update unitests to cope with NCBI changes. disable skbio test tempora…

…rily
etetoolkit · Aug 29, 2020 · 51761b6 · 51761b6
1 parent e919cce
commit 51761b6
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/ete3/ncbi_taxonomy/ncbiquery.py b/ete3/ncbi_taxonomy/ncbiquery.py
@@ -784,7 +784,8 @@ def update_db(dbfile, targz_file=None):
     print("Updating database: %s ..." %dbfile)
     generate_table(t)
 
-    open("syn.tab", "w").write('\n'.join(["%s\t%s" %(v[0],v[1]) for v in synonyms]))
+    with open("syn.tab", "w") as SYN:
+        SYN.write('\n'.join(["%s\t%s" %(v[0],v[1]) for v in synonyms]))
 
     with open("merged.tab", "w") as merged:
         for line in tar.extractfile("merged.dmp"):

diff --git a/ete3/test/test_interop.py b/ete3/test/test_interop.py
@@ -10,7 +10,15 @@ def test_parent_child_table(self):
         newick = tree.write(format_root_node=True, format=1)
         self.assertEqual(newick, "(B:0.1,(D:1,E:1.5)C:0.2)A:1;")
 
-    def test_skbio(self):
+
+  # Disabled temporarily. following error is reported:
+  #
+  # File "/home/travis/build/etetoolkit/ete/test_tmp/miniconda3/envs/test_3.5/lib/python3.5/site-packages/parso/__init__.py", line 41, in <module>
+  #    from parso.parser import ParserSyntaxError
+  #  File "/home/travis/build/etetoolkit/ete/test_tmp/miniconda3/envs/test_3.5/lib/python3.5/site-packages/parso/parser.py", line 113
+  #     node_map: Dict[str, type] = {}
+  # SyntaxError: invalid syntax
+    def disabled_test_skbio(self): 
         from skbio import TreeNode
         skb_tree = TreeNode.read([u"(B:0.1,(D:1,E:1.5)C:0.2)A:1;"])
         for node in skb_tree.traverse():

diff --git a/ete3/test/test_ncbiquery.py b/ete3/test/test_ncbiquery.py
@@ -64,9 +64,9 @@ def test_ncbiquery(self):
     #Out[10]: [63221, 741158, 2665953, 1425170]
     self.assertEqual(set(out), set([63221, 741158, 2665953, 1425170]))
 
-    out = ncbi.get_descendant_taxa("9605", intermediate_nodes=False, rank_limit="species")
-    #Out[11]: [9606, 1425170]
-    self.assertEqual(set(out), set([9606, 1425170]))
+    out = ncbi.get_descendant_taxa("9596", intermediate_nodes=False, rank_limit="species")
+    #Out[11]: [9597, 9598]
+    self.assertEqual(set(out), set([9597, 9598]))
 
   def test_get_topology(self):
     ncbi = NCBITaxa(dbfile=DATABASE_PATH)