Propose Casanovo GSoC project

[bittremieux]

Summary by CodeRabbit

• Documentation
  • Updated GSoC 2026 project pages to introduce Theme D: a Machine Learning Engineering track centered on real-time Casanovo de novo sequencing, including mentors, skills, and timelines.
  • Reworked Theme C and project goals to emphasize real-time sequencing, non‑autoregressive inference, transformer considerations, and concrete performance targets (20–100 Hz).
  • Shifted focus from visualization to performance, profiling, optimization, and model distillation.

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

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📝 Walkthrough

Walkthrough

Updates the GSoC 2026 news file to replace prior project content with a new Theme D focused on real-time Casanovo de novo sequencing, adding mentors, required skills, narrative project goals, performance targets (20–100 Hz), and emphasis on profiling, optimization, and model distillation.

Changes

Cohort / File(s)	Summary
GSoC 2026 News content/en/news/GSoC2026.md	Replaces earlier visualization/targeted-spectrum project text with a Casanovo-focused Theme D: adds mentor and skills details, converts goals to narrative form, sets real-time inference targets (20–100 Hz), and reorients Theme C/D content toward profiling, optimization, and model distillation.

Possibly related PRs

• Update GSoC2026.md with new project themes #243: Edited Theme C and related GSoC2026.md content (visualization/targeted-spectrum) that this PR replaces.

Suggested reviewers

• tjeerdijk

Poem

🐰 In the lab where mass specs hum and whirr,
I hop with models fast and sure,
Casanovo sings at fifty Hertz or more,
Profiles trimmed, distilled to core,
GSoC leaps — a rabbit's cheerful purr! ✨

🚥 Pre-merge checks | ✅ 3 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	No pull request description was provided by the author, but the template requires a brief description of what is fixed or changed.	Add a description explaining the Casanovo GSoC project proposal, including key details about the ML engineering project, real-time sequencing goals, and why this project was added to the GSoC offerings.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Propose Casanovo GSoC project' clearly and specifically summarizes the main change—introducing a new Machine Learning GSoC project focused on Casanovo de novo sequencing.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Merge Conflict Detection	✅ Passed	✅ No merge conflicts detected when merging into main

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

content/en/news/GSoC2026.md (1)

180-185: Minor formatting inconsistency in bullet point punctuation.

Line 185 has awkward spacing before the period ("the observed ones ."). Consider either removing the trailing period for consistency or fixing the spacing.

✏️ Proposed fix for spacing

-- Intuitive feature (m/z and mass) visualization for quantitative analysis validation, to support exact and quick comparison between theoretical feature traces of quantified proteoforms and the observed ones .
+- Intuitive feature (m/z and mass) visualization for quantitative analysis validation, to support exact and quick comparison between theoretical feature traces of quantified proteoforms and the observed ones.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@content/en/news/GSoC2026.md` around lines 180 - 185, Minor formatting
inconsistency: remove the extra space before the period in the bullet text "the
observed ones ." or remove the trailing period entirely for consistency with
other bullets; locate the bullet list in the GSoC2026.md content (the line
containing "Intuitive feature (m/z and mass) visualization for quantitative
analysis validation, to support exact and quick comparison between theoretical
feature traces of quantified proteoforms and the observed ones .") and fix the
spacing so it reads either "...the observed ones." or "...the observed ones" to
match the punctuation style of the other list items.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@content/en/news/GSoC2026.md`:
- Line 200: Replace the misspelled token "spectometer" with the correct spelling
"spectrometer" in the sentence that begins "A version of Casanovo capable of
real-time sequencing..." so the line reads "...will enable the mass spectrometer
to make decisions..." (replace "spectometer" → "spectrometer").

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Nitpick comments:
In `@content/en/news/GSoC2026.md`:
- Around line 180-185: Minor formatting inconsistency: remove the extra space
before the period in the bullet text "the observed ones ." or remove the
trailing period entirely for consistency with other bullets; locate the bullet
list in the GSoC2026.md content (the line containing "Intuitive feature (m/z and
mass) visualization for quantitative analysis validation, to support exact and
quick comparison between theoretical feature traces of quantified proteoforms
and the observed ones .") and fix the spacing so it reads either "...the
observed ones." or "...the observed ones" to match the punctuation style of the
other list items.