Improve workflow-to-tools

[lldelisle]

Finally solve #206

I hope this will make some admins happy...

This PR improves workflow-to-tools:

• remove duplicated tools (due to the deletion of item while looping through it, some items were not seen and stayed duplicated. I solved it with a while loop that make sure that there was no modification to the tool list before returning the final deduplicated tool list).
• in addition to the default tool_panel_section_label, users can now provide a json that specifies a tool_panel_section_label. You can for example reuse the work done by @hexylena for the GTN by using https://training.galaxyproject.org/api/toolcats.json (@hexylena you know how much I am a fan).

Dear reviewers, feel free to change the name of the parameters I used.

[lldelisle]

Here is the error I get with the test under 3.9:

ImportError while loading conftest '/home/runner/work/ephemeris/ephemeris/tests/conftest.py'.
tests/conftest.py:6: in <module>
    from galaxy_test.driver.driver_util import GalaxyTestDriver
.tox/py39-pytest/lib/python3.9/site-packages/galaxy_test/driver/driver_util.py:45: in <module>
    from galaxy.webapps.galaxy.fast_app import initialize_fast_app as init_galaxy_fast_app
.tox/py39-pytest/lib/python3.9/site-packages/galaxy/webapps/galaxy/fast_app.py:24: in <module>
    from galaxy.webapps.openapi.utils import get_openapi
.tox/py39-pytest/lib/python3.9/site-packages/galaxy/webapps/openapi/utils.py:16: in <module>
    from fastapi._compat import (
E   ImportError: cannot import name 'GenerateJsonSchema' from 'fastapi._compat' (/home/runner/work/ephemeris/ephemeris/.tox/py39-pytest/lib/python3.9/site-packages/fastapi/_compat/__init__.py)
An error occurred: module 'importlib.metadata' has no attribute 'packages_distributions'
py39-pytest: exit 4 (10.45 seconds) /home/runner/work/ephemeris/ephemeris> pytest -v --cov=/home/runner/work/ephemeris/ephemeris/.tox/py39-pytest/lib/python3.9/site-packages/ephemeris --cov-report xml tests pid=2524
  py39-pytest: FAIL code 4 (74.74=setup[64.29]+cmd[10.45] seconds)
  evaluation failed :( (74.79 seconds)

[nsoranzo]

You can try to bump the minimum Python version to 3.10, 3.9 is EOL.

[nsoranzo]

For "3.10, pytest" we are hitting the issue fixed by galaxyproject/galaxy@31720da , which is only in Galaxy dev currently (future galaxy-files 26.0).

[nsoranzo]

Thanks for the code cleanups!

[lldelisle]

Should we pin pydantic? Or leave it with a bug...

[nsoranzo]

It may be worth to backport the one-line fix to 25.1 and release a new galaxy-files 25.1.1 package. @mvdbeek thoughts?

[martenson]

Let's move this forward with a pydantic pin if that is sufficient?

[mvdbeek]

pydantic pin is problematic, that's a widely used dependency we use in planemo, where we also use ephemeris. Let's just backport the fix.

[mvdbeek]

I see, the backport has happened already -- galaxyproject/galaxy#21518. I can create a new release.

[lldelisle]

The error in the test is always the same while it is using 25.1.1...

[nsoranzo]

Yep, 25.1.1 only fixed the pydantic error you had in commit a8bdd7c , now we are back to a FastAPI breaking change.

[nsoranzo]

Also I just noticed the py312-tests don't actually run any tests, tox.ini needs a rewrite.

[lldelisle]

For tox.ini should I simply copy paste what is in py310-pytest and put it with py312-pytest?

[nsoranzo]

For tox.ini should I simply copy paste what is in py310-pytest and put it with py312-pytest?

I'm on it, I'll tag you for a review.