Skip to content

DOC: fix doctests in pca.py for newer NumPy output format #5301

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Kd1880 wants to merge 2 commits into
base: develop
Choose a base branch
from
+14 −12
Open

DOC: fix doctests in pca.py for newer NumPy output format #5301

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
09c580f
DOC: fix doctests in pca.py for newer NumPy output format
Kd1880 Mar 11, 2026
394b382
DOC: update CHANGELOG for PR #5301
Kd1880 Mar 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions package/CHANGELOG
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ The rules for this file:
* 2.11.0

Fixes
* Fix doctests in pca.py for newer NumPy output format and testsetup blocks
(Issue #3925, PR #5301)
* Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
* Fixed bug in add_transformations allowing non-callable transformations
(Issue #2558, PR #2558)
Expand Down
24 changes: 12 additions & 12 deletions package/MDAnalysis/analysis/pca.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -688,10 +688,10 @@ def rmsip(self, other, n_components=None):

.. testsetup::

>>> import MDAnalysis as mda
>>> import MDAnalysis.analysis.pca as pca
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
import MDAnalysis as mda
import MDAnalysis.analysis.pca as pca
from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)


You can compare the RMSIP between different intervals of the same trajectory.
Expand All @@ -703,9 +703,9 @@ def rmsip(self, other, n_components=None):
>>> second_interval = pca.PCA(u, select="backbone").run(start=25, stop=50)
>>> last_interval = pca.PCA(u, select="backbone").run(start=75)
>>> round(first_interval.rmsip(second_interval, n_components=3), 6)
0.381476
np.float64(0.381476)
>>> round(first_interval.rmsip(last_interval, n_components=3), 6)
0.174782
np.float64(0.174782)


See also
Expand Down Expand Up @@ -870,10 +870,10 @@ def rmsip(a, b, n_components=None):

.. testsetup::

>>> import MDAnalysis as mda
>>> import MDAnalysis.analysis.pca as pca
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
import MDAnalysis as mda
import MDAnalysis.analysis.pca as pca
from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)


You can compare the RMSIP between different intervals of the same trajectory.
Expand All @@ -887,11 +887,11 @@ def rmsip(a, b, n_components=None):
>>> round(pca.rmsip(first_interval.results.p_components.T,
... second_interval.results.p_components.T,
... n_components=3), 6)
0.381476
np.float64(0.381476)
>>> round(pca.rmsip(first_interval.results.p_components.T,
... last_interval.results.p_components.T,
... n_components=3), 6)
0.174782
np.float64(0.174782)


.. versionadded:: 1.0.0
Expand Down
Loading