update tests

test/test_unit/test_pangenome/test_mmseq_func.py

@@ -50,6 +50,7 @@ def setup_teardown_module():
             os.remove(f)
     print("teardown")
 
+
 # Clusters expected for the given databank (ref: [members]
 EXP_CLUSTERS = {"GEN2.1017.00001.i0002_00004": ["GEN2.1017.00001.i0002_00004",
                                                 "GEN4.1111.00001.i0001_00002",
@@ -232,7 +233,6 @@ def test_create_mmseqdb_not_all_exist(caplog):
     assert caplog.records[8].levelname == "DETAIL"
 
 
-
 def test_do_mmseqdb_existok(caplog):
     """
     Check that, when trying to run create_mmseqs_db while all output files already exist,
@@ -250,12 +250,12 @@ def test_do_mmseqdb_existok(caplog):
     # Check files created/existing
     for file in [filename + ext for ext in outext]:
         assert os.path.isfile(file)
-    assert ("Creating database") in caplog.text
+    # assert ("Creating database") in caplog.text
     assert ("mmseqs database "
             "test/data/pangenome/generated_by_unit-tests/test_create_mmseqsdb_exist.msdb "
             "already exists. The program will use it.") in caplog.text
-    assert caplog.records[0].levelname == "INFO"
-    assert caplog.records[1].levelname == "WARNING"
+    # assert caplog.records[0].levelname == "INFO"
+    assert caplog.records[0].levelname == "WARNING"
 
 
 def test_do_mmseqdb_quiet(caplog):
@@ -412,7 +412,7 @@ def test_mmseq2pan_givenout():
                 break
         assert found
     exp_pan = os.path.join(PATH_EXP_FILES, "exp_pangenome-4genomes.lst")
-    #Check that families written in output file are as expected
+    # Check that families written in output file are as expected
     with open(exp_pan, "r") as ep, open(outfile, "r") as pan:
         lines_exp = []
         lines_out = []
@@ -593,7 +593,7 @@ def test_do_pangenome_justdone_panexists(caplog):
     -> removes mmseqs_clust to rerun it
     -> check content of generated panfile
     """
-    caplog.set_level(15) # set level to detail
+    caplog.set_level(15)  # set level to detail
     outdir = os.path.join(GENEPATH, "test_do_pangenome_outdir_exist")
     prt_bank = "exp_EXEM.All.prt"
     mmseqdb = os.path.join(PATH_TEST_FILES, "mmseq_db")
@@ -626,7 +626,7 @@ def test_do_pangenome_justdone_panexists(caplog):
                 found = True
                 break
         assert found
-    # Check content of output pangenome file. Should contain families, and not empty 
+    # Check content of output pangenome file. Should contain families, and not empty
     # as it was before running do_pangenome
     exp_pan = os.path.join(PATH_EXP_FILES, "exp_pangenome-4genomes.lst")
     with open(exp_pan, "r") as ep, open(panfile, "r") as pan:
@@ -947,7 +947,7 @@ def test_run_all_pangenome_panexists_wrong(caplog):
     open(panfile_out, "w").close()
     with pytest.raises(SystemExit):
         mmseqs.run_all_pangenome(min_id, clust_mode, outdir, prt_path,
-                                             threads, panfile=panfile, quiet=quiet)
+                                 threads, panfile=panfile, quiet=quiet)
 
     # check that tmp dir was created and not empty
     tmp_dir = os.path.join(outdir, "tmp_exp_EXEM.All.prt_0.8-mode1")