Give duplicated test method names distinct names so both run

lint.sh

@@ -5,3 +5,6 @@ set -e
 
 # lint for Python syntax errors or undefined names\
 ruff check --format=github --select=E9,F63,F7,F82,W605 --extend-exclude=docs/source/schemas/interfaces,src/dendropy/dataio/_beast2_v2_7_8_lark_standalone.py --target-version=py37 .
+
+# lint for duplicated test names, which discards tests
+ruff check --format=github --select=F811 --target-version=py37 tests/unittests

tests/unittests/test_dataio_newick_reader_rooting.py

@@ -76,7 +76,7 @@ def test_with_unrooted_token_ucase(self):
         nr = newickreader.NewickReader(rooting="force-unrooted")
         self.assertIs(nr._parse_tree_rooting_state("&u"), False)
 
-    def test_with_unrooted_token_ucase(self):
+    def test_with_unrooted_token_Ucase(self):
         nr = newickreader.NewickReader(rooting="force-unrooted")
         self.assertIs(nr._parse_tree_rooting_state("&U"), False)
 
@@ -106,7 +106,7 @@ def test_with_unrooted_token_ucase(self):
         nr = newickreader.NewickReader(rooting="force-rooted")
         self.assertIs(nr._parse_tree_rooting_state("&u"), True)
 
-    def test_with_unrooted_token_ucase(self):
+    def test_with_unrooted_token_Ucase(self):
         nr = newickreader.NewickReader(rooting="force-rooted")
         self.assertIs(nr._parse_tree_rooting_state("&U"), True)
 
@@ -136,7 +136,7 @@ def test_with_unrooted_token_ucase(self):
         nr = newickreader.NewickReader(rooting="default-unrooted")
         self.assertIs(nr._parse_tree_rooting_state("&u"), False)
 
-    def test_with_unrooted_token_ucase(self):
+    def test_with_unrooted_token_Ucase(self):
         nr = newickreader.NewickReader(rooting="default-unrooted")
         self.assertIs(nr._parse_tree_rooting_state("&U"), False)
 
@@ -166,7 +166,7 @@ def test_with_unrooted_token_ucase(self):
         nr = newickreader.NewickReader(rooting="default-rooted")
         self.assertIs(nr._parse_tree_rooting_state("&u"), False)
 
-    def test_with_unrooted_token_ucase(self):
+    def test_with_unrooted_token_Ucase(self):
         nr = newickreader.NewickReader(rooting="default-rooted")
         self.assertIs(nr._parse_tree_rooting_state("&U"), False)
 

tests/unittests/test_dataio_newick_reader_tree.py

@@ -29,8 +29,6 @@
 import dendropy
 from dendropy.utility import error
 from dendropy.dataio import newickreader
-import os
-import sys
 sys.path.insert(0, os.path.dirname(__file__))
 from support import dendropytest
 from support import standard_file_test_trees

tests/unittests/test_dataio_newick_reader_tree_iter.py

@@ -26,7 +26,6 @@
 import unittest
 import dendropy
 import os
-import sys
 sys.path.insert(0, os.path.dirname(__file__))
 from support import dendropytest
 from support import standard_file_test_trees

tests/unittests/test_dataio_newick_reader_tree_list.py

@@ -26,7 +26,6 @@
 import unittest
 import dendropy
 import os
-import sys
 sys.path.insert(0, os.path.dirname(__file__))
 from support import dendropytest
 from support import standard_file_test_trees

tests/unittests/test_dataio_tokenizer.py

@@ -117,7 +117,7 @@ def test_captured_delimiters(self):
                 ]
         self.check_tokenization(input_str, expected)
 
-    def test_comments(self):
+    def test_capture_comments(self):
         input_str = "([the quick]apple[brown],([fox]banjo,([jumps]cucumber[over the],[really]dogwood)[lazy]eggplant)) rhubarb[dog];";
         expected_comments = {
             "apple"    : ["the quick", "brown"],

tests/unittests/test_datamodel_charmatrix.py

@@ -142,7 +142,7 @@ def test_setitem_by_idx_not_in_namespace(self):
         with self.assertRaises(IndexError):
             char_matrix[len(tns)] = []
 
-    def test_setitem_by_idx_not_in_namespace(self):
+    def test_setitem_by_label_not_in_namespace(self):
         tns = get_taxon_namespace(3)
         char_matrix = charmatrixmodel.CharacterMatrix()
         with self.assertRaises(KeyError):
@@ -301,7 +301,7 @@ def test_fill_taxa(self):
         for taxon in tns:
             self.assertIn(taxon, char_matrix)
 
-    def test_fill_taxa(self):
+    def test_pack_pads_taxa_to_equal_length(self):
         tns = get_taxon_namespace(5)
         char_matrix = charmatrixmodel.CharacterMatrix(taxon_namespace=tns)
         s = ["z"] * 10
@@ -1151,7 +1151,7 @@ def setUp(self):
     def test_basic_taxa(self):
         self.assertEqual(self.char_matrix.poll_taxa(), self.expected_taxa)
 
-class TestCharacterMatrixTaxa(dendropytest.ExtendedTestCase):
+class TestCharacterMatrixPurgeTaxonNamespace(dendropytest.ExtendedTestCase):
 
     def setUp(self):
         self.char_matrix = charmatrixmodel.CharacterMatrix()

tests/unittests/test_datamodel_tree_construction_copying_and_identity.py

@@ -177,13 +177,6 @@ def test_construction_from_another_tree_different_label(self):
         self.assertNotEqual(tree1.label, "tree2")
         self.assertNotEqual(tree1.label, tree2.label)
 
-    def test_construction_from_given_seed_node(self):
-        tree1, anodes1, lnodes1, inodes1 = self.get_tree(
-                suppress_internal_node_taxa=False,
-                suppress_leaf_node_taxa=False)
-        tree2 = dendropy.Tree(seed_node=tree1.seed_node)
-        self.assertIs(tree2.seed_node, tree1.seed_node)
-
     def test_construction_from_given_seed_node(self):
         tree1, anodes1, lnodes1, inodes1 = self.get_tree(
                 suppress_internal_node_taxa=False,

tests/unittests/test_datamodel_tree_list.py

@@ -474,7 +474,7 @@ def test_remove(self):
         self.assertEqual(len(tlist), 4)
         self.assertNotIn(t, tlist)
 
-    def test_remove(self):
+    def test_reverse(self):
         tlist = curated_test_tree_list.get_tree_list(5)
         clist = list(tlist._trees)
         tlist.reverse()

tests/unittests/test_datamodel_tree_structure_and_iteration.py

@@ -400,7 +400,7 @@ def test_ageorder_node_iter_unfiltered_reversed(self):
         exp = [x[1] for x in nda]
         self.assertSequenceEqual(visited_labels, exp)
 
-    def test_leaf_node_iter_filtered(self):
+    def test_ageorder_node_iter_filtered(self):
         tree, anodes, lnodes, inodes = self.get_tree()
         f = lambda x: x.edge.length > 13
         nodes = [nd for nd in tree.ageorder_node_iter(filter_fn=f)]

tests/unittests/test_fitch.py

@@ -27,7 +27,6 @@
 import random
 import unittest
 import math
-import sys
 import dendropy
 from dendropy.calculate.treescore import fitch_down_pass
 sys.path.insert(0, os.path.dirname(__file__))

tests/unittests/test_phylogenetic_distance_matrix.py

@@ -265,18 +265,6 @@ def test_max_pairwise_weighted_distance_taxa(self):
             obs_maxt = self.pdm.max_pairwise_distance_taxa(is_weighted_edge_distances=True)
             self.assertEqual(set(obs_maxt), maxt)
 
-        def test_max_pairwise_weighted_distance_taxa(self):
-            maxd = None
-            maxt = None
-            for taxon1 in self.tree.taxon_namespace:
-                for taxon2 in self.tree.taxon_namespace:
-                    d = self.reference_pdm_weighted_table[taxon1.label, taxon2.label]
-                    if maxd is None or d > maxd:
-                        maxd = d
-                        maxt = set([taxon1, taxon2])
-            obs_maxt = self.pdm.max_pairwise_distance_taxa(is_weighted_edge_distances=True)
-            self.assertEqual(set(obs_maxt), maxt)
-
         def test_max_pairwise_unweighted_distance_taxa(self):
             maxd = None
             maxts = []