Issue 137: unify argument patterns (#138)

pipelines/build_model.py

@@ -48,7 +48,7 @@ def build_model_from_dir(model_dir):
         - 1
     )
 
-    priors = runpy.run_path(prior_path)
+    priors = runpy.run_path(str(prior_path))
 
     right_truncation_offset = model_data["right_truncation_offset"]
 

pipelines/fit_model.py

@@ -54,7 +54,7 @@ def fit_and_save_model(
         description="Fit the hospital-only wastewater model."
     )
     parser.add_argument(
-        "--model_run_dir",
+        "model_run_dir",
         type=Path,
         help=(
             "Path to a directory containing model fitting data. "

pipelines/generate_predictive.py

@@ -53,7 +53,7 @@ def generate_and_save_predictions(
         description=("Do posterior prediction from a pyrenew-hew fit.")
     )
     parser.add_argument(
-        "model-run-dir",
+        "model_run_dir",
         type=Path,
         help=(
             "Path to a directory containing the model fitting data "

pipelines/iteration_helpers/loop_fit.sh

@@ -13,5 +13,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the Python script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    python fit_model.py --model_run_dir "$SUBDIR"
+    python fit_model.py "$SUBDIR"
 done

pipelines/iteration_helpers/loop_generate_predictive.sh

@@ -14,5 +14,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the Python script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    python generate_predictive.py --model_dir "$SUBDIR" --n_forecast_points 28
+    python generate_predictive.py "$SUBDIR" --n-forecast-points 28
 done

pipelines/iteration_helpers/loop_postprocess.sh

@@ -13,5 +13,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the R script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    Rscript postprocess_state_forecast.R --model-run-dir "$SUBDIR"
+    Rscript postprocess_state_forecast.R "$SUBDIR"
 done

pipelines/score_forecast.R

@@ -236,7 +236,7 @@ read_and_score_location <- function(model_run_dir,
 # Create a parser
 p <- arg_parser("Score a single location forecast") |>
   add_argument(
-    "model-run-dir",
+    "model_run_dir",
     help = "Directory containing the model data and output."
   )