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Fix: Align.py doctest error #4373
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Fix: Align.py doctest error #4373
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I will update the change log when reviewed by maintainers, such that unnecessary merge conflicts can be avoided. |
Linter Bot Results:Hi @HeetVekariya! Thanks for making this PR. We linted your code and found the following: Some issues were found with the formatting of your code.
Please have a look at the Please note: The |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4373 +/- ##
==========================================
Coverage 93.41% 93.41%
==========================================
Files 171 185 +14
Lines 22512 23626 +1114
Branches 4129 4129
==========================================
+ Hits 21029 22070 +1041
- Misses 963 1036 +73
Partials 520 520 ☔ View full report in Codecov by Sentry. |
@HeetVekariya CI is still showing errors with I'd also ask to change the "Fixes #3925" into something else like "Partially address #3925", otherwise the issue will be automatically closed when we merge this PR. |
/mdanalysis/package/MDAnalysis$ pytest -v --disable-pytest-warnings --doctest-modules analysis/align.py
============================================================= test session starts ==============================================================
platform linux -- Python 3.10.13, pytest-7.4.3, pluggy-1.3.0 -- /home/heet/anaconda3/envs/mdanalysis-dev/bin/python
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/home/heet/Work/Development/mdanalysis/package/MDAnalysis/.hypothesis/examples'))
rootdir: /home/heet/Work/Development/mdanalysis/package
plugins: anyio-4.0.0, hypothesis-6.92.1
collected 2 items
analysis/align.py::MDAnalysis.analysis.align PASSED [ 50%]
analysis/align.py::MDAnalysis.analysis.align.rotation_matrix PASSED [100%]
======================================================= 2 passed, 23 warnings in 12.43s ======================================================== |
@HeetVekariya I'm referring to the errors in the doctest CI. |
For 1: >>> ref = mda.Universe(PDB_small)
>>> mobile = mda.Universe(PSF, DCD)
>>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions, center=True)
21.892591663632704 For 2: >>> ref = mda.Universe(PDB_small)
>>> mobile = mda.Universe(PSF, DCD)
>>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions,
... superposition=True)
6.809396586471815 |
Thanks for looking into it. I'm not very well versed in doctests for MDAnalysis, I'll need a bit of time to understand why your setup is different from what we have in CI. |
@RMeli are you able to do a review here or should I try to find someone else? |
Sorry, I completely missed this. =/ I'm cycling the PR so we can have access to the logs. |
Partially address #3925
Changes made in this Pull Request:
>
from the Expected output such that error can be solved.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4373.org.readthedocs.build/en/4373/