feat: Prefer papermill to nbconvert#2857
Conversation
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@johanneskoester Any concerns with this PR? |
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Awesome. Have wanted to do this for a while, I use papermill + notebooks implemented manually for most of my workflows. |
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Just triggered the update from main. I am curious what this will look like, once ready, and will try to incorporate it into some teaching material. |
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@cmeesters What do you mean by "once ready"? This should be ready and is waiting for review. I see a CI failure but it doesn't look like anything I touched? |
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@zmbc my bad. I should have written "released" instead of "ready". The CI-error is indeed weird. I triggered the merge from main to give this PR a little push. Alas, I don't understand the cause of the error either. |
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@cmeesters are you able to review this PR, or poke a maintainer who can? Also could you try re-running the CI? |
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Just did the re-trigger: The tests keep failing and produce output for a test, which should fail. It requires |
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@cmeesters How sure are we that this test passes on |
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I am pretty sure that it will not pass - after all, I merged main into this branch to subject it to testing (and re-requested review). But I know we are all busy with our little sidelines, being researchers ... |
📝 Walkthrough""" WalkthroughThis pull request introduces three new test functions in the testing module to validate Jupyter notebook execution in a conda environment, updates documentation to clarify the use of Papermill and nbconvert for notebook execution, and refines the Changes
Sequence Diagram(s)sequenceDiagram
participant Test
participant JupyterNotebook
participant Subprocess
Test->>JupyterNotebook: call execute_script(fname, edit, fname_out)
JupyterNotebook->>Subprocess: Execute "papermill --version"
Subprocess-->>JupyterNotebook: Return version info or error
alt Papermill available
JupyterNotebook->>Subprocess: Execute notebook with papermill (using fname or fname_out)
else Papermill unavailable
JupyterNotebook->>Subprocess: Execute notebook with jupyter-nbconvert
end
JupyterNotebook-->>Test: Return execution result
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Actionable comments posted: 1
Outside diff range and nitpick comments (1)
snakemake/notebook.py (1)
82-96: LGTM, but consider using a ternary operator.The updates to the command construction for executing notebooks look good:
- The conditional logic based on
papermillavailability ensures the appropriate execution command is used.- Falling back to
jupyter-nbconvertwhenpapermillis not available maintains compatibility.However, consider simplifying the code by using a ternary operator for setting
output_parameter, as suggested by the static analysis hint from Ruff:-if fname_out is None: - output_parameter = fname -else: - output_parameter = "{fname_out}" +output_parameter = fname if fname_out is None else "{fname_out}"This change makes the code more concise without sacrificing readability.
Tools
Ruff
83-86: Use ternary operator
output_parameter = fname if fname_out is None else "{fname_out}"instead ofif-else-blockReplace
if-else-block withoutput_parameter = fname if fname_out is None else "{fname_out}"(SIM108)
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Files selected for processing (9)
- snakemake/notebook.py (2 hunks)
- tests/test_jupyter_notebook/env.yaml (1 hunks)
- tests/test_jupyter_notebook_draft/env.yaml (1 hunks)
- tests/test_jupyter_notebook_nbconvert/Notebook.ipynb (1 hunks)
- tests/test_jupyter_notebook_nbconvert/Snakefile (1 hunks)
- tests/test_jupyter_notebook_nbconvert/env.yaml (1 hunks)
- tests/test_jupyter_notebook_nbconvert/expected-results/result_final.txt (1 hunks)
- tests/test_jupyter_notebook_nbconvert/expected-results/result_intermediate.txt (1 hunks)
- tests/tests.py (1 hunks)
Files skipped from review due to trivial changes (1)
- tests/test_jupyter_notebook_draft/env.yaml
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Path-based instructions (2)
snakemake/notebook.py (1)
Pattern
**/*.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.tests/tests.py (1)
Pattern
**/*.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
LanguageTool
tests/test_jupyter_notebook_nbconvert/expected-results/result_intermediate.txt
[style] ~1-~1: Using many exclamation marks might seem excessive (in this case: 3 exclamation marks for a text that’s 32 characters long)
Context: result of serious computation!!!(EN_EXCESSIVE_EXCLAMATION)
tests/test_jupyter_notebook_nbconvert/expected-results/result_final.txt
[style] ~1-~1: Using many exclamation marks might seem excessive (in this case: 6 exclamation marks for a text that’s 35 characters long)
Context: result of serious computation!!!!!!(EN_EXCESSIVE_EXCLAMATION)
yamllint
tests/test_jupyter_notebook_nbconvert/env.yaml
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
Ruff
snakemake/notebook.py
83-86: Use ternary operator
output_parameter = fname if fname_out is None else "{fname_out}"instead ofif-else-blockReplace
if-else-block withoutput_parameter = fname if fname_out is None else "{fname_out}"(SIM108)
Additional comments not posted (15)
tests/test_jupyter_notebook_nbconvert/expected-results/result_intermediate.txt (1)
1-1: The file content is appropriate for an expected test result.The text "result of serious computation!!!" seems to be an intentionally emphatic expected output for a test case. In this context, the use of multiple exclamation marks is acceptable.
While the static analysis tool flagged this as excessive, it's a false positive in this case since the exact content of the expected output file needs to match the actual output for the test to pass.
Tools
LanguageTool
[style] ~1-~1: Using many exclamation marks might seem excessive (in this case: 3 exclamation marks for a text that’s 32 characters long)
Context: result of serious computation!!!(EN_EXCESSIVE_EXCLAMATION)
tests/test_jupyter_notebook_nbconvert/expected-results/result_final.txt (1)
1-1: Skip the style issue flagged by the static analysis tool.The use of multiple exclamation marks in this expected result file is not a concern, as it seems to be intentional to convey emphasis or excitement. The style of the text in an expected result file is not critical as long as it matches the actual output of the test.
Tools
LanguageTool
[style] ~1-~1: Using many exclamation marks might seem excessive (in this case: 6 exclamation marks for a text that’s 35 characters long)
Context: result of serious computation!!!!!!(EN_EXCESSIVE_EXCLAMATION)
tests/test_jupyter_notebook/env.yaml (1)
7-7: LGTM!The addition of the
papermilldependency aligns with the PR objective of preferringpapermilltonbconvertfor notebook execution.The existing comments discussing the removal of the
nbformatdependency are still valid and applicable here. No additional comments are necessary.tests/test_jupyter_notebook_nbconvert/env.yaml (1)
1-6: LGTM!The Conda environment configuration looks good. It specifies the appropriate channels (conda-forge and bioconda) and includes the necessary dependencies (Python >=3.5 and jupyter) for the notebook execution functionality.
Tools
yamllint
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
tests/test_jupyter_notebook_nbconvert/Snakefile (5)
3-6: LGTM!The
allrule correctly specifies the final output files of the workflow.
8-13: LGTM!The
foorule correctly generates the intermediate data file used by subsequent rules.
15-23: LGTM!The
barrule correctly processes the intermediate data file using a Jupyter notebook with the specified conda environment.
25-35: LGTM!The
bazrule correctly processes the intermediate result file using a Jupyter notebook with the specified conda environment and log file.
38-46: LGTM!The
wildrule correctly demonstrates the use of wildcards in notebook execution with the specified conda environment.tests/test_jupyter_notebook_nbconvert/Notebook.ipynb (3)
9-10: LGTM!The code changes are approved.
19-19: LGTM!The code changes are approved.
28-29: LGTM!The code changes are approved.
snakemake/notebook.py (2)
69-73: LGTM!The changes to introduce
papermillsupport look good:
- Checking
papermillavailability by executingpapermill --versionis a reasonable approach.- Setting the
has_papermillflag allows for clear conditional logic based onpapermillsupport.- Falling back to
jupyter-nbconvertwhenpapermillis not available ensures backward compatibility.
77-81: LGTM!The updates to the command construction for editing notebooks look good:
- Including the IP address and port in the logging message enhances clarity and aids in debugging.
- Switching to
--ServerApp.quit_button=Truereflects the change in the underlying server application.tests/tests.py (1)
1507-1511: LGTM!The new
test_jupyter_notebook_nbconverttest function looks good. It is properly decorated with@condaand callsrunwith the appropriate arguments to test the nbconvert functionality in a conda environment.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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@johanneskoester can you give this PR another look? Seems fine to me. |
This reverts commit c3aa979.
johanneskoester
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Thanks! Looks good in principle. However, can you please also extend the notebook section in the docs to mention that if papermill is available (e.g. in the conda env), snakemake will use papermill instead of jupyter-nbconvert to run the notebook in non-edit mode (and maybe shortly mention there the rationale why this is considered to be advantageous)?
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🧹 Nitpick comments (1)
docs/snakefiles/rules.rst (1)
1693-1699: Clarify the Advantages of Papermill over nbconvertThe revised text now explains the standard headless execution mode for notebooks. However, given that this PR aims to prefer Papermill over nbconvert, it would be beneficial to briefly mention Papermill’s advantages (such as incremental output and error retention) to guide users on why its usage is preferred. For example, you might add a phrase that emphasizes that Papermill not only executes notebooks headlessly but also provides incremental output and preserves outputs even in error cases.
Suggested Diff:
-Normally, notebooks are executed headlessly (without a Jupyter interface being presented to you). -This is achieved with Papermill_ if that is installed in your software environment, -or `nbconvert`_ otherwise. -The latter will be installed automatically along with Jupyter, but will not output -an executed (logfile) notebook until the entire execution is complete, and won't output -a notebook if execution encounters an error. +Normally, notebooks are executed headlessly (without a Jupyter interface being presented to you). +This is achieved with Papermill_ if that is installed in your software environment, which additionally +provides incremental output and retains notebook output even upon execution errors, +or `nbconvert`_ otherwise. +Note that while nbconvert is automatically installed alongside Jupyter, it only produces +an executed notebook after complete success and will omit output if execution fails.
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📓 Common learnings
Learnt from: zmbc
PR: snakemake/snakemake#2857
File: snakemake/notebook.py:84-90
Timestamp: 2025-03-14T16:09:08.165Z
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.
docs/snakefiles/rules.rst (1)
Learnt from: zmbc
PR: snakemake/snakemake#2857
File: snakemake/notebook.py:84-90
Timestamp: 2025-03-14T16:09:08.165Z
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.
🔇 Additional comments (1)
docs/snakefiles/rules.rst (1)
1700-1703: Verify Reference Links for Papermill and nbconvertThe reference hyperlinks for both Papermill and nbconvert are now explicitly defined. They appear accurate and well integrated with the text. Make sure that these links remain up-to-date as new releases occur.
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🧹 Nitpick comments (3)
src/snakemake/notebook.py (3)
70-75: Add logging when falling back to nbconvertThe code elegantly checks for papermill availability, but there's no notification to the user when falling back to nbconvert.
try: self._execute_cmd("papermill --version", read=True) has_papermill = True except sp.CalledProcessError: has_papermill = False + logger.debug("Papermill not available, falling back to nbconvert.")
83-91: Consider adding a timeout parameter to papermill commandThe nbconvert command includes
--ExecutePreprocessor.timeout=-1to prevent timeouts, but the papermill command doesn't have an equivalent parameter. For consistency and to prevent potential timeouts with long-running notebooks, consider adding a timeout parameter.cmd = ( "papermill --log-level ERROR {{fname:q}} " - "{output_parameter}".format(output_parameter=output_parameter) + "{output_parameter} --execution-timeout -1".format(output_parameter=output_parameter) )🧰 Tools
🪛 Ruff (0.8.2)
84-87: Use ternary operator
output_parameter = fname if fname_out is None else "{fname_out}"instead ofif-else-blockReplace
if-else-block withoutput_parameter = fname if fname_out is None else "{fname_out}"(SIM108)
84-87: Simplify output parameter logic with a ternary operatorThe static analysis tool suggests using a ternary operator for better readability.
- if fname_out is None: - output_parameter = fname - else: - output_parameter = "{fname_out}" + output_parameter = fname if fname_out is None else "{fname_out}"🧰 Tools
🪛 Ruff (0.8.2)
84-87: Use ternary operator
output_parameter = fname if fname_out is None else "{fname_out}"instead ofif-else-blockReplace
if-else-block withoutput_parameter = fname if fname_out is None else "{fname_out}"(SIM108)
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`**/*.py`: Do not try to improve formatting. Do not suggest ...
**/*.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
src/snakemake/notebook.py
🧠 Learnings (1)
src/snakemake/notebook.py (1)
Learnt from: zmbc
PR: snakemake/snakemake#2857
File: snakemake/notebook.py:84-90
Timestamp: 2025-03-14T16:09:08.165Z
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.
🪛 Ruff (0.8.2)
src/snakemake/notebook.py
84-87: Use ternary operator output_parameter = fname if fname_out is None else "{fname_out}" instead of if-else-block
Replace if-else-block with output_parameter = fname if fname_out is None else "{fname_out}"
(SIM108)
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🔇 Additional comments (3)
src/snakemake/notebook.py (3)
4-4: LGTM: Import subprocess for checking papermill availabilityAdding the subprocess import is necessary for executing shell commands to check if papermill is available.
78-82: LGTM: Improved logging and updated Jupyter server configurationThe logging now provides more detailed information by including the IP and port. The change from
--NotebookApp.quit_button=Trueto--ServerApp.quit_button=Truereflects updates in the Jupyter API.
70-104: LGTM: Great implementation of papermill with fallback to nbconvertThe implementation aligns perfectly with the PR objective of preferring papermill while maintaining backward compatibility with nbconvert. This approach ensures seamless execution regardless of the environment setup while taking advantage of papermill's features when available.
🧰 Tools
🪛 Ruff (0.8.2)
84-87: Use ternary operator
output_parameter = fname if fname_out is None else "{fname_out}"instead ofif-else-blockReplace
if-else-block withoutput_parameter = fname if fname_out is None else "{fname_out}"(SIM108)
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@johanneskoester I've added something to the docs. Feel free to make edits directly! |
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The CI failures look completely unrelated, having to do with internet access on the CI runner. |
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Thank you for working this in. Looking forward to giving this a try. |
🤖 I have created a release *beep* *boop* --- ## [9.6.0](v9.5.1...v9.6.0) (2025-06-16) ### Features * Prefer papermill to nbconvert ([#2857](#2857)) ([4263b03](4263b03)) ### Bug Fixes * DeprecationWarning when using snakemake.utils.validate ([#3420](#3420)) ([cf72427](cf72427)) * display group jobs on dryrun ([#3435](#3435)) ([3bebef4](3bebef4)) * expandvars for special profile keys ([#3597](#3597)) ([4020188](4020188)) * fix bug causing --precommand to not being executed before each remote job ([#3625](#3625)) ([e59d125](e59d125)) * improved toggle switch behavior in reports ([#3623](#3623)) ([0c4bd23](0c4bd23)) * pass envvars defined via the envvars directive to remote jobs ([#3626](#3626)) ([d4890b4](d4890b4)) * remove wms arg, update logging cli docs ([#3622](#3622)) ([3a9a5ac](3a9a5ac)) * typo in CondaEnvDirSpec.__eq__ (issue [#3192](#3192)) ([#3613](#3613)) ([f4c107f](f4c107f)) * Unclear handling of params overriding with inheritance ([#3624](#3624)) ([077ac4a](077ac4a)) ### Documentation * Added snakemake command to execute the rule plot_with_python ([#3608](#3608)) ([bd99c11](bd99c11)) * Updated Reporting Section of The Tutorial(Interaction, Visualization, and Reporting with Snakemake) ([#3606](#3606)) ([91e90ba](91e90ba)) * Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually ([#3607](#3607)) ([3bd114b](3bd114b)) * Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease ([#3605](#3605)) ([b3bcc21](b3bcc21)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
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Thanks @johanneskoester! 🎉 |
Turns out I cannot since this regression has me stuck at 9.5.x for now. So if anyone has an idea what I could try to get around that, I would greatly appreciate it as this feature would be very convenient for debugging notebooks. |
As described in snakemake#348, the current notebook integration has some downsides, and they are due to limitations in the `nbconvert` tool. [`papermill`](https://papermill.readthedocs.io/en/latest/index.html) is a more feature-rich alternative. In particular, it outputs the executed notebook incrementally for progress tracking, and outputs the notebook (with errors) even when it fails. ### 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). I didn't see `nbconvert` anywhere in the docs, so I think this was always an implementation detail. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Tests** - Added new test functions for verifying Jupyter notebook execution in various scenarios. - **Documentation** - Updated guidance to clarify headless notebook execution and expectations during errors. - **Refactor** - Enhanced error handling and improved command execution logic for more reliable Jupyter notebook processing. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
🤖 I have created a release *beep* *boop* --- ## [9.6.0](snakemake/snakemake@v9.5.1...v9.6.0) (2025-06-16) ### Features * Prefer papermill to nbconvert ([snakemake#2857](snakemake#2857)) ([4263b03](snakemake@4263b03)) ### Bug Fixes * DeprecationWarning when using snakemake.utils.validate ([snakemake#3420](snakemake#3420)) ([cf72427](snakemake@cf72427)) * display group jobs on dryrun ([snakemake#3435](snakemake#3435)) ([3bebef4](snakemake@3bebef4)) * expandvars for special profile keys ([snakemake#3597](snakemake#3597)) ([4020188](snakemake@4020188)) * fix bug causing --precommand to not being executed before each remote job ([snakemake#3625](snakemake#3625)) ([e59d125](snakemake@e59d125)) * improved toggle switch behavior in reports ([snakemake#3623](snakemake#3623)) ([0c4bd23](snakemake@0c4bd23)) * pass envvars defined via the envvars directive to remote jobs ([snakemake#3626](snakemake#3626)) ([d4890b4](snakemake@d4890b4)) * remove wms arg, update logging cli docs ([snakemake#3622](snakemake#3622)) ([3a9a5ac](snakemake@3a9a5ac)) * typo in CondaEnvDirSpec.__eq__ (issue [snakemake#3192](snakemake#3192)) ([snakemake#3613](snakemake#3613)) ([f4c107f](snakemake@f4c107f)) * Unclear handling of params overriding with inheritance ([snakemake#3624](snakemake#3624)) ([077ac4a](snakemake@077ac4a)) ### Documentation * Added snakemake command to execute the rule plot_with_python ([snakemake#3608](snakemake#3608)) ([bd99c11](snakemake@bd99c11)) * Updated Reporting Section of The Tutorial(Interaction, Visualization, and Reporting with Snakemake) ([snakemake#3606](snakemake#3606)) ([91e90ba](snakemake@91e90ba)) * Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually ([snakemake#3607](snakemake#3607)) ([3bd114b](snakemake@3bd114b)) * Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease ([snakemake#3605](snakemake#3605)) ([b3bcc21](snakemake@b3bcc21)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
As described in #348, the current notebook integration has some downsides, and they are due to limitations in the
nbconverttool.papermillis a more feature-rich alternative. In particular, it outputs the executed notebook incrementally for progress tracking, and outputs the notebook (with errors) even when it fails.QC
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 didn't see
nbconvertanywhere in the docs, so I think this was always an implementation detail.Summary by CodeRabbit
Tests
Documentation
Refactor