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Docs: Missing references in BibTex format in reference page.

1

## Expected behavior ## In docs, the [references](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/doc/sphinx/source/documentation_pages/references.rst) should display citations following the BibTex format. Note: This change was left on purpose given that PR #3663 was getting too large....

ojeda-e

type hints for Visualization module

3

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

umak1106

No need to redirect to the original frame explicitly during deserialization

17

Fixes #3723 Partial fix: #3721 Changes made in this Pull Request: - no redirection to the original frame (explicitly) during deserialization - TextIOPicklable serializes the raw class instance instead of...

yuxuanzhuang

Change mmtf reading of formal charges from the `charges` attribute to `formalcharges`

3

## Expected behavior ## The contents of `charges` is always expected to contain partial charges. ## Actual behavior ## For mmtf, formal charges are fed into `charges`, which a) leads...

IAlibay

Remove use of `trajectory.timeseries` from `ENCORE`

1

## Expected behavior ## The `ENCORE` module should work with all kinds of readers. As revealed by the use of the DUMPReader in [this](https://groups.google.com/g/mdnalysis-discussion/c/PEqfPk_aVvo ) mailing list question this is...

hmacdope

modernize testing code

20

## Is your feature request related to a problem? ## The testing code uses pytest and relies on numpy.testing. It contains some deprecated testing constructs such as [`assert_almost_equal()`](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_almost_equal.html), [`assert_array_almost_equal()`](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_array_almost_equal.html) and...

orbeckst

Issue 3449 lammps dump parser

10

Fixes # Changes made in this Pull Request: - LAMMPS standard atom styles are added to `DATAParser`, so it can now handle all LAMMPS atom styles as listed in [read_data](https://docs.lammps.org/read_data.html)...

amirhs1

Add optional dtype argument to box routines

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Fixes #3500 Changes made in this Pull Request: - Add an optional dtype argument to the box routines. As we don't guarantee the input is an `ndarray` we can't pass...

hmacdope

XYZWriter odd behaviour

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## Expected behavior ## If I reorder some atoms I expect to get the right name along the right coordinates. Original coordinates: O 0.00000 0.00000 0.00000 N 2.00000 0.00000 0.00000...

rafaelpap

Automate removal of old `-dev0` tagged doc builds

3

As of writing, the MDAnalysis docs have `-dev0` entries for 1.0.1, 1.0.2 (which never existed), 2.0.0, 2.1.0, 2.2.0, and 2.3.0. Ideally the `dev` version should be limited to unreleased versions...

IAlibay