iqtree / piqtree / 13985423968

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ENH: provide piqtree_nj and nj_tree option for positive branch lengths (#165)

* ENH: parameter to restrict negative value of branch length

* TST: allow_negative correctly control the behavior of branch length in nj_tree

* ENH: add parameter allow_negative in piqtree_nj app

* MAINT: fix double return error in merge

* MAINT: ruff formatting

* TST: Use full fasta file for checking `nj_tree` negative branch lengths

* MAINT: move from `ArrayAlignment` to `Alignment` in preparation for `new_type` default

* MAINT: simplify logic for negative branch lengths

* MAINT: Sort fixtures by number of taxa

* MAINT: Remove unused test data file

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Co-authored-by: Robert McArthur <robert.mcarthur@anu.edu.au>

35 of 35 new or added lines in 8 files covered. (100.0%)

1181 of 1196 relevant lines covered (98.75%)

5.92 hits per line