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galaxyproject / planemo

Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
https://planemo.readthedocs.io/
MIT License
86 stars 85 forks source link

Don't crash autoupdate on non-PEP440-compliant tool versions #1422

Closed nsoranzo closed 6 months ago

nsoranzo commented 6 months ago

Fix errors like:

File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/commands/cmd_autoupdate.py", line 120, in cli
    tools_to_update = autoupdate.get_tools_to_update(ctx, workflow, tools_to_skip)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 363, in get_tools_to_update
    return outdated_tools(ctx, wf_dict, ts, tools_to_skip)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 349, in outdated_tools
    outdated_tools_rec(wf_dict)
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 337, in outdated_tools_rec
    outdated_tool_dict.update(check_tool_step(tool_id))
                              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 324, in check_tool_step
    updated_tool_id = get_newest_tool_id(matching_tool_ids)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 290, in get_newest_tool_id
    return sorted(
           ^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/planemo/autoupdate.py", line 292, in <lambda>
    key=lambda n: packaging.version.parse(n.split("/")[-1]),
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/packaging/version.py", line 54, in parse
    return Version(version)
           ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/packaging/version.py", line 200, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
packaging.version.InvalidVersion: Invalid version: '0.8.1+galaxy0+galaxy0'

seen e.g. in https://github.com/planemo-autoupdate/autoupdate/actions/runs/7443075417/job/20247438333 by using parse_version from galaxy.tool_util.version.