Merge branch 'ete4' into ete4_#750

etetoolkit · May 30, 2024 · 7739f27 · 7739f27
2 parents 8ccac7c + 2fabb2e
commit 7739f27
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diff --git a/ete4/smartview/renderer/drawer.py b/ete4/smartview/renderer/drawer.py
@@ -90,9 +90,7 @@ def __init__(self, tree, viewport=None, panel=0, zoom=(1, 1),
         self.layouts = layouts or []
         self.include_props = include_props
         self.exclude_props = exclude_props
-        self.tree_style = tree_style
-        if not self.tree_style:
-            self.tree_style = TreeStyle()
+        self.tree_style = tree_style or TreeStyle()
 
     def draw(self):
         "Yield graphic elements to draw the tree"

diff --git a/run_tests.py b/run_tests.py
@@ -4,6 +4,7 @@
 A simple program to coordinate which tests to run.
 """
 
+import sys
 import os
 from argparse import ArgumentParser
 
@@ -25,6 +26,13 @@
 def main():
     args = get_args()
 
+    if args.list:
+        print('Tests included in each category:')
+        for category, ctests in tests.items():
+            print(f'\n{category}')
+            print(' ', '\n  '.join(ctests))
+        sys.exit()
+
     run_pytest(tests['fast'], args.verbose)
 
     if args.include_interactive:
@@ -43,10 +51,9 @@ def get_args():
     parser = ArgumentParser(description=__doc__)
 
     add = parser.add_argument  # shortcut
-    add('-i', '--include-interactive', action='store_true',
-        help='run tests that require user input')
-    add('-s', '--include-slow', action='store_true',
-        help='run tests that take a long time')
+    add('-l', '--list', action='store_true', help='list the tests in each category and exit')
+    add('-i', '--include-interactive', action='store_true', help='run tests that require user input')
+    add('-s', '--include-slow', action='store_true', help='run tests that take a long time')
     add('-v', '--verbose', action='store_true', help='be verbose')
 
     return parser.parse_args()

diff --git a/tests/redundant/test_ncbiquery.py b/tests/redundant/test_ncbiquery.py
@@ -0,0 +1,141 @@
+import os
+import unittest
+
+from ete4 import PhyloTree, NCBITaxa, ETE_DATA_HOME
+from ete4.ncbi_taxonomy import ncbiquery
+
+DATABASE_PATH = ETE_DATA_HOME + '/tests/test_ncbiquery.taxa.sqlite'
+
+class Test_ncbiquery(unittest.TestCase):
+
+  def test_00_update_database(self):
+
+    if not os.path.exists(DATABASE_PATH):
+      ncbiquery.update_db(DATABASE_PATH)
+
+
+  def test_01tree_annotation(self):
+    # using name as species attribute
+    t = PhyloTree( "((9598, 9606), 10090);", sp_naming_function=lambda name: name)
+    t.annotate_ncbi_taxa(dbfile=DATABASE_PATH)
+    self.assertEqual(t.props.get('sci_name'), 'Euarchontoglires')
+
+    homi = t['9606'].up
+    self.assertEqual(homi.props.get('sci_name'), 'Homininae')
+    self.assertEqual(homi.props.get('taxid'), 207598)
+    self.assertEqual(homi.props.get('rank'), 'subfamily')
+    self.assertEqual(homi.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae'])
+    self.assertEqual(homi.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598] )
+
+    human = t['9606']
+    self.assertEqual(human.props.get('sci_name'), 'Homo sapiens')
+    self.assertEqual(human.props.get('taxid'), 9606)
+    self.assertEqual(human.props.get('rank'), 'species')
+    self.assertEqual(human.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae', u'Homo', u'Homo sapiens'])
+    self.assertEqual(human.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605, 9606])
+
+  def test_02tree_annotation(self):
+    # assign species attribute via sp_naming_function
+    t = PhyloTree( "((9598|protA, 9606|protB), 10090|propC);", sp_naming_function=lambda name: name.split('|')[0])
+    t.annotate_ncbi_taxa(dbfile=DATABASE_PATH, taxid_attr='species')
+
+    homi = t['9606|protB'].up
+    self.assertEqual(homi.props.get('sci_name'), 'Homininae')
+    self.assertEqual(homi.props.get('taxid'), 207598)
+    self.assertEqual(homi.props.get('rank'), 'subfamily')
+    self.assertEqual(homi.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae'])
+    self.assertEqual(homi.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598] )
+
+    human = t['9606|protB']
+    self.assertEqual(human.props.get('sci_name'), 'Homo sapiens')
+    self.assertEqual(human.props.get('taxid'), 9606)
+    self.assertEqual(human.props.get('rank'), 'species')
+    self.assertEqual(human.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae', u'Homo', u'Homo sapiens'])
+    self.assertEqual(human.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605, 9606])
+
+  def test_03tree_annotation(self):
+    # Using custom property as taxonomic identifier 
+    t = PhyloTree( "((protA, protB), propC);")
+    # add property called "spcode"
+    t['protA'].add_prop('spcode', 9598)
+    t['protB'].add_prop('spcode', 9606)
+    t['propC'].add_prop('spcode', 10090)
+    t.annotate_ncbi_taxa(dbfile=DATABASE_PATH, taxid_attr='spcode')
+
+    homi = t['protB'].up
+    self.assertEqual(homi.props.get('sci_name'), 'Homininae')
+    self.assertEqual(homi.props.get('taxid'), 207598)
+    self.assertEqual(homi.props.get('rank'), 'subfamily')
+    self.assertEqual(homi.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae'])
+    self.assertEqual(homi.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598] )
+
+    human = t['protB']
+    self.assertEqual(human.props.get('sci_name'), 'Homo sapiens')
+    self.assertEqual(human.props.get('taxid'), 9606)
+    self.assertEqual(human.props.get('rank'), 'species')
+    self.assertEqual(human.props.get('named_lineage'), [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa', u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata', u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi', u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota', u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires', u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea', u'Hominidae', u'Homininae', u'Homo', u'Homo sapiens'])
+    self.assertEqual(human.props.get('lineage'), [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742, 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347, 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605, 9606])
+
+  def test_ncbiquery(self):
+    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
+
+    id2name = ncbi.get_taxid_translator(['9606', '7507'])
+    self.assertEqual(id2name[7507], 'Mantis religiosa')
+    self.assertEqual(id2name[9606], 'Homo sapiens')
+
+    name2id = ncbi.get_name_translator(['Mantis religiosa', 'homo sapiens'])
+    self.assertEqual(name2id['Mantis religiosa'], [7507])
+    self.assertEqual(name2id['homo sapiens'], [9606])
+
+    name2id = ncbi.get_name_translator(['Bacteria'])
+    self.assertEqual(set(name2id['Bacteria']), {2})
+
+    out = ncbi.get_descendant_taxa("9605", intermediate_nodes=True)
+    self.assertEqual(set(out), {9606, 63221, 741158, 1425170, 2665952, 2665953, 2813598, 2813599})
+
+    out = ncbi.get_descendant_taxa("9605", intermediate_nodes=False)
+    self.assertEqual(set(out), {63221, 741158, 2665953, 1425170, 2813599})
+
+    out = ncbi.get_descendant_taxa("9596", intermediate_nodes=False, rank_limit="species")
+    self.assertEqual(set(out), {9597, 9598})
+
+  def test_get_topology(self):
+    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
+    t1 = ncbi.get_topology([9606, 7507, 9604])
+    t2 = ncbi.get_topology([9606, 7507, 678])
+
+    self.assertEqual(sorted(t1.leaf_names()), ["7507", "9606"])
+    self.assertEqual(sorted(t2.leaf_names()), ["678", "7507", "9606"])
+
+    # Test taxid synonyms
+    self.assertEqual(ncbi.get_topology(["42099"]).write(format_root_node=True), "1223560;")
+    # The id 42099 is for https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=42099
+    # which corresponds to "Phytopythium vexans DAOM BR484", which has id 1223560
+    # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1223560
+
+    for target in [9604, 9443, "9443"]:
+      t1 = ncbi.get_descendant_taxa(target, return_tree=True)
+      t2 = ncbi.get_topology([target])
+      t3 = ncbi.get_topology(ncbi.get_descendant_taxa(target))
+      t4 = ncbi.get_topology(list(map(str, ncbi.get_descendant_taxa(target))))
+
+      self.assertEqual(set(t1.leaf_names()), set(t2.leaf_names()))
+      self.assertEqual(set(t2.leaf_names()), set(t3.leaf_names()))
+      self.assertEqual(set(t3.leaf_names()), set(t4.leaf_names()))
+      diffs1 = t1.compare(t2, unrooted=True)
+      diffs2 = t2.compare(t3, unrooted=True)
+      diffs3 = t3.compare(t4, unrooted=True)
+      self.assertEqual(diffs1["rf"], 0.0)
+      self.assertEqual(diffs2["rf"], 0.0)
+      self.assertEqual(diffs3["rf"], 0.0)
+
+  def test_merged_id(self):
+    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
+    t1 = ncbi.get_lineage(649756)
+    self.assertEqual(t1, [1, 131567, 2, 1783272, 1239, 186801, 186802, 186803, 207244, 649756])
+    t2 = ncbi.get_lineage("649756")
+    self.assertEqual(t2, [1, 131567, 2, 1783272, 1239, 186801, 186802, 186803, 207244, 649756])
+
+if __name__ == '__main__':
+  unittest.main()
+
diff --git a/tests/slow/test_ncbiquery_force_download.py b/tests/slow/test_ncbiquery_force_download.py
@@ -2,9 +2,7 @@
 Test the functionality of ncbiquery.py. To run with pytest.
 """
 
-import os
-
-from ete4 import PhyloTree, NCBITaxa, ETE_DATA_HOME
+from ete4 import ETE_DATA_HOME
 from ete4.ncbi_taxonomy import ncbiquery
 
 DATABASE_PATH = ETE_DATA_HOME + '/tests/test_ncbiquery.taxa.sqlite'
@@ -14,112 +12,3 @@ def test_update_database():
     ncbiquery.update_db(DATABASE_PATH)
     # It will download the full NCBI taxa database and process it. Slow!
     # Should raise an error if things go wrong.
-
-
-def test_tree_annotation():
-    t = PhyloTree('((9598,9606),10090);',
-                  sp_naming_function=lambda name: name)
-
-    t.annotate_ncbi_taxa(dbfile=DATABASE_PATH)
-
-    assert t.props['sci_name'] == 'Euarchontoglires'
-
-    homi = t['9606'].up
-    assert homi.props['sci_name'] == 'Homininae'
-    assert homi.props['taxid'] == 207598
-    assert homi.props['rank'] == 'subfamily'
-    assert homi.props['named_lineage'] == [
-        'root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa',
-        'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata',
-        'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi',
-        'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota',
-        'Mammalia', 'Theria', 'Eutheria', 'Boreoeutheria', 'Euarchontoglires',
-        'Primates', 'Haplorrhini', 'Simiiformes', 'Catarrhini', 'Hominoidea',
-        'Hominidae', 'Homininae']
-    assert homi.props['lineage'] == [
-        1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-        7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-        1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598]
-
-    human = t['9606']
-    assert human.props['sci_name'] == 'Homo sapiens'
-    assert human.props['taxid'] == 9606
-    assert human.props['rank'] == 'species'
-    assert human.props['named_lineage'] == [
-        'root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa',
-        'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata',
-        'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi',
-        'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota',
-        'Mammalia', 'Theria', 'Eutheria', 'Boreoeutheria', 'Euarchontoglires',
-        'Primates', 'Haplorrhini', 'Simiiformes', 'Catarrhini', 'Hominoidea',
-        'Hominidae', 'Homininae', 'Homo', 'Homo sapiens']
-    assert human.props['lineage'] == [
-        1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-        7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-        1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598,
-        9605, 9606]
-
-
-def test_ncbiquery():
-    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
-
-    id2name = ncbi.get_taxid_translator(['9606', '7507'])
-    assert id2name[7507] == 'Mantis religiosa'
-    assert id2name[9606] == 'Homo sapiens'
-
-    name2id = ncbi.get_name_translator(['Mantis religiosa', 'homo sapiens'])
-    assert name2id['Mantis religiosa'] == [7507]
-    assert name2id['homo sapiens'] == [9606]
-
-    name2id = ncbi.get_name_translator(['Bacteria'])
-    assert set(name2id['Bacteria']) == {2}
-
-    out = ncbi.get_descendant_taxa('9605', intermediate_nodes=True)
-    assert set(out) == {9606, 63221, 741158, 1425170, 2665952, 2665953, 2813598, 2813599}
-
-    out = ncbi.get_descendant_taxa('9605', intermediate_nodes=False)
-    assert set(out) == {63221, 741158, 2665953, 1425170, 2813599}
-
-    out = ncbi.get_descendant_taxa('9596', intermediate_nodes=False, rank_limit='species')
-    assert set(out) == {9597, 9598}
-
-
-def test_get_topology():
-    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
-
-    t1 = ncbi.get_topology([9606, 7507, 9604])
-    t2 = ncbi.get_topology([9606, 7507, 678])
-
-    assert sorted(t1.leaf_names()) == ['7507', '9606']
-    assert sorted(t2.leaf_names()) == ['678', '7507', '9606']
-
-    # Test taxid synonyms
-    assert ncbi.get_topology(['42099']).write(format_root_node=True) == '1223560;'
-    # The id 42099 is for https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=42099
-    # which corresponds to 'Phytopythium vexans DAOM BR484', which has id 1223560
-    # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1223560
-
-    for target in [9604, 9443, '9443']:
-        t1 = ncbi.get_descendant_taxa(target, return_tree=True)
-        t2 = ncbi.get_topology([target])
-        t3 = ncbi.get_topology(ncbi.get_descendant_taxa(target))
-        t4 = ncbi.get_topology(list(map(str, ncbi.get_descendant_taxa(target))))
-
-        assert (set(t1.leaf_names()) == set(t2.leaf_names()) ==
-                set(t3.leaf_names()) == set(t4.leaf_names()))
-
-        diffs1 = t1.compare(t2, unrooted=True)
-        diffs2 = t2.compare(t3, unrooted=True)
-        diffs3 = t3.compare(t4, unrooted=True)
-
-        assert diffs1['rf'] == diffs2['rf'] == diffs3['rf'] == 0.0
-
-
-def test_merged_id():
-    ncbi = NCBITaxa(dbfile=DATABASE_PATH)
-
-    t1 = ncbi.get_lineage(649756)
-    assert t1 == [1, 131567, 2, 1783272, 1239, 186801, 186802, 186803, 207244, 649756]
-
-    t2 = ncbi.get_lineage('649756')
-    assert t2 == [1, 131567, 2, 1783272, 1239, 186801, 186802, 186803, 207244, 649756]