Copy soil layer setting csv to input folder + add a BMI MODFLOW coupling notebook

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/ecoextreml/stemmus_scope:1.6.0
+FROM ghcr.io/ecoextreml/stemmus_scope:1.6.1
 
 LABEL maintainer="Bart Schilperoort <[email protected]>"
 LABEL org.opencontainers.image.source = "https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing"

PyStemmusScope/bmi/docker_process.py

@@ -83,7 +83,7 @@ class StemmusScopeDocker:
     """Communicate with a STEMMUS_SCOPE Docker container."""
 
     # Default image, can be overridden with config:
-    compatible_tags = ("1.6.0",)
+    compatible_tags = ("1.6.1",)
 
     _process_ready_phrase = b"Select BMI mode:"
     _process_finalized_phrase = b"Finished clean up."

PyStemmusScope/bmi/variable_reference.py

@@ -114,6 +114,15 @@ class BmiVariable:
         grid=0,
         keys=["gwfluxes", "recharge"],
     ),
+    BmiVariable(
+        name="groundwater_recharge_index",
+        dtype="int64",
+        input=False,
+        output=True,
+        units="-",
+        grid=0,
+        keys=["gwfluxes", "indxRchrg"],
+    ),
     # groundwater (coupling) vars
     BmiVariable(
         name="groundwater_coupling_enabled",

PyStemmusScope/config_io.py

@@ -126,6 +126,16 @@ def _copy_data(input_dir: Path, config: dict) -> None:
 
     # copy input_data.xlsx
     shutil.copy(str(config["input_data"]), str(input_dir))
+    # copy soil_layers_thickness, this is optional
+    if "soil_layers_thickness" in config:
+        if Path(config["soil_layers_thickness"]).is_file():
+            shutil.copy(str(config["soil_layers_thickness"]), str(input_dir))
+        else:
+            raise FileNotFoundError(
+                "The key `soil_layers_thickness` is provided in the config file, "
+                f"but file {config['soil_layers_thickness']} not found. "
+                "Remove the key from the config file or provide the file."
+            )
 
 
 def _update_config_file(

docs/bmi.md

@@ -19,10 +19,10 @@ To use the Docker image, use the `DockerImage` setting in the configuration file
 ```sh
 WorkDir=/home/username/tmp/stemmus_scope
 ...
-DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.6.0
+DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.6.1
 ```
 
-It is best to add the version tag here too (`:1.6.0`), this way the BMI will warn you if the version might be incompatible.
+It is best to add the version tag here too (`:1.6.1`), this way the BMI will warn you if the version might be incompatible.
 
 Note that the `docker` package for python is required here. Install this with `pip install PyStemmusScope[docker]`.
 Additionally, [Docker](https://docs.docker.com/get-docker/) itself has to be installed.
@@ -52,7 +52,7 @@ If you need access to other model variables that are not yet available in the BM
 
 A [Docker image is available](https://ghcr.io/ecoextreml/stemmus_scope-grpc4bmi) in which the model as well as the Python BMI have been wrapped in a container. The Docker image is created using the Docker file [here](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/blob/main/Dockerfile) and allows communication with a STEMMUS_SCOPE BMI through [grpc4bmi](https://grpc4bmi.readthedocs.io/en/latest/).
 
-Doing so avoids the needs to install PyStemmusScope yourself, only Docker/apptainer and a python environment with grpc4bmi are required. Please note you should not specify `DockerImage` or `ExeFilePath` in the config file if you are using the grpc4bmi interface. 
+Doing so avoids the needs to install PyStemmusScope yourself, only Docker/apptainer and a python environment with grpc4bmi are required. Please note you should not specify `DockerImage` or `ExeFilePath` in the config file if you are using the grpc4bmi interface.
 
 A demonstration is available [here](notebooks/grpc4bmi_demo.ipynb)