Fix github action job: Version 3.9 with arch x64 not found

[rugeli]

Merge this pr first

Problem

What is the problem this work solves, including
CI/CD issue: Error: Version 3.9 with arch x64 not found

Solution

What I/we did to solve this problem
Made a few adjustments, and turns out using python 3.10 - currently the most stable version for cellPACK.
updated checkout and setup-python

Type of change

Please delete options that are not relevant.

• Bug fix and version update (non-breaking change which fixes an issue)

[github-actions]

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name	Encapsulating radius	Average number packed
ext_A	25	236.0

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[mogres]

Is there any reason we are using Python 3.10 for testing? The base cellpack environment still uses Python 3.9

[meganrm]

you could define this as a variable that you then reference in the matrix and down here

[rugeli]

Oh I just realized sharing values across jobs might require some tweaks, like adding another job to define and output the python version and using needs in other jobs. The way we have it now looks cleaner.

[rugeli]

Is there any reason we are using Python 3.10 for testing? The base cellpack environment still uses Python 3.9

Because one of our github actions failed, with the error described in the title, it seems that the version of ubuntu-latest macos-latest is the cause.

To solve the issue, we can either specify an older ubuntu macos version(20.04) or upgrade the python version, and I chose the latter solution in this pr. I tried a few python versions but ran into issues with deprecations and module not found, version 3.10 finally passed all the tests.

We may need to upgrade the base environment to python 3.10 soon to maintain consistency.

[mogres]

To solve the issue, we can either specify an older ubuntu version(20.04) or upgrade the python version, and I chose the latter solution in this pr. I tried a few python versions but ran into issues with deprecations and module not found, version 3.10 finally passed all the tests.

We may need to upgrade the base environment to python 3.10 soon to maintain consistency.

While I do agree we should move to python 3.10 eventually, I am not sure if this is the right approach. The ideal path would be to first create a branch to migrate cellPACK to Python 3.10, check whether this breaks anything beyond our unit tests and then upgrade our CI workflows, requirements, etc. to use the new python version.

Another reasoning for sticking with python 3.9 is because the cellPACK package is a dependency in other analysis packages including simulariumio and cellpack-analysis and we want to make sure these work as expected when we eventually release a newer version with python 3.10.

For the time being, I would recommend using Ubuntu 20.04 in our tests to be compatible with the base cellPACK version. If that is not feasible, we can discuss ways to ensure that the tests are run on the same python version as the base package in one of the WG meetings.

[mogres]

Updating the setup-python version here might also be useful

Added a suggestion comment for this here

[rugeli]

To solve the issue, we can either specify an older ubuntu version(20.04) or upgrade the python version, and I chose the latter solution in this pr. I tried a few python versions but ran into issues with deprecations and module not found, version 3.10 finally passed all the tests.
We may need to upgrade the base environment to python 3.10 soon to maintain consistency.

While I do agree we should move to python 3.10 eventually, I am not sure if this is the right approach. The ideal path would be to first create a branch to migrate cellPACK to Python 3.10, check whether this breaks anything beyond our unit tests and then upgrade our CI workflows, requirements, etc. to use the new python version.

Another reasoning for sticking with python 3.9 is because the cellPACK package is a dependency in other analysis packages including simulariumio and cellpack-analysis and we want to make sure these work as expected when we eventually release a newer version with python 3.10.

For the time being, I would recommend using Ubuntu 20.04 in our tests to be compatible with the base cellPACK version. If that is not feasible, we can discuss ways to ensure that the tests are run on the same python version as the base package in one of the WG meetings.

I see your concern, sure I'll try a different approach and we can discuss it at our next meeting.

[mogres]

Maybe updating the setup-python version would help?

[mogres]

Suggested change

	uses: actions/setup-python@v1
	uses: actions/setup-python@v5

[rugeli]

you are absolutely right!

[mogres]

Yay!