PMDA with refactored `_single_frame`

[yuxuanzhuang]

Fix #131

Still on-going, showing some possible simplifications after Universe can be serialized.

PR Checklist

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

[pep8speaks]

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

• In the file pmda/custom.py:

Line 86:80: E501 line too long (83 > 79 characters) Line 137:25: E126 continuation line over-indented for hanging indent Line 139:52: E127 continuation line over-indented for visual indent

• In the file pmda/density.py:

Line 302:80: E501 line too long (86 > 79 characters) Line 315:44: W291 trailing whitespace

• In the file pmda/leaflet.py:

Line 102:9: E265 block comment should start with '# ' Line 133:51: W504 line break after binary operator Line 135:52: W504 line break after binary operator Line 137:54: W504 line break after binary operator Line 139:54: W504 line break after binary operator Line 141:54: W504 line break after binary operator Line 143:52: W504 line break after binary operator

• In the file pmda/parallel.py:

Line 236:80: E501 line too long (81 > 79 characters) Line 352:80: E501 line too long (80 > 79 characters) Line 353:70: E128 continuation line under-indented for visual indent Line 353:80: E501 line too long (80 > 79 characters) Line 381:30: E126 continuation line over-indented for hanging indent Line 383:34: E123 closing bracket does not match indentation of opening bracket's line Line 409:14: E131 continuation line unaligned for hanging indent Line 413:28: E226 missing whitespace around arithmetic operator Line 428:80: E501 line too long (83 > 79 characters) Line 448:80: E501 line too long (91 > 79 characters) Line 451:80: E501 line too long (86 > 79 characters)

• In the file pmda/rms/rmsd.py:

Line 147:80: E501 line too long (85 > 79 characters) Line 149:80: E501 line too long (88 > 79 characters)

• In the file pmda/rms/rmsf.py:

Line 187:39: E226 missing whitespace around arithmetic operator Line 187:80: E501 line too long (90 > 79 characters) Line 189:80: E501 line too long (83 > 79 characters) Line 204:34: E127 continuation line over-indented for visual indent

Comment last updated at 2020-07-16 10:59:39 UTC

[kain88-de]

This is pretty cool. I'm do not expect this to work for everything. But it could make a neat little wrapper for some analysis functions. It could definitely be working on 'AnalysisFromFunction'.

[yuxuanzhuang]

m not sold on how to unify the two _single_frame() methods.

I'd rather have a simple PR that just upgrades PMDA to use serializable universes but leaves everything else intact. Then we can worry about massive API changes. First make it work in a simple manner where you immediately reap the benefits of the serialization.

yeah, makes sense.

[orbeckst]

It makes sense to have this PR as a test case and to try out what might be possible. To make immediate progress, I'll continue with your PR #132 for now.