Pre-commit workflow

[laserkelvin]

This PR adds a configuration file for pre-commit as the preferred mechanism for maintaining git hooks, replacing the setup_git_hooks.sh and related pre-commit and post-commit execution scripts.

The configuration adds more to the git commit workflow, with some replacements:

Additions

Style/formatting

Style and formatting changes enforce best practices tied to Python 3.9+

• Trailing whitespace
• EOF line
• Pretty JSON formatting
• Python import ordering and style
• Black 23.7.0
• Absolute imports over relative ones

Linting

We replace pylint with flake8, which also includes additional plugins such as flake8-bandit and flake8-black for example.

Security

Adds bandit as part of the workflow which will identify security vulnerabilities with committed code.

Replacements

• pylint is replaced by flake8
• autopep8 is replaced by black

Removal

• unittest was removed for now. pre-commit doesn't have a supported workflow and we could write one ourselves. It might also be a bit extreme to have unit tests run every single commit, and we may want to just have that as CI instead. We can do a follow up PR.

Partially addresses #18 by replacing pylint with flake8 as configured in .pre-commit-config.yaml

[laserkelvin]

Some further improvements could be had, if we want to segment into specific git commit stages

[Pennycook]

CONTRIBUTING.md still refers to pylint and the old hooks. Would you mind reviewing that and updating the text to reflect the changes here?

[laserkelvin]

CONTRIBUTING.md still refers to pylint and the old hooks. Would you mind reviewing that and updating the text to reflect the changes here?

Done in 24728d0. I'll update again with pyproject.toml

[Pennycook]

Done in 24728d0. I'll update again with pyproject.toml

This is good, but I think there are some more parts to change. There are a few references to pylint remaining.

I think we should remove the pre-commit and post-commit bullets from the "Hooks" section, and remove the reference to pylint from "Submitting a Patch". I think the 99 character limit is right (because I think that's the black default) but please double check that too.

[laserkelvin]

Done in 24728d0. I'll update again with pyproject.toml

This is good, but I think there are some more parts to change. There are a few references to pylint remaining.

I think we should remove the pre-commit and post-commit bullets from the "Hooks" section, and remove the reference to pylint from "Submitting a Patch". I think the 99 character limit is right (because I think that's the black default) but please double check that too.

black is actually 88 characters - should I update to that?

[Pennycook]

black is actually 88 characters - should I update to that?

I'm not sure. For the P3 Analysis Library we apparently set it to 79:
https://github.com/intel/p3-analysis-library/blob/fec67d5c7f319fbcb4e37d5c7075e055127f4b34/pyproject.toml#L66-L68

Maybe we should just go to 79? It would make it easier to share code between the two projects, which is quite likely.

[laserkelvin]

79 is PEP8, we can do that sure

[Pennycook]

Changes look good. As discussed offline, I don't think we should actually run these hooks until the next release, but I've tested things locally and everything seems to work.