docs: document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax by johanneskoester · Pull Request #4116 · snakemake/snakemake

johanneskoester · 2026-03-18T08:49:12Z

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).
I, as a human being, have checked each line of code in this pull request

AI-assistance disclosure

I used AI assistance for:

Code generation (e.g., when writing an implementation or fixing a bug)
Test/benchmark generation
Documentation (including examples)
Research and understanding

Summary by CodeRabbit

Chores
- Reduced the module's public import surface and adjusted internal type annotations to streamline exports; no runtime behavior changes.
Tests
- Added an end-to-end test and a simple sample workflow that runs a script and verifies the expected "Hello world!" output.
Documentation
- Updated the Python-scripts example to show a type-checking-safe import pattern.

…ripts

coderabbitai · 2026-03-18T08:49:32Z

📝 Walkthrough

Walkthrough

Reduced the public import surface of src/snakemake/script/__init__.py, added a test scenario tests/test_script_import_snakemake_obj (Snakefile, script, expected output) to validate script import/usage, and introduced a module-level snakemake annotation in src/snakemake/io/container.py. No runtime control-flow changes.

Changes

Cohort / File(s)	Summary
Script module export cleanup `src/snakemake/script/__init__.py`	Removed several public imports: `Dict`, `Optional`, `TypeVar`, `Union` (from `typing`); `PathLike` (from `snakemake.io.container`); `sourcecache` (top-level `snakemake`); and `get_report_id` (`snakemake.common`). Export surface reduced; behavior unchanged.
New test scenario — files `tests/tests.py`, `tests/test_script_import_snakemake_obj/Snakefile`, `tests/test_script_import_snakemake_obj/script.py`, `tests/test_script_import_snakemake_obj/expected-results/test.txt`	Added `test_script_import_snakemake_obj()`; new Snakefile rule runs `script.py` which writes `Hello world!` to `test.txt`. Expected output file added.
Docs update (example snippet) `docs/snakefiles/rules.rst`	Replaced direct example import with a TYPE_CHECKING conditional import pattern for typed `snakemake` usage in Python script examples. Documentation-only change.
Container module annotation `src/snakemake/io/container.py`	Added module-level type annotation `snakemake: Snakemake`, introducing a publicly declared name for typing; no runtime logic changes.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main changes: documenting a breaking change in type checking compatibility for Python scripts with a new recommended syntax.
Description check	✅ Passed	The description follows the required template with all QC checkboxes completed and AI-assistance disclosure section included, though lacking detailed context about the breaking change.

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

✨ Finishing Touches

📝 Generate docstrings

Create stacked PR
Commit on current branch

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch dbg/snakemake-type-check

📝 Coding Plan

Generate coding plan for human review comments

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

…snakemake object in scripts

🤖 I have created a release *beep* *boop* --- ## [9.17.3](v9.17.2...v9.17.3) (2026-03-24) ### Bug Fixes * add curl when containerize with wrapper ([#4115](#4115)) ([44979e4](44979e4)) * ensure proper wrapper prefix is passed to CWL and shown in wrapper error messages ([#4121](#4121)) ([11b6f29](11b6f29)) * ensure that strings that purely contain integers or floats (e.g. "42") remain strings when parsing profiles ([#4119](#4119)) ([3ca08e1](3ca08e1)) * incorrect highlighting in HTML report ([#4120](#4120)) ([1ef224d](1ef224d)) ### Documentation * document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax ([#4116](#4116)) ([013bc43](013bc43)) * Rework tutorial ([#4068](#4068)) ([4bba4a9](4bba4a9)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).  ## Summary by CodeRabbit * **Chores** * Released version 9.17.3

chore: testing type checking compatibility for snakemake object in sc…

eac70bd

…ripts

johanneskoester changed the title ~~Dbg/snakemake-type-check~~ chore: testing type-checking compatibility for snakemake object in scripts Mar 18, 2026

johanneskoester mentioned this pull request Mar 18, 2026

Can no longer explicitely import snakemake from snakemake.script #4113

Closed

johanneskoester added 4 commits March 18, 2026 09:58

missing files

3625282

add script

6d8545a

fix: document accidental breaking change around type checking of the …

d17e61f

…snakemake object in scripts

fmt

16cd804

johanneskoester changed the title ~~chore: testing type-checking compatibility for snakemake object in scripts~~ docs: document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax Mar 19, 2026

johanneskoester merged commit 013bc43 into main Mar 19, 2026
63 checks passed

johanneskoester deleted the dbg/snakemake-type-check branch March 19, 2026 12:41

snakemake-bot mentioned this pull request Mar 19, 2026

chore(main): release 9.17.3 #4112

Merged

vandalt mentioned this pull request Mar 28, 2026

Enable linting for rule F821 (undefined names) showyourwork/showyourwork#698

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

docs: document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax#4116

docs: document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax#4116
johanneskoester merged 5 commits intomainfrom
dbg/snakemake-type-check

johanneskoester commented Mar 18, 2026 •

edited

Loading

Uh oh!

coderabbitai bot commented Mar 18, 2026 •

edited

Loading

Walkthrough

Changes

Estimated code review effort

❌ Failed checks (1 warning)

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Conversation

johanneskoester commented Mar 18, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

QC

AI-assistance disclosure

Summary by CodeRabbit

Uh oh!

coderabbitai bot commented Mar 18, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Walkthrough

Changes

Estimated code review effort

❌ Failed checks (1 warning)

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

johanneskoester commented Mar 18, 2026 •

edited

Loading

coderabbitai bot commented Mar 18, 2026 •

edited

Loading