[REF] Replace duecredit with BibTeX

[tsalo]

Closes #873.

Changes proposed in this pull request:

• Remove duecredit as a dependency and remove all due decorators.
• Remove the RefLGR and have BibTeX citations in the RepLGR strings.
  • We still need to figure out how to load the references BibTeX file, select the references that are actually used in the report string, and output those to the report. Done!
• Add references.bib BibTeX file.
• Use sphinxcontrib-bibtex for docstring references.
  • We can also use this throughout the documentation, outside of docstrings!

[codecov]

Codecov Report

Merging #875 (aab1cdf) into main (a008689) will increase coverage by 0.02%.
The diff coverage is 95.50%.

@@            Coverage Diff             @@
##             main     #875      +/-   ##
==========================================
+ Coverage   93.26%   93.28%   +0.02%     
==========================================
  Files          27       28       +1     
  Lines        2315     2337      +22     
==========================================
+ Hits         2159     2180      +21     
- Misses        156      157       +1     

Impacted Files	Coverage Δ
tedana/__init__.py	100.00% <ø> (ø)
tedana/combine.py	90.62% <ø> (-0.81%)	⬇️
tedana/decay.py	97.26% <ø> (-0.02%)	⬇️
tedana/decomposition/_utils.py	0.00% <ø> (ø)
tedana/decomposition/ica.py	82.14% <ø> (-0.62%)	⬇️
tedana/decomposition/pca.py	89.51% <0.00%> (+0.45%)	⬆️
tedana/gscontrol.py	100.00% <ø> (ø)
tedana/io.py	94.00% <ø> (-0.03%)	⬇️
tedana/metrics/collect.py	94.94% <ø> (-0.03%)	⬇️
tedana/metrics/dependence.py	97.72% <ø> (-0.02%)	⬇️
... and 12 more

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[tsalo]

@eurunuela this PR is now ready for review, if you have the time for it.

[eurunuela]

This is great. Thank you @tsalo!

I built the docs on my computer and the references look perfect.

I guess my only question is regarding GitHub's supported citations. Is that something we have to do once the PR is merged?

[tsalo]

Sorry, what do you mean by "GitHub's supported citations"? Do you mean the "Cite this repository" option available when repositories have a CFF file?

[eurunuela]

Sorry, what do you mean by "GitHub's supported citations"? Do you mean the "Cite this repository" option available when repositories have a CFF file?

Sorry, yes. That's what I was referring to.

[tsalo]

We can tackle that in a separate PR. We can add the CFF file with the JOSS paper citation, but I'm still concerned about getting folks to cite individual releases' Zenodo DOIs. The two problems are (1) CFF can support multiple citations, but will only show one of them to users on GitHub, and (2) the Zenodo DOI is minted after the release is made, so any code in tedana will only reflect the previous release.

This PR doesn't address the second problem, but it does let us put as many references as we want in the reports (as we already do), so we could have both the JOSS and Zenodo citations in the boilerplate.

[dowdlelt]

I haven't had a chance to do an in depth look at this so maybe I'm completely missing the mark...but before I forget: I looked at the docs generated for this PR and duecredit is mentioned right at the beginning under the Citation heading as well as in the Installation section. Should reference to duecredit be removed there (it is also in the FAQ section, but that may be wise if someone is encountering duecredit in an older version).

[tsalo]

I forgot about the docs. Thanks for catching that! I've removed all mentions of duecredit.

[eurunuela]

Good catch @dowdlelt! I missed it too.

[jbteves]

This looks good, but could we move all of the bibtex utils into a new file, perhaps bibtex.py? I just feel like it will be difficult to figure out how they're distinct from other utilities with the current names, and there's several of them so it makes sense to split them off.

[tsalo]

@jbteves that's a great idea. I think everything should now be sufficiently separated.

[jbteves]

I'm biased because it's my idea but looks good to me 😉

[eurunuela]

LGTM! Thank you @tsalo

[tsalo]

Thanks all! Merging now.