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ci: bump pixi version in actions#3903

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cademirch merged 3 commits intosnakemake:mainfrom
cademirch:ci-max-parallel
Jan 5, 2026
Merged

ci: bump pixi version in actions#3903
cademirch merged 3 commits intosnakemake:mainfrom
cademirch:ci-max-parallel

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@cademirch cademirch commented Jan 4, 2026 •
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Pixi install github action is failing with "failed to parse pypi name mapping" errors likely due to rate limiting when 30+ jobs are kicked off nearly simultaneously

I tested this fix on #3820 since the tests kept failing due to the pixi install action failing. After committing this change, the actions ran successfully.

In this failing run's debug logs we see:

pixi install -e py311
[...]
   WARN resolve_conda{group=py313 platform=win-64}: reqwest_retry::middleware: Retry attempt #1. Sleeping 1.225245051s before the next attempt
  Error:   × failed to parse pypi name mapping
    ├─▶ error decoding response body
    ╰─▶ expected value at line 1 column 1

This warning is repeated many times until finally pixi stops retrying - this is what suggested to me that some sort of rate limit was the issue.

One downside is that this does make the CI take a bit longer to run. We could consider using the cache feature of the pixi action. And turning up the max-parallel, or reducing the number of test-groups

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

Summary by CodeRabbit

  • Chores
    • Updated development toolchain dependencies for improved build and test infrastructure.

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@cademirch
ci: reduce concurrent jobs to fix install failures
3d45380 
Pixi install is failing with "failed to parse pypi name mapping" errors
likely due to rate limiting when 30+ jobs are kicked off nearly simultaneously
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coderabbitai bot commented Jan 4, 2026 •
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📝 Walkthrough

Walkthrough

Bumps pixi-version from v0.42.1 to v0.62.2 in two Install Pixi steps within the GitHub Actions workflow; no other logic, step, or file changes were introduced.

Changes

Cohort / File(s) Summary
GitHub Actions Workflow
.github/workflows/main.yml		 Updated two Install Pixi steps to change pixi-version from v0.42.1 → v0.62.2. No other workflow steps or logic modified.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)
Check name Status Explanation
Description check ✅ Passed The description is comprehensive and addresses the root cause analysis, provides testing evidence, and includes QC checklist items, though the checklist items remain unchecked.
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Title check ✅ Passed The PR title states 'ci: bump pixi version in actions' which directly corresponds to the main change in the pull request—updating the pixi version from v0.42.1 to v0.62.2 in CI workflow steps.
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Actionable comments posted: 0

🧹 Nitpick comments (1)
.github/workflows/main.yml (1)

81-82: Consider enabling cache for additional reliability improvements.

The Pixi version is consistently upgraded across both jobs, which is good. However, the PR description mentions "considering using the Pixi action's cache feature." Enabling caching could further reduce install load and improve reliability, potentially complementing the max-parallel fix.

If the "no pixi.lock" comment indicates a blocker for enabling cache, consider if adding a lock file would be beneficial for this project.

💡 Suggested change to enable cache

If a pixi.lock file can be added to the repository:

-          cache: false # no pixi.lock
-          locked: false
+          cache: true
+          locked: true

Note: This would require generating and committing a pixi.lock file first.

📜 Review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between f46d904 and 218c6f6.

📒 Files selected for processing (1)
  • .github/workflows/main.yml
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (9)
  • GitHub Check: tests (2, windows-2022, py313)
  • GitHub Check: tests (2, ubuntu-latest, py311)
  • GitHub Check: tests (2, ubuntu-latest, py312)
  • GitHub Check: tests (1, ubuntu-latest, py313)
  • GitHub Check: tests (2, ubuntu-latest, py313)
  • GitHub Check: tests (1, windows-2022, py313)
  • GitHub Check: tests (1, macos-latest, py313)
  • GitHub Check: tests (1, ubuntu-latest, py311)
  • GitHub Check: tests (1, ubuntu-latest, py312)
🔇 Additional comments (2)
.github/workflows/main.yml (2)

49-49: Good solution to mitigate rate limiting.

Setting max-parallel: 10 effectively addresses the rate limiting issue by preventing all ~50 matrix jobs from starting simultaneously. This reduces concurrent Pixi installs from 50 to 10, which should stay well below the rate limit threshold mentioned in the PR description.

Note: This will increase total CI runtime as jobs queue, but it's a reasonable trade-off for reliability.

28-28: No action needed. Pixi v0.62.2 is a compatible stable release that works with setup-pixi@v0.9.3. The version bump is safe and includes caching-related bug fixes relevant to your CI configuration.

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melund commented Jan 4, 2026 •
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@cademirch Did you try just updating the pixi version by it self?

I guess the guys at prefix may want to know about this. I have mentioned the issue on their discord..

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cademirch commented Jan 4, 2026

@cademirch Did you try just updating the pixi version by it self?

I guess the guys at prefix may want to know about this. I have mentioned the issue on their discord?

Yeah good question - I'll test that

@cademirch cademirch changed the title ci: reduce concurrent jobs to fix install failures ci: bump pixi version in actions Jan 5, 2026
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cademirch commented Jan 5, 2026

Seems like bumping the version worked by itself. If we see more failures like in my initial comment we reevaluate.

@cademirch cademirch merged commit 3dffc17 into snakemake:main Jan 5, 2026
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@melund melund melund approved these changes

@johanneskoester johanneskoester Awaiting requested review from johanneskoester johanneskoester is a code owner

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@cademirch @melund