add packaging

[gonuke]

This adds the python packaging module to support updated pymoab installation in MOAB master branch.

Successful testing is demonstrated here.

[shimwell]

oh this is very cool, just repeating to check i have understood

the most recent versions of MOAB come with PyMoab that was causing a few installation issue. Consequently a few of us have stayed with MOAB 5.3.1 as the newest version that we have installed pymoab with.

However adding python3-packaging brings in the necessary components that make PyMoab installable again.

My only question is should python3-packaging should instead be added to the pymoab install process in the pyproject.toml build section?

perhaps to this location
https://bitbucket.org/fathomteam/moab/src/aa7fca46f7f3d8d7d6cbadbc9b70f4fe29edec75/pymoab/pyproject.toml#lines-2

which already appears to have a packaging package in the list 👀

[gonuke]

Your understanding is correct (with the minor variation that DAGMC briefly worked with newer MOAB versions on 22.04 until the most recent update broke it again).

I am not sure how the pyptoject.toml is being used in the pymoab install process and why it's not being installed in an accessible way for DAGMC MOAB to access at build time.

Any ideas @pshriwise ?

[gonuke]

You can see a failure here: https://github.com/svalinn/DAGMC/actions/runs/6209143428/job/16856049951

[shimwell]

setuptools and packaging are mentioned in the pyproject.toml of pymoab so ideally they would have been installed by python during the instal process.

I see adding them to the docker works which is great but I would be keen to understand why they are not being installed automatically like other build dependencies

[shimwell]

You can see a failure here: https://github.com/svalinn/DAGMC/actions/runs/6209143428/job/16856049951

I see it is running python setup.py and then failing with ModuleNotFoundError: No module named 'packaging' so this might bypass the use of the pyproject.toml file and the list of things to install contained within

I also notice there is a requirements.txt file which somewhat doubles up on the pyproject.toml as well
https://bitbucket.org/fathomteam/moab/src/master/pymoab/requirements.txt

[gonuke]

I wonder if it needs to use pip install instead of python setup.py? I thought that the change to pip install had already happened.

[pshriwise]

@shimwell is right, we can do away with the requirements.txt file. The pyproject.toml isn't being copied to the build directory, which is where we call pip as part of the make install target, so the packaging build dependency isn't accounted for.

I'll submit a PR to MOAB shortly to fix this.

[pshriwise]

MOAB PR cros-reference: https://bitbucket.org/fathomteam/moab/pull-requests/651

[vijaysm]

In the future, we would appreciate it if you can raise issues or submit PRs when something fails in DagMC due to MOAB. This will help keep the library up to date in general as workflows evolve. @shimwell In general, I do not recommend sticking to old versions unless absolutely necessary.

[gonuke]

We are trying to get out of the habit of pinning to old versions @vijaysm but bandwidth limitations sometimes put us there. It's often not a MOAB bug/issue, but important progress in MOAB or other dependencies that we don't have the bandwidth to adapt to.

[gonuke]

MOAB PR cros-reference: https://bitbucket.org/fathomteam/moab/pull-requests/651

When this merges to MOAB/master, I can try our current test without this PR; if it works I'll withdraw this.

[shimwell]

Suggested change

python3-packaging \

shall we remove this and retrigger the CI

[pshriwise]

🤞🏻

[gonuke]

It looks like develop passes now that MOAB master has been updated, so I'm withdrawing this PR

[shimwell]

we might be able to remove these from the dockerfile as well

                        python3-setuptools \
                        python3-dev \
                        libpython3-dev \