Remove entry point for cellfinder workflow (#93)

* remove entry point for cellfinder workflow

* make black happy

* remove entry point test

* remove unused import

brainglobe_workflows/cellfinder_core/cellfinder_core.py

@@ -437,27 +437,12 @@ def main(
     return cfg
 
 
-def main_app_wrapper():
-    """Parse command line arguments and
-    run cellfinder setup and workflow
-
-    This function is used to define an entry-point,
-    that allows the user to run the cellfinder workflow
-    for a given input config file as:
-    `cellfinder-workflow --config <path-to-input-config>`.
-
-    If no input config file is provided, the default is used.
-
-    """
+if __name__ == "__main__":
     # parse CLI arguments
     args = config_parser(
-        sys.argv[1:],  # sys.argv[0] is the script name
+        sys.argv[1:],
         str(DEFAULT_JSON_CONFIG_PATH_CELLFINDER),
     )
 
     # run setup and workflow
     _ = main(args.config)
-
-
-if __name__ == "__main__":
-    main_app_wrapper()

pyproject.toml

@@ -74,7 +74,6 @@ napari = ["napari[pyqt5]", "brainglobe-napari-io", "cellfinder[napari]>=1.0.0"]
 "Source Code" = "https://github.com/brainglobe/brainglobe-workflows"
 
 [project.scripts]
-cellfinder-workflow = "brainglobe_workflows.cellfinder_core.cellfinder_core:main_app_wrapper"
 brainmapper = "brainglobe_workflows.brainmapper.main:main"
 
 [build-system]

tests/cellfinder_core/test_integration/test_cellfinder.py

@@ -1,4 +1,3 @@
-import subprocess
 from pathlib import Path
 from typing import Optional
 
@@ -50,21 +49,3 @@ def test_main_w_inputs(
 
     # check output files exist
     assert Path(cfg._detected_cells_path).is_file()
-
-
-def test_entry_point_help():
-    """
-    Smoke test the cellfinder workflow entry point by checking
-    help is printed out successfully
-    """
-
-    # define CLI input
-    subprocess_input = ["cellfinder-workflow", "--help"]
-
-    # run workflow
-    subprocess_output = subprocess.run(
-        subprocess_input,
-    )
-
-    # check returncode
-    assert subprocess_output.returncode == 0