[DNM] Update guesser docs #4741
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…lysis into guesser-basics
* updating some docs and removing docs of removed modules *updating are_value_missing() method
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
- updated guess_TopologyAttrs docs - fixed some tests - capitalize atomtypes from elements in RDKitParser
Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Bumps the github-actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish). Updates `actions/setup-python` from 4 to 5 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.2 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.10.0...v1.10.2) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* add black configuration, ignoring all files * black * black version * adios 39
…lysis (MDAnalysis#4718) - Fixes MDAnalysis#4664 - Parallelization of the backend support to the class HydrogenBondAnalysis in hbond_analysis.py - Moved setting up of donors and acceptors from _prepare() to __init__() (needed to make parallel processing work) - Addition of parallelization tests in test_hydrogenbonds_analysis.py and fixtures in conftest.py - Updated Changelog --------- Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu> Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
…alysis#4721) - Fixes MDAnalysis#4674 - Parallelization of the backend support to the class DSSP in dssp.py - Addition of parallelization tests in test_dssp.py and fixtures in conftest.py - Updated Changelog --------- Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
* Add Python 3.13 to minimal CI testing, and include some minor test shims to accommodate.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #4741 +/- ##
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+ Coverage 93.60% 93.62% +0.02%
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Files 173 187 +14
Lines 21464 22627 +1163
Branches 2993 3023 +30
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+ Hits 20091 21185 +1094
- Misses 929 998 +69
Partials 444 444 ☔ View full report in Codecov by Sentry. |
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Closing to cherry-pick commits into new PR once #3753 is merged. |
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Relates to #4696
Do not merge -- I'll cherry-pick these commits into a real PR that's more easily reviewable after #3753 is merged. Just checking docs rendering for now.
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📚 Documentation preview 📚: https://mdanalysis--4741.org.readthedocs.build/en/4741/