fix: fix modification checks for scripts and and notebooks containing wildcards or params in their paths by mawenzy · Pull Request #2751 · snakemake/snakemake

mawenzy · 2024-03-12T13:42:11Z

Fixes #2750

Description

Parse wildcards in script names before checking file timestamps.

Summary by CodeRabbit

New Features
- Enhanced script path handling for improved flexibility in dynamic resolution based on provided parameters.
Bug Fixes
- Improved control flow to ensure accurate script path determination before further operations.

sonarqubecloud · 2024-03-12T13:42:55Z

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sonarqubecloud · 2024-04-12T08:44:02Z

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sonarqubecloud · 2024-06-03T12:55:46Z

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coderabbitai · 2024-09-06T12:53:39Z

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📥 Commits

Reviewing files that changed from the base of the PR and between e390c9a and fd5e336.

📒 Files selected for processing (1)

snakemake/jobs.py (5 hunks)

📝 Walkthrough

Walkthrough

The changes introduce a new import statement and modify the logic of the outputs_older_than_script_or_notebook asynchronous function in the snakemake/jobs.py file. The updated logic incorporates dynamic path resolution using the infer_source_file function, allowing for improved handling of script paths based on provided wildcards and parameters.

Changes

Files	Change Summary
`snakemake/jobs.py`	Added import statement and modified `outputs_older_than_script_or_notebook` function to include dynamic path resolution using `infer_source_file`.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Snakemake
    participant JobHandler

    User->>Snakemake: Request job execution
    Snakemake->>JobHandler: Check outputs older than script or notebook
    JobHandler->>JobHandler: Check if wildcards or params are not None
    alt Wildcards or Params present
        JobHandler->>JobHandler: Format path using wildcards/params
        JobHandler->>infer_source_file: Resolve script path
    else No wildcards or Params
        JobHandler->>JobHandler: Use default script path
    end
    JobHandler->>Snakemake: Return output status
    Snakemake->>User: Respond with job execution result

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Actionable comments posted: 1

Review details

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Commits

Files that changed from the base of the PR and between 2ec61f4 and e390c9a.

Files selected for processing (1)

snakemake/jobs.py (2 hunks)

Additional context used

Path-based instructions (1)

snakemake/jobs.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/jobs.py (1)

44-44: New Import: infer_source_file

The addition of infer_source_file from snakemake.sourcecache is crucial for the new functionality to dynamically resolve script names using wildcards and parameters. This change aligns with the PR's objective to handle file timestamps more accurately when wildcards are used in script names.

snakemake/jobs.py

sonarqubecloud · 2024-09-27T11:32:14Z

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

sonarqubecloud · 2024-12-21T16:32:00Z

Quality Gate passed

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See analysis details on SonarQube Cloud

@laf070810

🤖 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>

… wildcards or params in their paths (snakemake#2751) Fixes snakemake#2750 ### Description Parse wildcards in script names before checking file timestamps.  ## Summary by CodeRabbit - **New Features** - Enhanced script path handling for improved flexibility in dynamic resolution based on provided parameters. - **Bug Fixes** - Improved control flow to ensure accurate script path determination before further operations.  --------- Co-authored-by: mawenzy <mawenzy@users.noreply.github.com> Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com> Co-authored-by: Johannes Koester <johannes.koester@uni-due.de> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

@laf070810

🤖 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>

Parse script name when deciding whether job needs updating

6eff1dd

mawenzy requested a review from johanneskoester as a code owner March 12, 2024 13:42

mawenzy changed the title ~~Closes #2750~~ fix: #2750, does not correctly check time stamps of scripts with wildcards Mar 12, 2024

Merge branch 'main' into script_wildcard_update

60c3b26

updated formatting

ec9b6b0

Merge branch 'main' into script_wildcard_update

e390c9a

coderabbitai bot reviewed Sep 6, 2024

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snakemake/jobs.py Outdated Show resolved Hide resolved

Merge branch 'main' into script_wildcard_update

ff13b6c

johanneskoester added 2 commits December 21, 2024 16:34

refactoring

de2a29d

fmt

5a48b2c

johanneskoester approved these changes Dec 21, 2024

View reviewed changes

johanneskoester and others added 4 commits December 21, 2024 16:58

fix

6157d2e

fix

97ad3d4

fix

57ec26a

Merge branch 'main' into script_wildcard_update

fd5e336

johanneskoester changed the title ~~fix: #2750, does not correctly check time stamps of scripts with wildcards~~ fix: fix modification checks for scripts and and notebooks containing wildcards or params in their paths Dec 21, 2024

johanneskoester merged commit 773568d into snakemake:main Dec 21, 2024

github-actions bot mentioned this pull request Dec 21, 2024

chore(main): release 8.26.0 #3229

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fix: fix modification checks for scripts and and notebooks containing wildcards or params in their paths#2751

fix: fix modification checks for scripts and and notebooks containing wildcards or params in their paths#2751
johanneskoester merged 11 commits intosnakemake:mainfrom
mawenzy:script_wildcard_update

mawenzy commented Mar 12, 2024 •

edited by johanneskoester

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