[WIP] Citation

[luizirber]

Fixes #259 #255

Uses duecredit to implement citation. This is pretty nice because it will collect appropriate citations for other software too. As an example, running sourmash compute results in

$ DUECREDIT_ENABLE=yes sourmash compute ...

DueCredit Report:
- Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences / sourmash/ (v 2.0.0a6) [1]

1 packages cited
0 modules cited
0 functions cited

References
----------

[1] Brown, C.T. & Irber, L., 2016. sourmash: a library for MinHash sketching of DNA. The Journal of Open Source Software, 1(5), p.27.

but running sourmash compare gives us the numpy citation too:

$ DUECREDIT_ENABLE=yes sourmash compare ...

DueCredit Report:
- Scientific tools library / numpy (v 1.14.3) [1]
- Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences / sourmash/ (v 2.0.0a6) [2]

2 packages cited
0 modules cited
0 functions cited

References
----------

[1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
[2] Brown, C.T. & Irber, L., 2016. sourmash: a library for MinHash sketching of DNA. The Journal of Open Source Software, 1(5), p.27.

TODO:

• Provide the basic sourmash citation thru argparse too (see https://github.com/dib-lab/khmer/blob/9323ca4e17bccac9ec1a7d5e8321eeec61cd17cd/khmer/khmer_args.py#L78 for example)
• Wait for a duecredit version that allows outputting to stderr by default (check Default collector to stderr instead of stdout duecredit/duecredit#135) (see [WIP] Citation #478 (comment))
• Add tests (see https://github.com/MDAnalysis/mdanalysis/pull/1822/files#diff-61cf2a678e9b5f5d6d2338f797266a30 for example)

Checklist

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov-io]

Codecov Report

Merging #478 into master will decrease coverage by 0.21%.
The diff coverage is 51.85%.

@@            Coverage Diff            @@
##           master    #478      +/-   ##
=========================================
- Coverage   90.51%   90.3%   -0.22%     
=========================================
  Files          33      34       +1     
  Lines        4892    4919      +27     
  Branches       36      36              
=========================================
+ Hits         4428    4442      +14     
- Misses        463     476      +13     
  Partials        1       1

Impacted Files	Coverage Δ
sourmash/__init__.py	100% <100%> (ø)	⬆️
sourmash/due.py	45.83% <45.83%> (ø)

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[luizirber]

Outputting only to stderr by default will not happen, but there is an env var to control it. In our case, we would run

$ DUECREDIT_ENABLE=yes DUECREDIT_OUTPUTS=pickle sourmash compare ...

and that won't generate any output, or

$ DUECREDIT_ENABLE=yes DUECREDIT_OUTPUTS=stderr,pickle sourmash compare ...

to generate the report to stderr.

Discussion: duecredit/duecredit#135 (comment) and duecredit/duecredit#135 (comment)

[luizirber]

I still think duecredit is a cool idea, but this has been open for 5 years, so I'm closing it =]