Python 3.12 support #193
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Python 3.12 support #193
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standage
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Apr 30, 2025
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| from pkg_resources import resource_filename | ||
| from importlib.resources import files |
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The pkg_resources package is also removed in Python 3.12, so it was replaced by importlib.resources.
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| result, | ||
| "analysis/{}/03typing/callplots".format(wildcards.sample), | ||
| sample=wildcards.sample, |
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Snakemake has weird problems with f-strings in Python 3.12, so calling the str.format function in a few places.
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| linkfile = f"{params.outdir}/R{end}-fastqc.html" | ||
| # Snakemake f-strings break with Python 3.12: https://github.com/snakemake/snakemake/issues/2648 | ||
| linkfile = "{}/R{}-fastqc.html".format(params.outdir, end) |
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This PR is enabling Python 3.12 support. This involved a versioneer upgrade, not only for the main package but also for accessory packages. The happer package was integrated into MicroHapulator as it probably never should have been an independent package. This eliminated one additional source of 3.12 incompatibility. The remaining source of incompatibility is MicroHapDB, whose version 0.12 release will be required before this PR can be merged.