Separating command line argument parsing from code

Author: MichaelClerx

.coverage

@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.10', 3.11, 3.12, 3.13, 3.14]
-        
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -36,16 +36,15 @@ jobs:
         wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
         tar xvf tests/test_data.tar.xz -C tests/
 
-    - name: Test with pytest
-      run: |
-        python -m pip install -e .
-        python -m pytest --cov --cov-config=.coveragerc
-
     - name: Install TeX dependencies
       timeout-minutes: 15
       run: |
         sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
 
+    - name: Run unit tests and check coverage
+      run: |
+        coverage run python -m unittest
+
     - name: Test running QC
       timeout-minutes: 15
       run: |

.github/workflows/pytest.yml

@@ -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'
 

example_export_config.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/_version.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()