fix: use relpath for configfiles added to the source archive (thanks to @sposadac for the initial solution) #3240
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📝 WalkthroughWalkthroughThe pull request introduces modifications to three files in the Snakemake project: Changes
Sequence DiagramsequenceDiagram
participant Workflow
participant DAG
Workflow->>DAG: get_sources()
DAG-->>Workflow: Return relative configuration file paths
Workflow->>Workflow: write_source_archive()
Workflow-->>User: Display enhanced warning message
This sequence diagram illustrates the high-level interaction between the Workflow and DAG components, highlighting the changes in path handling and logging mechanisms. Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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🧹 Nitpick comments (1)
snakemake/workflow.py (1)
298-303: Consider refining grammar and consolidating the f-string.
- The phrase "spawned jobs will not properly work" can be more standardly phrased as "spawned jobs will not work properly."
- (Optional) Use one unified f-string for clearer readability across multiple lines.
A possible edit for grammar:
logger.warning( - f"Ignoring source file {f}! Only files relative " - "to the working directory are allowed. Most likely the " - "spawned jobs will not properly work. Make sure to start " - "the workflow from a directory below which all the sources " - "are located (may be in subfolders) and also ensure that any " - "config files you refer to are inside that directory." f"Ignoring source file {f}! Only files relative to the working " f"directory are allowed. Most likely the spawned jobs will not work " f"properly. Make sure to start the workflow from a directory below " f"which all the sources are located (may be in subfolders), and " f"also ensure that any config files you refer to are inside that directory." )
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snakemake/dag.py(1 hunks)snakemake/workflow.py(1 hunks)
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- snakemake/dag.py
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snakemake/workflow.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.
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johanneskoester
changed the title
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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>
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
Bug Fixes