Oliver Beckstein

**Describe the bug** CI fails in **build_docs** with ``` Traceback (most recent call last): File "/home/runner/work/UserGuide/UserGuide/doc/source/scripts/gen_topologyparser_attrs.py", line 29, in from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParser ImportError: cannot import name 'TestDumpParser' from...

update psf insertion codes

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update notes on PSF file format https://github.com/MDAnalysis/mdanalysis/issues/2053 was closed by PR https://github.com/MDAnalysis/mdanalysis/pull/4582 on 2024-05-30 and PSF files with insertion codes can now be read. ---- 📚 Documentation preview 📚: https://mdanalysisuserguide--420.org.readthedocs.build/en/420/

There hasn't been any development on the package for more than half a year. We should make clear that the package is currently not really maintained (or correct me @ojeda-e...

update docs GHA workflow

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The docs.yml workflow needs to be updated - use modern mambaforge setup action - version bumps

Sphinx/RTD says > WARNING: sphinx-sitemap: html_baseurl is required in conf.py.Sitemap not built. html_baseurl should be said to the correct baseurl ... possibly from an env var.

replaced lib.transformations with transformations package

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Fixes #5061 Changes made in this Pull Request: - removed old lib.transformations code - use transformations package instead (which is the updated version of our old vendored code) - **Makes...

compile failure due to numpy issues in transformations.c

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## Expected behavior ## pip install build/compiles cleanly ## Actual behavior ## See https://discord.com/channels/807348386012987462/808088023957897258/1381767573611483176 by @ljwoods2 Curious if I'm missing something, is anyone else getting a Numpy compatibility issue when...

fix inclusion of PRO in secondary structure

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Fixes #4913 Changes made in this Pull Request: - ported fix from PyDSSP 0.9.1 by @ShintaroMinami to analysis.dssp.DSSP (see also https://github.com/ShintaroMinami/PyDSSP/issues/2) - new kwarg ignore_proline_donor=True for DSSP (the new default...

## Is your feature request related to a problem? ## WHen looking at the tests in testsuite/MDAnalysisTests/lib I'd expect to find one test file for each of the major sub...

update license string to SPDX

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Use a string from https://spdx.org/licenses/ to update https://github.com/MDAnalysis/mdanalysis/blob/1cdb055ea95c7d1cddb788296227eef026164bb6/package/pyproject.toml#L53 (and elsewhere). See output from a [recent CI run on azure](https://dev.azure.com/mdanalysis/mdanalysis/_build/results?buildId=8062&view=logs&j=a2a7f4f3-7a8f-538b-6d27-7072c87d6fd3&t=98b69802-e87c-5933-6a7a-52e710b30a1f) ``` !! ******************************************************************************** Please use a simple string containing a SPDX...