Change flag for experiment path for better intuition. #60

src/mednet/scripts/upload.py

@@ -72,24 +72,24 @@ def _create_temp_copy(source, target):
 
    .. code:: sh
 
-      mednet upload --output-folder=path/to/results
+      mednet upload --experiment-folder=/path/to/results
 
 2. Upload an existing experiment result with an experiment name:
 
    .. code:: sh
 
-      mednet upload--output-folder=path/to/results --experiment-name=exp-pasa_mc
+      mednet upload --experiment-folder=/path/to/results --experiment-name=exp-pasa_mc
 
 3. Upload an existing experiment result with a run name:
 
    .. code:: sh
 
-      mednet upload--output-folder=path/to/results --run-name=run-1
+      mednet upload --experiment-folder=/path/to/results --run-name=run-1
 """,
 )
 @click.option(
-    "--output-folder",
-    "-o",
+    "--experiment-folder",
+    "-f",
     help="Directory in which to upload results from",
     required=True,
     type=click.Path(
@@ -114,12 +114,12 @@ def _create_temp_copy(source, target):
 )
 @verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
 def upload(
-    output_folder: pathlib.Path,
+    experiment_folder: pathlib.Path,
     experiment_name: str,
     run_name: str,
     **_,  # ignored
 ) -> None:  # numpydoc ignore=PR01
-    """Upload results from an experiment output folder."""
+    """Upload results from an experiment folder."""
 
     logger.info("Getting Gitlab credentials for accessing to MLFlow server...")
     gitlab, config = _get_gitlab_config()
@@ -130,10 +130,10 @@ def upload(
     )
 
     # prepare train files
-    train_output_folder = output_folder / "model"
-    train_meta_file = train_output_folder / "meta.json"
-    train_log_file = train_output_folder / "trainlog.pdf"
-    train_model_file = [f for f in train_output_folder.glob("*lowest*")][0]
+    train_folder = experiment_folder / "model"
+    train_meta_file = train_folder / "meta.json"
+    train_log_file = train_folder / "trainlog.pdf"
+    train_model_file = [f for f in train_folder.glob("*lowest*")][0]
     train_model_temp_file = train_model_file.parts[-1].replace("=", "_")
     train_model_temp_file = _create_temp_copy(
         train_model_file, train_model_temp_file
@@ -142,9 +142,9 @@ def upload(
         meta_data = json.load(f)
 
     # prepare evaluation files
-    evaluation_file = output_folder / "evaluation.json"
-    evaluation_meta_file = output_folder / "evaluation.meta.json"
-    evaluation_log_file = output_folder / "evaluation.pdf"
+    evaluation_file = experiment_folder / "evaluation.json"
+    evaluation_meta_file = experiment_folder / "evaluation.meta.json"
+    evaluation_log_file = experiment_folder / "evaluation.pdf"
     with evaluation_file.open("r") as f:
         evaluation_data = json.load(f)
     test_data = evaluation_data["test"]