Merge branch 'release_21.01' into release_21.05 (85ad2a0a) · Commits · NDIP / Galaxy

lib/galaxy/tool_util/deps/conda_util.py

+18 −43

Original line number	Diff line number	Diff line
		@@ -26,12 +26,10 @@ SHELL_UNSAFE_PATTERN = re.compile(r"[\s\"']")

		IS_OS_X = sys.platform == "darwin"

		# BSD 3-clause
		CONDA_LICENSE = "http://docs.continuum.io/anaconda/eula"
		VERSIONED_ENV_DIR_NAME = re.compile(r"__(.)@(.)")
		UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
		USE_PATH_EXEC_DEFAULT = False
		CONDA_VERSION = "4.6.14"
		CONDA_PACKAGE_SPECS = ("conda=4.6.14", "'pyopenssl>=22.1.0'")
		CONDA_BUILD_VERSION = "3.17.8"
		USE_LOCAL_DEFAULT = False

		@@ -105,7 +103,6 @@ class CondaContext(installable.InstallableContext):
		ensure_channels = None
		self.ensure_channels = ensure_channels
		self._conda_version = None
		self._miniconda_version = None
		self._conda_build_available = None
		self.use_local = use_local

		@@ -122,35 +119,16 @@ class CondaContext(installable.InstallableContext):
		return self._conda_build_available

		def _guess_conda_properties(self):
		conda_meta_path = self._conda_meta_path
		# Perhaps we should call "conda info --json" and parse it but for now we are going
		# to assume the default.
		conda_version = packaging.version.parse(CONDA_VERSION)
		conda_build_available = False
		miniconda_version = "3"

		if os.path.exists(conda_meta_path):
		for package in os.listdir(conda_meta_path):
		package_parts = package.split("-")
		if len(package_parts) < 3:
		continue
		package = '-'.join(package_parts[:-2])
		version = package_parts[-2]
		# build = package_parts[-1]
		if package == "conda":
		conda_version = packaging.version.parse(version)
		if package == "python" and version.startswith("2"):
		miniconda_version = "2"
		if package == "conda-build":
		conda_build_available = True

		self._conda_version = conda_version
		self._miniconda_version = miniconda_version
		self._conda_build_available = conda_build_available

		@property
		def _conda_meta_path(self):
		return os.path.join(self.conda_prefix, "conda-meta")
		info = self.conda_info()
		self._conda_version = packaging.version.parse(info["conda_version"])
		self._conda_build_available = False
		conda_build_version = info.get("conda_build_version")
		if conda_build_version != "not installed":
		try:
		self._conda_version = packaging.version.parse(conda_build_version)
		self._conda_build_available = True
		except Exception:
		pass

		@property
		def _override_channels_args(self):
		@@ -248,10 +226,9 @@ class CondaContext(installable.InstallableContext):
		"""
		Return the process exit code (i.e. 0 in case of success).
		"""
		create_args = [
		"-y",
		"--quiet"
		]
		create_args = ["-y", "--quiet"]
		if self.conda_version >= packaging.version.parse("4.7.5"):
		create_args.append("--strict-channel-priority")
		if allow_local and self.use_local:
		create_args.extend(["--use-local"])
		create_args.extend(self._override_channels_args)
		@@ -275,9 +252,9 @@ class CondaContext(installable.InstallableContext):
		"""
		Return the process exit code (i.e. 0 in case of success).
		"""
		install_args = [
		"-y"
		]
		install_args = ["-y"]
		if self.conda_version >= packaging.version.parse("4.7.5"):
		install_args.append("--strict-channel-priority")
		if allow_local and self.use_local:
		install_args.append("--use-local")
		install_args.extend(self._override_channels_args)
		@@ -432,9 +409,7 @@ def install_conda(conda_context, force_conda_build=False):
		script_path = temp.name
		download_cmd = commands.download_command(conda_link(), to=script_path)
		install_cmd = ['bash', script_path, '-b', '-p', conda_context.conda_prefix]
		package_targets = [
		"conda=%s" % CONDA_VERSION,
		]
		package_targets = list(CONDA_PACKAGE_SPECS)
		if force_conda_build or conda_context.use_local:
		package_targets.append("conda-build=%s" % CONDA_BUILD_VERSION)
		log.info("Installing conda, this may take several minutes.")