=prefix)
delete_trash()
if args.all:
if prefix == context.root_prefix:
raise CondaEnvironmentError(
'cannot remove root environment,\n'
' add -n NAME or -p PREFIX option')
print("\nRemove all packages in environment %s:\n" % prefix,
file=sys.stderr)
actions = defaultdict(list)
actions[PREFIX] = prefix
for dist in sorted(iterkeys(index)):
add_unlink(actions, dist)
actions['ACTION'] = 'REMOVE_ALL'
action_groups = (actions, index),
if not context.json:
confirm_yn()
rm_rf(prefix)
if context.json:
stdout_json({
'success': True,
'actions': tuple(x[0] for x in action_groups)
})
return
else:
if args.features:
specs = tuple(
MatchSpec(track_features=f) for f in set(args.package_names))
channel_urls = context.channels
subdirs = context.subdirs
else:
specs = specs_from_args(args.package_names)
channel_urls = ()
subdirs = ()
solver = Solver(prefix, channel_urls, subdirs, specs_to_remove=specs)
txn = solver.solve_for_transaction(force_remove=args.force)
pfe = txn.get_pfe()
handle_txn(pfe, txn, prefix, args, False, True)
def remove(args, parser):
if not (args.all or args.package_names):
raise CondaValueError('no package names supplied,\n'
' try "mamba remove -h" for more details')
prefix = context.target_prefix
check_non_admin()
if args.all and prefix == context.default_prefix:
raise CondaEnvironmentError("cannot remove current environment. \
deactivate and run mamba remove again")
if args.all and path_is_clean(prefix):
# full environment removal was requested, but environment doesn't exist anyway
return 0
if args.all:
if prefix == context.root_prefix:
raise CondaEnvironmentError(
'cannot remove root environment,\n'
' add -n NAME or -p PREFIX option')
print("\nRemove all packages in environment %s:\n" % prefix,
file=sys.stderr)
if 'package_names' in args:
stp = PrefixSetup(
target_prefix=prefix,
unlink_precs=tuple(PrefixData(prefix).iter_records()),
link_precs=(),
remove_specs=(),
update_specs=(),
)
txn = UnlinkLinkTransaction(stp)
handle_txn(txn, prefix, args, False, True)
rm_rf(prefix, clean_empty_parents=True)
unregister_env(prefix)
return
else:
if args.features:
specs = tuple(
MatchSpec(track_features=f) for f in set(args.package_names))
else:
specs = [s for s in specs_from_args(args.package_names)]
if not context.quiet:
print("Removing specs: {}".format(specs))
channel_urls = ()
subdirs = ()
installed_json_f = get_installed_jsonfile(prefix)
mamba_solve_specs = [s.conda_build_form() for s in specs]
solver_options.append((api.SOLVER_FLAG_ALLOW_UNINSTALL, 1))
to_link, to_unlink = api.solve([], installed_json_f.name,
mamba_solve_specs, solver_options,
api.SOLVER_ERASE, False, context.quiet)
conda_transaction = to_txn(specs, prefix, to_link, to_unlink)
handle_txn(conda_transaction, prefix, args, False, True)
def bypass_satsolver_on_install(
pkg_names, conda_channel="ggd-genomics", debug=False, prefix=None
):
"""Method to bypass the sat solver used by conda when a cached recipe is being installed
bypass_satsolver_on_install
============================
This method is used to run the conda install steps to install a ggd aws cahced reicpe. The
intsallation will skip the sat solver step, ignore packages that may be additionaly installed
or uninstalled, and performs other steps in order to install the data package without using
the sat solver.
The majority of the work is still done by conda through the use of the conda module. This method
should only be used when a cached recipe is being installed.
Parameters:
-----------
#1) pkg_name: The name of the ggd package to install. (Example: hg19-gaps)
1) pkg_names: A list of the names of the ggd packages to install. (Example: [hg19-gaps])
2) conda_channel: The ggd conda channel that package is being installed from. (Example: ggd-genomics)
"""
# -------------------------------------------------------------------------
# import statments
# -------------------------------------------------------------------------
from conda.base.context import context
from conda.cli import common
from conda.cli import install
from conda.core.solve import Solver
from conda.core.solve import SolverStateContainer
from conda.common.io import Spinner
from conda.core.link import PrefixSetup
from conda.core.link import UnlinkLinkTransaction
from argparse import Namespace
from conda._vendor.boltons.setutils import IndexedSet
from conda.models.prefix_graph import PrefixGraph
from conda.core.solve import diff_for_unlink_link_precs
from conda.common.compat import iteritems, itervalues, odict, text_type
from conda._vendor.toolz import concat, concatv
from conda.resolve import Resolve
from conda.models.match_spec import MatchSpec
from conda.base.constants import UpdateModifier
from conda.common.io import ProgressBar
from conda.gateways.logging import set_all_logger_level, set_conda_log_level
from conda.gateways.logging import VERBOSITY_LEVELS
from conda.gateways.logging import log
from logging import (
DEBUG,
ERROR,
Filter,
Formatter,
INFO,
StreamHandler,
WARN,
getLogger,
)
import sys
print(
"\n:ggd:utils:bypass: Installing %s from the %s conda channel\n"
% (", ".join(pkg_names), conda_channel)
)
# -------------------------------------------------------------------------
# Nested functions
# -------------------------------------------------------------------------
# def bypass_sat(package_name,ssc_object): ## Package_name will be used as a key
def bypass_sat(package_names, ssc_object): ## Package_name will be used as a key
"""Method used to extract information during sat solving, but to bypass the sat solving step
bypass_sat
==========
This method is used to extract and process information that would have been done during the sat
solvering step, (Solving Enviroment), bypass the sat solver, and return a filtered set of packages
to install.
Parameters:
-----------
#1) package_name: The name of the package to extract. (This is the package that will be installed)
1) package_names: A list of package names of the packages to extract. (This is the package that will be installed)
2) ssc_object: A processed conda SolverStateContainer object.
Returns:
+++++++
1) The updated ssc object based off the sat bypass and package filtering.
"""
## From Solver.run_sat
specs_map_set = set(itervalues(ssc_object.specs_map))
## Get the specs from ssc filtered by the package name
new_odict = odict(
[(p_name, ssc_object.specs_map[p_name]) for p_name in package_names]
)
final_environment_specs = IndexedSet(
concatv(
itervalues(new_odict),
ssc_object.track_features_specs,
ssc_object.pinned_specs,
)
)
## Run the resolve process and get info for desired package
ssc_object.solution_precs = ssc_object.r.solve(tuple(final_environment_specs))
wanted_indices = []
for i, info in enumerate(ssc_object.solution_precs):
for p_name in package_names:
if p_name in ssc_object.solution_precs[i].namekey:
wanted_indices.append(i)
filtered_ssc_solution_precs = [
ssc_object.solution_precs[x] for x in wanted_indices
]
ssc_object.solution_precs = filtered_ssc_solution_precs
## Add the final environment specs to ssc
ssc_object.final_environment_specs = final_environment_specs
return ssc_object
# -------------------------------------------------------------------------
# Run install
# -------------------------------------------------------------------------
## Set the context.always_yes to True to bypass user input
context.always_yes = True
target_prefix = context.target_prefix if prefix == None else prefix
# Setup solver object
# solve = Solver(target_prefix, (conda_channel,u'default'), context.subdirs, [pkg_name])
solve = Solver(
target_prefix, (conda_channel, u"default"), context.subdirs, pkg_names
)
## Create a solver state container
### Make sure to Freeze those packages already installed in the current env in order to bypass update checking.
ssc = SolverStateContainer(
prefix=target_prefix,
update_modifier=UpdateModifier.FREEZE_INSTALLED,
deps_modifier=context.deps_modifier,
prune=True,
ignore_pinned=context.ignore_pinned,
force_remove=context.force_remove,
should_retry_solve=False,
)
## Get channel metadata
with Spinner(
"Collecting package metadata",
not context.verbosity and not context.quiet,
context.json,
):
ssc = solve._collect_all_metadata(ssc)
## Set specs map to an empty map. (No need to check other specs)
add_spec = []
for p_name, spec in iteritems(ssc.specs_map):
for pkg_name in pkg_names:
if str(p_name) in pkg_name:
add_spec.append((pkg_name, MatchSpec(pkg_name)))
ssc.specs_map = odict(add_spec)
## Process the data in the solver state container
with Spinner(
"Processing data", not context.verbosity and not context.quiet, context.json
):
ssc = solve._add_specs(ssc)
ssc = bypass_sat(pkg_names, ssc)
ssc = solve._post_sat_handling(ssc)
## create an IndexedSet from ssc.solution_precs
ssc.solution_precs = IndexedSet(PrefixGraph(ssc.solution_precs).graph)
## Get linked and unlinked
unlink_precs, link_precs = diff_for_unlink_link_precs(
target_prefix, ssc.solution_precs, solve.specs_to_add
)
# set unlinked to empty indexed set so we do not unlink/remove any pacakges
unlink_precs = IndexedSet()
## Create a PrefixSetup
stp = PrefixSetup(
solve.prefix,
unlink_precs,
link_precs,
solve.specs_to_remove,
solve.specs_to_add,
solve.neutered_specs,
)
## Create an UnlinkLinkTransaction with stp
unlink_link_transaction = UnlinkLinkTransaction(stp)
# create Namespace
args = Namespace(
channel=None,
cmd="install",
deps_modifier=context.deps_modifier,
json=False,
packages=pkg_names,
)
## Set logger level
if debug:
WARN, INFO, DEBUG, TRACE = VERBOSITY_LEVELS
set_all_logger_level(DEBUG)
## Install package
install.handle_txn(unlink_link_transaction, solve.prefix, args, False)
## Retrun True if finished
return True