Merge branch 'main' into update_docs

Author: SarahAlidoost

Dockerfile

@@ -1,7 +1,7 @@
-FROM ghcr.io/ecoextreml/stemmus_scope:1.6.1
+FROM ghcr.io/ecoextreml/stemmus_scope:1.6.2
 
 LABEL maintainer="Bart Schilperoort <b.schilperoort@esciencecenter.nl>"
-LABEL org.opencontainers.image.source = "https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing"
+LABEL org.opencontainers.image.source="https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing"
 
 # Requirements for building Python 3.10
 RUN apt-get update && apt-get -y upgrade
@@ -26,8 +26,8 @@ RUN pip3.10 install grpc4bmi==0.5.0
 
 # # Set the STEMMUS_SCOPE environmental variable, so the BMI can find the executable
 WORKDIR /
-ENV STEMMUS_SCOPE /STEMMUS_SCOPE
+ENV STEMMUS_SCOPE=/STEMMUS_SCOPE
 
 EXPOSE 55555
 # Start grpc4bmi server
-CMD run-bmi-server --name "PyStemmusScope.bmi.implementation.StemmusScopeBmi" --port 55555 --debug
+CMD ["run-bmi-server", "--name", "PyStemmusScope.bmi.implementation.StemmusScopeBmi", "--port", "55555", "--debug"]

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 = ("1.6.1",)
+    compatible_tags = ("1.6.2",)
 
     _process_ready_phrase = b"Select BMI mode:"
     _process_finalized_phrase = b"Finished clean up."

PyStemmusScope/bmi/local_process.py

@@ -86,6 +86,7 @@ def __init__(self, cfg_file: str) -> None:
         """Initialize the process."""
         self.cfg_file = cfg_file
         config = read_config(cfg_file)
+        self.sleep_duration = int(config.get("SleepDuration", 10))
 
         exe_file = find_exe(config)
         args = [exe_file, cfg_file, "bmi"]
@@ -154,7 +155,7 @@ def finalize(self) -> None:
         """Finalize the model."""
         self.process = alive_process(self.process)
         self.process.stdin.write(b"finalize\n")  # type: ignore
-        sleep(10)
+        sleep(self.sleep_duration)
         if self.process.poll() != 0:
             try:
                 self.process.terminate()

PyStemmusScope/bmi/variable_reference.py

@@ -28,15 +28,43 @@ class BmiVariable:
         keys=["fluxes", "Resp"],
     ),
     BmiVariable(
-        name="evaporation_total",
+        name="precipitation",
+        dtype="float64",
+        input=True,
+        output=False,
+        units="cm s-1",
+        grid=0,
+        keys=["ForcingData", "Precip_msr"],
+        all_timesteps=True,
+    ),
+    BmiVariable(
+        name="applied_infiltration",
         dtype="float64",
         input=False,
         output=True,
         units="cm s-1",
         grid=0,
-        keys=["EVAP"],
+        keys=["ForcingData", "applied_inf"],
         all_timesteps=True,
     ),
+    BmiVariable(
+        name="soil_evaporation",
+        dtype="float64",
+        input=False,
+        output=True,
+        units="cm s-1",
+        grid=0,
+        keys=["Evap"],
+    ),
+    BmiVariable(
+        name="transpiration",
+        dtype="float64",
+        input=False,
+        output=True,
+        units="cm s-1",
+        grid=0,
+        keys=["Trap"],
+    ),
     # soil vars:
     BmiVariable(
         name="soil_temperature",

docs/bmi.md

@@ -21,10 +21,10 @@ 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:1.6.1
+DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.6.2
 ```
 
-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.
+It is best to add the version tag here too (`:1.6.2`), 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.

tests/test_data/config_file_docker.txt

@@ -13,4 +13,4 @@ StartTime=1996-01-01T00:00
 EndTime=1996-01-01T02:00
 InputPath=
 OutputPath=
-DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.6.1
+DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.6.2