mdanalysis

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Some initial testing with awkward array

4

I've been meaning to give [awkward array](https://awkward-array.readthedocs.io/en/latest/) a try because lipid and protein "residues" with different numbers of atoms seemed like a potentially good fit for the description: > Awkward...

tylerjereddy

AuxReader for EDR Files

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Fixes #3629 With ~~panedrlite now closer to~~ pyedr now being a thing, and the actual code itself less likely to still change, I have now finally started work on the...

BFedder

Add a reader for TNG files using pytng

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Fixes #3237 and partially addresses #865 (reading TNG) This PR adds functionality for reading TNG files using pytng (finally). :smile: The limitations of reading a TNG file using pytng are...

hmacdope

[DOC]: Updated references to BibTex format

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Fixes #3766 and entirely fixes #2837 Changes made in this Pull Request: - Updated all references in `references.rst` to BibTex format. - Added references to `references.bib`. - Fixed typos. -...

ojeda-e

Type hint for analysis module

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Fixes # Changes made in this Pull Request: - PR Checklist ------------ - [ ] Tests? - [ ] Docs? - [ ] CHANGELOG updated? - [ ] Issue raised/referenced?

umak1106

Type hints for topology module

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Fixes # Changes made in this Pull Request: - PR Checklist ------------ - [ ] Tests? - [ ] Docs? - [ ] CHANGELOG updated? - [ ] Issue raised/referenced?

umak1106

basic guesser features

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Fixes # Changes made in this Pull Request: - I have created a guesser package that will contain all upcoming the context aware guessers. it contain the following so far:...

aya9aladdin

Type hints for lib module

10

Fixes # Changes made in this Pull Request: - PR Checklist ------------ - [ ] Tests? - [ ] Docs? - [ ] CHANGELOG updated? - [ ] Issue raised/referenced?

umak1106

PCA not showing progress bar on mean structure calculation

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## Expected behavior ## Progress bar should be shown when computing mean structure for PCA when `verbose=True`. ## Actual behavior ## Progress bar is shown for PCA calculation but not...

rsexton2

Modernize more tests, ref #3743

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Ref #3743 Changes made in this Pull Request: - Changed more tests to use `approx` and `assert_allclose` rather than `assert_almost_equals` and `assert_array_almost_equals`. PR Checklist ------------ - [x] Tests? - [x]...

rzhao271