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fix: Ensure pixi tasks may be run as advertised#4046

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johanneskoester merged 6 commits intosnakemake:mainfrom
TRON-Bioinformatics:4045-build-docs-pixi-task-not-working-as-advertised
Mar 11, 2026
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fix: Ensure pixi tasks may be run as advertised#4046
johanneskoester merged 6 commits intosnakemake:mainfrom
TRON-Bioinformatics:4045-build-docs-pixi-task-not-working-as-advertised

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@jonasfreimuth
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@jonasfreimuth jonasfreimuth commented Mar 11, 2026

Add a constraint to the Pixi workspace for pixi>=0.63 and pin Pixi to v0.63.2 on the CI to ensure the default-environment field is available for tasks and set it for all tasks. This is to ensure that there are no changes to the formula pixi run task, when currently pixi either requires user input or an additional -e environment specification when the environment for a task is ambiguous. This helps to ensure existing workflows depending on the simple formula above don't break.

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).

Existing tests should cover this. Also this PR ensures current documentation is accurate, rather than updating docs to reflect a changed state.

Summary by CodeRabbit

  • Chores
    • Updated CI/CD workflows to remove explicit Pixi version specifications, allowing workflows to use the default Pixi version instead of previously pinned versions.

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coderabbitai bot commented Mar 11, 2026

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 9ff3f74a-be94-4e4c-a620-0bb3025ed9a2

📥 Commits

Reviewing files that changed from the base of the PR and between 45883c5 and ae350f4.

⛔ Files ignored due to path filters (1)
  • pyproject.toml is excluded by !pyproject.toml
📒 Files selected for processing (3)
  • .github/workflows/docs.yml
  • .github/workflows/main.yml
  • .github/workflows/release-please.yml
💤 Files with no reviewable changes (3)
  • .github/workflows/docs.yml
  • .github/workflows/release-please.yml
  • .github/workflows/main.yml

📝 Walkthrough

Walkthrough

Removed explicit Pixi version specifications from GitHub Actions workflow steps across three workflow files. The steps will now use the default or latest available Pixi version instead of pinned versions (v0.42.1, v0.62.2, and v0.47.0).

Changes

Cohort / File(s) Summary
Workflow Configuration
.github/workflows/docs.yml, .github/workflows/main.yml, .github/workflows/release-please.yml
Removed Pixi version pinning from "Install Pixi" or "Set up Pixi" steps. Docs and apidocs jobs removed v0.42.1, formatting and tests jobs removed v0.62.2, and release-please removed v0.47.0. Steps will now use default/latest Pixi version.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

🚥 Pre-merge checks | ✅ 3
✅ Passed checks (3 passed)
Check name Status Explanation
Title check ✅ Passed The title accurately summarizes the main change: ensuring pixi tasks work as advertised by pinning versions and configuring default environments.
Description check ✅ Passed The PR description is comprehensive, explaining the rationale, implementation, and impact of changes, and properly addresses all QC checklist items.
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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@jonasfreimuth jonasfreimuth force-pushed the 4045-build-docs-pixi-task-not-working-as-advertised branch from 2b93adb to 0660835 Compare March 11, 2026 09:37
@jonasfreimuth
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Closes #4046.

@jonasfreimuth jonasfreimuth force-pushed the 4045-build-docs-pixi-task-not-working-as-advertised branch from 0660835 to 0d0cd41 Compare March 11, 2026 09:51
@jonasfreimuth jonasfreimuth changed the title 4045 build docs pixi task not working as advertised fix: Ensure pixi tasks may be run as advertised Mar 11, 2026
To be able to use  for tasks later on.
Latest version should be fine.
So pixi does not ask every time without manual env specification.
So pixi does not ask every time without manual env specification.
So pixi does not ask every time without manual env specification
Not strictly necessary at the moment, but a precaution against
pixi beginning to ask in the future when the publish feature is
added to multiple environments.
@jonasfreimuth jonasfreimuth force-pushed the 4045-build-docs-pixi-task-not-working-as-advertised branch from 50c86eb to ae350f4 Compare March 11, 2026 10:20
@jonasfreimuth jonasfreimuth marked this pull request as ready for review March 11, 2026 10:22
@johanneskoester johanneskoester merged commit 88253c2 into snakemake:main Mar 11, 2026
60 checks passed
@jonasfreimuth jonasfreimuth deleted the 4045-build-docs-pixi-task-not-working-as-advertised branch March 11, 2026 11:22
johanneskoester pushed a commit that referenced this pull request Mar 13, 2026
🤖 I have created a release *beep* *boop*
---


##
[9.17.0](v9.16.3...v9.17.0)
(2026-03-13)


### Features

* Allow storing snakemake metadata in files or databases
([#4012](#4012))
([dd75f31](dd75f31))
* Allow to specify comparison command per-unit test
([#3956](#3956))
([b88171c](b88171c))
* job table orderd topological when run is started
([#4018](#4018))
([75cf506](75cf506))
* lambda functions for priority in rules
([#3253](#3253))
([d2aa226](d2aa226))
* Make on... directive of modules accessible
([#4050](#4050))
([e9f2e1c](e9f2e1c))


### Bug Fixes

* adjust conda tests to not fail on apple silicon; fix
[#4040](#4040)
([#4049](#4049))
([f5b0142](f5b0142))
* allow "--containerize apptainer" to output apptainer format instead of
dockerfile ([#4030](#4030))
([f5cac30](f5cac30))
* apptainer command not recognized when singularity is absent
([#4010](#4010))
([b8162e2](b8162e2))
* capture stderr when tests fail
([#3995](#3995))
([97d74ba](97d74ba))
* **docs:** make Data-dependent conditional execution a complete example
([#4043](#4043))
([3a1d7f2](3a1d7f2))
* don't build the DAG when running unlock. Fixes
[#4000](#4000) and
[#198](#198)
([#4007](#4007))
([acf79fd](acf79fd))
* Ensure pixi tasks may be run as advertised
([#4046](#4046))
([88253c2](88253c2))
* fix checkpoint handling corner cases
([#3870](#3870) and
[#3559](#3559))
([#4015](#4015))
([63f4257](63f4257))
* issue 3642
([#4054](#4054))
([76e6fc2](76e6fc2))
* issue 3815
([#4026](#4026))
([b0eec96](b0eec96))
* logging None in shellcmd context causes error
([#4064](#4064))
([d0652cd](d0652cd))
* lookup function returns default value for empty DataFrame queries
([#4056](#4056))
([f71de97](f71de97))
* make `cache: omit-software` a rule specific property
([#4085](#4085))
([034a9e7](034a9e7))
* reduce number of tests leaving temporary files behind
([#4033](#4033))
([a3a1c97](a3a1c97))
* regression in dynamic resource handling
([#4038](#4038))
([f2c554a](f2c554a))
* somewhat shorter announce message
([#4080](#4080))
([57efc71](57efc71))


### Performance Improvements

* switch reretry with tenacity; decouple container classes (with Python
3.7 compat for old scripts) from rest of the codebase (enabling moving
to newer python versions)
([#4032](#4032))
([ffb19e7](ffb19e7))


### Documentation

* Add AI-assisted contributions policy to contributing guidelines
([#4051](#4051))
([dd70526](dd70526))
* **codebase:** Update & simplify plugin architecture section
([#4052](#4052))
([176cf63](176cf63))
* Correct workflow.source_path() description in documentation
([#4036](#4036))
([45883c5](45883c5))
* fixed wrong code example for collect() function
([#4037](#4037))
([5c85ed8](5c85ed8))
* Minor docs improvements
([#4089](#4089))
([29ea226](29ea226))
* switch to sphinx_design for tabs
([#3976](#3976))
([9674614](9674614))
* typo in the migration table breaking a pip install command
([#4024](#4024))
([66f9dda](66f9dda))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
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