Skip to content

DOC: fix doctest output in transformations.py for newer NumPy #5283

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 7 commits into
base: develop
Choose a base branch
from
Open

DOC: fix doctest output in transformations.py for newer NumPy #5283

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
219a9a5
DOC: fix doctest output in transformations.py for newer NumPy
Kd1880 Mar 6, 2026
7493437
DOC: add myself to AUTHORS
Kd1880 Mar 6, 2026
b1f0f29
DOC: resolve merge conflict in AUTHORS
Kd1880 Mar 6, 2026
d0e2e54
DOC: update CHANGELOG for PR #5283
Kd1880 Mar 10, 2026
044c5d5
DOC: fix CHANGELOG to only include transformations.py entry
Kd1880 Mar 11, 2026
059a83f
DOC: fix CHANGELOG and AUTHORS as per review
Kd1880 Mar 19, 2026
f6865c3
Merge branch 'develop' into fix/doctest-transformations
Kd1880 Mar 19, 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
1 change: 1 addition & 0 deletions package/AUTHORS
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -273,6 +273,7 @@ Chronological list of authors
- Kushagar Garg
- Jeremy M. G. Leung
- Harshit Gajjela
- Kriti Dogra
Copy link
Copy Markdown
Contributor

@jeremyleung521 jeremyleung521 Mar 16, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Place your name at the bottom of the list.

- Kunj Sinha

External code
Expand Down
4 changes: 4 additions & 0 deletions package/CHANGELOG
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,10 @@ The rules for this file:

Fixes
* Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
* Fix doctest output in transformations.py for newer NumPy
Copy link
Copy Markdown
Contributor

@jeremyleung521 jeremyleung521 Mar 16, 2026 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Your changes deleted someone else's line. Please restore that.

Also the two lines you added should be a single line.

Copy link
Copy Markdown
Author

@Kd1880 Kd1880 Mar 19, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hi, I’ve addressed the requested changes and resolved merge conflicts.
Kindly review again. Thanks!

(Issue #3925, PR #5283)
* Fix doctest in util.py for platform-dependent path output
(Issue #3925, PR #5285)
* Fixed bug in add_transformations allowing non-callable transformations
(Issue #2558, PR #2558)
* Drop/Replace lock file test in test_xdr (Issue #5236, PR #5237)
Expand Down
2 changes: 1 addition & 1 deletion package/MDAnalysis/lib/transformations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -795,7 +795,7 @@ def decompose_matrix(matrix):
>>> S = scale_matrix(0.123)
>>> scale, shear, angles, trans, persp = decompose_matrix(S)
>>> scale[0]
0.123
np.float64(0.123)
>>> R0 = euler_matrix(1, 2, 3)
>>> scale, shear, angles, trans, persp = decompose_matrix(R0)
>>> R1 = euler_matrix(*angles)
Expand Down
Loading