Coding standard automated checks for Python projects

[giorgiosironi]

Coding standards common problems:

• mixture of formatting patterns (single and double quotes)
• enforcement of type hints
• unused variables, leftover unused imports

Standard tools for enforcing used at elife:

• flake8 for code style
• autopep8 for reformatting code automatically
• pylint and pyflakes for static analysis
• proofreader-python as an eLife-specific tool that wraps some of the above to ensure a consistent configuration

We may use some of these tools directly and find a way to extract a common configuration later.
/cc @thewilkybarkid for common proofreader-python problems

[de-code]

Just to be sure, we don't want to use proofreader-python for now?

[giorgiosironi]

It may be too eLife-specific and/or force too many pinned versions of dependencies. I'd welcome an experiment.

[thewilkybarkid]

IIRC there are pinned dependency problems. Would rather static tools weren't part of the app too (to avoid other dependency incompatibilities). But it's somewhere to start.

[de-code]

Also worth adding a markdown linter. The one used in VSCode is https://github.com/DavidAnson/markdownlint but requires an extra dependency. Perhaps use a separate docker image for that.

[de-code]

First PR to introduce pylint: libero/content-store#9

[de-code]

I wasn't planning on adding autopep8 as part of the pipeline. It's probably more useful for developers to make 'legacy' code compliant. Unless there are strong opinions.

[de-code]

Actually wondering whether we should split the ticket instead, I can create one for pylint (currently in checking), flake8.

Optionally:

• pyflakes (do we need it if we use pylint?)
• markdown linting

[de-code]

The scope of the ticket isn't well defined, can we now define it as please:

• pylint
• flake8
• markdownlint

It mention Python projects. I believe at the time of creation it was just the content-store (and it is has the corresponding title). I think we should have separate tickets for each project (e.g. now validator?). So this ticket is just about the content-store.

[giorgiosironi]

I'd stop with content-store and extract knowledge and tools from there after the setup is stable.

The current tools cover both style (flake8) and semantics (pylint) so I wouldn't add anything else at the moment unless you have something in the pipeline to try.

[de-code]

No, there was nothing else I was going to add.

Apart from markdownlint (if you consider markdown as code).

[giorgiosironi]

markdownlint approved and merged, it's useful to get feedback on minimal documentation changes. Let's consider it experimental if we have doubts about its stability.

[giorgiosironi]

Can probably be closed now?