fix: Pass host attribute to GitlabFile instantiation within class methods#3155
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe changes involve enhancements to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant GitlabFile
User->>GitlabFile: Create instance (repo, path)
GitlabFile->>GitlabFile: Set host to "gitlab.com" (if not provided)
User->>GitlabFile: Call get_basedir()
GitlabFile->>GitlabFile: Create new instance with same attributes
User->>GitlabFile: Call join(path)
GitlabFile->>GitlabFile: Create new instance with appended path
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🧹 Outside diff range and nitpick comments (1)
tests/test_sourcecache.py (1)
3-12: LGTM: Test function is well-structured. Consider minor improvements.The test function
test_GitlabFile_host_propagationis well-implemented and covers the main scenarios forhostattribute propagation in theGitlabFileclass. It correctly verifies that thehostis maintained both in the base directory and when joining paths.To further enhance the test:
- Consider adding a docstring to explain the purpose of the test.
- You might want to add more assertions to cover edge cases or different
hostvalues.Here's a suggested improvement with a docstring:
def test_GitlabFile_host_propagation(): """ Test that the 'host' attribute is correctly propagated in GitlabFile. This test verifies that: 1. The 'host' attribute is correctly set when creating a GitlabFile instance. 2. The 'host' is properly propagated when getting the base directory. 3. The 'host' is maintained when joining with a new path. """ file = GitlabFile( repo="owner/repo", path="parent/path", tag="tag", host="host.com" ) assert file.get_basedir().host == file.host assert file.join("another/path").host == file.host # Additional assertions could be added here to test different host values # or edge cases
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snakemake/sourcecache.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/test_sourcecache.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.
🔇 Additional comments (7)
tests/test_sourcecache.py (2)
1-1: LGTM: Import statement is correct.The import statement correctly imports the
GitlabFileclass from thesnakemake.sourcecachemodule, which is necessary for the test function.
1-12: Overall, the test file is well-implemented and addresses the PR objectives.This test file successfully implements a test case for the
GitlabFileclass, focusing on the propagation of thehostattribute. It aligns well with the PR objectives of ensuring that thehostattribute is appropriately handled during the instantiation of new class instances.The test covers the main scenarios:
- Creating a
GitlabFileinstance with a specifichost.- Verifying
hostpropagation when getting the base directory.- Ensuring
hostis maintained when joining paths.These test cases provide good coverage for the changes made in the
GitlabFileclass. The implementation is concise and effective, meeting the quality control measures mentioned in the PR description.snakemake/sourcecache.py (5)
293-293: LGTM: Constructor change improves flexibilityThe modification to set a default value for the
hostparameter enhances theGitlabFileclass's flexibility. This change aligns well with the PR objective and follows Python best practices.
308-316: LGTM:get_basedirmethod correctly implementedThe new
get_basedirmethod is well-implemented, preserving all attributes including thehostwhen creating a newGitlabFileinstance. This addition aligns with the PR objective and maintains consistency with the base class implementation.
318-331: LGTM:joinmethod well-implemented with cross-platform considerationsThe new
joinmethod is correctly implemented, preserving all attributes including thehostwhen creating a newGitlabFileinstance. The method handles path normalization and includes Windows-specific adjustments, which is excellent for cross-platform compatibility. This addition aligns with the PR objective and maintains consistency with the base class implementation.
301-301: LGTM:get_path_or_urimethod updated for consistencyThe
get_path_or_urimethod has been updated to useself.hostinstead of a hardcoded value. This change is consistent with the constructor modification and supports custom GitLab hosts, aligning with the PR objective.
293-331: Summary: Excellent implementation ofhostattribute handling inGitlabFileThe changes to the
GitlabFileclass effectively address the PR objective of passing thehostattribute to new instantiations. The modifications to the constructor,get_basedir,join, andget_path_or_urimethods are well-implemented, consistent, and follow Python best practices. These changes enhance the flexibility of theGitlabFileclass by supporting custom GitLab hosts while maintaining backward compatibility.The implementation also demonstrates good cross-platform considerations, particularly in the
joinmethod. Overall, these changes improve the functionality and usability of theGitlabFileclass within the Snakemake source cache system.
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🤖 I have created a release *beep* *boop* --- ## [8.26.0](v8.25.5...v8.26.0) (2024-12-23) ### Features * add helpers for deferred input/output etc. item access ([#2927](#2927)) ([2cca9bc](2cca9bc)) ### Bug Fixes * convert parameters so they can be serialized ([#2925](#2925)) ([9e653fb](9e653fb)) * correct formatting of R preamble ([#2425](#2425)) ([5380cae](5380cae)) * fix modification checks for scripts and and notebooks containing wildcards or params in their paths ([#2751](#2751)) ([773568d](773568d)) * Improved handling of missing output files in group job postprocessing, accounting for temporary files. ([#1765](#1765)) ([bac06ba](bac06ba)) * mtime of script or notebook not triggering workflow without metadata ([#3148](#3148)) ([e8a0b83](e8a0b83)) * Pass `host` attribute to `GitlabFile` instantiation within class methods ([#3155](#3155)) ([9ef52de](9ef52de)) * problem with spaces in path ([#3236](#3236)) ([2d08c63](2d08c63)) * require current yte release which contains an important bug fix for cases where numpy/pandas data is passed to templates ([#3227](#3227)) ([c3339da](c3339da)) * rerun jobs if previously failed but rule was changed afterwards (thanks to [@laf070810](https://github.com/laf070810) for bringing this up) ([#3237](#3237)) ([1dc0084](1dc0084)) * use relpath for configfiles added to the source archive (thanks to [@sposadac](https://github.com/sposadac) for the initial solution) ([#3240](#3240)) ([bff3844](bff3844)) --- 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>
… methods (snakemake#3155) Updates `GitlabFile` to re-implement the `HostingProviderFile` methods `get_basedir` and `join` that create new class instances to include handling for the `GitlabFile` specific `host` attribute. ### QC <!-- Make sure that you can tick the boxes below. --> * [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). <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced `GitlabFile` class with a default host parameter and added methods for better file path management. - Introduced `get_basedir` and `join` methods for improved functionality. - **Bug Fixes** - Updated `get_path_or_uri` method for consistent host attribute usage. - **Tests** - Added a new test to ensure the `host` attribute is correctly propagated in the `GitlabFile` class. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Johannes Koester <johannes.koester@uni-due.de>
🤖 I have created a release *beep* *boop* --- ## [8.26.0](snakemake/snakemake@v8.25.5...v8.26.0) (2024-12-23) ### Features * add helpers for deferred input/output etc. item access ([snakemake#2927](snakemake#2927)) ([2cca9bc](snakemake@2cca9bc)) ### Bug Fixes * convert parameters so they can be serialized ([snakemake#2925](snakemake#2925)) ([9e653fb](snakemake@9e653fb)) * correct formatting of R preamble ([snakemake#2425](snakemake#2425)) ([5380cae](snakemake@5380cae)) * fix modification checks for scripts and and notebooks containing wildcards or params in their paths ([snakemake#2751](snakemake#2751)) ([773568d](snakemake@773568d)) * Improved handling of missing output files in group job postprocessing, accounting for temporary files. ([snakemake#1765](snakemake#1765)) ([bac06ba](snakemake@bac06ba)) * mtime of script or notebook not triggering workflow without metadata ([snakemake#3148](snakemake#3148)) ([e8a0b83](snakemake@e8a0b83)) * Pass `host` attribute to `GitlabFile` instantiation within class methods ([snakemake#3155](snakemake#3155)) ([9ef52de](snakemake@9ef52de)) * problem with spaces in path ([snakemake#3236](snakemake#3236)) ([2d08c63](snakemake@2d08c63)) * require current yte release which contains an important bug fix for cases where numpy/pandas data is passed to templates ([snakemake#3227](snakemake#3227)) ([c3339da](snakemake@c3339da)) * rerun jobs if previously failed but rule was changed afterwards (thanks to [@laf070810](https://github.com/laf070810) for bringing this up) ([snakemake#3237](snakemake#3237)) ([1dc0084](snakemake@1dc0084)) * use relpath for configfiles added to the source archive (thanks to [@sposadac](https://github.com/sposadac) for the initial solution) ([snakemake#3240](snakemake#3240)) ([bff3844](snakemake@bff3844)) --- 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>
Updates
GitlabFileto re-implement theHostingProviderFilemethodsget_basedirandjointhat create new class instances to include handling for theGitlabFilespecifichostattribute.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
New Features
GitlabFileclass with a default host parameter and added methods for better file path management.get_basedirandjoinmethods for improved functionality.Bug Fixes
get_path_or_urimethod for consistent host attribute usage.Tests
hostattribute is correctly propagated in theGitlabFileclass.