fix: Add support for pathlib in `notebook` field by staadecker · Pull Request #3636 · snakemake/snakemake

staadecker · 2025-06-18T22:43:15Z

The following:

from pathlib import Path

DIR = Path("scripts")

rule my_rule:
    input:
        "data.csv",
    output:
        "result.csv",
    notebook:
        DIR / "process_data.ipynb"

Produces an error:

TypeError in file "C:\Users\staadeck\Software\pyoframe\Snakefile", line 61:
expected str, got WindowsPath
  File "C:\Users\staadeck\AppData\Roaming\uv\python\cpython-3.13.3-windows-x86_64-none\Lib\string.py", line 190, in format
  File "C:\Users\staadeck\AppData\Roaming\uv\python\cpython-3.13.3-windows-x86_64-none\Lib\string.py", line 194, in vformat
  File "C:\Users\staadeck\AppData\Roaming\uv\python\cpython-3.13.3-windows-x86_64-none\Lib\string.py", line 204, in _vformat
  File "C:\Users\staadeck\AppData\Roaming\uv\python\cpython-3.13.3-windows-x86_64-none\Lib\string.py", line 288, in parse

This PR adds support for Path objects in the notebook field. I did not have time (to learn how) to make a test case.

Summary by CodeRabbit

Bug Fixes
- Improved compatibility by ensuring file paths are correctly handled when provided as Path objects.

coderabbitai · 2025-06-18T22:43:21Z

📝 Walkthrough

Walkthrough

The notebook function in src/snakemake/notebook.py was updated to check if the path parameter is a Path object and convert it to a string if necessary, prior to formatting. No other logic or public interfaces were changed.

Changes

File(s)	Change Summary
src/snakemake/notebook.py	Added type check and string conversion for `path` if it is a `Path`

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant notebook
    Caller->>notebook: Call notebook(path, ...)
    alt path is Path object
        notebook->>notebook: Convert path to string
    end
    notebook->>notebook: Format path with wildcards and params
    notebook-->>Caller: Return result

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coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/notebook.py (1)
281-282: Prefer os.fspath for converting path-like objects.

Instead of restricting the conversion to pathlib.Path, use os.fspath(path) so that any os.PathLike (and strings) are handled uniformly:
-    if isinstance(path, Path):
-        path = str(path)
+    path = os.fspath(path)
Also, please add a unit test to verify that passing a pathlib.Path (and other PathLike) to notebook() works as expected.

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Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 8bd1df9 and 4445bb8.

📒 Files selected for processing (1)

src/snakemake/notebook.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/notebook.py

mschilli87 · 2025-10-08T09:24:09Z

@staadecker: Are you still interested in finishing this PR? I could help you with test design etc.

staadecker · 2025-10-09T19:07:51Z

I'm afraid I don't quite have the time. Feel free to close the PR if needed.

@staadecker

PR snakemake#3636 added support for Pathlike `notebook` specifications but @staadecker (the original author of that PR) did not provide a matching test. This commit add such a test based on @staadecker's example. I have verified that this test * fails (with the expected `TypeError`: ``` TypeError in file "</path/to/testdir>/Snakefile", line 7: expected str, got PosixPath ``` ) at commit 8bd1df9 (v9.6.0; parent of @staadecker's original PR snakemake#3636), * passes after applying the changes of commit 4445bb8 (@staadecker's original PR snakemake#3636), * still fails (with the same expected `TypeError`, see above) at commit f8b8620 (v.913.4; current `main`), and * still passes at commit 37a017d (after merging the current `main` (see above) on top of @staadecker's original PR snakemake#3636).

mschilli87 · 2025-10-27T15:30:26Z

@staadecker: I added a test on top of your work. Since I don't have write permission to your branch, I opened a new PR (#3811). This one should automatically be closed once mine gets merged.

Thank you for your contribution.

@staadecker

PR snakemake#3636 added support for Pathlike `notebook` specifications but @staadecker (the original author of that PR) did not provide a matching test. This commit add such a test based on @staadecker's example. I have verified that this test * fails (with the expected `TypeError`: ``` TypeError in file "</path/to/testdir>/Snakefile", line 7: expected str, got PosixPath ``` ) at commit 8bd1df9 (v9.6.0; parent of @staadecker's original PR snakemake#3636), * passes after applying the changes of commit 4445bb8 (@staadecker's original PR snakemake#3636), * still fails (with the same expected `TypeError`, see above) at commit f8b8620 (v.913.4; current `main`), and * still passes at commit 37a017d (after merging the current `main` (see above) on top of @staadecker's original PR snakemake#3636).

@staadecker

PR snakemake#3636 added support for Pathlike `notebook` specifications but @staadecker (the original author of that PR) did not provide a matching test. This commit add such a test based on @staadecker's example. I have verified that this test * fails (with the expected `TypeError`: ``` TypeError in file "</path/to/testdir>/Snakefile", line 7: expected str, got PosixPath ``` ) at commit 8bd1df9 (v9.6.0; parent of @staadecker's original PR snakemake#3636), * passes after applying the changes of commit 4445bb8 (@staadecker's original PR snakemake#3636), * still fails (with the same expected `TypeError`, see above) at commit 395a5e6 (current `main`), and * still passes at commit 756656d (after merging the current `main` (see above) on top of @staadecker's original PR snakemake#3636).

@staadecker

PR #3636 added support for Pathlike `notebook` specifications but @staadecker (the original author of that PR) did not provide a matching test. This PR superseeds @staadecker's original PR #3636 by merging in current `main` and adding a commit that adds such a test based on @staadecker's example. I have verified that this test * fails (with the expected `TypeError`: ``` TypeError in file "</path/to/testdir>/Snakefile", line 7: expected str, got PosixPath ``` ) at commit 8bd1df9 (v9.6.0; parent of @staadecker's original PR #3636), * passes after applying the changes of commit 4445bb8 (@staadecker's original PR #3636), * still fails (with the same expected `TypeError`, see above) at commit 395a5e6 (current `main`), and * still passes at commit 756656d merging the current `main` (see above) on top of @staadecker's original PR #3636). --- closes #3636  ## Summary by CodeRabbit * **Bug Fixes** * Ensure pathlike notebook resources are converted to strings before processing to avoid inconsistent handling. * **Tests** * Added test coverage verifying Jupyter notebook pathlike object support with Conda deployment.  --------- Co-authored-by: Martin <machstg@gmail.com>

@staadecker

PR snakemake#3636 added support for Pathlike `notebook` specifications but @staadecker (the original author of that PR) did not provide a matching test. This PR superseeds @staadecker's original PR snakemake#3636 by merging in current `main` and adding a commit that adds such a test based on @staadecker's example. I have verified that this test * fails (with the expected `TypeError`: ``` TypeError in file "</path/to/testdir>/Snakefile", line 7: expected str, got PosixPath ``` ) at commit 8bd1df9 (v9.6.0; parent of @staadecker's original PR snakemake#3636), * passes after applying the changes of commit 4445bb8 (@staadecker's original PR snakemake#3636), * still fails (with the same expected `TypeError`, see above) at commit 395a5e6 (current `main`), and * still passes at commit 756656d merging the current `main` (see above) on top of @staadecker's original PR snakemake#3636). --- closes snakemake#3636  ## Summary by CodeRabbit * **Bug Fixes** * Ensure pathlike notebook resources are converted to strings before processing to avoid inconsistent handling. * **Tests** * Added test coverage verifying Jupyter notebook pathlike object support with Conda deployment.  --------- Co-authored-by: Martin <machstg@gmail.com>

Add support for pathlib in notebook field

4445bb8

staadecker requested a review from johanneskoester as a code owner June 18, 2025 22:43

coderabbitai Bot reviewed Jun 18, 2025

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staadecker changed the title ~~Add support for pathlib in notebook field~~ fix: Add support for pathlib in notebook field Oct 9, 2025

mschilli87 mentioned this pull request Oct 27, 2025

fix: Add support for pathlib in notebook field #3811

Merged

johanneskoester closed this in #3811 Nov 27, 2025

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fix: Add support for pathlib in `notebook` field#3636

fix: Add support for pathlib in `notebook` field#3636
staadecker wants to merge 1 commit into
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