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fix(tree): check for all synonyms of conflicting default args #1547

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fix(tree): check for all synonyms of conflicting default args #1547

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Commits on Jul 17, 2024

  1. fix(tree): check for all synonyms of conflicting args 

    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`
    @corneliusroemer
    corneliusroemer committed Jul 17, 2024
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  2. chore(tests): more robust test by adding -redo to iqtree args 

    If `-redo` is not added, one can get errors like this:
```
   >  --tree-builder-args="-czb -bb 1000 -bnni" \
   >  --override-default-args \
   >  --output "$TMP/tree_raw.nwk" > /dev/null
+
+  ERROR: Shell exited 2 when running: iqtree2 --threads-max 1 -s tree/full_aligned-delim.fasta -m GTR -czb -bb 1000 -bnni > tree/full_aligned-delim.iqtree.log
+  Command output was:
+    Checkpoint (tree/full_aligned-delim.fasta.ckp.gz) indicates that a previous run successfully finished
+    Use `-redo` option if you really want to redo the analysis and overwrite all output files.
+    Use `--redo-tree` option if you want to restore ModelFinder and only redo tree search.
+    Use `--undo` option if you want to continue previous run when changing/adding options.
+
+  [1]
```
    @corneliusroemer
    corneliusroemer committed Jul 17, 2024
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  3. Add changelog entry

    @corneliusroemer
    corneliusroemer committed Jul 17, 2024
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  4. chore(tree): use new, preferred iqtree option names (those mentioned … 

    …by `iqtree2 -h`)
    @corneliusroemer
    corneliusroemer committed Jul 17, 2024
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