docs: Add AI-assisted contributions policy to contributing guidelines by matthewfeickert · Pull Request #4051 · snakemake/snakemake

matthewfeickert · 2026-03-11T11:01:02Z

Add an AI-assisted contributions policy taken mostly from Awkward Array's (https://github.com/scikit-hep/awkward/), which was based on Scikit-learn's Automated Contributions Policy.
Add AI-assistance disclosure checkboxes to pull request template.
c.f.
- docs: add automated contributions policy to CONTRIBUTING.md scikit-hep/awkward#3831
- DOC add paragraph on "AI usage disclosure" to Automated Contributions Policy and PR Template scikit-learn/scikit-learn#32566

Note that the Awkward Array language is more pro-AI-usage while the Scikit-learn language is more neutral.

Context

This was discussed in the AI section of the 2026 Snakemake Hackathon at TUM (GitHub project board).

QC

[N/A] 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 an "AI-assisted contributions" subsection to the contribution guide covering attribution, limits on automation, reviewer expectations, and when to disclose significant AI assistance.
- Updated the pull request template to include an AI-assistance disclosure section and checklist to ensure contributors declare use of AI tools during submission and review.

coderabbitai · 2026-03-11T11:01:24Z

📝 Walkthrough

Walkthrough

Adds AI-assistance disclosure guidance: a new checklist and disclosure block in the PR template, and a new "AI-assisted contributions" subsection in the contributing guide outlining attribution and disclosure practices.

Changes

Cohort / File(s)	Summary
PR template `.github/pull_request_template.md`	Inserted an AI-assistance disclosure block under QC with policy reference text and a checklist of AI-assistance options.
Contributing guide `docs/project_info/contributing.rst`	Added an "AI-assisted contributions" subsection describing attribution, limits on end-to-end automation, reviewer-time considerations, and disclosure expectations.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately and concisely describes the main change: adding an AI-assisted contributions policy to the contributing guidelines, which is the primary objective of this PR.
Description check	✅ Passed	The description provides context, references, and notes on the policy approach. It includes the QC checklist with documentation confirmed as updated, though test case status is marked N/A.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

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🧹 Nitpick comments (1)

docs/project_info/contributing.rst (1)
91-92: Add an explicit anchor for this new subsection.

This new second-level section is missing a .. _...: target, so any link back to the policy has to rely on generated heading IDs instead of the stable cross-reference style documented later in this file.
Suggested change
+.. _project_info-ai_assisted_contributions:
+
 AI-assisted contributions
 -------------------------
As per coding guidelines, "Provide hyperlink targets <...>, at least for the first two section levels."
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@docs/project_info/contributing.rst` around lines 91 - 92, Add an explicit
reStructuredText target anchor immediately above the "AI-assisted contributions"
second-level heading so links can use a stable cross-reference; create a target
named ai-assisted-contributions (or similar) and place it on the line directly
before the "AI-assisted contributions" heading so other parts of the docs can
reference it by name.

🤖 Prompt for all review comments with AI agents

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

Nitpick comments:
In `@docs/project_info/contributing.rst`:
- Around line 91-92: Add an explicit reStructuredText target anchor immediately
above the "AI-assisted contributions" second-level heading so links can use a
stable cross-reference; create a target named ai-assisted-contributions (or
similar) and place it on the line directly before the "AI-assisted
contributions" heading so other parts of the docs can reference it by name.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: cfcfaaf9-fa81-44d4-8744-a1a38180e06e

📥 Commits

Reviewing files that changed from the base of the PR and between 6677775 and c69cfe9.

📒 Files selected for processing (2)

.github/pull_request_template.md
docs/project_info/contributing.rst

🚧 Files skipped from review as they are similar to previous changes (1)

.github/pull_request_template.md

jonasfreimuth · 2026-03-11T11:46:30Z

Cool, thanks for setting this up!

.github/pull_request_template.md

* Add an AI-assisted contributions policy taken mostly from Awkward Array's (https://github.com/scikit-hep/awkward/), which was based on Scikit-learn's Automated Contributions Policy. * Add AI-assistance disclosure checkboxes to pull request template. * c.f. - https://github.com/scikit-hep/awkward/ PR 3831 - https://github.com/scikit-learn/scikit-learn/ PR 2566 Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

coderabbitai

🧹 Nitpick comments (1)

.github/pull_request_template.md (1)

16-20: Add an explicit “no AI assistance” option.

As written, an entirely unchecked section is ambiguous between “no AI was used” and “the author skipped the disclosure.” Adding a dedicated checkbox for the no-AI case would make the template easier to interpret and enforce consistently.

✏️ Proposed tweak

 I used AI assistance for:
+* [ ] No AI assistance
 * [ ] Code generation (e.g., when writing an implementation or fixing a bug)
 * [ ] Test/benchmark generation
 * [ ] Documentation (including examples)
 * [ ] Research and understanding

🤖 Prompt for AI Agents

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

In @.github/pull_request_template.md around lines 16 - 20, Add an explicit "No
AI assistance" checkbox to the existing "I used AI assistance for:" checklist so
an unchecked list cannot be confused with skipping disclosure; specifically,
update the checklist under the "I used AI assistance for:" heading to include a
distinct option like "* [ ] No AI assistance used" (in addition to the current
items such as "Code generation", "Test/benchmark generation", "Documentation",
"Research and understanding") and adjust the template copy to make it clear one
box should be selected before submitting.

🤖 Prompt for all review comments with AI agents

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

Nitpick comments:
In @.github/pull_request_template.md:
- Around line 16-20: Add an explicit "No AI assistance" checkbox to the existing
"I used AI assistance for:" checklist so an unchecked list cannot be confused
with skipping disclosure; specifically, update the checklist under the "I used
AI assistance for:" heading to include a distinct option like "* [ ] No AI
assistance used" (in addition to the current items such as "Code generation",
"Test/benchmark generation", "Documentation", "Research and understanding") and
adjust the template copy to make it clear one box should be selected before
submitting.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: bd90cf7a-a28d-4693-ab39-26330d970b93

📥 Commits

Reviewing files that changed from the base of the PR and between 052389a and 194b324.

📒 Files selected for processing (2)

.github/pull_request_template.md
docs/project_info/contributing.rst

🚧 Files skipped from review as they are similar to previous changes (1)

docs/project_info/contributing.rst

matthewfeickert · 2026-03-12T22:55:40Z

Not necessarily actionable information for this PR, but interesting post that was shared on the Scientific Python Discord: https://redmonk.com/kholterhoff/2026/02/26/generative-ai-policy-landscape-in-open-source/

johanneskoester · 2026-03-13T15:24:54Z

Thanks!

🤖 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).

matthewfeickert self-assigned this Mar 11, 2026

matthewfeickert requested a review from johanneskoester as a code owner March 11, 2026 11:01

matthewfeickert force-pushed the docs/add-automated-contributions-guidelines branch from 6677775 to c69cfe9 Compare March 11, 2026 11:03

coderabbitai bot reviewed Mar 11, 2026

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matthewfeickert added this to Snakemake Hackathon 2026 Mar 11, 2026

johanneskoester reviewed Mar 11, 2026

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matthewfeickert force-pushed the docs/add-automated-contributions-guidelines branch from 052389a to 194b324 Compare March 11, 2026 15:34

matthewfeickert requested a review from johanneskoester March 11, 2026 15:34

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johanneskoester approved these changes Mar 11, 2026

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johanneskoester approved these changes Mar 13, 2026

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johanneskoester merged commit dd70526 into snakemake:main Mar 13, 2026
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github-project-automation bot moved this to Done in Snakemake Hackathon 2026 Mar 13, 2026

snakemake-bot mentioned this pull request Mar 13, 2026

chore(main): release 9.17.0 #3977

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matthewfeickert deleted the docs/add-automated-contributions-guidelines branch March 13, 2026 16:10

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