Standardize atomicdistances to use results#5347
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charity-g wants to merge 4 commits intoMDAnalysis:developfrom
Draft
Standardize atomicdistances to use results#5347charity-g wants to merge 4 commits intoMDAnalysis:developfrom
charity-g wants to merge 4 commits intoMDAnalysis:developfrom
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BradyAJohnston
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Mar 28, 2026
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BradyAJohnston
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BradyAJohnston
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Some suggestions that should fix the issues with running tests.
The black formatter is also failing. You can run it like this:
uvx black~=24.0 package| # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. | ||
| # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 | ||
| # | ||
| from mdanalysis.package.MDAnalysis.analysis.results import Results |
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This is what's causing your tests to fail - this mdanalysis.package.MDAnalysis only exists on local file system. You should always just import directly from MDAnalysis - which will become available if you us pip install -e . or uv pip install -e ..
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| from mdanalysis.package.MDAnalysis.analysis.results import ( |
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same issue with imports as in other comment.
| Changes | ||
| * The msd.py inside analysis is changed, and ProgressBar is implemented inside | ||
| _conclude_simple and _conclude_fft functions instead of tqdm (Issue #5144, PR #5153) | ||
| * `MDAnalysis.analysis.atomicdistances.AtomicDistances` results are now consistent with expected`analysis` documentation data type = Results (Issue #4819) |
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needs a space between "expected analysis"
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Fixes #4819
Changes made in this Pull Request:
MDAnalysis.analysis.atomicdistances.AtomicDistancesresults are now consistent with expectedanalysisdocumentation data type = Results (Issueanalysis.atomicdistances.AtomicDistancesdoes not use Results #4819)LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no
PR Checklist
package/CHANGELOGfile updated?package/AUTHORS? (If it is not, add it!)Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
📚 Documentation preview 📚: https://mdanalysis--5347.org.readthedocs.build/en/5347/