CLI

maxsmi/full_workflow.py

@@ -50,7 +50,9 @@
     NB_EPOCHS,
 )
 
-if __name__ == "__main__":
+
+def main():
+
     warnings.filterwarnings("ignore")
     parser = argparse.ArgumentParser()
 
@@ -432,3 +434,7 @@
     )
     results_metrics = results_metrics.to_pickle(f"{folder}/results_metrics.pkl")
     logging.info("Script completed. \n \n")
+
+
+if __name__ == "__main__":
+    main()

maxsmi/full_workflow_earlystopping.py

@@ -50,7 +50,9 @@
     NB_EPOCHS,
 )
 
-if __name__ == "__main__":
+
+def main():
+
     warnings.filterwarnings("ignore")
     parser = argparse.ArgumentParser()
 
@@ -451,3 +453,7 @@
     )
     results_metrics = results_metrics.to_pickle(f"{folder}/results_metrics.pkl")
     logging.info("Script completed. \n \n")
+
+
+if __name__ == "__main__":
+    main()

maxsmi/prediction_unlabeled_data.py

@@ -2,6 +2,7 @@
 From smiles to predictions
 
 """
+from pathlib import Path
 import argparse
 import logging
 import logging.handlers
@@ -36,7 +37,11 @@
 from maxsmi.pytorch_evaluation import out_of_sample_prediction
 from maxsmi.utils_optimal_model import retrieve_optimal_model
 
-if __name__ == "__main__":
+PATH_MAXSMI = Path(__file__).parent
+
+
+def main():
+
     warnings.filterwarnings("ignore")
     parser = argparse.ArgumentParser()
 
@@ -170,7 +175,7 @@
 
     (ml_model_name, ml_model) = model_type(ml_model, device, smi_dict, max_length_smi)
     logging.info(f"Summary of ml model used for the prediction: {ml_model} ")
-    file_path = f"maxsmi/prediction_models/{args.task}"
+    file_path = PATH_MAXSMI / f"prediction_models/{args.task}"
     ml_model.load_state_dict(
         torch.load(f"{file_path}/model_dict.pth", map_location=device)
     )
@@ -246,3 +251,7 @@
 
     logging.info("Script completed. \n \n")
     print(f"Script completed. Output can be found at {folder}/")
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -38,6 +38,13 @@
     # Customize MANIFEST.in if the general case does not suit your needs
     # Comment out this line to prevent the files from being packaged with your software
     include_package_data=True,
+    entry_points={
+        "console_scripts": [
+            "maxsmi = maxsmi.full_workflow:main",
+            "maxsmi-earlystopping = maxsmi.full_workflow_earlystopping:main",
+            "maxsmi-pred = maxsmi.prediction_unlabeled_data:main",
+        ]
+    },
     # Allows `setup.py test` to work correctly with pytest
     setup_requires=[] + pytest_runner,
     # Additional entries you may want simply uncomment the lines you want and fill in the data