minor tweaks

test_suite/process_test_suite.py

@@ -3,10 +3,8 @@
 """
 produce a markdown table of the results of running various tests on the SBML Test Suite
 
-get the version of the test suite that includes sedml versions
+get this version of the test suite that includes sedml versions or the sedml validation will fail:
 https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip
-
-
 """
 
 import os
@@ -74,7 +72,7 @@ def add_case_url(case,fpath,url_base):
     '''
     insert URL link to original test case file online
     effectively replaces args.suite_path with args.suite_url_base
-    this should produce a valid link for all the main intended use case
+    this should produce a valid link for all the main intended use cases
     of testing the sbml test suite using the default args
     but will not handle all possible variations of globs and base directories
     in which case it should be disabled by setting --suite-url-base=''
@@ -85,26 +83,28 @@ def add_case_url(case,fpath,url_base):
     return new_item
 
 def process_cases(args):
-    "process the test cases and write results out as a markdown table"
+    """
+    process the test cases and write results out as a markdown table
+    with links to the test case files online (as noted above the sedml files are actually in a zip file)
+    with a summary of how many cases were tested and how many tests failed
+    """
 
     header = "|case|valid-sbml|valid-sbml-units|valid-sedml|"
     sep = "|---|---|---|---|"
-    row = "|{case}|{valid_sbml}|{valid_sbml_units}|{valid_sedml}|"
     summary="|cases={n_cases}|fails={n_failing[valid_sbml]}|fails={n_failing[valid_sbml_units]}|fails={n_failing[valid_sedml]}|"
+    row = "|{case}|{valid_sbml}|{valid_sbml_units}|{valid_sedml}|"
 
     with open(args.output_file, "w") as fout:
-        output = []
-        n_cases = 0
-        n_failing = {"valid_sbml":0, "valid_sbml_units":0, "valid_sedml":0 }
-
-        os.chdir(args.suite_path)
-
         #accumulate output in memory so we can put the nifty summary at the top
-        #instead of at the end of 1800 lines
+        #instead of at the end of a very long table
+        output = []
         output.append(header)
         output.append(sep)
         output.append("<results summary goes here>")
+        n_cases = 0
+        n_failing = {"valid_sbml":0, "valid_sbml_units":0, "valid_sedml":0 }
 
+        os.chdir(args.suite_path)
         for fpath in sorted(glob.glob(args.suite_glob)):
             sedml_path = fpath.replace(".xml", "-sedml.xml")
             print(fpath)
@@ -117,14 +117,14 @@ def process_cases(args):
             valid_sedml = pass_or_fail(validate_sedml_files([sedml_path]))
             output.append(row.format(**locals()))
 
-            #tally results so we provide a summary
+            #tally results so we can provide a summary
             global okay,fail
             n_cases +=1
             if valid_sbml != okay: n_failing["valid_sbml"] += 1
             if valid_sbml_units != okay: n_failing["valid_sbml_units"] += 1
             if valid_sedml != okay: n_failing["valid_sedml"] += 1
-            output[2] = summary.format(**locals())
 
+        output[2] = summary.format(**locals())
         for line in output: fout.write(line+'\n')