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This printed the reason for each executed rule but was already deprecated and always true in v7 [1] and has been removed entirely in later snakemake versions. The upgrade path is clear [2]: "Deprecated: Drop it and don't worry about anything" [1] <https://snakemake.readthedocs.io/en/v7.22.0/executing/cli.html#output> [2] <https://snakemake.readthedocs.io/en/stable/getting_started/migration.html>
j23414
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jameshadfield
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This printed the reason for each executed rule but was already deprecated and always true in v7 [1] and has been removed entirely in later snakemake versions. The upgrade path is clear [2]: "Deprecated: Drop it and don't worry about anything" Note: The same changes were applied to zika [3] [1] <https://snakemake.readthedocs.io/en/v7.22.0/executing/cli.html#output> [2] <https://snakemake.readthedocs.io/en/stable/getting_started/migration.html> [3] <nextstrain/zika#88>
jameshadfield
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This printed the reason for each executed rule but was already deprecated and always true in v7 [1] and has been removed entirely in later snakemake versions. The upgrade path is clear [2]: "Deprecated: Drop it and don't worry about anything" Note: The same changes were applied to zika [3] [1] <https://snakemake.readthedocs.io/en/v7.22.0/executing/cli.html#output> [2] <https://snakemake.readthedocs.io/en/stable/getting_started/migration.html> [3] <nextstrain/zika#88>
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The only change needed to support Snakemake v9 was to remove a snakemake argument which was already deprecated and a no-op in v7. So I think this can be merged now (while our runtimes are still pinned to v7).
Closes #87
Tested in a conda environment with python 3.12.2, snakemake 9.6.2, augur e6245ebd (current master, v31.2.1).