[fmt] Automatically renormalize line endings to \n (LF) (Fixes #5315) by jeremyleung521 · Pull Request #5446 · MDAnalysis/mdanalysis

jeremyleung521 · 2026-07-22T16:52:58Z

Regardless of whether #5445 gets merged in due to AI usage or not, the scope of that PR is to check whether bad commits went through. This preemptively deals with problems before commit + combs through existing files. This PR should be merged before #5445 (since this will solve CI failure on that PR anyways) should #5445 be deemed still needed.

Changes made in this Pull Request:

Added a .gitattributes file to enforce line endings to \n (LF). All files within /testsuite/MDAnalysisTests/data are outside of the scope.
Ran git add --renormalize . to comb over existing files and implement the .gitattributes changes.

With this PR, when staging a file with CRLF, the following message will be displayed:
warning: in the working copy of '/package/MDAnalysis/blahblah', CRLF will be replaced by LF the next time Git touches it
And the changes will be implemented during commit.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

I guess this is a "yes" now that I read the copilot AI overview on GitHub and implemented changes (not exact) based on what was suggested? Otherwise all done manually (i.e. "no").

PR Checklist

Issue raised/referenced?
Tests updated/added?
Documentation updated/added?
package/CHANGELOG file updated?
Is your name in package/AUTHORS? (If it is not, add it!)
LLM/AI disclosure was updated.

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.

Other Considerations:

Thought about just listing .py and .pyx but then there's the .c and .h and .ini and .txt (and the list goes on with README and CHANGELOG...). Might as well let git figure it out instead.

All files in testsuite/MDAnalysisTests/data/ are excluded from the renormalization.

Also for transparency, there were some problems with the following files which required me to manually remove \r (don't know why--they were pesky and behavior very much reproducible with git reset --hard HEAD~1 and rerunning git add --renormalize .) but otherwise should be good now. Rerunning git add --renormalize . after the manual replacement in a fresh clone does not retrigger this problem so I assume it's a one-time thing.

modified: testsuite/MDAnalysisTests/data/adk_closed_NAMD.psf modified: testsuite/MDAnalysisTests/data/gms/surf2wat.gms modified: testsuite/MDAnalysisTests/data/gms/symopt.gms modified: testsuite/MDAnalysisTests/data/gms/symopt.inp modified: testsuite/MDAnalysisTests/data/mol2/BrokenMolecule.mol2 modified: testsuite/MDAnalysisTests/data/mol2/Molecule.mol2 modified: testsuite/MDAnalysisTests/data/mol2/Molecules.mol2

Copilot

Pull request overview

This PR introduces repository-wide line-ending normalization by adding a .gitattributes policy and renormalizing existing files to reduce noisy diffs and prevent CRLF-related CI/lint issues (Fixes #5315).

Changes:

Added .gitattributes intended to enforce LF line endings.
Renormalized existing repository files (many changes are EOL-only).
Updated package/CHANGELOG to record the change.

Reviewed changes

Copilot reviewed 2 out of 94 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
testsuite/MDAnalysisTests/lib/test_log.py	Renormalized line endings (no functional change intended).
testsuite/MDAnalysisTests/lib/test_augment.py	Renormalized line endings (no functional change intended).
testsuite/MDAnalysisTests/data/windows/WIN_wat.lammpstrj	Renormalized line endings in Windows/DOS fixture.
testsuite/MDAnalysisTests/data/windows/WIN_test.arc	Renormalized line endings in Windows/DOS fixture.
testsuite/MDAnalysisTests/data/mol2/Molecule.mol2	Renormalized line endings in test data file.
testsuite/MDAnalysisTests/data/mol2/BrokenMolecule.mol2	Renormalized line endings in test data file.
testsuite/MDAnalysisTests/data/gms/symopt.inp	Renormalized line endings in test input file.
testsuite/MDAnalysisTests/data/gms/surf2wat.gms	Renormalized line endings in test data file.
package/MDAnalysis/lib/_cutil.pxd	Renormalized line endings in Cython declarations.
package/MDAnalysis/coordinates/NAMDBIN.py	Renormalized line endings in coordinate reader/writer module.
package/CHANGELOG	Added an entry describing the `.gitattributes`/renormalization work.
mypy.ini	Renormalized line endings (config file).
mypy_requirements.txt	Renormalized line endings (requirements file).
benchmarks/benchmarks/topology.py	Renormalized line endings in benchmark code.
.gitattributes	New attributes file to define line-ending policy.

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Copilot

Pull request overview

Copilot reviewed 2 out of 94 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (2)

.gitattributes:2

Using * text eol=lf forces Git to treat all files as text, which can corrupt binary assets by applying EOL normalization. This repo contains many binary files (e.g., testsuite/MDAnalysisTests/data/adk_dims.dcd, testsuite/MDAnalysisTests/data/surface.trr, and various *.png docs images), so this should be text=auto (or explicit binary patterns) instead of text.

* text=auto eol=lf

package/CHANGELOG:72

The CHANGELOG entry has minor formatting/wording issues (extra spaces, awkward phrasing, and trailing whitespace). Consider rewording to match surrounding entries and avoid the literal \n being interpreted ambiguously.

 * Added `.gitattributes` to enforce LF (\n)  as line ending, did a renormalize to
   existing files (Issue #5315, PR #5446)

read-the-docs-community · 2026-07-22T17:02:19Z

Documentation build overview

📚 MDAnalysis | 🛠️ Build #33818173 | 📁 Comparing 686c1d7 against latest (0803d88)

🔍 Preview build

8 files changed · ± 8 modified

± Modified

Copilot

Pull request overview

Copilot reviewed 2 out of 94 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

package/CHANGELOG:72

The CHANGELOG entry has awkward phrasing ("did a renormalize") and extra whitespace (double space after ")" and trailing spaces). Rewording it improves clarity and avoids unnecessary whitespace churn.

 * Added `.gitattributes` to enforce LF (\n)  as line ending, did a renormalize to
   existing files (Issue #5315, PR #5446)

IAlibay

May I suggest keeping these changes solely for ".py" files and not everything else? Doing this for binary files (especially TPR files) doesn't seem like a good idea given this isn't "code that was generated with the wrong line endings", but just "how the file actually is".

Copilot

Pull request overview

Copilot reviewed 2 out of 9 changed files in this pull request and generated 2 comments.

jeremyleung521 · 2026-07-22T17:20:27Z

May I suggest keeping these changes solely for ".py" files and not everything else? Doing this for binary files (especially TPR files) doesn't seem like a good idea given this isn't "code that was generated with the wrong line endings", but just "how the file actually is".

Done with a new renormalization commit (force pushed). .gitattributes pattern matching was a bit weird but was able to excluded all files in testsuite/MDAnalysisTests/data/. Thought about just listing .py and .pyx but then there's the .c and .h and .ini and .txt (and the list goes on...)

Copilot

Pull request overview

Copilot reviewed 2 out of 9 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (2)

.gitattributes:6

The current attributes mark all files under testsuite/MDAnalysisTests/data/ as binary, which will also disable text diffs and LF normalization for text-based test data (e.g., .pdb, .gro, .psf). This makes future reviews/blame harder and undermines the goal of consistent LF endings for text files. Consider only marking known binary trajectory/topology formats as binary and leaving text formats as text (so they still get eol=lf).

# Do not touch testsuite data files
testsuite/MDAnalysisTests/data/* binary
testsuite/MDAnalysisTests/data/**/* binary

package/CHANGELOG:72

This new CHANGELOG entry has trailing whitespace at the end of the lines, which tends to create noisy diffs and can trip whitespace-checking tools.

 * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized 
   existing files to conform (Issue #5315, PR #5446)

Copilot

Pull request overview

Copilot reviewed 2 out of 21 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

.gitattributes:7

The testsuite/MDAnalysisTests/data/windows/* fixtures are explicitly intended to have DOS/CRLF line endings (see testsuite/MDAnalysisTests/coordinates/test_windows.py docstring and testsuite/MDAnalysisTests/data/windows/README.md). With text=auto eol=crlf, Git will normalize these files to LF in the committed blob, so any source archives generated from the repository contents (e.g., git archive/sdist) will contain LF files and the “DOS line endings” tests/fixtures won’t actually exercise CRLF.

To preserve CRLF in the repository for these fixtures, they should be marked as -text (no normalization) and the files should be re-added with CRLF line endings (or alternatively, adjust the tests to generate CRLF copies at runtime instead of relying on committed CRLF fixtures).

# Tread carefully with testsuite data files
testsuite/MDAnalysisTests/data/* text=auto eol=lf
testsuite/MDAnalysisTests/data/**/* text=auto eol=lf
testsuite/MDAnalysisTests/data/windows/* text=auto eol=crlf

Copilot

Pull request overview

Copilot reviewed 2 out of 21 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

.gitattributes:7

The .gitattributes rules contradict the comment "Do not touch testsuite data files" and also apply CRLF checkout to every file in testsuite/MDAnalysisTests/data/windows/ (including __init__.py and README.md). This risks reintroducing CRLF into Python/Markdown sources and makes the intent of the Windows fixtures less clear. Consider removing the redundant testsuite/MDAnalysisTests/data/*/**/* overrides (the global * text=auto eol=lf already covers them) and scoping the CRLF rule to the actual Windows fixture files only (e.g., WIN_*).

# Do not touch testsuite data files
testsuite/MDAnalysisTests/data/* text=auto eol=lf
testsuite/MDAnalysisTests/data/**/* text=auto eol=lf
testsuite/MDAnalysisTests/data/windows/* text=auto eol=crlf

Copilot

Pull request overview

Copilot reviewed 2 out of 21 changed files in this pull request and generated 1 comment.

jeremyleung521 · 2026-07-22T19:04:13Z

All should be well now (bar CI to finish). Latest commits fixes problem where turning everything in data/* as binary breaks git diff for text files within data/.

For transparency, there were some problems with the following files which required me to manually remove \r (don't know why--they were pesky and behavior very reproducible) but otherwise should be good now. Rerunning git add --renormalize . (nor does a fresh clone) after the manual replacement does not retrigger this problem so I assume it's a one-time thing.

	modified:   testsuite/MDAnalysisTests/data/adk_closed_NAMD.psf
	modified:   testsuite/MDAnalysisTests/data/gms/surf2wat.gms
	modified:   testsuite/MDAnalysisTests/data/gms/symopt.gms
	modified:   testsuite/MDAnalysisTests/data/gms/symopt.inp
	modified:   testsuite/MDAnalysisTests/data/mol2/BrokenMolecule.mol2
	modified:   testsuite/MDAnalysisTests/data/mol2/Molecule.mol2
	modified:   testsuite/MDAnalysisTests/data/mol2/Molecules.mol2

Copilot

Pull request overview

Copilot reviewed 2 out of 21 changed files in this pull request and generated 1 comment.

jeremyleung521 · 2026-07-22T19:19:51Z

+# Data files from testsuite/MDAnalysisTests/data/windows/* need to end with CRLF for Windows testing
+testsuite/MDAnalysisTests/data/windows/* text=auto eol=crlf


Rather leave auto in so any future windows-only test binary files are exempted so no one has to think about it in the future. I don't think text attribute determination is ever documented to have different behaviors across platforms. There were some problems with git <2.10 but that is over 10 years old at this point.

codecov · 2026-07-22T20:48:40Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (83bc9a2) to head (686c1d7).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5446   +/-   ##
========================================
  Coverage    93.87%   93.87%           
========================================
  Files          182      182           
  Lines        22510    22510           
  Branches      3202     3202           
========================================
  Hits         21131    21131           
  Misses         917      917           
  Partials       462      462

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orbeckst

Can you structure the commit history as two commits

line ending fixes
changes to config and metadata (gitattributes, CHANGELOG, ...) AND add the SHA256 of commit (1) to .git-blame-ignore-revs

Then we can merge the whole PR and be sure that git-blame is not polluted by the line changes.

…Analysis#5446)

IAlibay

Thanks, this looks good to me.

Copilot AI review requested due to automatic review settings July 22, 2026 16:52

jeremyleung521 added the enhancement label Jul 22, 2026

Copilot started reviewing on behalf of jeremyleung521 July 22, 2026 16:53 View session