feat: python 3.13 support #3602

maarten-k · 2025-05-23T09:27:58Z

This should provide initial support for Python 3.13. The main issue was that conda-forge dependencies were not built for Python 3.13 (immutables and pulp). The immutables issue is solved, and for pulp, the pull request is ready conda-forge/pulp-feedstock#50

Also the pixi lock file needs to be updated (I assume this will be done automatically)

This should fix #3354

QC

[ x] 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

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- Updated testing environments to include Python 3.13 in the continuous integration workflow.

coderabbitai · 2025-05-23T09:28:05Z

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📝 Walkthrough

Walkthrough

The continuous integration workflow configuration was updated to include Python 3.13 in the test matrix. This ensures that automated tests are now executed on Python 3.11, 3.12, and 3.13 across supported operating systems. No other logic or configuration changes were made.

Changes

File(s)	Change Summary
.github/workflows/main.yml	Added Python 3.13 ("py313") to the CI test matrix for all OS targets

Assessment against linked issues

Objective	Addressed	Explanation
Add/support Python 3.13 in CI test matrix (#3354)	✅

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🎯 1 (Trivial) | ⏱️ ~3 minutes

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johanneskoester

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maarten-k · 2025-05-23T09:41:33Z

Since pulp is not supported yet, I converted to a draft

maarten-k · 2025-06-02T16:08:44Z

PuLP works for python 3.13. The next tool on the list is CWLtool, which requires cheetah3 (https://github.com/conda-forge/cheetah3-feedstock/pulls).

maarten-k · 2025-06-04T23:11:31Z

Cheetah3 is done, now waiting on conda-forge/cwltool-feedstock#166 , which is depended on pydot.

maarten-k · 2025-06-18T12:36:00Z

It looks like all tests succeeded except the CWL involved test, since I commented the dependency out because of no python 3.13 compatibility. I will wait until python 3.13 compatibly version of cwltool is released (there is a fix implemented ).

corneliusroemer · 2025-07-22T12:44:40Z

I can't find an issue on cwltool regarding Python 3.13, is it already supported or should I make a signpost issue?

maarten-k · 2025-07-22T12:47:02Z

I can't find an issue on cwltool regarding Python 3.13, is it already supported or should I make a signpost issue?

There is now in trunk/main of cwltool a patch to support 3.13, but there is not a release of cwltool with this patch. We are waiting on this. Maybe you can gently nudge a bit.

corneliusroemer · 2025-07-22T12:52:40Z

How important is cwltool for snakemake? Maybe it could be made an optional dependency?

I've made an issue to ask for a new release: common-workflow-language/cwltool#2136

maarten-k · 2025-07-22T13:23:24Z

It is needed for testng. You can disable this test, but often it is forgotten to reenable which makes me uncomfortable.

corneliusroemer · 2025-07-22T14:11:05Z

There's a new release already!

maarten-k · 2025-07-23T15:54:19Z

https://github.com/conda-forge/cwltool-feedstock does not build py313 packages. A fresh pull request is being made as we speak by the conda-forge-admin bot.

maarten-k · 2025-07-24T00:16:10Z

It looks like one test failed due to a network issue. first try to fix it is to rerun the tests.

maarten-k · 2025-07-24T13:53:54Z

@johanneskoester Python 3.13 seems to work now. Can you merge this request?

🤖 I have created a release *beep* *boop* --- ## [9.9.0](v9.8.2...v9.9.0) (2025-07-29) ### Features * python 3.13 support ([#3602](#3602)) ([429cff4](429cff4)) ### Bug Fixes * dag mermaid-js edges (bug:[#3556](#3556)) ([#3669](#3669)) ([c6e2e71](c6e2e71)) * if asset is present and no sha256 provided assume pass ([#3685](#3685)) ([7731175](7731175)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- ## [9.9.0](snakemake/snakemake@v9.8.2...v9.9.0) (2025-07-29) ### Features * python 3.13 support ([snakemake#3602](snakemake#3602)) ([429cff4](snakemake@429cff4)) ### Bug Fixes * dag mermaid-js edges (bug:[snakemake#3556](snakemake#3556)) ([snakemake#3669](snakemake#3669)) ([c6e2e71](snakemake@c6e2e71)) * if asset is present and no sha256 provided assume pass ([snakemake#3685](snakemake#3685)) ([7731175](snakemake@7731175)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

Update pyproject.toml to include python 3.13

7811f58

maarten-k requested a review from johanneskoester as a code owner May 23, 2025 09:27

maarten-k changed the title ~~python 3.13 support~~ feat: python 3.13 support May 23, 2025

added python 3.13 for testing

c25eefe

maarten-k marked this pull request as draft May 23, 2025 09:40

johanneskoester approved these changes Jun 6, 2025

View reviewed changes

maarten-k and others added 3 commits June 18, 2025 00:17

Merge branch 'main' into python_313

a7422e2

add python 3.13 to let github know it is needed

50a3a1f

disabled cwltool since it can not be installed now under python 3.12

eedc6c2

corneliusroemer mentioned this pull request Jul 22, 2025

Please make a new release so that Python 3.13 support is official common-workflow-language/cwltool#2136

Closed

maarten-k added 2 commits July 22, 2025 16:15

Merge branch 'main' into python_313

c2fac8a

uncommented cwltool

a5f5144

maarten-k marked this pull request as ready for review July 23, 2025 23:11

maarten-k marked this pull request as draft July 23, 2025 23:11

maarten-k added 3 commits July 24, 2025 01:36

small whiteline change to trigger ci rerun

4c67a7d

reverted small whiteline change to trigger ci rerun

249b50e

Update pyproject.toml

a9f3945

maarten-k marked this pull request as ready for review July 24, 2025 00:16

cademirch approved these changes Jul 25, 2025

View reviewed changes

cademirch merged commit 429cff4 into snakemake:main Jul 25, 2025
151 of 152 checks passed

snakemake-bot mentioned this pull request Jul 25, 2025

chore(main): release 9.9.0 #3683

Merged

coderabbitai bot mentioned this pull request Sep 12, 2025

feat: support python 3.14 #3739

Draft

27 tasks

kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025

feat: python 3.13 support (snakemake#3602)

1eb8221

feat: python 3.13 support #3602

feat: python 3.13 support #3602

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