fix: remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions by johanneskoester · Pull Request #3767 · snakemake/snakemake

johanneskoester · 2025-10-02T12:57:32Z

Description

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

Bug Fixes
- Standardized notebook read/write to a single, consistent nbformat version to reduce format mismatch issues and improve interoperability.
- Added a stable, public notebook format version reference for consistent I/O behavior.
- Improved compatibility with various Jupyter versions by omitting cell ID metadata when inserting the preamble cell, reducing related errors or warnings.

coderabbitai · 2025-10-02T12:57:40Z

📝 Walkthrough

Walkthrough

Added module-level constant NBFORMAT_VERSION = 4 to src/snakemake/notebook.py and standardized all nbformat read/write calls in that module to use this version (reads use as_version=NBFORMAT_VERSION, writes use version=NBFORMAT_VERSION).

Changes

Cohort / File(s)	Summary
Notebook nbformat versioning `src/snakemake/notebook.py`	Added `NBFORMAT_VERSION = 4`. Standardized nbformat I/O: reads use `as_version=NBFORMAT_VERSION` and writes use `version=NBFORMAT_VERSION` across draft, write_script, and execute_script notebook operations.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Pre-merge checks and finishing touches

❌ Failed checks (3 warnings)

Check name	Status	Explanation	Resolution
Title Check	⚠️ Warning	The pull request title claims to remove the id field from notebook cells, but the changeset instead adds an NBFORMAT_VERSION constant and standardizes nbformat I/O versioning without mentioning id removal, making the title misleading.	Please update the title to clearly reflect the main change, for example “standardize notebook I/O to NBFORMAT_VERSION constant (version 4)” or similar that highlights the versioning update.
Description Check	⚠️ Warning	The pull request description still contains the placeholder prompt and does not include an actual summary of the changes made, so it fails to inform reviewers of the modifications.	Please replace the placeholder in the Description section with a concise overview of the new NBFORMAT_VERSION constant addition and how notebook I/O was standardized to that version.
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

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src/snakemake/notebook.py

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github-actions · 2025-10-02T12:58:34Z

Please format your code with black: black snakemake tests/*.py.

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/notebook.py (1)

142-142: LGTM—also strip “id” from the default code cell in draft()
The cell created at line 39 via nbformat.v4.new_code_cell("# start coding here") may include an "id" field in its metadata—assign it to a variable, call pop("id", None), then append.

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coderabbitai

Actionable comments posted: 1

🧹 Nitpick comments (2)

src/snakemake/notebook.py (2)
23-28: Consider standardizing version handling in get_cell_sources.

The get_cell_sources function uses nbformat.NO_CONVERT when reading notebooks (line 26), while other read operations in this file now use as_version=NBFORMAT_VERSION.

For consistency with the standardization effort in this PR, consider whether this function should also use as_version=NBFORMAT_VERSION. If NO_CONVERT is intentional here (to preserve the original notebook version structure), this is acceptable, but it creates an inconsistency.

If consistency is desired, apply this diff:
 def get_cell_sources(source):
     import nbformat
 
-    nb = nbformat.reads(source, as_version=nbformat.NO_CONVERT)
+    nb = nbformat.reads(source, as_version=NBFORMAT_VERSION)
 
     return [cell["source"] for cell in nb["cells"]]
20-21: Consider backwards compatibility with existing notebooks.

Forcing all notebooks to version 5 might cause issues when reading notebooks created with older nbformat versions. While as_version=NBFORMAT_VERSION will convert on read, this could potentially alter the notebook structure in unexpected ways for users with legacy notebooks.

Consider documenting this change and its implications for users with existing notebooks, or provide a migration path if needed.

Consider adding a comment explaining the version choice and its implications:
+# nbformat version to use for all notebook I/O operations.
+# Version 5 is used to ensure compatibility with modern Jupyter versions.
+# Note: Notebooks in older formats will be automatically converted on read.
 NBFORMAT_VERSION = 5

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**/*.py

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Do not suggest type annotations for functions that are defined inside of functions or methods.
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Do not suggest return type annotation if a function or method does not contain a return statement.

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🧠 Learnings (1)

📚 Learning: 2024-10-29T17:14:13.585Z

Learnt from: zmbc
PR: snakemake/snakemake#2857
File: snakemake/notebook.py:84-90
Timestamp: 2024-10-29T17:14:13.585Z
Learning: In `snakemake/notebook.py`, when suggesting enhancements to the `execute_script` method in the `JupyterNotebook` class, ensure that changes align with both papermill and nbconvert use cases.

Applied to files:

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🔇 Additional comments (3)

src/snakemake/notebook.py (3)

56-64: LGTM! Standardized version handling in write_script.

The changes correctly standardize both the read (as_version=NBFORMAT_VERSION) and write (version=NBFORMAT_VERSION) operations. This ensures consistent notebook format handling when generating script files.

46-47: Verify notebook format version compatibility and add tests
No existing tests cover the version=NBFORMAT_VERSION change; confirm that current workflows support this notebook version or add tests to prevent regressions.

66-137: Standardizing to nbformat v5 is safe
Papermill 2.0+ (which uses nbclient requiring nbformat v5) and nbconvert 6+ (and all 7.x releases) support nbformat v5 without issues. No further changes needed.

🤖 I have created a release *beep* *boop* --- ## [9.11.9](v9.11.8...v9.11.9) (2025-10-03) ### Bug Fixes * Raise WorkflowError on empty file path in _IOFile.check ([#3769](#3769)) ([4249ff7](4249ff7)) * remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions ([#3767](#3767)) ([46cf3ed](46cf3ed)) * show failed logs in generated unit tests ([#3771](#3771)) ([61f4e9b](61f4e9b)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

…ncreasing compatibility with different jupyter versions (snakemake#3767) ### Description  ### QC  * [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).  ## Summary by CodeRabbit * **Bug Fixes** * Standardized notebook read/write to a single, consistent nbformat version to reduce format mismatch issues and improve interoperability. * Added a stable, public notebook format version reference for consistent I/O behavior. * Improved compatibility with various Jupyter versions by omitting cell ID metadata when inserting the preamble cell, reducing related errors or warnings.

🤖 I have created a release *beep* *boop* --- ## [9.11.9](snakemake/snakemake@v9.11.8...v9.11.9) (2025-10-03) ### Bug Fixes * Raise WorkflowError on empty file path in _IOFile.check ([snakemake#3769](snakemake#3769)) ([4249ff7](snakemake@4249ff7)) * remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions ([snakemake#3767](snakemake#3767)) ([46cf3ed](snakemake@46cf3ed)) * show failed logs in generated unit tests ([snakemake#3771](snakemake#3771)) ([61f4e9b](snakemake@61f4e9b)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

dbg

cdf17d8

coderabbitai Bot reviewed Oct 2, 2025

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set version to 5

2ede3fb

coderabbitai Bot reviewed Oct 2, 2025

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Comment thread src/snakemake/notebook.py Outdated

version 4, not 5

b64db38

johanneskoester merged commit 46cf3ed into main Oct 3, 2025
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johanneskoester deleted the fix/ci branch October 3, 2025 09:49

snakemake-bot mentioned this pull request Oct 3, 2025

chore(main): release 9.11.9 #3770

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johanneskoester mentioned this pull request Oct 3, 2025

Notebook validation failed. #1032

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fix: remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions#3767

fix: remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions#3767
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