Added cover pragmas to command line handling

Author: MichaelClerx

pcpostprocess/scripts/run_herg_qc.py

@@ -40,7 +40,7 @@ def starmap(n, func, iterable):
             return pool.starmap(func, iterable)
 
 
-def run_from_command_line():
+def run_from_command_line():  # pragma: no cover
     """
     Reads arguments from the command line and an ``export_config.py`` and then
     runs herg QC.

pcpostprocess/scripts/summarise_herg_export.py

@@ -37,7 +37,7 @@ def get_protocol_list(input_dir, experiment_name):
     return list(np.unique(protocols))
 
 
-def run_from_command_line():
+def run_from_command_line():  # pragma: no cover
     """
     Parses arguments from the command line and then ???
     """

pcpostprocess/tests/test_directory_builder.py

@@ -35,7 +35,7 @@ def test_directory_builder(self):
             self.assertRegex(info_dict['Commit'], r'^g[0-9a-fA-F]{9}$')
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     if '-store' in sys.argv:
         store_output = True
         sys.argv.remove('-store')

pcpostprocess/tests/test_herg_qc.py

@@ -870,7 +870,7 @@ def test_run_qc(self):
             self.assertEqual(QC.all_passed(), ex_pass, trace)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     if '-store' in sys.argv:
         sys.argv.remove('-store')
         store_output = True

pcpostprocess/tests/test_infer_reversal.py

@@ -62,7 +62,7 @@ def test_infer_reversal(self):
         self.assertAlmostEqual(erev, -89.57184, 5)
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     if '-store' in sys.argv:
         store_output = True
         sys.argv.remove('-store')

pcpostprocess/tests/test_leak_correct.py

@@ -77,7 +77,7 @@ def test_get_leak_correct(self):
         self.assertEqual(x.shape, (30784,))
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     if '-store' in sys.argv:
         sys.argv.remove('-store')
         store_output = True

pcpostprocess/tests/test_scripts.py

@@ -54,7 +54,7 @@ def test_run_herg_qc_and_summarise_herg_export(self):
         run_summarise(d1, d2, '13112023_MW2', reversal_potential=erev)
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     if '-store' in sys.argv:
         sys.argv.remove('-store')
         store_output = True

pcpostprocess/tests/test_subtraction_plots.py

@@ -67,7 +67,7 @@ def test_do_subtraction_plot(self):
         fig.savefig(os.path.join(self.plot_dir, f'{well}.png'))
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     if '-store' in sys.argv:
         sys.argv.remove('-store')
         store_output = True

pyproject.toml

@@ -68,4 +68,7 @@ include = [
 source = [
     'pcpostprocess',
 ]
+omit = [
+    'pcpostprocess/__main__.py',
+]