fixes flake8 of 2d_filter_segmentation_by_features

[kostrykin]

FOR CONTRIBUTOR:

• [x] - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• [x] - License permits unrestricted use (educational + commercial)
• [ ] - This PR adds a new tool or tool collection
• [x] - This PR updates an existing tool or tool collection
• [ ] - This PR does something else (explain below)

[kostrykin]

From this it seems that the build is failing due to

+ read -r -a TOOL_GROUP
+ '[' '!' -s tool_list_chunk.txt ']'
+ planemo merge_test_reports 'json_output/*.json' tool_test_output.json
Total reclaimed space: 3.612GB
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.17/x64/bin/planemo", line 5, in <module>
    from planemo.cli import planemo
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/planemo/cli.py", line 24, in <module>
    from planemo.galaxy import profiles
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/planemo/galaxy/__init__.py", line 4, in <module>
    from .config import galaxy_config
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/planemo/galaxy/config.py", line 38, in <module>
    from planemo.galaxy.workflows import remote_runnable_to_workflow_id
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/planemo/galaxy/workflows.py", line 14, in <module>
    from ephemeris import (
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/ephemeris/generate_tool_list_from_ga_workflow_files.py", line 13, in <module>
    from .shed_tools import InstallRepoDict
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/ephemeris/shed_tools.py", line 62, in <module>
    from typing_extensions import (
ImportError: cannot import name 'NamedTuple' from 'typing_extensions'

which seems unrelated to the tool.

[bgruening]

Thanks @kostrykin! This looks good to me, but do we need to ship this to the ToolShed? It has not features or bug fixes, does it? I would merge it and not push to the TS, if you agree.

[kostrykin]

Thanks @kostrykin! This looks good to me, but do we need to ship this to the ToolShed? It has not features or bug fixes, does it? I would merge it and not push to the TS, if you agree.

Nope, no new features or bug fixes. I was searching for a bug, but couldn't reproduce it locally. Still, while searching it, I fixed the flake8. Please continue merging it if you think it is appropriate!

Still, I was wondering, why the Status checks were failing in the first place. It initially failed as described here. Then, I noticed that the action for PRs has been changed recently. So I created another branch (pr-fix), on which I reverted the changed made back then, and created another PR from kostrykin:2d_filter_segmentation_by_features to BMCV:pr-fix. Subsequently, both PRs failed the Status checks, but when looking at the workflow runs, I saw that the workflow run for this PR here was successful and only failed for the other PR. Isn't this weird, since I neither made any changes to kostrykin:2d_filter_segmentation_by_features nor to BMCV:master? It gets even weirder: I explicitly triggered the workflow run for this PR only, and doing that, GitHub reported that the Status checks passed for both PRs.

No need to ship this to the ToolShed.

[bgruening]

Let me know if there is anything to do ...