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Fix bug in PCA trajectory iteration -- avoid explicit usage of self.start #4423

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merged 11 commits into from
Jan 20, 2024
Merged

Fix bug in PCA trajectory iteration -- avoid explicit usage of self.start #4423

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211cbcf
Fix bug in PCA trajectory iteration -- avoid explicit usage of self.s…
marinegor Jan 12, 2024
d4de910
update changelog and tests for PCA fix
marinegor Jan 12, 2024
be05e9b
Update test_pca.py
Jan 12, 2024
9743827
Replace self._u.trajectory[...] with self._sliced_trajectory
marinegor Jan 17, 2024
e146863
Update documentaiton
marinegor Jan 17, 2024
dbe2dbc
Merge branch 'develop' into bugfix/pca-frames-iteration
IAlibay Jan 18, 2024
a4b2f4a
Update testsuite/MDAnalysisTests/analysis/test_pca.py
Jan 18, 2024
0c95e34
Update package/MDAnalysis/analysis/pca.py
Jan 18, 2024
39965ee
Update package/CHANGELOG
Jan 18, 2024
3b270c8
revert back to testing with mean=None
marinegor Jan 18, 2024
7e915a4
Enforce mean=None when testing with frames
marinegor Jan 18, 2024
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -19,6 +19,7 @@ The rules for this file:
* 2.8.0

Fixes
* Fix bug in PCA -- wasn't possible to use `frames=...` syntax before.
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* Fix deploy action to use the correct version of the pypi upload action.

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3 changes: 2 additions & 1 deletion package/MDAnalysis/analysis/pca.py
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Expand Up @@ -247,7 +247,8 @@ def __init__(self, universe, select='all', align=False, mean=None,

def _prepare(self):
# access start index
self._u.trajectory[self.start]
# self._u.trajectory[self.start]
self._sliced_trajectory[0]
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# reference will be start index
self._reference = self._u.select_atoms(self._select)
self._atoms = self._u.select_atoms(self._select)
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6 changes: 6 additions & 0 deletions testsuite/MDAnalysisTests/analysis/test_pca.py
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Expand Up @@ -133,6 +133,12 @@ def test_no_frames(u):
PCA(u, select=SELECTION).run(stop=1)


def test_can_run_frames(u):
atoms = u.select_atoms(SELECTION)
u.transfer_to_memory()
PCA(u, select=SELECTION).run(frames=[0, 1])
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def test_transform(pca, u):
ag = u.select_atoms(SELECTION)
pca_space = pca.transform(ag, n_components=1)
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