Working on adding coverage testing for scripts

Author: MichaelClerx

.gitignore

@@ -3,3 +3,4 @@
 *__pycache__*
 *.egg-info
 *.DS_Store
+.coverage

example_export_config.py

@@ -4,9 +4,6 @@
 
 # Copy this config file to the top-level data directory and modify fields.
 
-# Data output directory
-savedir = './data'
-
 # Save name for this set of data
 saveID = 'EXPERIMENT_NAME'
 

pcpostprocess/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.1.dev374+dirty'
+__version_tuple__ = version_tuple = (0, 1, 'dev374', 'dirty')
+
+__commit_id__ = commit_id = 'g9ee4de552'

pcpostprocess/scripts/__main__.py

@@ -18,7 +18,7 @@ def main():
     sys.argv.pop(1)  # Subcommand's argparser shouldn't see this
 
     if args.subcommand == "run_herg_qc":
-        run_herg_qc.main()
+        run_herg_qc.run_from_command_line()
 
     elif args.subcommand == "summarise_herg_export":
         summarise_herg_export.main()