closes #13

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changes
 
+## [Unreleased]
+
+- Fixed bug whereby the correct precedence of taxa labels was not obeyed when
+  translating trees.
+
+
 ## [v1.6.0] - 2023-08-09
 
 - `tools.normalise.normalise` now accepts a `remove_taxa` argument, making

src/commonnexus/blocks/trees.py

@@ -328,13 +328,13 @@ def validate(self, log=None):
     @functools.cached_property
     def translate_mapping(self):
         mapping = {}
-        if 'TRANSLATE' in self.commands:
-            mapping.update(self.TRANSLATE.mapping)
         if 'TAXA' in self.linked_blocks:
             mapping.update({
                 str(k): v for k, v in self.linked_blocks['TAXA'].TAXLABELS.labels.items()})
         elif self.nexus.TAXA and self.nexus.TAXA.TAXLABELS:
             mapping.update({str(k): v for k, v in self.nexus.TAXA.TAXLABELS.labels.items()})
+        if 'TRANSLATE' in self.commands:
+            mapping.update(self.TRANSLATE.mapping)
         return mapping
 
     def translate(self, tree: typing.Union[Tree, newick.Node]) -> newick.Node:

src/commonnexus/tools/combine.py

@@ -7,7 +7,7 @@
  - CHARACTERS/DATA: Characters are aggregated across NEXUS files (with character labels prefixed,
    for disambiguation).
  - TREES: Trees are (translated and) aggregated across NEXUS files.
- - DISTANCES?
+
 """
 import collections
 

tests/test_blocks_trees.py

@@ -31,6 +31,19 @@ def test_Tree_translate_with_taxa_from_linked_block(nexus):
     assert nex.TREES.translate(nex.TREES.TREE).newick == '(A,B)C'
 
 
+def test_Tree_translate_with_numeric_labels():
+    nex = Nexus("""#NEXUS
+    BEGIN TAXA;
+        TAXLABELS Scarabaeus Drosophila Aranaeus;
+    END;
+    BEGIN TREES;
+        TRANSLATE 0 Scarabaeus, 1 Drosophila, 2 Aranaeus;
+        TREE tree = ((0,1),2);
+    END;""")
+    tree = nex.TREES.translate(nex.TREES.TREE)
+    assert {n.name for n in tree.walk() if n.name} == {'Scarabaeus', 'Drosophila', 'Aranaeus'}
+
+
 def test_Trees_complex_newick():
     s = """#nexus
 BEGIN TAXA;