codecov: show patch

exclude cluster.py script from coverage (as we cannot properly test it inside
the pytest environment while recording coverage)

Author: orbeckst

.codecov.yml

@@ -1,7 +1,9 @@
 # Codecov configuration to make it a bit less noisy
 coverage:
   status:
-    patch: false
+    patch:
+      default:
+        threshold: 5%
     project:
       default:
         threshold: 50%
@@ -13,4 +15,4 @@ comment:
   flags: null
   paths: null
 ignore:
-  - "basicrta/_version.py"
+  - "*/tests/*"

basicrta/cluster.py

@@ -212,7 +212,9 @@ def b_color_structure(self, structure):
         u.select_atoms('protein').write('tau_bcolored.pdb')
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  #pragma: no cover
+    # the script is tested in the test_cluster.py but cannot be accounted for
+    # in the coverage report
     import argparse
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument('--nproc', type=int, default=1)