Fix alignment filename assumptions #1206
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…g in .fasta Applies only when using IQ-TREE. Demonstrates an issue reported by Jon Bråte in a discussion post.¹ ¹ <https://discussion.nextstrain.org/t/is-this-the-expected-behaviour-of-augur-tree/1375>
For example, .fa is another common suffix for FASTA filenames, but using it in the input alignment filename here resulted in both the temporary output alignment filename and the log file name being the same as the input alignment filename. This bug meant the input alignment file was overwritten! (twice!) and tree building failed when using IQ-TREE with such a filename. We should assume as little as possible about filenames and use pathlib for all manipulations. The use of str.replace() here was particularly naive as it wasn't even anchored to the end of the string. The change here would read a bit cleaner if build_iqtree() used Path objects internally instead of using strings, but that's a larger change for another commit/time. Reported by Jon Bråte in a discussion post.¹ ¹ <https://discussion.nextstrain.org/t/is-this-the-expected-behaviour-of-augur-tree/1375>
…ommand log_file was missed by "shell-quote all user-defined filenames" (1b28739). substition_model comes straight from the user via --substitution-model.
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1206 +/- ##
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Coverage 68.81% 68.81%
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Files 64 64
Lines 6936 6936
Branches 1693 1693
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Hits 4773 4773
Misses 1856 1856
Partials 307 307
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jameshadfield
approved these changes
May 4, 2023
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