Allow ChainReader to accept format keyword

[lilyminium]

Fixes #2334

Changes made in this Pull Request:

• Passed format argument from ChainReader through to core._get_readers.get_reader_for

PR Checklist

• Tests?
• Docs? <-- leaving this until after Tidying Universe.__init__ #2322
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #2335 into develop will decrease coverage by 0.09%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           develop    #2335     +/-   ##
==========================================
- Coverage    89.89%   89.79%   -0.1%     
==========================================
  Files          173      173             
  Lines        21778    21786      +8     
  Branches      2861     2861             
==========================================
- Hits         19577    19563     -14     
- Misses        1609     1625     +16     
- Partials       592      598      +6

Impacted Files	Coverage Δ
package/MDAnalysis/core/universe.py	94.98% <100%> (ø)	⬆️
package/MDAnalysis/coordinates/core.py	100% <100%> (ø)	⬆️
package/MDAnalysis/analysis/base.py	93.57% <0%> (-3.67%)	⬇️
package/MDAnalysis/coordinates/TRZ.py	81.74% <0%> (-1.53%)	⬇️
package/MDAnalysis/analysis/lineardensity.py	62.38% <0%> (-0.92%)	⬇️
package/MDAnalysis/lib/util.py	87.59% <0%> (-0.89%)	⬇️
package/MDAnalysis/analysis/gnm.py	95.38% <0%> (-0.77%)	⬇️
package/MDAnalysis/lib/formats/libdcd.pyx	78.31% <0%> (-0.65%)	⬇️
package/MDAnalysis/lib/transformations.py	78.18% <0%> (-0.44%)	⬇️
package/MDAnalysis/core/topologyobjects.py	98.02% <0%> (-0.4%)	⬇️
... and 4 more

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[orbeckst]

See comments.

Also, what happens if one provides a list of formats that parallels the list of files?

We actually have the functionality to provide tuples [(file, format), (file, format), ...] – how does your change interact with that feature?

[lilyminium]

We actually have the functionality to provide tuples [(file, format), (file, format), ...] – how does your change interact with that feature?

Tuples override the format.
mda.Universe(PSF, [file, (file, 'pdb'), file, file, (file, 'gro')], format='xyz') results in readers = [XYZReader, PDBReader, XYZReader, XYZReader, GroReader]. This probably also merits a test. Incidentally, I didn't know about this feature until I was looking at the testsuite -- noting it down for documentation!

[orbeckst]

Please just ping me when you need me to have a final look and 👍 .

[orbeckst]

Incidentally, I didn't know about this feature until I was looking at the testsuite -- noting it down for documentation!

Well, the ChainReader is a bit of an oddity, but really quite useful and something that other packages can't do, as far as I know. It could do with good documentation.

[lilyminium]

Please just ping me when you need me to have a final look and 👍 .

@orbeckst Added tests.

[orbeckst]

Thanks!