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docs: Updating contributing guidelines with new pixi dev setup#3415

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johanneskoester merged 7 commits intosnakemake:mainfrom
jjjermiah:jjjermiah/3414-docs-add-contributing-guidelines-for-dev-setup-using-pixi
Mar 13, 2025
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docs: Updating contributing guidelines with new pixi dev setup#3415
johanneskoester merged 7 commits intosnakemake:mainfrom
jjjermiah:jjjermiah/3414-docs-add-contributing-guidelines-for-dev-setup-using-pixi

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@jjjermiah jjjermiah commented Mar 13, 2025 •
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closes #3414

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

  • Documentation
    • Added a new section on "Development with pixi" outlining its features and advantages.
    • Introduced a "Testing Guide using pixi" with instructions for activating environments and running tests.
    • Updated the "Documentation Setup" section to reflect the use of pixi for building documentation with improved commands.
    • Enhanced overall documentation to facilitate the transition from conda to pixi in development and testing workflows.

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📝 Walkthrough

Walkthrough

The pull request introduces updates to the contribution documentation by integrating the pixi tool for environment management in place of conda. It includes new sections on installation, environment switching, testing across various Python versions, and building documentation with pixi. Additionally, the GitHub Actions workflow for documentation builds is overhauled to utilize pixi, reflecting a significant shift in dependency management and command execution.

Changes

File(s) Change Summary
docs/.../contributing.rst Added new sections: Development with pixi, Testing Guide using pixi, and Documentation Setup detailing commands for environment management, various test executions, and documentation builds using pixi.
.github/workflows/docs.yml Updated the documentation build process to use pixi for managing dependencies and executing build commands, replacing the previous Python and pip setup.

Sequence Diagram(s)

sequenceDiagram
    participant Dev as Developer
    participant CLI as Terminal/CLI
    participant Pixi as pixi Tool
    participant Env as Environment Manager
    participant Test as Test Runner

    Dev->>CLI: Execute pixi command for environment setup
    CLI->>Pixi: Parse command to switch environment (dev, py311, py312)
    Pixi->>Env: Activate specified environment
    Env-->>Pixi: Environment activated
    Pixi-->>CLI: Confirmation message
    Dev->>CLI: Execute pixi test command (test-all, test-simple, individual tests)
    CLI->>Pixi: Forward testing command
    Pixi->>Test: Run tests in the active environment
    Test-->>Pixi: Test results
    Pixi-->>CLI: Display test output
Loading 
sequenceDiagram
    participant Dev as Developer
    participant CLI as Terminal/CLI
    participant Pixi as pixi Tool
    participant Doc as Documentation Builder

    Dev->>CLI: Execute pixi command for documentation build or live server
    CLI->>Pixi: Parse documentation task (list tasks, build docs, launch live server)
    Pixi->>Doc: Trigger documentation build process or start live-reload server
    Doc-->>Pixi: Deliver build output/status
    Pixi-->>CLI: Display documentation build result or server URL
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Possibly related PRs

Suggested labels

enhancement, hackathon-2025

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  • matthewfeickert

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🔇 Additional comments (2)
docs/project_info/contributing.rst (2)

144-211: Clear and Informative "Testing Guide using pixi" Section

The "Testing Guide using pixi" section is well structured and clearly explains prerequisites, environment activation, and the available testing commands. The inclusion of code blocks makes it easy for contributors to follow along. Excellent work integrating these details.

267-306: Concise "Documentation Setup" Section Using pixi

The updated "Documentation Setup" section provides clear instructions on managing the docs environment with pixi. The step-by-step command examples—including listing tasks, building docs, and running a live server—enhance the contributor experience. Great clarity and organization.

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Actionable comments posted: 1

🧹 Nitpick comments (2)
docs/project_info/contributing.rst (2)

88-125: Header Underline and Punctuation in "Development with pixi" Section

The new "Development with pixi" section (lines 88–125) is clear and well structured. However, the header underline on line 91 appears too short compared to the header text, which is triggering a pipeline warning. Please extend the underline so that its length meets or exceeds the length of "Development with pixi". Also, on line 93, there is a missing space after the period in "environment.It"—adding a space will improve readability.

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[warning] 91-91: Title underline too short.

144-147: Testing Guide Header Underline Too Short

The header for "Testing Guide using pixi" (lines 146–147) has an underline that is shorter than the header text, as highlighted by the pipeline warning. Please update the underline on line 147 to match or exceed the title's length to meet reStructuredText formatting requirements.

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[warning] 147-147: Title underline too short.

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docs/project_info/contributing.rst

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[warning] 5-5: Duplicate explicit target name: 'sphinx'.

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sonarqubecloud bot commented Mar 13, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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Actionable comments posted: 0

🧹 Nitpick comments (2)
.github/workflows/docs.yml (1)

28-28: Remove Trailing Spaces
YAMLlint has flagged trailing spaces on this line. Please remove any extraneous whitespace to conform to YAML best practices.

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[error] 28-28: trailing spaces

(trailing-spaces)

docs/project_info/contributing.rst (1)

88-97: New "Development with pixi" Section Introduced
This section clearly explains the role of Pixi as a modern alternative to Conda, providing benefits such as easy installation, streamlined environment management, and multiple environment support.
Minor nitpick: On line 93, there is a punctuation issue where "development environment.It" should read "development environment. It" to improve readability.

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🔇 Additional comments (8)
.github/workflows/docs.yml (5)

21-27: Pixi Installation Step Configuration is Clear
The new step uses the prefix-dev/setup-pixi action (v0.8.3) to install Pixi with the specified settings (i.e. environments: "docs", pixi-version: v0.42.1, and caching/locking disabled). This is aligned with the updated documentation build process.

29-32: Build Docs Step Using Pixi
Switching the build command to use pixi run --environment docs build-docs correctly reflects the new workflow. Verify that this command is fully compatible with your Pixi configuration.

44-52: Pixi Installation for API Docs is Configured Correctly
The API documentation job replicates the Pixi installation step and uses the correct settings (same Pixi version and environment) as the docs job. This consistency helps ensure that both documentation types are built similarly.

53-56: Build API Docs Step is Up-to-Date
The build step now runs pixi run --environment docs build-apidocs, which aligns with the new documentation process. Double-check that the API docs build output is generated in the expected location.

57-62: Artifact Uploads are Consistent
Both artifact upload steps (for docs and apidocs) use the proper paths. Ensure that the directory names match those produced by the Pixi build commands.

docs/project_info/contributing.rst (3)

144-147: Anchor for Pixi Testing Guide Added
The addition of the anchor .. _pixi-test-guide: prepares the document well for cross-referencing the new Testing Guide section.

146-210: Comprehensive Testing Guide using Pixi
The new section, "Testing Guide using pixi", provides detailed instructions on how to activate the different testing environments (dev, py311, py312) and run various test suites using Pixi commands. Ensure that the references (for example, to pyproject.toml for environment definitions) remain accurate as the project evolves.

271-306: Updated Documentation Setup Section with Pixi Tasks
The "Documentation Setup" section now leverages Pixi to list available tasks and execute documentation builds or start a live-reload server. The command examples (e.g., $ ➜ pixi task list --environment docs) are clear and instructive. Double-check that these examples render correctly and that any specialized symbols (like the arrow) do not cause confusion.

@jjjermiah jjjermiah added the documentation Improvements or additions to documentation label Mar 13, 2025
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Actionable comments posted: 0

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

28-28: Remove Trailing Spaces
YAMLlint detected trailing spaces on line 28. Removing these trailing whitespaces will help avoid linter errors.

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[error] 28-28: trailing spaces

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🔇 Additional comments (4)
.github/workflows/docs.yml (4)

21-27: Pixi Installation Step Updated
The new "Install Pixi" step uses prefix-dev/setup-pixi@v0.8.3 with proper parameters for the docs environment (including version, cache, and lock settings). This aligns with the new Pixi-based development setup.

29-31: Build Docs Command Update
The build command has been updated to use pixi run --environment docs build-docs, which correctly reflects the new documentation build process. Ensure this command executes successfully in the CI environment.

45-51: Pixi Installation in API Docs Job
The API docs job now also installs Pixi with the same configuration as the docs job. This maintains consistency across the workflows and meets the updated guidelines.

53-55: Build API Docs Command Update
The command pixi run --environment docs build-apidocs correctly replaces the old make-based build command for API documentation, aligning with the new Pixi setup.

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Actionable comments posted: 1

🧹 Nitpick comments (2)
docs/project_info/contributing.rst (2)

144-211: Good: Comprehensive and Clear Testing Guide Using pixi

The "Testing Guide using pixi" section is well-organized and provides clear, step-by-step instructions for:

  • Verifying prerequisites,
  • Activating various testing environments (e.g., dev, py311, py312), and
  • Running different test suites through concrete command examples.

One minor suggestion is to include a reference (or a hyperlink) to the official Pixi installation instructions for contributors who might be new to Pixi. This would further enhance the clarity and self-containment of the guide.

271-306: Approval: Clear Documentation Setup with pixi Integration

The updated "Documentation Setup" section effectively outlines how to:

  • Check available documentation tasks,
  • Build the documentation (via the build-docs task), and
  • Serve the documentation locally with live reload (via the docs task).

The use of practical code blocks with console commands enhances readability. One minor nitpick: consider verifying that the Unicode arrow (➜) used in the command prompt (line 278) displays consistently across all terminal environments. If there's any compatibility concern, you might opt for a plain dollar sign prompt.

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@johanneskoester johanneskoester merged commit 8e95a12 into snakemake:main Mar 13, 2025
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@github-project-automation github-project-automation bot moved this from In review to Done in Snakemake Hackathon March 2025 Mar 13, 2025
@github-actions github-actions bot mentioned this pull request Mar 13, 2025
Merged
@coderabbitai coderabbitai bot mentioned this pull request Mar 14, 2025
Merged
johanneskoester pushed a commit that referenced this pull request Mar 14, 2025
@github-actions @snakemake-bot
chore(main): release 9.0.0 (#3380)
4d778fb 
🤖 I have created a release *beep* *boop*
---


##
[9.0.0](v8.30.0...v9.0.0)
(2025-03-14)


### ⚠ BREAKING CHANGES

* Logging refactor & add LoggerPluginInterface
([#3107](#3107))

### Features

* [#3412](#3412) - keep
shadow folder of failed job if --keep-incomplete flag is set.
([#3430](#3430))
([22978c3](22978c3))
* add flag --report-after-run to automatically generate the report after
a successfull workflow run
([#3428](#3428))
([b0a7f03](b0a7f03))
* add flatten function to IO utils
([#3424](#3424))
([67fa392](67fa392))
* add helper functions to parse input files
([#2918](#2918))
([63e45a7](63e45a7))
* Add option to print redacted file names
([#3089](#3089))
([ba4d264](ba4d264))
* add support for validation of polars dataframe and lazyframe
([#3262](#3262))
([c7473a6](c7473a6))
* added support for rendering dag with mermaid js
([#3409](#3409))
([7bf8381](7bf8381))
* adding --replace-workflow-config to fully replace workflow configs
(from config: directive) with --configfile, instead of merging them
([#3381](#3381))
([47504a0](47504a0))
* Dynamic module name
([#3401](#3401))
([024dc32](024dc32))
* Enable saving and reloading IOCache object
([#3386](#3386))
([c935953](c935953))
* files added in rule params with workflow.source_path will be available
in used containers
([#3385](#3385))
([a6e45bf](a6e45bf))
* Fix keep_local in storage directive and more freedom over remote
retrieval behaviour
([#3410](#3410))
([67b4739](67b4739))
* inherit parameters of use rule and extend/replace individual items
them when using 'with' directive
([#3365](#3365))
([93e4b92](93e4b92))
* Logging refactor & add LoggerPluginInterface
([#3107](#3107))
([86f1d6e](86f1d6e))
* Maximal file size for checksums
([#3368](#3368))
([b039f8a](b039f8a))
* Modernize package configuration using Pixi
([#3369](#3369))
([77992d8](77992d8))
* multiext support for named input/output
([#3372](#3372))
([05e1378](05e1378))
* optionally auto-group jobs via temp files in case of remote execution
([#3378](#3378))
([cc9bba2](cc9bba2))


### Bug Fixes

* `--delete-all-output` ignores `--dry-run`
([#3265](#3265))
([23fef82](23fef82))
* 3342 faster touch runs and warning messages for non-existing files
([#3398](#3398))
([cd9c3c3](cd9c3c3))
* add default value to max-jobs-per-timespan
([#3043](#3043))
([2959abe](2959abe))
* checkpoints inside modules are overwritten
([#3359](#3359))
([fba3ac7](fba3ac7))
* Convert Path to IOFile
([#3405](#3405))
([c58684c](c58684c))
* Do not perform storage object cleanup with --keep-storage-local-copies
set ([#3358](#3358))
([9a6d14b](9a6d14b))
* edgecases of source deployment in case of remote execution
([#3396](#3396))
([5da13be](5da13be))
* enhance error message formatting for strict DAG-building mode
([#3376](#3376))
([a1c39ee](a1c39ee))
* fix bug in checkpoint handling that led to exceptions in case
checkpoint output was missing upon rerun
([#3423](#3423))
([8cf4a2f](8cf4a2f))
* force check all required outputs
([#3341](#3341))
([495a4e7](495a4e7))
* group job formatting
([#3442](#3442))
([f0b10a3](f0b10a3))
* in remote jobs, upload storage in topological order such that
modification dates are preserved (e.g. in case of group jobs)
([#3377](#3377))
([eace08f](eace08f))
* only skip eval when resource depends on input
([#3374](#3374))
([4574c92](4574c92))
* Prevent execution of conda in apptainer when not explicitly requested
in software deployment method
([#3388](#3388))
([c43c5c0](c43c5c0))
* print filenames with quotes around them in RuleException
([#3269](#3269))
([6baeda5](6baeda5))
* Re-evaluation of free resources
([#3399](#3399))
([6371293](6371293))
* ReadTheDocs layout issue due to src directory change
([#3419](#3419))
([695b127](695b127))
* robustly escaping quotes in generated bash scripts (v2)
([#3297](#3297))
([#3389](#3389))
([58720bd](58720bd))
* Show apptainer image URL in snakemake report
([#3407](#3407))
([45f0450](45f0450))
* Update ReadTheDocs configuration for documentation build to use Pixi
([#3433](#3433))
([3f227a6](3f227a6))


### Documentation

* Add pixi setup instructions to general use tutorial
([#3382](#3382))
([115e81b](115e81b))
* fix contribution section heading levels, fix docs testing setup order
([#3360](#3360))
([051dc53](051dc53))
* fix link to github.com/snakemake/poetry-snakemake-plugin
([#3436](#3436))
([ec6d97c](ec6d97c))
* fix quoting
([#3394](#3394))
([b40f599](b40f599))
* fix rerun-triggers default
([#3403](#3403))
([4430e23](4430e23))
* fix typo 'safe' -&gt; 'save'
([#3384](#3384))
([7755861](7755861))
* mention code formatting in the contribution section
([#3431](#3431))
([e8682b7](e8682b7))
* remove duplicated 'functions'.
([#3356](#3356))
([7c595db](7c595db))
* update broken links documentation
([#3437](#3437))
([e3d0d88](e3d0d88))
* Updating contributing guidelines with new pixi dev setup
([#3415](#3415))
([8e95a12](8e95a12))

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

Co-authored-by: snakemake-bot <snakemake-bot-admin@googlegroups.com>
@coderabbitai coderabbitai bot mentioned this pull request May 19, 2025
Merged
2 tasks
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@jjjermiah @kjohnsen
docs: Updating contributing guidelines with new pixi dev setup (snake…
8553d80 
…make#3415)

closes snakemake#3414 

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] 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).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Documentation**
- Added a new section on "Development with pixi" outlining its features
and advantages.
- Introduced a "Testing Guide using pixi" with instructions for
activating environments and running tests.
- Updated the "Documentation Setup" section to reflect the use of pixi
for building documentation with improved commands.
- Enhanced overall documentation to facilitate the transition from conda
to pixi in development and testing workflows.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@github-actions @snakemake-bot @kjohnsen
chore(main): release 9.0.0 (snakemake#3380)
9ab6028 
🤖 I have created a release *beep* *boop*
---


##
[9.0.0](snakemake/snakemake@v8.30.0...v9.0.0)
(2025-03-14)


### ⚠ BREAKING CHANGES

* Logging refactor & add LoggerPluginInterface
([snakemake#3107](snakemake#3107))

### Features

* [snakemake#3412](snakemake#3412) - keep
shadow folder of failed job if --keep-incomplete flag is set.
([snakemake#3430](snakemake#3430))
([22978c3](snakemake@22978c3))
* add flag --report-after-run to automatically generate the report after
a successfull workflow run
([snakemake#3428](snakemake#3428))
([b0a7f03](snakemake@b0a7f03))
* add flatten function to IO utils
([snakemake#3424](snakemake#3424))
([67fa392](snakemake@67fa392))
* add helper functions to parse input files
([snakemake#2918](snakemake#2918))
([63e45a7](snakemake@63e45a7))
* Add option to print redacted file names
([snakemake#3089](snakemake#3089))
([ba4d264](snakemake@ba4d264))
* add support for validation of polars dataframe and lazyframe
([snakemake#3262](snakemake#3262))
([c7473a6](snakemake@c7473a6))
* added support for rendering dag with mermaid js
([snakemake#3409](snakemake#3409))
([7bf8381](snakemake@7bf8381))
* adding --replace-workflow-config to fully replace workflow configs
(from config: directive) with --configfile, instead of merging them
([snakemake#3381](snakemake#3381))
([47504a0](snakemake@47504a0))
* Dynamic module name
([snakemake#3401](snakemake#3401))
([024dc32](snakemake@024dc32))
* Enable saving and reloading IOCache object
([snakemake#3386](snakemake#3386))
([c935953](snakemake@c935953))
* files added in rule params with workflow.source_path will be available
in used containers
([snakemake#3385](snakemake#3385))
([a6e45bf](snakemake@a6e45bf))
* Fix keep_local in storage directive and more freedom over remote
retrieval behaviour
([snakemake#3410](snakemake#3410))
([67b4739](snakemake@67b4739))
* inherit parameters of use rule and extend/replace individual items
them when using 'with' directive
([snakemake#3365](snakemake#3365))
([93e4b92](snakemake@93e4b92))
* Logging refactor & add LoggerPluginInterface
([snakemake#3107](snakemake#3107))
([86f1d6e](snakemake@86f1d6e))
* Maximal file size for checksums
([snakemake#3368](snakemake#3368))
([b039f8a](snakemake@b039f8a))
* Modernize package configuration using Pixi
([snakemake#3369](snakemake#3369))
([77992d8](snakemake@77992d8))
* multiext support for named input/output
([snakemake#3372](snakemake#3372))
([05e1378](snakemake@05e1378))
* optionally auto-group jobs via temp files in case of remote execution
([snakemake#3378](snakemake#3378))
([cc9bba2](snakemake@cc9bba2))


### Bug Fixes

* `--delete-all-output` ignores `--dry-run`
([snakemake#3265](snakemake#3265))
([23fef82](snakemake@23fef82))
* 3342 faster touch runs and warning messages for non-existing files
([snakemake#3398](snakemake#3398))
([cd9c3c3](snakemake@cd9c3c3))
* add default value to max-jobs-per-timespan
([snakemake#3043](snakemake#3043))
([2959abe](snakemake@2959abe))
* checkpoints inside modules are overwritten
([snakemake#3359](snakemake#3359))
([fba3ac7](snakemake@fba3ac7))
* Convert Path to IOFile
([snakemake#3405](snakemake#3405))
([c58684c](snakemake@c58684c))
* Do not perform storage object cleanup with --keep-storage-local-copies
set ([snakemake#3358](snakemake#3358))
([9a6d14b](snakemake@9a6d14b))
* edgecases of source deployment in case of remote execution
([snakemake#3396](snakemake#3396))
([5da13be](snakemake@5da13be))
* enhance error message formatting for strict DAG-building mode
([snakemake#3376](snakemake#3376))
([a1c39ee](snakemake@a1c39ee))
* fix bug in checkpoint handling that led to exceptions in case
checkpoint output was missing upon rerun
([snakemake#3423](snakemake#3423))
([8cf4a2f](snakemake@8cf4a2f))
* force check all required outputs
([snakemake#3341](snakemake#3341))
([495a4e7](snakemake@495a4e7))
* group job formatting
([snakemake#3442](snakemake#3442))
([f0b10a3](snakemake@f0b10a3))
* in remote jobs, upload storage in topological order such that
modification dates are preserved (e.g. in case of group jobs)
([snakemake#3377](snakemake#3377))
([eace08f](snakemake@eace08f))
* only skip eval when resource depends on input
([snakemake#3374](snakemake#3374))
([4574c92](snakemake@4574c92))
* Prevent execution of conda in apptainer when not explicitly requested
in software deployment method
([snakemake#3388](snakemake#3388))
([c43c5c0](snakemake@c43c5c0))
* print filenames with quotes around them in RuleException
([snakemake#3269](snakemake#3269))
([6baeda5](snakemake@6baeda5))
* Re-evaluation of free resources
([snakemake#3399](snakemake#3399))
([6371293](snakemake@6371293))
* ReadTheDocs layout issue due to src directory change
([snakemake#3419](snakemake#3419))
([695b127](snakemake@695b127))
* robustly escaping quotes in generated bash scripts (v2)
([snakemake#3297](snakemake#3297))
([snakemake#3389](snakemake#3389))
([58720bd](snakemake@58720bd))
* Show apptainer image URL in snakemake report
([snakemake#3407](snakemake#3407))
([45f0450](snakemake@45f0450))
* Update ReadTheDocs configuration for documentation build to use Pixi
([snakemake#3433](snakemake#3433))
([3f227a6](snakemake@3f227a6))


### Documentation

* Add pixi setup instructions to general use tutorial
([snakemake#3382](snakemake#3382))
([115e81b](snakemake@115e81b))
* fix contribution section heading levels, fix docs testing setup order
([snakemake#3360](snakemake#3360))
([051dc53](snakemake@051dc53))
* fix link to github.com/snakemake/poetry-snakemake-plugin
([snakemake#3436](snakemake#3436))
([ec6d97c](snakemake@ec6d97c))
* fix quoting
([snakemake#3394](snakemake#3394))
([b40f599](snakemake@b40f599))
* fix rerun-triggers default
([snakemake#3403](snakemake#3403))
([4430e23](snakemake@4430e23))
* fix typo 'safe' -&gt; 'save'
([snakemake#3384](snakemake#3384))
([7755861](snakemake@7755861))
* mention code formatting in the contribution section
([snakemake#3431](snakemake#3431))
([e8682b7](snakemake@e8682b7))
* remove duplicated 'functions'.
([snakemake#3356](snakemake#3356))
([7c595db](snakemake@7c595db))
* update broken links documentation
([snakemake#3437](snakemake#3437))
([e3d0d88](snakemake@e3d0d88))
* Updating contributing guidelines with new pixi dev setup
([snakemake#3415](snakemake#3415))
([8e95a12](snakemake@8e95a12))

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

Co-authored-by: snakemake-bot <snakemake-bot-admin@googlegroups.com>
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docs: add contributing guidelines for dev setup using pixi

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