fix(tree): check for all synonyms of conflicting default args#1547
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corneliusroemer merged 5 commits intomasterfrom Nov 10, 2024
Merged
fix(tree): check for all synonyms of conflicting default args#1547corneliusroemer merged 5 commits intomasterfrom
corneliusroemer merged 5 commits intomasterfrom
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## master #1547 +/- ##
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+ Coverage 72.27% 72.30% +0.03%
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Files 79 79
Lines 8273 8273
Branches 1691 1691
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+ Hits 5979 5982 +3
+ Misses 2009 2006 -3
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Would be nice if someone could look at this, e.g. @huddlej @victorlin @tsibley @genehack @joverlee521 @jameshadfield |
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Thanks, @corneliusroemer! Nice to have the check for modern synonyms and also clearer to use those throughout the docs and tests (-czb has always confused me, for example, and --polytomy is much clearer).
IQtree2 has multiple synonyms for default args We were only checking for one of the synonyms. This PR fixes that. It also uses the currently preferred name for all IQtree options, where "preferred" is defined as the name shown in `iqtree2 -h` List of changes: `-nt` -> `-T` `--ntmax` -> `--threads-max` `-czb` -> `--polytomy` List of synonyms: `-ntmax`==`--threads-max` `-s`==`--aln`==`--msa` `-m`==`--model`
^ Conflicts: ^ CHANGES.md
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-redoto iqtree argsDescription of proposed changes
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Inspired by iqtree/iqtree2#273
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