fix: record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important.#3314
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johanneskoester merged 2 commits intomainfrom Feb 27, 2025
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fix: record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important.#3314johanneskoester merged 2 commits intomainfrom
johanneskoester merged 2 commits intomainfrom
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…rds in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important.
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Sequence Diagram(s)sequenceDiagram
participant Caller
participant Cache as AbstractOutputFileCache
participant PathLib as Path Library
Caller->>Cache: call get_outputfiles(job)
Cache->>PathLib: compute file extension from job.output[0]
PathLib-->>Cache: return file extension
Cache->>Caller: yield (job.output[0], extension)
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johanneskoester
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Feb 27, 2025
🤖 I have created a release *beep* *boop* --- ## [8.29.0](v8.28.0...v8.29.0) (2025-02-27) ### Features * provide mechanism to link between report items (snakemake.report_href, see docs) ([#3224](#3224)) ([a024e60](a024e60)) * toggles for binary labels in report ([#3296](#3296)) ([7690998](7690998)) ### Bug Fixes * add missing [@conda](https://github.com/conda) annotations ([#3298](#3298)) ([0b541cc](0b541cc)) * properly handle remote storage when waiting for pipes ([#3317](#3317)) ([9f7e092](9f7e092)) * provide proper error messages if output file preparation (pipe, mkdir) fails ([#3309](#3309)) ([77ef176](77ef176)) * record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. ([#3314](#3314)) ([4912f00](4912f00)) * sort results lexicographically by labels in their order of appearance ([#3293](#3293)) ([a19a0ac](a19a0ac)) ### Documentation * update best practices ([7270eb3](7270eb3)) --- 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>
kjohnsen
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Dec 15, 2025
…rds in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. (snakemake#3314) <!--Add a description of your PR here--> ### 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** - Improved caching of job outputs by incorporating file extensions. This update ensures that output files are more accurately identified and retrieved from the cache, reducing potential mismatches. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen
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Dec 15, 2025
🤖 I have created a release *beep* *boop* --- ## [8.29.0](snakemake/snakemake@v8.28.0...v8.29.0) (2025-02-27) ### Features * provide mechanism to link between report items (snakemake.report_href, see docs) ([snakemake#3224](snakemake#3224)) ([a024e60](snakemake@a024e60)) * toggles for binary labels in report ([snakemake#3296](snakemake#3296)) ([7690998](snakemake@7690998)) ### Bug Fixes * add missing [@conda](https://github.com/conda) annotations ([snakemake#3298](snakemake#3298)) ([0b541cc](snakemake@0b541cc)) * properly handle remote storage when waiting for pipes ([snakemake#3317](snakemake#3317)) ([9f7e092](snakemake@9f7e092)) * provide proper error messages if output file preparation (pipe, mkdir) fails ([snakemake#3309](snakemake#3309)) ([77ef176](snakemake@77ef176)) * record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. ([snakemake#3314](snakemake#3314)) ([4912f00](snakemake@4912f00)) * sort results lexicographically by labels in their order of appearance ([snakemake#3293](snakemake#3293)) ([a19a0ac](snakemake@a19a0ac)) ### Documentation * update best practices ([7270eb3](snakemake@7270eb3)) --- 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>
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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