fix: notebook execution for apptainer by laf070810 · Pull Request #3131 · snakemake/snakemake

laf070810 · 2024-10-11T07:00:46Z

At

snakemake/snakemake/deployment/singularity.py

Lines 118 to 125 in afa7bad

    
           if is_python_script: 
        
               # mount host snakemake module into container 
        
               args += " ".join( 
        
                   f" --bind {repr(searchpath)}:{repr(mountpoint)}" 
        
                   for searchpath, mountpoint in zip( 
        
                       get_snakemake_searchpaths(), get_snakemake_searchpath_mountpoints() 
        
                   ) 
        
               )

snakemake searchpaths are only bound into apptainer when is_python_script is True. For notebook directive, is_python_script will be False and snakemake searchpaths are not bound into apptainer, causing ModuleNotFoundError: No module named 'snakemake' error in the preamble. This PR sets is_python_script to True for notebook directive.

Also, the name, is_python_script, could then be somewhat confusing. Changing it to something like is_script or has_preamble might be better.

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

New Features
- Introduced a new parameter to enhance script execution for Python scripts in Jupyter notebooks.
- Added functionality to determine whether a notebook should be drafted or executed based on user input.
Bug Fixes
- Improved validation for local notebook paths to ensure editing is only allowed for local files.

coderabbitai · 2024-10-11T07:00:54Z

Walkthrough

The changes introduce a new parameter, is_python_script, to the _execute_cmd method within the execute_script method of the JupyterNotebook class in snakemake/notebook.py. This parameter is set to True to indicate that the executed script is a Python script. Additionally, the notebook function now checks the edit parameter to determine if a notebook should be drafted or executed, refining logic for local path validation and file extension checks. The overall structure of the classes and methods remains unchanged.

Changes

File	Change Summary
snakemake/notebook.py	Added `is_python_script=True` parameter to `_execute_cmd` call in `execute_script`. Updated `notebook` function to check `edit` parameter and validate local paths.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant JupyterNotebook
    participant CommandExecutor

    User->>JupyterNotebook: execute_script(fname, edit)
    JupyterNotebook->>CommandExecutor: _execute_cmd(fname, is_python_script=True)
    CommandExecutor-->>JupyterNotebook: Execute script
    JupyterNotebook-->>User: Return execution result

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📥 Commits

Files that changed from the base of the PR and between afa7bad and e74b593.

📒 Files selected for processing (1)

snakemake/notebook.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

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 the self argument of methods.
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Do not suggest return type annotation if a function or method does not contain a return statement.

🔇 Additional comments (1)

snakemake/notebook.py (1)
97-97: LGTM! Verify impact on other parts of the codebase.

The addition of is_python_script=True to the _execute_cmd call aligns with the PR objective and should resolve the issue of Snakemake search paths not being integrated into Apptainer for notebook execution. This change is consistent and straightforward.

To ensure this change doesn't have unintended consequences, please run the following verification:

Also, consider updating the documentation to reflect this change in behavior for notebook execution.

✅ Verification successful

Verified! No issues found with the addition of is_python_script=True.

The change in snakemake/notebook.py is consistent with existing implementations and does not introduce any conflicts or unintended side effects.
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Check for other occurrences of _execute_cmd and verify if they need similar changes

# Search for other _execute_cmd calls
rg "_execute_cmd\(" --type python

# Search for references to is_python_script
rg "is_python_script" --type python
Length of output: 133

Script:
#!/bin/bash
# Description: Check for other occurrences of _execute_cmd and verify if they need similar changes

# Find all Python files and search for _execute_cmd calls
fd --extension py --type file | xargs rg "_execute_cmd\("

# Find all references to is_python_script in Python files
fd --extension py --type file | xargs rg "is_python_script"
Length of output: 1253

Script:
#!/bin/bash
# Description: Review all usages of is_python_script to ensure consistency and identify if further changes are needed

# Find all assignments of is_python_script
fd --extension py --type file | xargs rg "is_python_script\s*="

# Find all conditional checks of is_python_script
fd --extension py --type file | xargs rg "if\s+is_python_script"

# Find all docstrings or comments mentioning is_python_script
fd --extension py --type file | xargs rg "is_python_script.*(docstring|comment)"
Length of output: 609

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laf070810 · 2024-10-11T07:15:54Z

Also, it may be better to add some tests for notebook execution in apptainer, to prevent trivial bugs like this one here.

johanneskoester

Good catch! To me the name also sounds correct for a notebook.

johanneskoester · 2024-10-11T08:38:41Z

Also, it may be better to add some tests for notebook execution in apptainer, to prevent trivial bugs like this one here.

Indeed! I won't be able to do that now, but if you want to do it in this PR please feel free to do so. If not, it would be ok to merge this without or while adding a TODO.

laf070810 · 2024-10-11T08:45:56Z

Also, it may be better to add some tests for notebook execution in apptainer, to prevent trivial bugs like this one here.

Indeed! I won't be able to do that now, but if you want to do it in this PR please feel free to do so. If not, it would be ok to merge this without or while adding a TODO.

Thanks for the quick reply! I would recommend merging this first, as this bug makes notebook in apptainer unusable. I can open an issue to track on adding tests and do it later.

sonarqubecloud · 2024-10-11T10:07:17Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

🤖 I have created a release *beep* *boop* --- ## [8.21.0](v8.20.7...v8.21.0) (2024-10-12) ### Features * support for specifying conda envs as directories ([#3132](#3132)) ([c54c95d](c54c95d)) ### Bug Fixes * better error handling in evaluate function ([#3129](#3129)) ([04fb97f](04fb97f)) * notebook execution for apptainer ([#3131](#3131)) ([2e382c4](2e382c4)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

fix notebook execution for apptainer

e74b593

laf070810 requested a review from johanneskoester as a code owner October 11, 2024 07:00

johanneskoester approved these changes Oct 11, 2024

View reviewed changes

Merge branch 'main' into fix-apptainer-notebook

ebc30d6

johanneskoester merged commit 2e382c4 into snakemake:main Oct 11, 2024

github-actions bot mentioned this pull request Oct 11, 2024

chore(main): release 8.21.0 #3134

Merged

coderabbitai bot mentioned this pull request Feb 19, 2025

feat: New CLI argument --premable-only, acting as a flexible side-kick to --draft-notebook #3281

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fix: notebook execution for apptainer#3131

fix: notebook execution for apptainer#3131
johanneskoester merged 2 commits intosnakemake:mainfrom
laf070810:fix-apptainer-notebook

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	if is_python_script:
	# mount host snakemake module into container
	args += " ".join(
	f" --bind {repr(searchpath)}:{repr(mountpoint)}"
	for searchpath, mountpoint in zip(
	get_snakemake_searchpaths(), get_snakemake_searchpath_mountpoints()
	)
	)

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