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The test was passing even with the typo because a nonexistent file still raises AlignmentError.
This avoids the assumption that a file existence check has not run, which may change with implementations unrelated to what these tests are targeting.
This hasn't been useful in our workflows. Removing it now to simplify future work around --config to other commands. The same goes for the search_paths parameter to get_referenced_files. FIXME: add to changelog
To be used in the following commit. 2 additional improvements: 1. Made config_file optional 2. Added a clear docstring
This marks input files using a dedicated InputFile argparse type. Instead of simply treating it as a string to be evaluated downstream, it is now resolved to an absolute path. This is useful for workflows that define AUGUR_SEARCH_PATHS to support user analysis directories with `nextstrain run`. Tests have been updated to reflect that file paths are now stored internally as resolved absolute paths. FIXME: add changelog entry FIXME: apply to other commands too?
The InputFile type resolves values to an absolute path, which naturally includes a check for file existence and errors if it cannot be found anywhere. This commit removes similar checks from downstream code.
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2051 +/- ##
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+ Coverage 74.30% 74.39% +0.09%
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Files 86 86
Lines 10767 10743 -24
Branches 2099 2093 -6
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- Hits 8000 7992 -8
+ Misses 2378 2365 -13
+ Partials 389 386 -3 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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victorlin
removed this pull request from stack #2052
September 26, 2026 00:46
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Description of proposed changes
Snippet from main commit:
This marks input files using a dedicated InputFile argparse type. Instead of simply treating it as a string to be evaluated downstream, it is now resolved to an absolute path. This is useful for workflows that define AUGUR_SEARCH_PATHS to support user analysis directories with
nextstrain run.Related issue(s)
Follow-up to #2049 (comment)
Checklist