Make BioC links consistent

[sjspielman]

The docs hop around among lots of bioconductor releases versions for relevant links (packages and OSCA). We should pick one and go with it. For ease of maintenance, I propose release...

[jashapiro]

Alternatively, we might try to match the version we are using in the current scpca-nf. I suspect that release is usually fine, but we want to discuss.

[allyhawkins]

We're using 3.17 in scpca-nf. I feel like there must be a way we can fill the versions automatically to match the version in scpca-nf before we merge things into main. That would eliminate us needing to constantly go through and update all the links.

[sjspielman]

I feel like there must be a way we can fill the versions automatically to match the version in scpca-nf before we merge things into main.

I like this idea. We'd want to match the version in the scpcaTools container, and probably use something like this -

https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#substitutions

https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#substitution-definitions

[allyhawkins]

I think this is related to Josh's comment about versions in readthedocs (see https://github.com/AlexsLemonade/scpca-docs/pull/157#pullrequestreview-1671369413). We might want to have a separate discussion about how we want to manage versions for this repo first, and then address this.

[jashapiro]

W

I feel like there must be a way we can fill the versions automatically to match the version in scpca-nf before we merge things into main.

I like this idea. We'd want to match the version in the scpcaTools container, and probably use something like this -

Those links actually don't apply to our docs, as we are writing in markdown, not rst. What we might need to do is to enable a MyST extension and describe the replacements in the conf.py, as described in https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#substitutions-with-jinja2

Note that doing the substitution in a URL (our use case) is a bit more complicated!: https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#substitutions-and-urls