Add a reader for TNG files using pytng

[hmacdope]

Fixes #3237 and partially addresses #865 (reading TNG)

This PR adds functionality for reading TNG files using pytng (finally). 😄

The limitations of reading a TNG file using pytng are also clearly outlined in the docs.

Changes made in this Pull Request:

• Add a reader for TNG files using PyTNG

TODO

Need to add tests using an example data file

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[pep8speaks]

Hello @hmacdope! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/coordinates/TNG.py:

Line 29:80: E501 line too long (98 > 79 characters)
Line 195:80: E501 line too long (85 > 79 characters)
Line 201:80: E501 line too long (86 > 79 characters)
Line 207:80: E501 line too long (82 > 79 characters)
Line 261:80: E501 line too long (85 > 79 characters)
Line 467:80: E501 line too long (82 > 79 characters)

• In the file testsuite/MDAnalysisTests/coordinates/test_tng.py:

Line 136:80: E501 line too long (87 > 79 characters)
Line 140:80: E501 line too long (80 > 79 characters)
Line 144:80: E501 line too long (80 > 79 characters)

• In the file testsuite/MDAnalysisTests/datafiles.py:

Line 130:80: E501 line too long (96 > 79 characters)
Line 132:80: E501 line too long (95 > 79 characters)
Line 339:80: E501 line too long (92 > 79 characters)
Line 340:80: E501 line too long (95 > 79 characters)

Comment last updated at 2022-09-09 18:03:04 UTC

[orbeckst]

Does pytng have conda packages already?

[hmacdope]

Does pytng have conda packages already?

Yep ! https://github.com/conda-forge/pytng-feedstock

[richardjgowers]

@IAlibay I think your review comments have been addressed here

[IAlibay]

@IAlibay I think your review comments have been addressed here

Thanks, unless this has a time sensitive component (please let me know if that is the case), I'll re-review later this week (after the 13th).

[IAlibay]

Sorry about the lack of review here, this is still on my radar the week has just been a bit busy. I'll try to go over it tomorrow.

[hmacdope]

Any chance of a final review here @MDAnalysis/coredevs? :)

[IAlibay]

Yeah sorry I did note it down earlier today when I was looking at what PRs needed merging. I'll try to re-review over the weekend.

[IAlibay]

Sorry about the very long time back to review this. Just a couple of tiny things.

I'm concurrently updating CI on pytng just to make sure upstream is all good when we do a release.

[IAlibay]

readthedocs is having a field day here, can you confirm this renders fine locally @hmacdope ? https://mdanalysis--3765.org.readthedocs.build/en/3765/documentation_pages/coordinates/TNG.html

[hmacdope]

Seems to be ok locally, what specifically where you looking at?

[IAlibay]

This seems out of place https://mdanalysis--3765.org.readthedocs.build/en/3765/documentation_pages/coordinates/TNG.html#MDAnalysis.coordinates.TNG.HAS_PYTNG

There's also some weird placement of the author list.

[hmacdope]

Removing the comments of the form #: fixed it.

[IAlibay]

We can ignore most of the linter stuff, but do have a look at the output if there's anything you think is worth it. Specifically the assert calls might make more sense without the brackets.

[hmacdope]

@IAlibay I think i have addressed everything including formatting. :)

[IAlibay]

lgtm!

[jbarnoud]

This has been years in the making. Thank you for making this milestone happen!

[orbeckst]

Well done, everyone!