New upstream version 4.8.1+dfsg (bf12baa6) · Commits · Debian Med / conda

.gitignore

+3 −0

Original line number	Diff line number	Diff line
		@@ -36,3 +36,6 @@ miniconda*.exe
		docs/source/_build
		**/.vscode
		conda.tmp/
		*.iml
		*.ipr
		*.iws

CHANGELOG.md

+123 −3

Original line number	Diff line number	Diff line
		## 4.8.1 (2019-12-19)

		### Enhancements:

		* improve performance for conda run by avoiding Popen.communicate (#9381)
		* Put conda keyring in /usr/share/keyrings on Debian (#9424)
		* refactor common.logic to fix some bugs and prepare for better modularity (#9427)
		* Support nested configuration (#9449)
		* Support Object configuration parameters (#9465)
		* Use freeze_installed to speed up conda env update (#9511)
		* add networking args to conda env create (#9525)

		### Docs:

		* fix string concatenation running words together regarding CONDA_EXE (#9411)
		* Fix typo ("list" -> "info") (#9433)
		* typo in condarc key envs_dirs (#9478)
		* Clarify channel priority and package sorting (#9492)
		* improve description of DLL loading verification and activating environments (#9453)
		* Installing with specific build number (#9534)

		### Bug fixes:

		* Fix calling python api run_command with list and string arguments (#9331)
		* revert init bash completion (#9421)
		* set tmp to shortened path that excludes spaces (#9409)
		* avoid function redefinition upon resourcing conda.fish (#9444)
		* propagate pip error level when creating envs with conda env (#9460)
		* fix incorrect chown call (#9464)
		* Add subdir to PackageRecord dist_str (#9418)
		* Fix running conda activate in multiple processes on windows (#9477)
		* Don't check in pkgs for trash (#9472)
		* remove setuptools from run_constrained in recipe (#9485)
		* Fix `__conda_activate` function to correctly return exit code (#9532)
		* fix overly greedy capture done by subprocess for conda run (#9537)


		### Contributors:

		* @AntoinePrv
		* @brettcannon
		* @bwildenhain
		* @cjmartian
		* @felker
		* @forrestwaters
		* @gilescope
		* @isuruf
		* @jeremyjliu
		* @jjhelmus
		* @jhultman
		* @marcuscaisey
		* @mbargull
		* @mingwandroid
		* @msarahan
		* @okhoma
		* @osamoylenko
		* @rrigdon
		* @rulerofthehuns
		* @soapy1
		* @tartansandal


		## 4.8.0rc0 (2019-11-04)

		### Enhancements:

		* retry downloads if they fail, controlled by `remote_max_retries` and `remote_backoff_factor` configuration values (#9318)
		* redact authentication information in some URLs (#9341)
		* add osx version virtual package , `__osx` (#9349)
		* add glibc virtual package, `__glibc` (#9358)

		### Docs

		* removeed references to MD5s from docs (#9247)
		* Add docs on `CONDA_DLL_SEARCH_MODIFICATION_ENABLED` (#9286)
		* document threads, spec history and configuration (#9327)
		* more documentation on channels (#9335)
		* document the .condarc search order (#9369)
		* various minor documentation fixes (#9238, #9248, #9267, #9334, #9351, #9372, #9378, #9388, #9391, #9393)

		### Bug fixes

		* fix issues with xonsh activation on Windows (#8246)
		* remove unsupported --lock argument from conda clean (#8310)
		* do not add `sys_prefix_path` to failed activation or deactivation (#9282)
		* fix csh setenv command (#9284)
		* do not memorize `PackageRecord.combined_depends` (#9289)
		* use `CONDA_INTERNAL_OLDPATH` rather than `OLDPATH` in activation script (#9303)
		* fixes xonsh activation and tab completion (#9305)
		* fix what channels are queried when context.offline is True (#9385)


		### Contributors

		* @analog-cbarber
		* @andreasg123
		* @beckermr
		* @bryant1410
		* @colinbrislawn
		* @felker
		* @forrestwaters
		* @gabrielcnr
		* @isuruf
		* @jakirkham
		* @jeremyjliu
		* @jjhelmus
		* @jooh
		* @jpigla
		* @marcelotrevisani
		* @melund
		* @mfansler
		* @mingwandroid
		* @msarahan
		* @rrigdon
		* @scopatz
		* @soapy1
		* @WillyChen123
		* @xhochy


		## 4.7.12 (2019-09-12)

		### Enhancements:

circle.yml

+2 −2

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ main_test: &main_test
		if [[ $(git diff origin/master --name-only \| wc -l) == $(git diff origin/master --name-only \| grep docs \| wc -l) && $(git diff origin/master --name-only \| grep docs) ]]; then
		echo "Only docs changed detected, skipping tests"
		else
		echo "local_repodata_ttl: 1800" >> ~/.condarc
		echo "local_repodata_ttl: 1800" > ~/.condarc
		eval "$(sudo /opt/conda/bin/python -m conda init --dev bash)"
		conda info
		# remove the pkg cache. We can't hardlink from here anyway. Having it around causes log problems.
		@@ -74,7 +74,7 @@ conda_build_test: &conda_build_test
		# pre-populating the package cache helps avoid race conditions for testing in parallel
		command: \|
		eval "$(sudo /opt/conda/bin/python -m conda init --dev bash)"
		echo "safety_checks: disabled" >> ~/.condarc
		echo "safety_checks: disabled" > ~/.condarc
		echo "local_repodata_ttl: 1800" >> ~/.condarc
		conda create -n blarg -yq --download-only python=2.7
		conda create -n blarg -yq -c https://repo.anaconda.com/pkgs/free --download-only python=3.4

conda/activate.py

+121 −24

Original line number	Diff line number	Diff line
		@@ -10,10 +10,11 @@ from glob import glob
		from itertools import chain
		from logging import getLogger
		import os
		from os.path import abspath, basename, dirname, expanduser, expandvars, isdir, join
		from os.path import abspath, basename, dirname, expanduser, expandvars, isdir, join, exists
		import re
		import sys
		from textwrap import dedent
		import json

		# Since we have to have configuration context here, anything imported by
		# conda.base.context is fair game, but nothing more.
		@@ -23,6 +24,7 @@ from ._vendor.auxlib.compat import Utf8NamedTemporaryFile
		from .base.context import ROOT_ENV_NAME, context, locate_prefix_by_name
		from .common.compat import FILESYSTEM_ENCODING, PY2, iteritems, on_win, string_types, text_type
		from .common.path import paths_equal
		from .base.constants import PREFIX_STATE_FILE, PACKAGE_ENV_VARS_DIR, CONDA_ENV_VARS_UNSET_VAR

		log = getLogger(__name__)

		@@ -244,13 +246,24 @@ class _Activator(object):
		context.dev = True

		if command == 'activate':
		self.stack = context.auto_stack and context.shlvl <= context.auto_stack
		try:
		stack_idx = remainder_args.index('--stack')
		except ValueError:
		self.stack = False
		else:
		del remainder_args[stack_idx]
		stack_idx = -1
		try:
		no_stack_idx = remainder_args.index('--no-stack')
		except ValueError:
		no_stack_idx = -1
		if stack_idx >= 0 and no_stack_idx >= 0:
		from .exceptions import ArgumentError
		raise ArgumentError('cannot specify both --stack and --no-stack to ' + command)
		if stack_idx >= 0:
		self.stack = True
		del remainder_args[stack_idx]
		if no_stack_idx >= 0:
		self.stack = False
		del remainder_args[no_stack_idx]
		if len(remainder_args) > 1:
		from .exceptions import ArgumentError
		raise ArgumentError(command + ' does not accept more than one argument:\n'
		@@ -312,17 +325,34 @@ class _Activator(object):
		activate_scripts = self._get_activate_scripts(prefix)
		conda_default_env = self._default_env(prefix)
		conda_prompt_modifier = self._prompt_modifier(prefix, conda_default_env)
		conda_environment_env_vars = self._get_environment_env_vars(prefix)
		unset_env_vars = [k for k, v in conda_environment_env_vars.items()
		if v == CONDA_ENV_VARS_UNSET_VAR]
		[conda_environment_env_vars.pop(_) for _ in unset_env_vars]

		clobbering_env_vars = [k for k in conda_environment_env_vars.keys()
		if k in os.environ.keys()]

		for cvar in clobbering_env_vars:
		save_var = "__CONDA_SHLVL_%s_%s" % (old_conda_shlvl, cvar)
		conda_environment_env_vars[save_var] = os.environ.get(cvar)

		if clobbering_env_vars:
		print("WARNING: overwriting environment variables set in the machine", file=sys.stderr)
		print("overwriting variable %s" % ' '.join(clobbering_env_vars), file=sys.stderr)

		unset_vars = []
		if old_conda_shlvl == 0:
		new_path = self.pathsep_join(self._add_prefix_to_path(prefix))
		export_vars, unset_vars = self.get_export_unset_vars(
		odargs=OrderedDict((
		env_vars_to_export = OrderedDict((
		('path', new_path),
		('conda_prefix', prefix),
		('conda_shlvl', new_conda_shlvl),
		('conda_default_env', conda_default_env),
		('conda_prompt_modifier', conda_prompt_modifier))))
		('conda_prompt_modifier', conda_prompt_modifier)))
		for k, v in conda_environment_env_vars.items():
		env_vars_to_export[k] = v
		export_vars, unset_vars = self.get_export_unset_vars(odargs=env_vars_to_export)
		deactivate_scripts = ()
		else:
		if self.environ.get('CONDA_PREFIX_%s' % (old_conda_shlvl - 1)) == prefix:
		@@ -332,24 +362,30 @@ class _Activator(object):
		if stack:
		new_path = self.pathsep_join(self._add_prefix_to_path(prefix))
		deactivate_scripts = ()
		export_vars, unset_vars = self.get_export_unset_vars(odargs=OrderedDict((
		env_vars_to_export = OrderedDict((
		('path', new_path),
		('conda_prefix', prefix),
		('conda_shlvl', new_conda_shlvl),
		('conda_default_env', conda_default_env),
		('conda_prompt_modifier', conda_prompt_modifier))))
		('conda_prompt_modifier', conda_prompt_modifier)))
		for k, v in conda_environment_env_vars.items():
		env_vars_to_export[k] = v
		export_vars, unset_vars = self.get_export_unset_vars(odargs=env_vars_to_export)
		export_vars['CONDA_PREFIX_%d' % old_conda_shlvl] = old_conda_prefix
		export_vars['CONDA_STACKED_%d' % new_conda_shlvl] = 'true'
		else:
		new_path = self.pathsep_join(
		self._replace_prefix_in_path(old_conda_prefix, prefix))
		deactivate_scripts = self._get_deactivate_scripts(old_conda_prefix)
		export_vars, unset_vars = self.get_export_unset_vars(odargs=OrderedDict((
		env_vars_to_export = OrderedDict((
		('path', new_path),
		('conda_prefix', prefix),
		('conda_shlvl', new_conda_shlvl),
		('conda_default_env', conda_default_env),
		('conda_prompt_modifier', conda_prompt_modifier))))
		('conda_prompt_modifier', conda_prompt_modifier)))
		for k, v in conda_environment_env_vars.items():
		env_vars_to_export[k] = v
		export_vars, unset_vars = self.get_export_unset_vars(odargs=env_vars_to_export)
		export_vars['CONDA_PREFIX_%d' % old_conda_shlvl] = old_conda_prefix

		set_vars = {}
		@@ -381,6 +417,7 @@ class _Activator(object):
		'activate_scripts': (),
		}
		deactivate_scripts = self._get_deactivate_scripts(old_conda_prefix)
		old_conda_environment_env_vars = self._get_environment_env_vars(old_conda_prefix)

		new_conda_shlvl = old_conda_shlvl - 1
		set_vars = {}
		@@ -406,6 +443,7 @@ class _Activator(object):
		new_prefix = self.environ.get('CONDA_PREFIX_%d' % new_conda_shlvl)
		conda_default_env = self._default_env(new_prefix)
		conda_prompt_modifier = self._prompt_modifier(new_prefix, conda_default_env)
		new_conda_environment_env_vars = self._get_environment_env_vars(new_prefix)

		old_prefix_stacked = 'CONDA_STACKED_%d' % old_conda_shlvl in self.environ
		new_path = ''
		@@ -419,11 +457,14 @@ class _Activator(object):
		self._replace_prefix_in_path(old_conda_prefix, new_prefix)
		)

		export_vars, unset_vars2 = self.get_export_unset_vars(odargs=OrderedDict((
		env_vars_to_export = OrderedDict((
		('conda_prefix', new_prefix),
		('conda_shlvl', new_conda_shlvl),
		('conda_default_env', conda_default_env),
		('conda_prompt_modifier', conda_prompt_modifier))))
		('conda_prompt_modifier', conda_prompt_modifier)))
		for k, v in new_conda_environment_env_vars.items():
		env_vars_to_export[k] = v
		export_vars, unset_vars2 = self.get_export_unset_vars(odargs=env_vars_to_export)
		unset_vars += unset_vars2
		export_path = {'PATH': new_path, }
		activate_scripts = self._get_activate_scripts(new_prefix)
		@@ -431,6 +472,11 @@ class _Activator(object):
		if context.changeps1:
		self._update_prompt(set_vars, conda_prompt_modifier)

		for env_var in old_conda_environment_env_vars.keys():
		unset_vars.append(env_var)
		save_var = "__CONDA_SHLVL_%s_%s" % (new_conda_shlvl, env_var)
		if save_var in os.environ.keys():
		export_vars[env_var] = os.environ[save_var]
		return {
		'unset_vars': unset_vars,
		'set_vars': set_vars,
		@@ -456,19 +502,27 @@ class _Activator(object):
		conda_default_env = self.environ.get('CONDA_DEFAULT_ENV', self._default_env(conda_prefix))
		new_path = self.pathsep_join(self._replace_prefix_in_path(conda_prefix, conda_prefix))
		set_vars = {}

		conda_prompt_modifier = self._prompt_modifier(conda_prefix, conda_default_env)
		if context.changeps1:
		self._update_prompt(set_vars, conda_prompt_modifier)

		env_vars_to_unset = ()
		env_vars_to_export = OrderedDict([
		('PATH', new_path),
		('CONDA_SHLVL', conda_shlvl),
		('CONDA_PROMPT_MODIFIER', self._prompt_modifier(conda_prefix, conda_default_env)),
		])
		conda_environment_env_vars = self._get_environment_env_vars(conda_prefix)
		for k, v in conda_environment_env_vars.items():
		if v == CONDA_ENV_VARS_UNSET_VAR:
		env_vars_to_unset = env_vars_to_unset + (k,)
		else:
		env_vars_to_export[k] = v
		# environment variables are set only to aid transition from conda 4.3 to conda 4.4
		return {
		'unset_vars': (),
		'unset_vars': env_vars_to_unset,
		'set_vars': set_vars,
		'export_vars': OrderedDict([('PATH', new_path),
		('CONDA_SHLVL', conda_shlvl),
		('CONDA_PROMPT_MODIFIER', self._prompt_modifier(
		conda_prefix, conda_default_env))]),
		'export_vars': env_vars_to_export,
		'deactivate_scripts': self._get_deactivate_scripts(conda_prefix),
		'activate_scripts': self._get_activate_scripts(conda_prefix),
		}
		@@ -651,6 +705,31 @@ class _Activator(object):
		prefix, 'etc', 'conda', 'deactivate.d', '*' + self.script_extension
		)), reverse=True))

		def _get_environment_env_vars(self, prefix):
		env_vars_file = join(prefix, PREFIX_STATE_FILE)
		pkg_env_var_dir = join(prefix, PACKAGE_ENV_VARS_DIR)
		env_vars = OrderedDict()

		# First get env vars from packages
		if exists(pkg_env_var_dir):
		for pkg_env_var_file in sorted(os.listdir(pkg_env_var_dir)):
		with open(join(pkg_env_var_dir, pkg_env_var_file), 'r') as f:
		env_vars.update(json.loads(f.read(), object_pairs_hook=OrderedDict))

		# Then get env vars from environment specification
		if exists(env_vars_file):
		with open(env_vars_file, 'r') as f:
		prefix_state = json.loads(f.read(), object_pairs_hook=OrderedDict)
		prefix_state_env_vars = prefix_state.get('env_vars', {})
		dup_vars = [ev for ev in env_vars.keys() if ev in prefix_state_env_vars.keys()]
		for dup in dup_vars:
		print("WARNING: duplicate env vars detected. Vars from the environment "
		"will overwrite those from packages", file=sys.stderr)
		print("variable %s duplicated" % dup, file=sys.stderr)
		env_vars.update(prefix_state_env_vars)

		return env_vars


		def expand(path):
		return abspath(expanduser(expandvars(path)))
		@@ -833,25 +912,43 @@ class CshActivator(_Activator):

		class XonshActivator(_Activator):

		@staticmethod
		def path_conversion(paths):
		if not on_win:
		return path_identity(paths)
		elif isinstance(paths, string_types):
		return paths.replace('\\', '/')
		elif paths is None:
		return None
		else:
		return tuple([path.replace('\\', '/') for path in paths])

		def __init__(self, arguments=None):
		self.pathsep_join = ':'.join
		self.pathsep_join = ';'.join if on_win else ':'.join
		self.sep = '/'
		self.path_conversion = native_path_to_unix
		self.script_extension = '.xsh'
		self.tempfile_extension = None
		self.command_join = '\n'

		self.unset_var_tmpl = 'del $%s'
		self.export_var_tmpl = "$%s = '%s'"
		self.set_var_tmpl = "$%s = '%s'" # TODO: determine if different than export_var_tmpl
		self.run_script_tmpl = 'source "%s"'

		# 'scripts' really refer to de/activation scripts, not scripts in the language per se
		# xonsh can piggy-back activation scripts from other languages depending on the platform
		import platform
		if platform.system() == 'Windows':
		self.script_extension = '.bat'
		self.run_script_tmpl = 'source-cmd "%s"'
		else:
		self.script_extension = '.sh'
		self.run_script_tmpl = 'source-bash "%s"'

		self.hook_source_path = join(CONDA_PACKAGE_ROOT, 'shell', 'conda.xsh')

		super(XonshActivator, self).__init__(arguments)

		def _hook_preamble(self):
		return '$CONDA_EXE = "%s"' % context.conda_exe
		return '$CONDA_EXE = "%s"' % self.path_conversion(context.conda_exe)


		class CmdExeActivator(_Activator):

conda/base/constants.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -228,6 +228,10 @@ class SatSolverChoice(Enum):
		PACKAGE_CACHE_MAGIC_FILE = 'urls.txt'
		PREFIX_MAGIC_FILE = join('conda-meta', 'history')

		PREFIX_STATE_FILE = join('conda-meta', 'state')
		PACKAGE_ENV_VARS_DIR = join('etc', 'conda', 'env_vars.d')
		CONDA_ENV_VARS_UNSET_VAR = "*unset*"


		# TODO: should be frozendict(), but I don't want to import frozendict from auxlib here.
		NAMESPACES_MAP = { # base package name, namespace