Vendorise `packaging.versions.LegacyVersion`

Fix https://github.com/galaxyproject/galaxy/issues/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 @@ from typing import (
     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 @@ class MinimalJobWrapper(HasResourceParameters):
     @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 @@ class MinimalJobWrapper(HasResourceParameters):
     @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 @@ from typing import (
     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 @@ __all__ = (
 )
 
 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 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 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:
@@ -810,7 +810,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     @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
@@ -818,7 +818,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
         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

@@ -20,8 +20,9 @@ from typing import (
     Union,
 )
 
-import packaging.version
+from packaging.version import Version
 
+from galaxy.tool_util.version import parse_version
 from galaxy.util import (
     commands,
     download_to_file,
@@ -87,7 +88,7 @@ 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 +133,10 @@ class CondaContext(installable.InstallableContext):
         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 +148,12 @@ class CondaContext(installable.InstallableContext):
 
     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 +170,9 @@ class CondaContext(installable.InstallableContext):
     @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 +283,7 @@ class CondaContext(installable.InstallableContext):
         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 +314,7 @@ class CondaContext(installable.InstallableContext):
         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 +568,7 @@ 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: parse_version(hit["version"]), reverse=True)
     except commands.CommandLineException as e:
         log.error(f"Could not execute: '{e.command}'\n{e}")
         hits = []
@@ -632,8 +633,8 @@ 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 @@ from typing import (
     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 @@ from typing import (
     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 @@ class XmlToolSource(ToolSource):
 
     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 @@ class XmlToolSource(ToolSource):
 
         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 @@ class XmlToolSource(ToolSource):
     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 @@ from typing import (
     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 @@ from typing import (
 )
 
 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 @@ class GalaxyInteractorApi:
     @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

lib/galaxy/tool_util/version.py

@@ -0,0 +1,164 @@
+# Copyright (c) Donald Stufft and individual contributors.
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#     1. Redistributions of source code must retain the above copyright notice,
+#        this list of conditions and the following disclaimer.
+#     2. Redistributions in binary form must reproduce the above copyright
+#        notice, this list of conditions and the following disclaimer in the
+#        documentation and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# The following code derives from packaging 21.3 before the LegacyVersion class
+# was removed: https://github.com/pypa/packaging/blob/21.3/packaging/version.py
+
+import re
+from typing import (
+    Iterator,
+    List,
+    Tuple,
+    Union,
+)
+
+from packaging.version import (
+    _BaseVersion,
+    InvalidVersion,
+    Version,
+)
+
+__all__ = ["parse_version", "LegacyVersion"]
+
+LegacyCmpKey = Tuple[int, Tuple[str, ...]]
+
+
+def parse_version(version: str) -> Union["LegacyVersion", "Version"]:
+    """
+    Parse the given version string and return either a :class:`Version` object
+    or a :class:`LegacyVersion` object depending on if the given version is
+    a valid PEP 440 version or a legacy version.
+    """
+    try:
+        return Version(version)
+    except InvalidVersion:
+        return LegacyVersion(version)
+
+
+class LegacyVersion(_BaseVersion):
+    def __init__(self, version: str) -> None:
+        self._version = str(version)
+        self._key = _legacy_cmpkey(self._version)
+
+    def __str__(self) -> str:
+        return self._version
+
+    def __repr__(self) -> str:
+        return f"<LegacyVersion('{self}')>"
+
+    @property
+    def public(self) -> str:
+        return self._version
+
+    @property
+    def base_version(self) -> str:
+        return self._version
+
+    @property
+    def epoch(self) -> int:
+        return -1
+
+    @property
+    def release(self) -> None:
+        return None
+
+    @property
+    def pre(self) -> None:
+        return None
+
+    @property
+    def post(self) -> None:
+        return None
+
+    @property
+    def dev(self) -> None:
+        return None
+
+    @property
+    def local(self) -> None:
+        return None
+
+    @property
+    def is_prerelease(self) -> bool:
+        return False
+
+    @property
+    def is_postrelease(self) -> bool:
+        return False
+
+    @property
+    def is_devrelease(self) -> bool:
+        return False
+
+
+_legacy_version_component_re = re.compile(r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE)
+
+_legacy_version_replacement_map = {
+    "pre": "c",
+    "preview": "c",
+    "-": "final-",
+    "rc": "c",
+    "dev": "@",
+}
+
+
+def _parse_version_parts(s: str) -> Iterator[str]:
+    for part in _legacy_version_component_re.split(s):
+        part = _legacy_version_replacement_map.get(part, part)
+
+        if not part or part == ".":
+            continue
+
+        if part[:1] in "0123456789":
+            # pad for numeric comparison
+            yield part.zfill(8)
+        else:
+            yield "*" + part
+
+    # ensure that alpha/beta/candidate are before final
+    yield "*final"
+
+
+def _legacy_cmpkey(version: str) -> LegacyCmpKey:
+    # We hardcode an epoch of -1 here. A PEP 440 version can only have a epoch
+    # greater than or equal to 0. This will effectively put the LegacyVersion,
+    # which uses the defacto standard originally implemented by setuptools,
+    # as before all PEP 440 versions.
+    epoch = -1
+
+    # This scheme is taken from pkg_resources.parse_version setuptools prior to
+    # it's adoption of the packaging library.
+    parts: List[str] = []
+    for part in _parse_version_parts(version.lower()):
+        if part.startswith("*"):
+            # remove "-" before a prerelease tag
+            if part < "*final":
+                while parts and parts[-1] == "*final-":
+                    parts.pop()
+
+            # remove trailing zeros from each series of numeric parts
+            while parts and parts[-1] == "00000000":
+                parts.pop()
+
+        parts.append(part)
+
+    return epoch, tuple(parts)

lib/galaxy/tools/__init__.py

@@ -25,10 +25,10 @@ from typing import (
 )
 from urllib.parse import unquote_plus
 
-import packaging.version
 import webob.exc
 from lxml import etree
 from mako.template import Template
+from packaging.version import Version
 
 from galaxy import (
     exceptions,
@@ -79,6 +79,10 @@ from galaxy.tool_util.toolbox import (
 )
 from galaxy.tool_util.toolbox.views.sources import StaticToolBoxViewSources
 from galaxy.tool_util.verify.test_data import TestDataNotFoundError
+from galaxy.tool_util.version import (
+    LegacyVersion,
+    parse_version,
+)
 from galaxy.tools import expressions
 from galaxy.tools.actions import (
     DefaultToolAction,
@@ -223,28 +227,28 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
 # Tools that needed galaxy on the PATH in the past but no longer do along
 # with the version at which they were fixed.
 GALAXY_LIB_TOOLS_VERSIONED = {
-    "meme_fimo": packaging.version.parse("5.0.5"),
-    "Extract genomic DNA 1": packaging.version.parse("3.0.0"),
-    "fetchflank": packaging.version.parse("1.0.1"),
-    "gops_intersect_1": packaging.version.parse("1.0.0"),
-    "lastz_wrapper_2": packaging.version.parse("1.3"),
-    "PEsortedSAM2readprofile": packaging.version.parse("1.1.1"),
-    "sam_to_bam": packaging.version.parse("1.1.3"),
-    "sam_pileup": packaging.version.parse("1.1.3"),
-    "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
-    "secure_hash_message_digest": packaging.version.parse("0.0.2"),
-    "join1": packaging.version.parse("2.1.3"),
-    "wiggle2simple1": packaging.version.parse("1.0.1"),
-    "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
-    "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
-    "CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
-    "CONVERTER_tar_to_directory": packaging.version.parse("1.0.1"),
-    "tabular_to_dbnsfp": packaging.version.parse("1.0.1"),
-    "cufflinks": packaging.version.parse("2.2.1.3"),
-    "Convert characters1": packaging.version.parse("1.0.1"),
-    "substitutions1": packaging.version.parse("1.0.1"),
-    "winSplitter": packaging.version.parse("1.0.1"),
-    "Interval2Maf1": packaging.version.parse("1.0.1+galaxy0"),
+    "meme_fimo": parse_version("5.0.5"),
+    "Extract genomic DNA 1": parse_version("3.0.0"),
+    "fetchflank": parse_version("1.0.1"),
+    "gops_intersect_1": parse_version("1.0.0"),
+    "lastz_wrapper_2": parse_version("1.3"),
+    "PEsortedSAM2readprofile": parse_version("1.1.1"),
+    "sam_to_bam": parse_version("1.1.3"),
+    "sam_pileup": parse_version("1.1.3"),
+    "vcf_to_maf_customtrack1": parse_version("1.0.1"),
+    "secure_hash_message_digest": parse_version("0.0.2"),
+    "join1": parse_version("2.1.3"),
+    "wiggle2simple1": parse_version("1.0.1"),
+    "CONVERTER_wiggle_to_interval_0": parse_version("1.0.1"),
+    "aggregate_scores_in_intervals2": parse_version("1.1.4"),
+    "CONVERTER_fastq_to_fqtoc0": parse_version("1.0.1"),
+    "CONVERTER_tar_to_directory": parse_version("1.0.1"),
+    "tabular_to_dbnsfp": parse_version("1.0.1"),
+    "cufflinks": parse_version("2.2.1.3"),
+    "Convert characters1": parse_version("1.0.1"),
+    "substitutions1": parse_version("1.0.1"),
+    "winSplitter": parse_version("1.0.1"),
+    "Interval2Maf1": parse_version("1.0.1+galaxy0"),
 }
 
 REQUIRE_FULL_DIRECTORY = {
@@ -252,7 +256,7 @@ REQUIRE_FULL_DIRECTORY = {
 }
 IMPLICITLY_REQUIRED_TOOL_FILES: Dict[str, Dict] = {
     "deseq2": {
-        "version": packaging.version.parse("2.11.40.6"),
+        "version": parse_version("2.11.40.6"),
         "required": {"includes": [{"path": "*.R", "path_type": "glob"}]},
     },
     # minimum example:
@@ -277,21 +281,21 @@ IMPLICITLY_REQUIRED_TOOL_FILES: Dict[str, Dict] = {
 
 
 class safe_update(NamedTuple):
-    min_version: Union[packaging.version.LegacyVersion, packaging.version.Version]
-    current_version: Union[packaging.version.LegacyVersion, packaging.version.Version]
+    min_version: Union[LegacyVersion, Version]
+    current_version: Union[LegacyVersion, Version]
 
 
 # Tool updates that did not change parameters in a way that requires rebuilding workflows
 WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
-    "Filter1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.1.1")),
-    "__BUILD_LIST__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
-    "__APPLY_RULES__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
-    "__EXTRACT_DATASET__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
-    "Grep1": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.4")),
-    "Show beginning1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.2")),
-    "Show tail1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
-    "sort1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2")),
+    "Filter1": safe_update(parse_version("1.1.0"), parse_version("1.1.1")),
+    "__BUILD_LIST__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
+    "__APPLY_RULES__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
+    "__EXTRACT_DATASET__": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "Grep1": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
+    "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
+    "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
 }
 
 
@@ -757,7 +761,7 @@ class Tool(Dictifiable):
         # guid attribute since it is useful to have.
         self.guid = guid
         self.old_id: Optional[str] = None
-        self.python_template_version: Optional[packaging.version.Version] = None
+        self.python_template_version: Optional[Version] = None
         self._lineage = None
         self.dependencies: List = []
         # populate toolshed repository info, if available
@@ -835,7 +839,7 @@ class Tool(Dictifiable):
 
     @property
     def version_object(self):
-        return packaging.version.parse(self.version)
+        return parse_version(self.version)
 
     @property
     def sa_session(self):
@@ -1005,12 +1009,8 @@ class Tool(Dictifiable):
         if not dynamic and not self.id:
             raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
 
-        profile = packaging.version.parse(str(self.profile))
-        if (
-            self.app.name == "galaxy"
-            and profile >= packaging.version.parse("16.04")
-            and packaging.version.parse(VERSION_MAJOR) < profile
-        ):
+        profile = Version(str(self.profile))
+        if self.app.name == "galaxy" and profile >= Version("16.04") and Version(VERSION_MAJOR) < profile:
             message = f"The tool [{self.id}] targets version {self.profile} of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool."
             raise Exception(message)
 
@@ -1018,9 +1018,9 @@ class Tool(Dictifiable):
         if self.python_template_version is None:
             # If python_template_version not specified we assume tools with profile versions >= 19.05 are python 3 ready
             if self.profile >= 19.05:
-                self.python_template_version = packaging.version.Version("3.5")
+                self.python_template_version = Version("3.5")
             else:
-                self.python_template_version = packaging.version.Version("2.7")
+                self.python_template_version = Version("2.7")
 
         # Get the (user visible) name of the tool
         self.name = tool_source.parse_name()

lib/galaxy/tools/parameters/wrapped_json.py

@@ -7,7 +7,7 @@ from typing import (
     Sequence,
 )
 
-import packaging.version
+from packaging.version import Version
 
 log = logging.getLogger(__name__)
 
@@ -147,7 +147,7 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
         else:
             json_value = _cast_if_not_none(value_wrapper, bool, empty_to_none=input.optional)
     elif input_type == "select":
-        if packaging.version.parse(str(profile)) < packaging.version.parse("20.05"):
+        if Version(str(profile)) < Version("20.05"):
             json_value = _cast_if_not_none(value_wrapper, str)
         else:
             if input.multiple:

lib/galaxy/util/template.py

@@ -3,11 +3,11 @@
 import traceback
 from lib2to3.refactor import RefactoringTool
 
-import packaging.version
 from Cheetah.Compiler import Compiler
 from Cheetah.NameMapper import NotFound
 from Cheetah.Parser import ParseError
 from Cheetah.Template import Template
+from packaging.version import Version
 from past.translation import myfixes
 
 from . import unicodify
@@ -55,7 +55,7 @@ def fill_template(
     if not context:
         context = kwargs
     if isinstance(python_template_version, str):
-        python_template_version = packaging.version.parse(python_template_version)
+        python_template_version = Version(python_template_version)
     try:
         klass = Template.compile(source=template_text, compilerClass=compiler_class)
     except ParseError as e:

lib/galaxy/workflow/modules.py

@@ -17,7 +17,6 @@ from typing import (
     Union,
 )
 
-import packaging.version
 from cwl_utils.expression import do_eval
 from typing_extensions import TypedDict
 
@@ -48,6 +47,7 @@ from galaxy.schema.invocation import (
 )
 from galaxy.tool_util.cwl.util import set_basename_and_derived_properties
 from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
+from galaxy.tool_util.version import parse_version
 from galaxy.tools import (
     DatabaseOperationTool,
     DefaultToolState,
@@ -1679,11 +1679,7 @@ class ToolModule(WorkflowModule):
                 if safe_version and self.tool.lineage:
                     # tool versions are sorted from old to new, so check newest version first
                     for lineage_version in reversed(self.tool.lineage.tool_versions):
-                        if (
-                            safe_version.current_version
-                            >= packaging.version.parse(lineage_version)
-                            >= safe_version.min_version
-                        ):
+                        if safe_version.current_version >= parse_version(lineage_version) >= safe_version.min_version:
                             self.tool = trans.app.toolbox.get_tool(
                                 tool_id, tool_version=lineage_version, exact=True, tool_uuid=tool_uuid
                             )

pyproject.toml

@@ -72,7 +72,7 @@ Mercurial = "*"
 mrcfile = "*"
 nodeenv = "*"
 numpy = "*"
-packaging = "<22"  # packaging 22.0 dropped LegacyVersion
+packaging = "*"
 paramiko = "!=2.9.0, !=2.9.1"  # https://github.com/paramiko/paramiko/issues/1961
 Parsley = "*"
 Paste = "*"

test/unit/tool_util/test_version.py

@@ -0,0 +1,100 @@
+import pytest
+from packaging.version import Version
+
+from galaxy.tool_util.version import (
+    LegacyVersion,
+    parse_version,
+)
+
+# This list must be in the correct sorting order
+VERSIONS = [
+    # Implicit epoch of 0
+    "1.0.dev456",
+    "1.0a1",
+    "1.0a2.dev456",
+    "1.0a12.dev456",
+    "1.0a12",
+    "1.0b1.dev456",
+    "1.0b2",
+    "1.0b2.post345.dev456",
+    "1.0b2.post345",
+    "1.0b2-346",
+    "1.0c1.dev456",
+    "1.0c1",
+    "1.0rc2",
+    "1.0c3",
+    "1.0",
+    "1.0.post456.dev34",
+    "1.0.post456",
+    "1.1.dev1",
+    "1.2+123abc",
+    "1.2+123abc456",
+    "1.2+abc",
+    "1.2+abc123",
+    "1.2+abc123def",
+    "1.2+1234.abc",
+    "1.2+123456",
+    "1.2.r32+123456",
+    "1.2.rev33+123456",
+    # Explicit epoch of 1
+    "1!1.0.dev456",
+    "1!1.0a1",
+    "1!1.0a2.dev456",
+    "1!1.0a12.dev456",
+    "1!1.0a12",
+    "1!1.0b1.dev456",
+    "1!1.0b2",
+    "1!1.0b2.post345.dev456",
+    "1!1.0b2.post345",
+    "1!1.0b2-346",
+    "1!1.0c1.dev456",
+    "1!1.0c1",
+    "1!1.0rc2",
+    "1!1.0c3",
+    "1!1.0",
+    "1!1.0.post456.dev34",
+    "1!1.0.post456",
+    "1!1.1.dev1",
+    "1!1.2+123abc",
+    "1!1.2+123abc456",
+    "1!1.2+abc",
+    "1!1.2+abc123",
+    "1!1.2+abc123def",
+    "1!1.2+1234.abc",
+    "1!1.2+123456",
+    "1!1.2.r32+123456",
+    "1!1.2.rev33+123456",
+]
+
+LEGACY_VERSIONS = ["foobar", "a cat is fine too", "lolwut", "1.8.1+2+galaxy0"]
+
+
+@pytest.mark.parametrize("version", VERSIONS)
+def test_parse_pep440_versions(version: str) -> None:
+    assert isinstance(parse_version(version), Version)
+
+
+@pytest.mark.parametrize("version", LEGACY_VERSIONS)
+def test_legacy_version_fields(version: str) -> None:
+    parsed_version = parse_version(version)
+    assert isinstance(parsed_version, LegacyVersion)
+    assert parsed_version.public == version
+    assert parsed_version.base_version == version
+    assert parsed_version.epoch == -1
+    assert parsed_version.release is None
+    assert parsed_version.pre is None
+    assert parsed_version.post is None
+    assert parsed_version.dev is None
+    assert parsed_version.local is None
+    assert parsed_version.is_prerelease is False
+    assert parsed_version.is_postrelease is False
+    assert parsed_version.is_devrelease is False
+
+
+@pytest.mark.parametrize(
+    "lower_ver,greater_ver",
+    [(VERSIONS[i], VERSIONS[i + 1]) for i in range(len(VERSIONS) - 1)]
+    + [(lv, v) for v in VERSIONS for lv in LEGACY_VERSIONS],
+)
+def test_version_cmp(lower_ver: str, greater_ver: str) -> None:
+    assert parse_version(lower_ver) < parse_version(greater_ver)