feat: add helper functions to parse input files #2918
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CodeRabbit blocks several paths by default. You can override this behavior by explicitly including those paths in the path filters. For example, including You can disable this status message by setting the 📝 WalkthroughWalkthroughThe pull request introduces a new section in the Snakemake documentation for integrating Xonsh scripts, alongside updates to various modules and test files. Key changes include the addition of functions Changes
Sequence DiagramsequenceDiagram
participant User as Snakemake Workflow
participant ParseInput as parse_input()
participant ExtractChecksum as extract_checksum()
participant InputFile as Input File
User->>ParseInput: Call with input file and parser
ParseInput->>InputFile: Open and read file
alt No custom parser
ParseInput-->>User: Return file content
else Custom parser provided
ParseInput->>ExtractChecksum: Apply parser function
ExtractChecksum->>InputFile: Read specific data
ExtractChecksum-->>ParseInput: Return parsed value
ParseInput-->>User: Return parsed result
end
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🧹 Nitpick comments (1)
snakemake/ioutils/input.py (1)
1-9: Add error handling for file operations.The function should handle potential IOErrors when opening/reading the file and provide meaningful error messages.
def parse_input(infile=None, parser=None, **kwargs): def inner(wildcards, input, output): - with open(infile, "r") as fh: - if parser is None: - return fh.read().strip() - else: - return parser(fh, **kwargs) + try: + with open(infile, "r") as fh: + if parser is None: + return fh.read().strip() + else: + return parser(fh, **kwargs) + except IOError as e: + raise WorkflowError(f"Error reading input file {infile}: {str(e)}") return inner
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docs/snakefiles/rules.rst(2 hunks)snakemake/ioutils/__init__.py(2 hunks)snakemake/ioutils/input.py(1 hunks)tests/test_ioutils/Snakefile(4 hunks)tests/test_ioutils/expected-results/c/1.txt(1 hunks)tests/test_ioutils/expected-results/results/switch~someswitch.column~sample.txt(1 hunks)tests/test_ioutils/samples.md5(1 hunks)
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snakemake/ioutils/__init__.py (1)
Pattern **/*.py: Do not try to improve formatting.
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snakemake/ioutils/input.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.
Do not suggest type annotation of the cls argument of classmethods.
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snakemake/ioutils/input.py
15-15: Do not assign a lambda expression, use a def
Rewrite fix_file_name as a def
(E731)
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🔇 Additional comments (3)
snakemake/ioutils/__init__.py (1)
8-8: LGTM!The registration of new functions follows the established pattern correctly.
Also applies to: 25-26
tests/test_ioutils/Snakefile (1)
11-13: LGTM!The test coverage is comprehensive and demonstrates proper usage of the new functionality.
Also applies to: 22-29
docs/snakefiles/rules.rst (1)
550-592: LGTM!The documentation is clear, well-structured, and includes helpful examples.
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🧹 Nitpick comments (1)
docs/snakefiles/rules.rst (1)
573-593: Enhance theextract_checksumFunction DocumentationThe documentation for
extract_checksumsuccinctly states its purpose and signature. To further improve clarity, consider:
- Stating explicitly the expected format or structure of the
infile(for example, if it is a CSV, a text file with MD5 checksums, etc.) and what exact form thefileparameter should take.- Explaining that the function returns a string representing the extracted checksum.
- Noting that when used in conjunction with
parse_input, any additional keyword arguments (e.g.file=output.tsvin the usage example) are forwarded toextract_checksum.These additions would provide the reader with a fuller understanding of how to use the function and what to expect from its output.
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🔇 Additional comments (1)
docs/snakefiles/rules.rst (1)
550-572: Clarify theparse_inputFunction’s Signature and BehaviorThe newly added documentation for
parse_inputis clear in its intent. However, consider adding the following clarifications:
- Specify that the third parameter (referred to as
kwargsin the signature) is optional and is used to pass extra keyword arguments directly to the parser.- Emphasize that
parse_inputreturns a function which, when evaluated later by Snakemake, invokes the given parser with the supplied parameters.- As noted in previous reviews (), please ensure the implementation/documentation reminds users to validate the first argument—if it is not a callable,
parse_inputshould raise a descriptive error directing them to the updated documentation (see PR 2927).These clarifications will help users understand both the required types for each parameter and the deferred evaluation behavior of the helper function.
Co-authored-by: Johannes Köster <[email protected]>
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♻️ Duplicate comments (1)
snakemake/ioutils/input.py (1)
12-30:⚠️ Potential issueMultiple improvements needed for extract_checksum function.
- Replace lambda with a proper function per static analysis
- Import WorkflowError class
- Use proper exception chaining with
fromsyntax- Add more comprehensive error handling
+from snakemake.exceptions import WorkflowError + def extract_checksum(infile, **kwargs): + """Extract checksum from a CSV file. + + Args: + infile: Path to CSV file containing checksums + **kwargs: Additional arguments, must include 'file' key + + Returns: + str: The extracted checksum + + Raises: + WorkflowError: If pandas is not installed, file not found, or checksum extraction fails + """ + def fix_file_name(x): + return x.removeprefix("./") + try: import pandas as pd - - fix_file_name = lambda x: x.removeprefix("./") - return ( - pd.read_csv( - infile, - sep=" ", - header=None, - engine="python", - converters={1: fix_file_name}, - ) - .set_index(1) - .loc[fix_file_name(kwargs.get("file"))] - .item() - ) except ImportError: - raise WorkflowError("Pandas is required to extract checksum from file.") + raise WorkflowError("Pandas is required to extract checksum from file.") from None + + if "file" not in kwargs: + raise WorkflowError("'file' parameter is required for extract_checksum function") + + try: + df = pd.read_csv( + infile, + sep=" ", + header=None, + engine="python", + converters={1: fix_file_name}, + ) + return df.set_index(1).loc[fix_file_name(kwargs["file"])].item() + except FileNotFoundError: + raise WorkflowError(f"Checksum file not found: {infile}") from None + except KeyError: + raise WorkflowError(f"File {kwargs['file']} not found in checksum file") from None + except Exception as e: + raise WorkflowError(f"Error extracting checksum: {str(e)}") from e🧰 Tools
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16-16: Do not assign a
lambdaexpression, use adefRewrite
fix_file_nameas adef(E731)
30-30: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
30-30: Undefined name
WorkflowError(F821)
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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.
snakemake/ioutils/input.py
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snakemake/ioutils/input.py
16-16: Do not assign a lambda expression, use a def
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30-30: Undefined name WorkflowError
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🔭 Outside diff range comments (2)
snakemake/script/__init__.py (1)
1600-1736: 💡 Verification agent🧩 Analysis chain
Verify Xonsh is properly installed in the conda environment for this feature.
The new Xonsh script functionality will require the
xonshshell to be installed in the user's environment. Please ensure this dependency is documented for users who want to use this feature.
🏁 Script executed:
#!/bin/bash # Check if xonsh is mentioned in any conda environment files or documentation echo "Searching for xonsh in conda environment files:" find workflow -name "*.yaml" -o -name "*.yml" | xargs grep -l "xonsh" || echo "xonsh not found in conda environment files" echo "Searching for xonsh in documentation:" find docs -type f -name "*.rst" -o -name "*.md" | xargs grep -l "xonsh" || echo "xonsh not mentioned in documentation files"Length of output: 565
Update Required: Document the Xonsh Dependency
The new Xonsh script functionality requires the
xonshshell to be installed in the user's environment. However, our search did not find any references toxonshin the conda environment YAML files or in the documentation. Please ensure that:
- The dependency on
xonshis clearly mentioned in the installation or setup instructions (e.g., in the README or other docs).- The conda environment configuration is updated (if applicable) to include the
xonshpackage.Once these documentation updates are added, users will be properly guided on how to install
xonshto utilize the new feature.🧰 Tools
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1675-1675: Local variable
eis assigned to but never usedRemove assignment to unused variable
e(F841)
1676-1679: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
1725-1733: Use
dict.get()without default valueRemove default value
(SIM910)
tests/tests_using_conda.py (1)
332-346:⚠️ Potential issueDuplicate test functions detected
The test functions
test_get_log_both,test_get_log_stderr,test_get_log_stdout, andtest_get_log_complexare duplicated at the end of the file. This will cause issues when running tests, as pytest will discover each function twice.Remove the duplicate test functions:
-def test_get_log_both(): - run(dpath("test_get_log_both")) - - - -def test_get_log_stderr(): - run(dpath("test_get_log_stderr")) - - - -def test_get_log_stdout(): - run(dpath("test_get_log_stdout")) - - - -def test_get_log_complex(): - run(dpath("test_get_log_complex"))
🧹 Nitpick comments (3)
docs/snakefiles/rules.rst (2)
550-571: Clarify theparse_inputfunction signature and expected behavior.
The new documentation forparse_inputis clear and provides a good usage example. However, the signature is noted asparse_input(input_item, parser, kwargs)while the example only passes a string as the first argument (e.g.
"samples"). It would improve clarity to explicitly state what types are accepted forinput_item– for instance, that it may be a key referencing an input file or a callable—and what will happen if a non-callable is provided (per the suggestions in PR #2927). Consider adding a note or a brief explanation that an error will be raised with a reference to the updated docs section if the first argument is not of the expected type.
573-593: Review and enhance theextract_checksumfunction documentation.
The documentation clearly explains thatextract_checksumparses an input file and returns the checksum for a given filename. The usage example is helpful. To further aid users, consider clarifying how thefileparameter is used in cases where multiple matches might occur or if no matching filename is found. This additional detail would prevent potential ambiguities in usage and guide users to implement proper error handling in their parser implementations.snakemake/workflow.py (1)
1812-1813: Fix the boolean comparison style.The current comparison against
Falseis discouraged in Python. Use a simple truthiness check instead.-if not ruleinfo.template_engine and ruleinfo.container_img != False: +if not ruleinfo.template_engine and ruleinfo.container_img:🧰 Tools
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1812-1812: Avoid inequality comparisons to
False; useif ruleinfo.container_img:for truth checksReplace with
ruleinfo.container_img(E712)
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docs/snakefiles/rules.rst(1 hunks)docs/snakefiles/rules.rst(2 hunks)docs/snakefiles/rules.rst(3 hunks)docs/snakefiles/deployment.rst(4 hunks)docs/snakefiles/reporting.rst(4 hunks)snakemake/cli.py(3 hunks)snakemake/script/__init__.py(4 hunks)snakemake/workflow.py(4 hunks)docs/snakefiles/rules.rst(2 hunks)snakemake/cli.py(1 hunks)test-environment.yml(1 hunks)tests/tests_using_conda.py(1 hunks)docs/snakefiles/rules.rst(1 hunks)docs/snakefiles/deployment.rst(2 hunks)docs/snakefiles/reporting.rst(5 hunks)docs/snakefiles/rules.rst(1 hunks)snakemake/cli.py(1 hunks)snakemake/script/__init__.py(3 hunks)snakemake/workflow.py(1 hunks)test-environment.yml(2 hunks)tests/test_conda_python_3_7_script/Snakefile(1 hunks)tests/test_conda_python_3_7_script/test_script_python_3_7.py(1 hunks)tests/test_conda_run/Snakefile(1 hunks)tests/test_conda_run/expected-results/test.txt(1 hunks)tests/test_conda_run/test_python_env.yaml(1 hunks)tests/test_conda_run/test_script_run.py(1 hunks)tests/test_script_xsh/Snakefile(1 hunks)tests/test_script_xsh/envs/xonsh.yaml(1 hunks)tests/test_script_xsh/scripts/test.xsh(1 hunks)tests/tests_using_conda.py(1 hunks)
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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.
tests/tests_using_conda.pysnakemake/workflow.pysnakemake/cli.pysnakemake/script/__init__.py
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1812-1812: Avoid inequality comparisons to False; use if ruleinfo.container_img: for truth checks
Replace with ruleinfo.container_img
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snakemake/script/__init__.py
97-100: Use ternary operator anchor = f"#{urllib.parse.quote(self._anchor)}" if self._anchor else "" instead of if-else-block
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🔇 Additional comments (30)
tests/test_script_xsh/Snakefile (1)
1-13: Well-structured test Snakefile for Xonsh script integrationThis is a clean and minimal test case for the new Xonsh script integration feature. The file follows Snakemake conventions with a proper
allrule targeting the expected output, and a rule specifying both the conda environment and script to be executed.tests/test_conda_run/Snakefile (1)
1-13: Good test case with informative commentsThis rule demonstrates how to execute a Python script with a conda environment using the
rundirective. The comments clearly explain that this approach is mainly for testing purposes and provide guidance on the recommended approach for production workflows (using the script directive).snakemake/cli.py (3)
14-14: LGTM: Appropriate import additionAdded import for the caching module that will be used to reference environment variables.
48-48: LGTM: Updated import sourceChanged the import source for the
Batchclass to be fromsnakemake.settings.types.
479-479: LGTM: Improved variable reference in help textReplaced hardcoded environment variable name with a reference to
caching.LOCATION_ENVVAR, making the code more maintainable by centralizing the definition of this environment variable.test-environment.yml (2)
7-7: LGTM: Added setuptools dependencyAdded setuptools to the dependencies list, which is a common requirement for Python packaging.
61-62: LGTM: Moved packages from pip to conda dependenciesMoved
cwltoolandcwl-utilsfrom the pip section to direct conda dependencies. This is generally better practice as it allows conda to handle dependency resolution, potentially leading to better compatibility across packages.snakemake/workflow.py (4)
1779-1787: Good refactoring to centralize deployment method validation logic.The addition of this function improves code maintainability by centralizing the logic for checking if software deployment methods can be used with template engines, replacing the previously scattered inline checks.
1794-1794: Consistent use of the new validation function for envmodules.The code now calls the centralized validation function instead of using inline checks, improving consistency and maintainability.
1800-1800: Consistent use of the new validation function for conda.The code now calls the centralized validation function instead of using inline checks, improving consistency and maintainability.
1808-1808: Consistent use of the new validation function for container/singularity.The code now calls the centralized validation function instead of using inline checks, improving consistency and maintainability.
docs/snakefiles/deployment.rst (2)
288-293: Updated conda documentation to include the run directive.This change correctly clarifies that conda environments can also be used with the
rundirective, while explaining its special case nature since it has access to the Snakefile and must execute in the same process as Snakemake itself.
464-467: Updated apptainer documentation to include the run directive.This change correctly clarifies that apptainer integration can also be used with the
rundirective, while explaining the same special case constraints as with conda environments.snakemake/script/__init__.py (4)
1600-1603: Good implementation of XonshScript class.The new
XonshScriptclass extends the functionality of Snakemake to support Xonsh scripts by leveraging inheritance fromPythonScript. The implementation is minimal but sufficient, overriding only theexecute_scriptmethod to use the Xonsh shell.
1667-1668: Added language recognition for Xonsh scripts.This change correctly updates the
get_languagefunction to recognize files with the.xshextension as Xonsh scripts, enabling their proper handling.
1732-1732: Registered XonshScript as the handler for Xonsh scripts.The update to the language-to-executor class mapping properly associates the new
XonshScriptclass with the 'xonsh' language identifier.
1736-1736: Updated error message to include Xonsh scripts.The error message for unsupported script types now correctly includes Xonsh (.xsh) as a supported format, ensuring users receive accurate information about the available options.
docs/snakefiles/reporting.rst (7)
7-10: Improved introduction to reporting capabilities!The updated introduction provides a clearer description of Snakemake's reporting capabilities, highlighting the self-contained nature of reports and explaining the distinction between smaller HTML reports and more complex ZIP archives.
13-17: Well-structured new section headingThe new section "Including results in a report" with proper RST formatting helps organize the documentation logically.
105-105: Minor formatting correctionThe heading level indicator has been corrected from underlining with dashes to using carets, which maintains proper hierarchy in the RST document structure.
142-143: Consistent heading formattingThe RST formatting for the section on determining category, subcategory, and labels dynamically has been properly updated with carets to maintain consistent heading levels.
149-150: Proper section heading formattingThe heading level for "Linking between items" has been correctly formatted with carets to maintain proper document hierarchy.
152-153: Consistent subsection formattingThe subsection headings "From captions" and "From results" use consistent formatting with quotation marks as underlining, maintaining proper RST document structure.
Also applies to: 164-165
257-258: Well-structured new sections with proper RST formattingThe additions of new sections for rendering reports, including self-contained HTML files, ZIP archives, partial reports, and custom layouts, have been properly formatted with appropriate heading levels and RST syntax.
Also applies to: 265-269, 284-285, 286-290, 304-306, 318-320, 321-327, 329-331
tests/tests_using_conda.py (6)
1-5: Proper file header with attribution informationThe file includes appropriate author, copyright, email, and license information.
6-24: Comprehensive imports for test functionalityThe imports cover all necessary modules for testing conda functionality, including standard library modules, pytest, and Snakemake-specific modules.
26-28: Well-designed helper for Windows permission error handlingThe
xfail_permissionerror_on_winfunction provides a clean way to mark tests that might fail with permission errors on Windows.
31-39: Comprehensive test coverage for Conda functionalityThe test functions cover a wide range of Conda-related functionalities, including script execution, environment creation, custom prefixes, and integration with other tools like Apptainer.
Also applies to: 41-49, 51-54, 56-59, 66-81, 83-90, 93-96, 98-107, 109-117, 119-125, 127-135, 137-155, 157-167, 169-172, 174-182, 184-187, 189-193, 195-211, 213-221, 223-227, 229-236, 238-242, 244-252, 254-258, 260-263, 265-271, 273-280, 282-290, 292-295, 297-307, 314-316, 318-320, 322-324, 326-328, 330-332
61-65: Helpful TODO comment for Windows-specific issueThe TODO comment provides valuable information about a specific Windows permission error that needs to be addressed.
309-312: Informative comment about test dependenciesThe comment clearly explains that the following tests don't explicitly depend on Conda but will fail if 'conda info --json' doesn't work as expected.
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moved this from In review
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in Snakemake Hackathon March 2025
🤖 I have created a release *beep* *boop* --- ## [9.0.0](v8.30.0...v9.0.0) (2025-03-14) ### ⚠ BREAKING CHANGES * Logging refactor & add LoggerPluginInterface ([#3107](#3107)) ### Features * [#3412](#3412) - keep shadow folder of failed job if --keep-incomplete flag is set. ([#3430](#3430)) ([22978c3](22978c3)) * add flag --report-after-run to automatically generate the report after a successfull workflow run ([#3428](#3428)) ([b0a7f03](b0a7f03)) * add flatten function to IO utils ([#3424](#3424)) ([67fa392](67fa392)) * add helper functions to parse input files ([#2918](#2918)) ([63e45a7](63e45a7)) * Add option to print redacted file names ([#3089](#3089)) ([ba4d264](ba4d264)) * add support for validation of polars dataframe and lazyframe ([#3262](#3262)) ([c7473a6](c7473a6)) * added support for rendering dag with mermaid js ([#3409](#3409)) ([7bf8381](7bf8381)) * adding --replace-workflow-config to fully replace workflow configs (from config: directive) with --configfile, instead of merging them ([#3381](#3381)) ([47504a0](47504a0)) * Dynamic module name ([#3401](#3401)) ([024dc32](024dc32)) * Enable saving and reloading IOCache object ([#3386](#3386)) ([c935953](c935953)) * files added in rule params with workflow.source_path will be available in used containers ([#3385](#3385)) ([a6e45bf](a6e45bf)) * Fix keep_local in storage directive and more freedom over remote retrieval behaviour ([#3410](#3410)) ([67b4739](67b4739)) * inherit parameters of use rule and extend/replace individual items them when using 'with' directive ([#3365](#3365)) ([93e4b92](93e4b92)) * Logging refactor & add LoggerPluginInterface ([#3107](#3107)) ([86f1d6e](86f1d6e)) * Maximal file size for checksums ([#3368](#3368)) ([b039f8a](b039f8a)) * Modernize package configuration using Pixi ([#3369](#3369)) ([77992d8](77992d8)) * multiext support for named input/output ([#3372](#3372)) ([05e1378](05e1378)) * optionally auto-group jobs via temp files in case of remote execution ([#3378](#3378)) ([cc9bba2](cc9bba2)) ### Bug Fixes * `--delete-all-output` ignores `--dry-run` ([#3265](#3265)) ([23fef82](23fef82)) * 3342 faster touch runs and warning messages for non-existing files ([#3398](#3398)) ([cd9c3c3](cd9c3c3)) * add default value to max-jobs-per-timespan ([#3043](#3043)) ([2959abe](2959abe)) * checkpoints inside modules are overwritten ([#3359](#3359)) ([fba3ac7](fba3ac7)) * Convert Path to IOFile ([#3405](#3405)) ([c58684c](c58684c)) * Do not perform storage object cleanup with --keep-storage-local-copies set ([#3358](#3358)) ([9a6d14b](9a6d14b)) * edgecases of source deployment in case of remote execution ([#3396](#3396)) ([5da13be](5da13be)) * enhance error message formatting for strict DAG-building mode ([#3376](#3376)) ([a1c39ee](a1c39ee)) * fix bug in checkpoint handling that led to exceptions in case checkpoint output was missing upon rerun ([#3423](#3423)) ([8cf4a2f](8cf4a2f)) * force check all required outputs ([#3341](#3341)) ([495a4e7](495a4e7)) * group job formatting ([#3442](#3442)) ([f0b10a3](f0b10a3)) * in remote jobs, upload storage in topological order such that modification dates are preserved (e.g. in case of group jobs) ([#3377](#3377)) ([eace08f](eace08f)) * only skip eval when resource depends on input ([#3374](#3374)) ([4574c92](4574c92)) * Prevent execution of conda in apptainer when not explicitly requested in software deployment method ([#3388](#3388)) ([c43c5c0](c43c5c0)) * print filenames with quotes around them in RuleException ([#3269](#3269)) ([6baeda5](6baeda5)) * Re-evaluation of free resources ([#3399](#3399)) ([6371293](6371293)) * ReadTheDocs layout issue due to src directory change ([#3419](#3419)) ([695b127](695b127)) * robustly escaping quotes in generated bash scripts (v2) ([#3297](#3297)) ([#3389](#3389)) ([58720bd](58720bd)) * Show apptainer image URL in snakemake report ([#3407](#3407)) ([45f0450](45f0450)) * Update ReadTheDocs configuration for documentation build to use Pixi ([#3433](#3433)) ([3f227a6](3f227a6)) ### Documentation * Add pixi setup instructions to general use tutorial ([#3382](#3382)) ([115e81b](115e81b)) * fix contribution section heading levels, fix docs testing setup order ([#3360](#3360)) ([051dc53](051dc53)) * fix link to github.com/snakemake/poetry-snakemake-plugin ([#3436](#3436)) ([ec6d97c](ec6d97c)) * fix quoting ([#3394](#3394)) ([b40f599](b40f599)) * fix rerun-triggers default ([#3403](#3403)) ([4430e23](4430e23)) * fix typo 'safe' -> 'save' ([#3384](#3384)) ([7755861](7755861)) * mention code formatting in the contribution section ([#3431](#3431)) ([e8682b7](e8682b7)) * remove duplicated 'functions'. ([#3356](#3356)) ([7c595db](7c595db)) * update broken links documentation ([#3437](#3437)) ([e3d0d88](e3d0d88)) * Updating contributing guidelines with new pixi dev setup ([#3415](#3415)) ([8e95a12](8e95a12)) --- 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: snakemake-bot <[email protected]>
Add helper functions to parse input files. See example in snakemake/snakemake-wrappers#2725.
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).Summary by CodeRabbit
Release Notes
New Features
Bug Fixes
Documentation
Tests