clean up tests

src/python/tests/test_gather.py

@@ -58,7 +58,6 @@ def test_simple(runtmp, zip_against):
     assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'rank', 'intersect_bp'}
 
 
-
 @pytest.mark.parametrize('zip_against', [False, True])
 def test_simple_with_prefetch(runtmp, zip_against):
     # test basic execution!
@@ -135,7 +134,7 @@ def test_bad_query(runtmp, capfd, zip_against):
 
     # query doesn't need to be a sig anymore - sig, zip, or pathlist welcome
     # as long as there's only one sketch that matches params
-    make_file_list(query, [sig2,sig47]) # [sig2]
+    make_file_list(query, [sig2,sig47])
     make_file_list(against_list, [sig2, sig47, sig63])
 
     if zip_against:
@@ -161,11 +160,7 @@ def test_missing_against(runtmp, capfd, zip_against):
     query = get_test_data('SRR606249.sig.gz')
     against_list = runtmp.output('against.txt')
 
-    sig2 = get_test_data('2.fa.sig.gz')
-    sig47 = get_test_data('47.fa.sig.gz')
-    sig63 = get_test_data('63.fa.sig.gz')
-
-    #make_file_list(against_list, [sig2, sig47, sig63])
+    # don't make against list
     if zip_against:
         against_list = runtmp.output('against.zip')
 
@@ -207,7 +202,6 @@ def test_sig_against(runtmp, capfd):
     assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'rank', 'intersect_bp'}
 
 
-
 def test_bad_against(runtmp, capfd):
     # test bad 'against' file - in this case, one containing a bad filename.
     query = get_test_data('SRR606249.sig.gz')

src/python/tests/test_index.py

@@ -215,7 +215,6 @@ def test_index_zipfile_repeated_md5sums(runtmp, capfd):
     captured = capfd.readouterr()
     print(captured.err)
 
-    # assert 'Found 3 filepaths' in captured.err
     assert 'index is done' in runtmp.last_result.err
 
 

src/python/tests/test_multigather.py

@@ -182,8 +182,6 @@ def test_missing_querylist(runtmp, capfd, indexed, zip_query):
 
     captured = capfd.readouterr()
     print(captured.err)
-
-        # assert 'Error: failed to load query' in captured.err
     assert 'Error: No such file or directory' in captured.err
 
 
@@ -313,8 +311,6 @@ def test_nomatch_query(runtmp, capfd, indexed, zip_query):
 
     captured = capfd.readouterr()
     print(captured.err)
-
-    # assert "WARNING: no compatible sketches in path " in captured.err
     assert "WARNING: skipped 1 query paths - no compatible signatures." in captured.err
 
 
@@ -424,7 +420,6 @@ def test_bad_against_2(runtmp, capfd, zip_query):
 
 
 def test_empty_against(runtmp, capfd):
-    # like fastgather - exit gracefully.
     # test bad 'against' file - in this case, an empty one
     query = get_test_data('SRR606249.sig.gz')
     query_list = runtmp.output('query.txt')

src/python/tests/test_multisearch.py

@@ -133,7 +133,6 @@ def test_missing_query(runtmp, capfd, zip_query):
     sig47 = get_test_data('47.fa.sig.gz')
     sig63 = get_test_data('63.fa.sig.gz')
 
-    #make_file_list(query_list, [sig2, sig47, sig63])
     make_file_list(against_list, [sig2, sig47, sig63])
 
     output = runtmp.output('out.csv')
@@ -173,6 +172,7 @@ def test_sig_query(runtmp, capfd):
     df = pandas.read_csv(output)
     assert len(df) == 1
 
+
 def test_bad_query(runtmp, capfd):
     # test with a bad query list (a missing file)
     query_list = runtmp.output('query.txt')
@@ -238,7 +238,7 @@ def test_missing_against(runtmp, capfd, zip_db):
     # do not create against_list
 
     if zip_db:
-        #.zip but don't create the file
+        #specify .zip but don't create the file
         against_list = runtmp.output('db.zip')
 
     output = runtmp.output('out.csv')
@@ -263,7 +263,6 @@ def test_sig_against(runtmp, capfd):
     sig63 = get_test_data('63.fa.sig.gz')
 
     make_file_list(query_list, [sig2, sig47, sig63])
-    #make_file_list(against_list, [sig2, sig47, sig63])
 
     output = runtmp.output('out.csv')
 
@@ -277,6 +276,7 @@ def test_sig_against(runtmp, capfd):
     df = pandas.read_csv(output)
     assert len(df) == 1
 
+
 def test_bad_against(runtmp, capfd):
     # test with a bad against list (a missing file)
     query_list = runtmp.output('query.txt')

src/python/tests/test_pairwise.py

@@ -114,7 +114,6 @@ def test_simple_threshold(runtmp, zip_query):
     assert len(df) == 1
 
 
-
 def test_sig_query(runtmp, capfd):
     # sig query is ok now, but fails bc only one sig
     sig2 = get_test_data('2.fa.sig.gz')
@@ -152,7 +151,6 @@ def test_bad_query(runtmp, capfd):
 
 def test_bad_query_2(runtmp, capfd):
     # test with a bad query (a .sig.gz file renamed as zip file)
-
     sig2 = get_test_data('2.fa.sig.gz')
     sig47 = get_test_data('47.fa.sig.gz')
     sig63 = get_test_data('63.fa.sig.gz')
@@ -274,11 +272,6 @@ def test_load_only_one_bug(runtmp, capfd, zip_db):
     assert not 'WARNING: no compatible sketches in path ' in captured.err
 
 
-
-
-
-
-
 @pytest.mark.parametrize("zip_query", [False, True])
 def test_md5(runtmp, zip_query):
     # test that md5s match what was in the original files, not downsampled etc.
@@ -314,8 +307,6 @@ def test_md5(runtmp, zip_query):
     print(md5s)
 
 
-
-
 def test_simple_prot(runtmp):
     # test basic execution with protein sigs
     sigs = get_test_data('protein.zip')
@@ -368,7 +359,6 @@ def test_simple_prot(runtmp):
                 assert intersect_hashes == 342
 
 
-
 def test_simple_dayhoff(runtmp):
     # test basic execution with dayhoff sigs
     sigs = get_test_data('dayhoff.zip')

src/python/tests/test_search.py

@@ -229,7 +229,7 @@ def test_missing_query(runtmp, capfd, indexed, zip_query):
     sig47 = get_test_data('47.fa.sig.gz')
     sig63 = get_test_data('63.fa.sig.gz')
 
-    #make_file_list(query_list, [sig2, sig47, sig63])
+    #make_file_list(query_list, [sig2, sig47, sig63]) # don't make query
     make_file_list(against_list, [sig2, sig47, sig63])
 
     if indexed:
@@ -266,15 +266,9 @@ def test_sig_query(runtmp, capfd, indexed):
 
     output = runtmp.output('out.csv')
 
-    # with pytest.raises(utils.SourmashCommandFailed):
     runtmp.sourmash('scripts', 'manysearch', sig2, against_list,
                         '-o', output)
 
-    # captured = capfd.readouterr()
-    # print(captured.err)
-
-    # assert 'Error: invalid line in fromfile' in captured.err
-
 
 @pytest.mark.parametrize("indexed", [False, True])
 def test_bad_query_2(runtmp, capfd, indexed):
@@ -363,15 +357,13 @@ def test_nomatch_against(runtmp, capfd):
     sig2 = get_test_data('2.fa.sig.gz')
     sig47 = get_test_data('47.fa.sig.gz')
     sig63 = get_test_data('63.fa.sig.gz')
-    # nomatch_sketch = get_test_data('genome-s11.fa.gz.sig')
     nomatch_sketch = get_test_data('SRR606249.sig.gz')
 
     make_file_list(query_list, [sig2, sig47, sig63])
     make_file_list(against_list, [nomatch_sketch])
 
     output = runtmp.output('out.csv')
 
-    # with pytest.raises(utils.SourmashCommandFailed):
     runtmp.sourmash('scripts', 'manysearch', query_list, against_list,
                         '-o', output)
 
@@ -420,7 +412,6 @@ def test_empty_query(runtmp, indexed, capfd):
 
     output = runtmp.output('out.csv')
 
-    # with pytest.raises(utils.SourmashCommandFailed):
     runtmp.sourmash('scripts', 'manysearch', query_list, against_list,
                         '-o', output)