Allow csv to handle all newlines (#316)

* Add 9-species model weights link to FAQ (#303) * Add model weights link * Generate new screengrabs with rich-codex * Clarify that these weights should only be used for benchmarking --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <[email protected]> * Add FAQ entry about antibody sequencing (#304) * Add FAQ entry about antibody sequencing * Generate new screengrabs with rich-codex --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Melih Yilmaz <[email protected]> * Allow csv to handle all newlines The `csv` module tries to handle newlines itself. On Windows, this leads to line endings of `\r\r\n` instead of `\r\n`. Setting `newline=''` produces the intended output on both platforms. * Update CHANGELOG.md * Fix linting issue * Delete docs/images/help.svg --------- Co-authored-by: Melih Yilmaz <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: William Stafford Noble <[email protected]> Co-authored-by: Wout Bittremieux <[email protected]>
Noble-Lab · Mar 25, 2024 · cac0f4e · cac0f4e
1 parent 6eabd6e
commit cac0f4e
Show file tree

Hide file tree

Showing 3 changed files with 2 additions and 60 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Fixed
 
 - Fix beam search caching failure when multiple beams have an equal predicted peptide score by breaking ties randomly.
+- The mzTab output file now has proper line endings regardless of platform, fixing the extra `\r` found when run on Windows.
 
 ## [4.1.0] - 2024-02-16
 

diff --git a/casanovo/data/ms_io.py b/casanovo/data/ms_io.py
@@ -147,7 +147,7 @@ def save(self) -> None:
         """
         Export the spectrum identifications to the mzTab file.
         """
-        with open(self.filename, "w") as f:
+        with open(self.filename, "w", newline="") as f:
             writer = csv.writer(f, delimiter="\t", lineterminator=os.linesep)
             # Write metadata.
             for row in self.metadata:

diff --git a/docs/images/help.svg b/docs/images/help.svg