remove code smells #41

run_YACHT.py

@@ -57,9 +57,7 @@
     ani_thresh = config['ani_thresh']
 
     # Make sure the output can be written to
-    if os.access(os.path.abspath(os.path.dirname(out_filename)), os.W_OK):
-        pass
-    else:
+    if not os.access(os.path.abspath(os.path.dirname(out_filename)), os.W_OK):
         raise FileNotFoundError(f"Cannot write to the location: {os.path.abspath(os.path.dirname(out_filename))}.")
 
     # check if min_coverage is between 0 and 1

tests/test_workflow.py

@@ -74,14 +74,14 @@ def test_incorrect_workflow1():
 
 def test_demo_workflow():
     cmd = "cd demo; sourmash sketch dna -f -p k=31,scaled=1000,abund -o sample.sig.zip query_data/query_data.fq"
-    res = subprocess.run(cmd, shell=True, check=True)
+    _ = subprocess.run(cmd, shell=True, check=True)
     cmd = "cd demo; sourmash sketch fromfile ref_paths.csv -p dna,k=31,scaled=1000,abund -o ref.sig.zip --force-output-already-exists"
-    res = subprocess.run(cmd, shell=True, check=True)
+    _ = subprocess.run(cmd, shell=True, check=True)
     cmd = "cd demo; python ../make_training_data_from_sketches.py --force --ref_file ref.sig.zip --ksize 31 --num_threads 1 --ani_thresh 0.95 --prefix 'demo_ani_thresh_0.95' --outdir ./"
-    res = subprocess.run(cmd, shell=True, check=True)
+    _ = subprocess.run(cmd, shell=True, check=True)
     cmd = "cd demo; python ../run_YACHT.py --json demo_ani_thresh_0.95_config.json --sample_file sample.sig.zip --significance 0.99 --num_threads 1 --min_coverage_list 1 0.6 0.2 0.1 --out_filename result.xlsx"
-    res = subprocess.run(cmd, shell=True, check=True)
+    _ = subprocess.run(cmd, shell=True, check=True)
     cmd = "cd demo; python ../srcs/standardize_yacht_output.py --yacht_output result.xlsx --sheet_name min_coverage0.2 --genome_to_taxid toy_genome_to_taxid.tsv --mode cami --sample_name 'MySample' --outfile_prefix cami_result --outdir ./"
-    res = subprocess.run(cmd, shell=True, check=True)
+    _ = subprocess.run(cmd, shell=True, check=True)