Vendorise packaging.versions.LegacyVersion

Fix galaxyproject#15898 .

lib/galaxy/dependencies/dev-requirements.txt

@@ -66,7 +66,7 @@ myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.2 ; python_version >= "3.8" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
-packaging==21.3 ; python_version >= "3.7" and python_version < "3.12"
+packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -110,7 +110,7 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.2 ; python_version >= "3.8" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
-packaging==21.3 ; python_version >= "3.7" and python_version < "3.12"
+packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 paramiko==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 parse==1.19.0 ; python_version >= "3.7" and python_version < "3.12"
 parsley==1.3 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/jobs/__init__.py

@@ -22,8 +22,8 @@
     TYPE_CHECKING,
 )
 
-import packaging.version
 import yaml
+from packaging.version import Version
 from pulsar.client.staging import COMMAND_VERSION_FILENAME
 
 from galaxy import (
@@ -1089,7 +1089,7 @@ def job_io(self):
     @property
     def outputs_directory(self):
         """Default location of ``outputs_to_working_directory``."""
-        return None if self.created_with_galaxy_version < packaging.version.parse("20.01") else "outputs"
+        return None if self.created_with_galaxy_version < Version("20.01") else "outputs"
 
     @property
     def outputs_to_working_directory(self):
@@ -1098,7 +1098,7 @@ def outputs_to_working_directory(self):
     @property
     def created_with_galaxy_version(self):
         galaxy_version = self.get_job().galaxy_version or "19.05"
-        return packaging.version.parse(galaxy_version)
+        return Version(galaxy_version)
 
     @property
     def dependency_shell_commands(self):

lib/galaxy/jobs/runners/pulsar.py

@@ -14,9 +14,9 @@
     Dict,
 )
 
-import packaging.version
 import pulsar.core
 import yaml
+from packaging.version import Version
 from pulsar.client import (
     build_client_manager,
     CLIENT_INPUT_PATH_TYPES,
@@ -64,9 +64,9 @@
 )
 
 MINIMUM_PULSAR_VERSIONS = {
-    "_default_": packaging.version.parse("0.7.0.dev3"),
-    "remote_metadata": packaging.version.parse("0.8.0"),
-    "remote_container_handling": packaging.version.parse("0.9.1.dev0"),  # probably 0.10 ultimately?
+    "_default_": Version("0.7.0.dev3"),
+    "remote_metadata": Version("0.8.0"),
+    "remote_container_handling": Version("0.9.1.dev0"),  # probably 0.10 ultimately?
 }
 
 NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
@@ -498,7 +498,7 @@ def __prepare_job(self, job_wrapper, job_destination):
                 pulsar_version=pulsar_version,
             )
             rewrite_paths = not PulsarJobRunner.__rewrite_parameters(client)
-            if pulsar_version < packaging.version.parse("0.14.999") and rewrite_paths:
+            if pulsar_version < Version("0.14.999") and rewrite_paths:
                 job_wrapper.disable_commands_in_new_shell()
             container = None
             if remote_container is None:
@@ -810,15 +810,15 @@ def __client_outputs(self, client, job_wrapper):
 
     @staticmethod
     def pulsar_version(remote_job_config):
-        pulsar_version = packaging.version.parse(remote_job_config.get("pulsar_version", "0.6.0"))
+        pulsar_version = Version(remote_job_config.get("pulsar_version", "0.6.0"))
         return pulsar_version
 
     @staticmethod
     def check_job_config(remote_job_config, check_features=None):
         check_features = check_features or {}
         # 0.6.0 was newest Pulsar version that did not report it's version.
         pulsar_version = PulsarJobRunner.pulsar_version(remote_job_config)
-        needed_version = packaging.version.parse("0.0.0")
+        needed_version = Version("0.0.0")
         log.info(f"pulsar_version is {pulsar_version}")
         for feature, needed in list(check_features.items()) + [("_default_", True)]:
             if not needed:

lib/galaxy/tool_util/deps/conda_util.py

@@ -20,7 +20,7 @@
     Union,
 )
 
-import packaging.version
+from packaging.version import Version
 
 from galaxy.util import (
     commands,
@@ -87,7 +87,7 @@ def find_conda_prefix() -> str:
 class CondaContext(installable.InstallableContext):
     installable_description = "Conda"
     _conda_build_available: Optional[bool]
-    _conda_version: Optional[Union[packaging.version.Version, packaging.version.LegacyVersion]]
+    _conda_version: Optional[Version]
     _experimental_solver_available: Optional[bool]
 
     def __init__(
@@ -132,10 +132,10 @@ def _reset_conda_properties(self) -> None:
         self._experimental_solver_available = None
 
     @property
-    def conda_version(self) -> Union[packaging.version.Version, packaging.version.LegacyVersion]:
+    def conda_version(self) -> Version:
         if self._conda_version is None:
             self._guess_conda_properties()
-        assert isinstance(self._conda_version, (packaging.version.Version, packaging.version.LegacyVersion))
+        assert isinstance(self._conda_version, Version)
         return self._conda_version
 
     @property
@@ -147,12 +147,12 @@ def conda_build_available(self) -> bool:
 
     def _guess_conda_properties(self) -> None:
         info = self.conda_info()
-        self._conda_version = packaging.version.parse(info["conda_version"])
+        self._conda_version = Version(info["conda_version"])
         self._conda_build_available = False
         conda_build_version = info.get("conda_build_version")
         if conda_build_version and conda_build_version != "not installed":
             try:
-                packaging.version.parse(conda_build_version)
+                Version(conda_build_version)
                 self._conda_build_available = True
             except Exception:
                 pass
@@ -169,9 +169,9 @@ def _override_channels_args(self) -> List[str]:
     @property
     def _experimental_solver_args(self) -> List[str]:
         if self._experimental_solver_available is None:
-            self._experimental_solver_available = self.conda_version >= packaging.version.parse(
-                "4.12.0"
-            ) and self.is_package_installed("conda-libmamba-solver")
+            self._experimental_solver_available = self.conda_version >= Version("4.12.0") and self.is_package_installed(
+                "conda-libmamba-solver"
+            )
         if self._experimental_solver_available:
             return ["--experimental-solver", "libmamba"]
         else:
@@ -282,7 +282,7 @@ def exec_create(self, args: Iterable[str], allow_local: bool = True, stdout_path
         for try_strict in [True, False]:
             create_args = ["-y", "--quiet"]
             if try_strict:
-                if self.conda_version >= packaging.version.parse("4.7.5"):
+                if self.conda_version >= Version("4.7.5"):
                     create_args.append("--strict-channel-priority")
                 else:
                     continue
@@ -313,7 +313,7 @@ def exec_install(self, args: Iterable[str], allow_local: bool = True, stdout_pat
         for try_strict in [True, False]:
             install_args = ["-y"]
             if try_strict:
-                if self.conda_version >= packaging.version.parse("4.7.5"):
+                if self.conda_version >= Version("4.7.5"):
                     install_args.append("--strict-channel-priority")
                 else:
                     continue
@@ -567,7 +567,7 @@ def best_search_result(
         # the latest update time.
         hits = json.loads(res).get(conda_target.package, [])[::-1]
         hits = sorted(hits, key=lambda hit: hit["build_number"], reverse=True)
-        hits = sorted(hits, key=lambda hit: packaging.version.parse(hit["version"]), reverse=True)
+        hits = sorted(hits, key=lambda hit: Version(hit["version"]), reverse=True)
     except commands.CommandLineException as e:
         log.error(f"Could not execute: '{e.command}'\n{e}")
         hits = []
@@ -632,8 +632,8 @@ def build_isolated_environment(
         # Adjust fix if they fix Conda - xref
         # - https://github.com/galaxyproject/galaxy/issues/3635
         # - https://github.com/conda/conda/issues/2035
-        offline_works = (conda_context.conda_version < packaging.version.parse("4.3")) or (
-            conda_context.conda_version >= packaging.version.parse("4.4")
+        offline_works = (conda_context.conda_version < Version("4.3")) or (
+            conda_context.conda_version >= Version("4.4")
         )
         if offline_works:
             create_args.append("--offline")

lib/galaxy/tool_util/deps/mulled/util.py

@@ -17,11 +17,12 @@
     Union,
 )
 
-import packaging.version
 import requests
 from conda_package_streaming.package_streaming import stream_conda_info
 from conda_package_streaming.url import stream_conda_info as stream_conda_info_from_url
 
+from galaxy.tool_util.version import parse_version
+
 if TYPE_CHECKING:
     from galaxy.tool_util.deps.container_resolvers import ResolutionCache
 
@@ -189,8 +190,8 @@ def parse_tag(tag):
         build_number = -1
     return PARSED_TAG(
         tag=tag,
-        version=packaging.version.parse(version),
-        build_string=packaging.version.parse(build_string),
+        version=parse_version(version),
+        build_string=parse_version(build_string),
         build_number=build_number,
     )
 

lib/galaxy/tool_util/linters/general.py

@@ -1,7 +1,10 @@
 """This module contains linting functions for general aspects of the tool."""
 import re
 
-import packaging.version
+from galaxy.tool_util.version import (
+    LegacyVersion,
+    parse_version,
+)
 
 ERROR_VERSION_MSG = "Tool version is missing or empty."
 WARN_VERSION_MSG = "Tool version [%s] is not compliant with PEP 440."
@@ -34,10 +37,10 @@ def lint_general(tool_source, lint_ctx):
     else:
         tool_node = None
     version = tool_source.parse_version() or ""
-    parsed_version = packaging.version.parse(version)
+    parsed_version = parse_version(version)
     if not version:
         lint_ctx.error(ERROR_VERSION_MSG, node=tool_node)
-    elif isinstance(parsed_version, packaging.version.LegacyVersion):
+    elif isinstance(parsed_version, LegacyVersion):
         lint_ctx.warn(WARN_VERSION_MSG % version, node=tool_node)
     elif version != version.strip():
         lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ("Tool version", version), node=tool_node)

lib/galaxy/tool_util/parser/xml.py

@@ -9,7 +9,7 @@
     Optional,
 )
 
-import packaging.version
+from packaging.version import Version
 
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import (
@@ -525,7 +525,7 @@ def parse_stdio(self):
 
     def parse_strict_shell(self):
         command_el = self._command_el
-        if packaging.version.parse(self.parse_profile()) < packaging.version.parse("20.09"):
+        if Version(self.parse_profile()) < Version("20.09"):
             default = "False"
         else:
             default = "True"
@@ -558,7 +558,7 @@ def parse_tests_to_dict(self) -> ToolSourceTests:
 
         return rval
 
-    def parse_profile(self):
+    def parse_profile(self) -> str:
         # Pre-16.04 or default XML defaults
         # - Use standard error for error detection.
         # - Don't run shells with -e
@@ -573,7 +573,7 @@ def parse_license(self):
     def parse_python_template_version(self):
         python_template_version = self.root.get("python_template_version")
         if python_template_version is not None:
-            python_template_version = packaging.version.Version(python_template_version)
+            python_template_version = Version(python_template_version)
         return python_template_version
 
     def parse_creator(self):

lib/galaxy/tool_util/toolbox/lineages/interface.py

@@ -5,9 +5,9 @@
     List,
 )
 
-import packaging.version
 from sortedcontainers import SortedSet
 
+from galaxy.tool_util.version import parse_version
 from galaxy.util.tool_version import remove_version_from_guid
 
 
@@ -46,7 +46,7 @@ class ToolLineage:
 
     def __init__(self, tool_id, **kwds):
         self.tool_id = tool_id
-        self.tool_versions = SortedSet(key=packaging.version.parse)
+        self.tool_versions = SortedSet(key=parse_version)
 
     @property
     def tool_ids(self) -> List[str]:

lib/galaxy/tool_util/verify/interactor.py

@@ -25,10 +25,7 @@
 )
 
 import requests
-from packaging.version import (
-    parse as parse_version,
-    Version,
-)
+from packaging.version import Version
 from requests import Response
 from requests.cookies import RequestsCookieJar
 from typing_extensions import (
@@ -200,7 +197,7 @@ def __init__(self, **kwds):
     @property
     def target_galaxy_version(self):
         if self._target_galaxy_version is None:
-            self._target_galaxy_version = parse_version(self._get("version").json()["version_major"])
+            self._target_galaxy_version = Version(self._get("version").json()["version_major"])
         return self._target_galaxy_version
 
     @property