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 <wout@bittremieux.be>

* 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 <32707537+melihyilmaz@users.noreply.github.com>

* 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 <32707537+melihyilmaz@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Wout Bittremieux <wout@bittremieux.be>
Co-authored-by: William Stafford Noble <wnoble@uw.edu>
Co-authored-by: Wout Bittremieux <bittremieux@users.noreply.github.com>

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
 

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: