From 51761b6fb5312fc11fc0422c4679dad0caa732d0 Mon Sep 17 00:00:00 2001 From: Jaime Date: Sat, 29 Aug 2020 20:04:14 +0200 Subject: [PATCH] update unitests to cope with NCBI changes. disable skbio test temporarily --- ete3/ncbi_taxonomy/ncbiquery.py | 3 ++- ete3/test/test_interop.py | 10 +++++++++- ete3/test/test_ncbiquery.py | 6 +++--- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/ete3/ncbi_taxonomy/ncbiquery.py b/ete3/ncbi_taxonomy/ncbiquery.py index 77136ae8..a9729bdb 100644 --- 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 index fe4ebe90..0976d8a8 100644 --- 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 + # 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 index dbe631fa..15e64ec1 100644 --- 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)