fix: Migrate away from deprecated pulp API #2610
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Once this is merged, the bioconda recipe needs to include the new version constraints |
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Thanks! |
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Fixing old Snakemake releases on bioconda here: bioconda/bioconda-recipes#45203 |
johanneskoester
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Jan 12, 2024
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henrykironde
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Jan 12, 2024
by Handling backward compatibility within the code ref snakemake#2610 snakemake#2612
johanneskoester
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Jan 13, 2024
🤖 I have created a release *beep* *boop* --- ## [8.1.2](v8.1.1...v8.1.2) (2024-01-12) ### Bug Fixes * local mtime handling in case of storage plugins and cleaner error message for parallel storage retrieval ([#2611](#2611)) ([880b264](880b264)) * Migrate away from deprecated pulp API ([#2610](#2610)) ([fb26640](fb26640)) --- 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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I think the bioconda dependencies weren't adjusted 🙃 https://github.com/bioconda/bioconda-recipes/pull/45226/files |
| @@ -46,7 +46,7 @@ install_requires = | |||
| nbformat | |||
| packaging | |||
| psutil | |||
| pulp >=2.0 | |||
| pulp >=2.3.1,<2.9 # pulp introduced a breaking change from 2.7 to 2.8. Hence we should always pin to the minor version. | |||
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Mirrored to bioconda here: bioconda/bioconda-recipes#45234
Unfortunately not already for 8.1.2, just for 8.1.3
ireneisdoomed
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Feb 16, 2024
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Description
The latest update of pulp 2.8.0 removed deprecated API calls still used by snakemake.
This PR updates the calls to their modern equivalents, as well as constrains the pulp version to the moment these got introduced (v2.3.1).
Fixes the issues described in #2607 and #2606.
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).