def install(prefix, specs, args, env, *_, **kwargs):
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
new_specs = []
channel_urls = set()
for elem in specs:
if "::" in elem:
channel_urls.add(elem.split("::")[0])
new_specs.append(elem.split("::")[-1])
else:
new_specs.append(elem)
specs = new_specs
channel_urls = list(channel_urls)
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
channel_urls = channel_urls + [chan for chan in env.channels if chan != 'nodefaults']
if 'nodefaults' not in env.channels:
channel_urls.extend(context.channels)
_channel_priority_map = prioritize_channels(channel_urls)
channels = IndexedSet(Channel(url) for url in _channel_priority_map)
subdirs = IndexedSet(basename(url) for url in _channel_priority_map)
solver = Solver(prefix, channels, subdirs, specs_to_add=specs)
unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
pfe = unlink_link_transaction.get_pfe()
pfe.execute()
unlink_link_transaction.execute()
def install(prefix, specs, args, env, *_, **kwargs):
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
new_specs = []
channel_urls = set()
for elem in specs:
if "::" in elem:
channel_urls.add(elem.split("::")[0])
new_specs.append(elem.split("::")[-1])
else:
new_specs.append(elem)
specs = new_specs
channel_urls = list(channel_urls)
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
channel_urls = channel_urls + [chan for chan in env.channels if chan != 'nodefaults']
if 'nodefaults' not in env.channels:
channel_urls.extend(context.channels)
_channel_priority_map = prioritize_channels(channel_urls)
channels = IndexedSet(Channel(url) for url in _channel_priority_map)
subdirs = IndexedSet(basename(url) for url in _channel_priority_map)
solver = Solver(prefix, channels, subdirs, specs_to_add=specs)
unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
pfe = unlink_link_transaction._get_pfe()
pfe.execute()
unlink_link_transaction.execute()
def install(prefix, specs, args, env, *_, **kwargs):
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
channel_urls = [chan for chan in env.channels if chan != 'nodefaults']
if 'nodefaults' not in env.channels:
channel_urls.extend(context.channels)
_channel_priority_map = prioritize_channels(channel_urls)
channels = IndexedSet(Channel(url) for url in _channel_priority_map)
subdirs = IndexedSet(basename(url) for url in _channel_priority_map)
solver = Solver(prefix, channels, subdirs, specs_to_add=specs)
try:
unlink_link_transaction = solver.solve_for_transaction(
prune=getattr(args, 'prune', False),
update_modifier=UpdateModifier.FREEZE_INSTALLED)
except (UnsatisfiableError, SystemExit):
unlink_link_transaction = solver.solve_for_transaction(
prune=getattr(args, 'prune', False), update_modifier=NULL)
if unlink_link_transaction.nothing_to_do:
return None
unlink_link_transaction.download_and_extract()
unlink_link_transaction.execute()
return unlink_link_transaction._make_legacy_action_groups()[0]
def _create_env_conda_44(prefix, full_list_of_packages):
assert CONDA_VERSION_MAJOR_MINOR >= (4, 4)
from conda.models.match_spec import MatchSpec
from conda.core.solve import Solver
matched_list_of_packages = (MatchSpec(d) for d in full_list_of_packages)
m = Solver(prefix, (), specs_to_add=matched_list_of_packages)
txn = m.solve_for_transaction()
txn.execute()
def solve_for_packages(packages: List[str]) -> Tuple[IndexedSet, IndexedSet]:
"""
given a list of conda packages solve the environment for dependencies
:param packages: list of conda packages to be installed
:return: tuple of packages that will be removed and will be added to the current conda environment
"""
specs_to_add = [MatchSpec(p) for p in packages]
info = json.loads(conda.run_command(conda.Commands.INFO, '--json')[0])
prefix = info['conda_prefix'] if info['active_prefix'] == 'null' else info[
'active_prefix']
solver = Solver(prefix, info['channels'], specs_to_add=specs_to_add)
return solver.solve_for_diff()
def _solve(prefix, specs, args, env, *_, **kwargs):
# TODO: support all various ways this happens
# Including 'nodefaults' in the channels list disables the defaults
channel_urls = [chan for chan in env.channels if chan != 'nodefaults']
if 'nodefaults' not in env.channels:
channel_urls.extend(context.channels)
_channel_priority_map = prioritize_channels(channel_urls)
channels = IndexedSet(Channel(url) for url in _channel_priority_map)
subdirs = IndexedSet(basename(url) for url in _channel_priority_map)
solver = Solver(prefix, channels, subdirs, specs_to_add=specs)
return solver
def get_conda_solver(filepath=None,
prefix=None,
channels=None,
subdirs=None,
specs_to_add=None,
existing_solver=None):
'''
Initialize or update a conda environment solver from a file or spec
Parameters
----------
filepath : str, optional
Path to a yaml file to parse and solve. If not provided, ``prefix`` is
required and any transactions must be defined in ``channels``,
``subdirs``, and ``specs_to_add``.
prefix : str, optional
Name or path of the environment to be created/modified. Ignored if
``filepath`` is provided; required if omitted.
channels: list, optional
Conda channels. Ignored if ``filepath`` is provided.
subdirs: tuple, optional
Architecture subdirs. Ignored if ``filepath`` is provided.
specs_to_add: list, optional
List of strings of package specs to add to the environment. Ignored if
``filepath`` is provided.
existing_solver : conda.core.solve.Solver, optional
Optionally, upgrade a provided spec with the new dependencies provided
in an environment file. Default is to create a new environment.
Returns
-------
solver: conda.core.solve.Solver
Examples
--------
Initializing with an environment file:
.. code-block:: python
>>> get_conda_solver('notebook/environment.yml')
<conda.core.solve.Solver at ...>
Initializing with a spec
.. code-block:: python
>>> s = get_conda_solver(
... prefix='vis',
... channels=['pyviz', 'conda-forge'],
... specs_to_add=['python=3.7', 'holoviews', 'bokeh>=1.2'])
...
Testing for unsatisfiable environments:
.. code-block:: python
>>> s = get_conda_solver(
... prefix='base',
... specs_to_add=['xarray>=0.13.0', 'python<3.0'])
...
>>> s.solve_final_state() # doctest: +ELLIPSIS
...
Traceback (most recent calls last):
...
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
- xarray[version='>=0.13.0'] -> python[version='>=3.5.3']
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you've asked for.
Your current python version is (python[version='<3.0']).
The following specifications were found to be incompatible with each other:
- python[version='<3.0']
TODO
----
* figure out how to solve for/align pip dependencies. currently these are
ignored
'''
if filepath is not None:
with open(filepath, 'r') as f:
spec = yaml.safe_load(f)
else:
spec = {
'prefix': prefix,
'channels': channels if channels is not None else [],
'subdirs': subdirs if subdirs is not None else [],
'dependencies': specs_to_add if specs_to_add is not None else []
}
# exclude pip dependencies - these trip up the Solver
conda_packages = [
d for d in spec.get('dependencies', []) if not isinstance(d, dict)
]
if existing_solver is None:
solver = Solver(spec.get('name', 'base'),
channels=spec.get('channels', []),
specs_to_add=conda_packages)
else:
solver = Solver(
prefix=existing_solver.prefix,
channels=spec.get('channels', existing_solver.channels),
subdirs=spec.get('subdirs', existing_solver.subdirs),
specs_to_add=(list(existing_solver.specs_to_add) + conda_packages),
specs_to_remove=spec.get('specs_to_remove',
existing_solver.specs_to_remove))
return solver
def pkg_env(environment_file: Path, coex_path: Path, cache_dir: Path) -> None:
"""Resolve, fetch, and repackage conda env into coex /pkgs directory.
Resolve conda environment file to a specific package list via conda solver,
then fetch and unpack target packages. Repack into .coex package data in
cache_dir or reuse if pre-packed, and assemble into /pkgs under coex_path.
Args:
environment_file: Standard conda env file, can not contain pip deps.
coex_path: Output coex build path.
cache_dir: Coex build cache directory.
"""
# Resolve environment file to dependencies
# Logic culled from conda-env
spec = YamlFileSpec(filename=str(environment_file))
env = spec.environment
logging.info(env.dependencies)
assert set(env.dependencies) == {
"conda"
}, f"coex environments do not support pip dependencies: {env}"
channel_urls = [chan for chan in env.channels if chan != "nodefaults"]
if "nodefaults" not in env.channels:
channel_urls.extend(context.channels)
_channel_priority_map = prioritize_channels(channel_urls)
# Setup an dummpy environment resolution for install into /dev/null
# Execute fetch-and-extract operations for required conda packages
prefix = "/dev/null"
channels = IndexedSet(Channel(url) for url in _channel_priority_map)
subdirs = IndexedSet(
os.path.basename(url) for url in _channel_priority_map)
solver = Solver(prefix,
channels,
subdirs,
specs_to_add=env.dependencies["conda"])
transaction: UnlinkLinkTransaction = solver.solve_for_transaction()
logging.info(transaction)
transaction.download_and_extract()
# Resolve all the, now extracted, target packages in the filesystem
fetcher: ProgressiveFetchExtract = transaction._pfe
target_records: Set[PackageRecord] = set(fetcher.link_precs)
logging.debug("target_records=%s", target_records)
extracted: Set[PackageCacheRecord] = {
next(
(pcrec
for pcrec in chain(*(PackageCacheData(pkgs_dir).query(precord)
for pkgs_dir in context.pkgs_dirs))
if pcrec.is_extracted),
None,
)
for precord in target_records
}
logging.debug("extracted=%s", extracted)
# Repackage into a single-file .zst in the cache, then copy into the output
# package.
output_path = coex_path / "pkgs"
for e in extracted:
extracted_dir = Path(e.extracted_package_dir)
pkgname = extracted_dir.name + ".tar.zst"
cache_dir.mkdir(parents=True, exist_ok=True)
if not (cache_dir / pkgname).exists():
pkg_cmd = (
# tar filtered through zstd
# Seeing errors on macos 10.13 image when using --use-compress-program
# with arguments, consider (a) installing conda-forge tar or (b) using
# a wrapper script if zstd arguments are needed
[
"tar",
"--use-compress-program",
"zstd -T0" if platform.system() != "Darwin" else "zstd",
]
# write to archive file
+ ["-f", str(cache_dir / pkgname)]
# chdir to extracted package directory
+ ["-C", str(extracted_dir)]
# and add all package dirs
+ (["-c"] + [f.name for f in extracted_dir.iterdir()]))
logging.info("packaging: %s", pkg_cmd)
subprocess.check_call(pkg_cmd)
output_path.mkdir(parents=True, exist_ok=True)
shutil.copyfile(cache_dir / pkgname, output_path / pkgname)
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 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