fix: avoid error accessing superclass in ioutils by johanneskoester · Pull Request #3056 · snakemake/snakemake

johanneskoester · 2024-08-29T07:14:04Z

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
- Improved the method resolution for wildcards, enhancing stability and preventing potential issues in complex inheritance scenarios.

coderabbitai · 2024-08-29T07:14:11Z

Walkthrough

The changes involve modifying the needs_wildcards method in the QueryWildcardHandler class within the snakemake/ioutils.py file. The method now explicitly specifies the class when calling the superclass method, improving clarity and addressing potential issues related to multiple inheritance.

Changes

Files	Change Summary
snakemake/ioutils.py	Modified the `needs_wildcards` method in `QueryWildcardHandler` to explicitly specify the class in the `super()` call.

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github-actions · 2024-08-29T07:14:36Z

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

coderabbitai

Actionable comments posted: 0

Review details

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Review profile: CHILL

Commits

Files that changed from the base of the PR and between 86ed3cd and 7183327.

Files selected for processing (1)

snakemake/ioutils.py (1 hunks)

Additional context used

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snakemake/ioutils.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.
Do not suggest return type annotation if a function or method does not contain a return statement.

Additional comments not posted (1)

snakemake/ioutils.py (1)

90-90: LGTM!

The change to explicitly specify the class when calling the superclass method enhances clarity and prevents potential issues related to multiple inheritance scenarios.

The code changes are approved.

sonarqubecloud · 2024-08-29T07:30:20Z

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

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 7183327 and 9e5fd68.

Files selected for processing (1)

snakemake/ioutils.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

snakemake/ioutils.py

🤖 I have created a release *beep* *boop* --- ## [8.19.0](v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([#3050](#3050)) ([666cf62](666cf62)) * print host name when executing workflow ([#3048](#3048)) ([b0ff787](b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([#3040](#3040)) ([7530794](7530794)) * avoid error accessing superclass in ioutils ([#3056](#3056)) ([a66a5f5](a66a5f5)) * disable execute after print compilation ([#3041](#3041)) ([86ed3cd](86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [#2904](#2904)) ([#3026](#3026)) ([e8dad4b](e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([#3045](#3045)) ([9a4006d](9a4006d)) * Fix typo (seesee to see) ([#3037](#3037)) ([de201fb](de201fb)) * various documentation fixes ([#3052](#3052)) ([b11460c](b11460c)) --- 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>

### 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** - Improved the method resolution for wildcards, enhancing stability and preventing potential issues in complex inheritance scenarios.

🤖 I have created a release *beep* *boop* --- ## [8.19.0](snakemake/snakemake@v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([snakemake#3050](snakemake#3050)) ([666cf62](snakemake@666cf62)) * print host name when executing workflow ([snakemake#3048](snakemake#3048)) ([b0ff787](snakemake@b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([snakemake#3040](snakemake#3040)) ([7530794](snakemake@7530794)) * avoid error accessing superclass in ioutils ([snakemake#3056](snakemake#3056)) ([a66a5f5](snakemake@a66a5f5)) * disable execute after print compilation ([snakemake#3041](snakemake#3041)) ([86ed3cd](snakemake@86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [snakemake#2904](snakemake#2904)) ([snakemake#3026](snakemake#3026)) ([e8dad4b](snakemake@e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([snakemake#3045](snakemake#3045)) ([9a4006d](snakemake@9a4006d)) * Fix typo (seesee to see) ([snakemake#3037](snakemake#3037)) ([de201fb](snakemake@de201fb)) * various documentation fixes ([snakemake#3052](snakemake#3052)) ([b11460c](snakemake@b11460c)) --- 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>

- Fixes pip deployment import path in spawn_jobs.py because PIP_DEPLOYMENT_PATH was moved to snakemake/__init__.py in #3056 ### 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 - **Chores** - Simplified import statements for better clarity in the deployment path reference. - Improved readability of the code without altering existing functionality.

fix: avoid error accessing superclass in ioutils

7183327

coderabbitai bot reviewed Aug 29, 2024

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fix

9e5fd68

coderabbitai bot reviewed Aug 29, 2024

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johanneskoester merged commit a66a5f5 into main Aug 29, 2024

johanneskoester deleted the fix/ioutils-super-class branch August 29, 2024 07:37

github-actions bot mentioned this pull request Aug 29, 2024

chore(main): release 8.19.0 #3051

Merged

jakevc mentioned this pull request Aug 30, 2024

fix: pip deployment path #3062

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2 tasks

coderabbitai bot mentioned this pull request Sep 9, 2024

fix: ensure that CLI help is formatted deterministically and set defaults are displayed properly (based on preliminary work by @keszybz) #3081

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coderabbitai bot mentioned this pull request Oct 9, 2024

fix: better error handling in evaluate function #3129

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coderabbitai bot mentioned this pull request Nov 25, 2024

fix: ensure that intermediate files in job groups do not cause spurious mtime errors when checking for consistency with output files #3220

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fix: avoid error accessing superclass in ioutils#3056

fix: avoid error accessing superclass in ioutils#3056
johanneskoester merged 2 commits intomainfrom
fix/ioutils-super-class

johanneskoester commented Aug 29, 2024 •

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