Update POVME3 to Python3

[Seanny123]

Currently, POVME3 only supports Python 2. Given Python 2 will no longer be supported in 2020, it would be helpful to update POVME3 to Python 3.

Is there any work in this direction? Would the maintainers be open to a PR for this issue? Are you all working on a different piece of work which will make POVME3 obsolete?

[j-wags]

Hi @Seanny123,

I'm the head maintainer on POVME3. I've been weighing whether to make a sprint over the holidays to add python3 compatibility, update to a better build system, and distribute on conda-forge, or to archive the repo starting in 2020. At this point, I haven't gotten the sense that many people are using it, so I was leaning towards archiving. Computational chemistry is a bit (two decades?) behind on OSS best practices, so as I continue to learn about more of them, I realize that POVME has even further to go to modernize.

I'd be happy to accept PRs on this, and to bring new maintainers into the org. To the best of my knowledge, there is no ongoing work toward POVME4, so if folks have genuine interest in that, I'd be happy to share and/or turn over ownership.

Let me know your thoughts. I'm happy to take care of the "devops" side (updating to the common MolSSI cookiecutter infrastructure, conda packaging) if you want to take a swing at Python3.

[Seanny123]

I made an attempt in #34, but it is pretty pathetic. I wouldn't worry about it and archive this repo. I'm sure you have other projects which are more important to your career/field. I'll ping you again if further updating of this code becomes a priority for me.

[j-wags]

I'm also working on an attempt in #35. Updating pymolecule seems to be non-trivial, largely due to a change in numpy's data types.

In the long run, replacing pymolecule with MDAnalysis (#5) will provide a huge improvement in performance and reliability.

[hazho]

@j-wags I'm ready to contribute on this issue, let me know your workflow for that, especially if you take care of DevOps, I'll be taking care of modernizing POVME programmatically
cheers

[j-wags]

Awesome. Thanks, @hazho! This repo should be open to PRs from forks, so you can open one with updates for Python 3. I'll work on getting CI working on GitHub Actions, but if your PR to opens before that, I promise to give it a timely review + approval!

The steps for going forward here should be:

• On your fork, make changes to get the code working with python 3
• Open a PR to merge your fork into master in POVME/POVME
• I'll review the code and comment/request changes/approve
  • If I have CI working, we'll use that to determine whether the code is merge-ready, otherwise I'll test locally on linux and mac (this has been added to CI in Refactor testing to use GitHub Actions, add tests for python 3.6 and 3.8 #38)
  • The Python 3.6 and 3.8 mac/linux tests must pass
  • We don't currently have code format standards like black or isort, so I don't expect there to be major formatting issues
• Once the PR is approved, you will make any final changes and click "merge"
• I'll make a new release and upload it to pip

[j-wags]

Ok, for the above, I just merged #38, which adds CI builds for python 3.6 and 3.8. These are separate from the "main" CI, which only tests python 2.7.

Now we'll have an easy way to tell if a PR successfully adds python 3 compatibility!