Add --keep-invalid Flag for LCA #35
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standage
approved these changes
Mar 8, 2024
pytaxonkit.py
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| assert lca([11111111], skip_deleted=True, skip_unfound=True) == None | ||
| assert lca([22222222], skip_deleted=True, skip_unfound=True) == None |
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Minor quibble: is None instead of == None.
added 2 commits
March 8, 2024 14:54
standage
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Mar 8, 2024
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| TaxID Lineage LineageTaxIDs | ||
| 0 1325911 Eukaryota;Arthropoda;Insecta;Hymenoptera;Eucharitidae;Pogonocharis; 2759;6656;50557;7399;216140;1325911; | ||
| 1 1649473 Bacteria;Bacteroidota;Cytophagia;Cytophagales;Spirosomaceae;Nibrella; 2;976;768503;768507;2896860;1649473; | ||
| 2 1401311 Eukaryota;Arthropoda;Insecta;Coleoptera;Staphylinidae;Styngetus; 2759;6656;50557;7041;29026;1401311; | ||
| TaxID Lineage LineageTaxIDs | ||
| 0 1325911 Eukaryota;Arthropoda;Insecta;Hymenoptera;Eucharitidae;Pogonocharis; 2759;6656;50557;7399;216140;1325911; | ||
| 1 1649473 Bacteria;Bacteroidota;Cytophagia;Cytophagales;Spirosomataceae;Nibrella; 2;976;768503;768507;2896860;1649473; | ||
| 2 1401311 Eukaryota;Arthropoda;Insecta;Coleoptera;Staphylinidae;Styngetus; 2759;6656;50557;7041;29026;1401311; |
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Better update your taxonomy DB 🙃
standage
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Mar 8, 2024
.github/workflows/cibuild.yml
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| python-version: 3.7 | ||
| python-version: "3.8" | ||
| - os: ubuntu-latest | ||
| python-version: 3.8 | ||
| python-version: "3.9" | ||
| - os: ubuntu-latest | ||
| python-version: 3.9 | ||
| python-version: "3.10" | ||
| - os: macos-latest | ||
| python-version: 3.8 | ||
| python-version: "3.9" |
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GitHub automatically disabled CI builds after several months of inactivity. So I re-enabled that, and bumped these version numbers.
added 3 commits
March 8, 2024 15:02
standage
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Mar 8, 2024
| curl -L -O ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz | ||
| curl -L -O https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz |
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The MacOS build kept on failing, unable to download the taxonomy DB. This was an attempt at troubleshooting.
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| # - os: macos-latest | ||
| # python-version: "3.9" |
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Ended up dropping the MacOS build. 🙁
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This pull request adds the
-k/--keep-invalidflag for the LCA command. The-kflag was added with the v0.16.0 release of Taxonkit.