Fix deprecation warning regarding setup.py and pyproject.toml

[kinow]

While reviewing @naiaraAM 's code in !459 , I created a new Micromamba env on a new laptop, and doing everything over from scratch I got this warning with Py 3.9.12 running pip install -e .:

DEPRECATION: Legacy editable install of autosubmit==4.1.9 from file:///home/kinow/Development/python/workspace/autosubmit (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at pypa/pip#11457

It's probably better that we fix this earlier, instead of waiting until they remove it which may prevent AS from working with newer versions of Python for a simple issue that can be fixed in under one hour.

[kinow]

In GitLab by @edgano on Aug 12, 2024, 13:53

Looking for more info about these. I found this info here: https://packaging.python.org/en/latest/discussions/setup-py-deprecated/

What commands should be used instead?

Deprecated	Recomendation
python setup.py install	python -m pip install .
...	...

But not sure which could be the best strategy

[kinow]

I think calling python setup.py install directly has been considered old/deprecated for a long time. Some scripts that I used in the past did not work correctly when called directly like that.

I think either python -m pip install . or just pip install . should be OK.

The error, I believe, is due to the missing pyproject.toml. Other projects have added or migrated to pyproject.toml. It would be hard for us to migrate, I think, as I don't know if the way we retrieve the project version would work.

But we can add a pyproject.toml and move part of the metadata, to see if the deprecation warning goes away. Then in the future we can move more things, and follow the PEP's and see which direction we need/want to follow.

WDYT?

[kinow]

In GitLab by @edgano on Aug 12, 2024, 14:25

A ok!
yes, that sounds good ;) a good way to test without breaking anything. IDK what the others thinks about it

[dbeltrankyl]

In relation to this, we should also fix this:

https://autosubmit.readthedocs.io/en/master/installation/index.html#installation

The docs are still referring to the use

python3 setup.py install

Which won't work because it doesn't download the dependencies of Autosubmit.

git clone -b $current_display_version https://github.com/BSC-ES/autosubmit
cd autosubmit
pip install . 

Would be more appropriate.

I think this should be done for v4.1.13, to avoid external user issues which are always harder to track.

[dbeltrankyl]

It may be a good issue for @isimo00 or @VindeeR

[kinow]

Yeah, and this is a really annoying one, because I see this warning every week, nearly every day when I pip install -e . Autosubmit 😆

[isimo00]

@VindeeR I assigned us both so we can collaborate :) I think this should be fairly easy, based on How to modernize a setup.py based project? and the pyproject.toml specification
I will push an initial commit today

[isimo00]

I pushed a working first version of the file - I'm not very well versed on this type of files so it might be a rough draft, we'll see -.

To test, run python -m build and then pip install dist/autosubmit-4.1.12-py3-none-any.whl or pip install dist/autosubmit-4.1.12.tar.gz.

[kinow]

I pushed a working first version of the file - I'm not very well versed on this type of files so it might be a rough draft, we'll see -.

To test, run python -m build and then pip install dist/autosubmit-4.1.12-py3-none-any.whl or pip install dist/autosubmit-4.1.12.tar.gz.

I think there's no draft pull request yet? But looking at the commit, it's looking like a normal pyproject.toml to me 🙂 seems to be in the right direction.

We can remove things from setup.py once we move them to pyproject.toml. Then at some point we can have just an empty setup.py with an empty setup() call (saw that in some projects, not sure if still useful/recommended), or drop the setup.py file.

Great job, Irene!

[isimo00]

@kinow Just created the draft PR: #2079. I'll briefly work on some other issues to let @VindeeR have some time to look at this for now, and will come back to polish the content migration from setup,py to pypropject.toml later. Thanks Bruno!

[isimo00]

I forgot to mention; there's a few filler values for the author and member fields; I added Daniel's info but there's some extra random people in there. Besides eventually removing these placeholders, should we add other members of the team other than Daniel?

[kinow]

I forgot to mention; there's a few filler values for the author and member fields; I added Daniel's info but there's some extra random people in there. Besides eventually removing these placeholders, should we add other members of the team other than Daniel?

That may be hard to maintain. What I've seen in other projects is to use either the original creator of the project, or something like "Autosubmit Team" (so we don't have to update it when the team changes...)

[kinow]

That would be a good topic for the Thursday meeting, I think.