Add BMI tests w/ Docker (linux only on GH Actions)

Author: BSchilperoort

tests/test_data/config_file_docker.txt

@@ -0,0 +1,16 @@
+WorkDir=tests/test_data/directories/
+SoilPropertyPath=tests/test_data/directories/model_parameters/soil_property/
+ForcingPath=tests/test_data/directories/forcing/plumber2_data/
+Location=XX-Xxx
+directional=tests/test_data/directories/model_parameters/vegetation_property/directional/
+fluspect_parameters=tests/test_data/directories/model_parameters/vegetation_property/fluspect_parameters/
+leafangles=tests/test_data/directories/model_parameters/vegetation_property/leafangles/
+radiationdata=tests/test_data/directories/model_parameters/vegetation_property/radiationdata/
+soil_spectrum=tests/test_data/directories/model_parameters/vegetation_property/soil_spectrum/
+input_data=tests/test_data/directories/model_parameters/vegetation_property/dummy_data.xlsx
+InitialConditionPath=tests/test_data/directories/model_parameters/soil_initialcondition/
+StartTime=1996-01-01T00:00
+EndTime=1996-01-01T02:00
+InputPath=
+OutputPath=
+DockerImage=ghcr.io/ecoextreml/stemmus_scope:1.5.0

tests/test_data/directories/model_parameters/vegetation_property/.gitignore

@@ -0,0 +1,3 @@
+fluspect_parameters/Optipar2017_ProspectD.mat
+radiationdata/FLEX-S3_std.atm
+soil_spectrum/soilnew.txt

tests/test_data/directories/model_parameters/vegetation_property/input_data.xlsx

@@ -0,0 +1,105 @@
+from distutils.dir_util import copy_tree
+from pathlib import Path
+import docker
+import docker.errors
+import pytest
+import requests
+from PyStemmusScope import config_io
+from PyStemmusScope import forcing_io
+from PyStemmusScope import soil_io
+from PyStemmusScope.bmi.implementation import StemmusScopeBmi
+from PyStemmusScope.bmi.docker_utils import pull_image
+from . import data_folder
+import platform
+
+
+SCOPE_INPUTDATA_v2_1 = "https://github.com/Christiaanvandertol/SCOPE/raw/2.1/input/"
+SCOPE_INPUTDATA_v1_7 = (
+    "https://github.com/Christiaanvandertol/SCOPE/raw/1.73/data/input/"
+)
+
+
+def docker_available():
+    try:
+        docker.APIClient()
+        
+        # Github Actions windows runners couldn't pull the image:
+        if platform.system() == "Windows":
+            pull_image("ghcr.io/ecoextreml/stemmus_scope:1.5.0")
+
+        return True
+    except docker.errors.DockerException as err:
+        if "Error while fetching server API version" in str(err):
+            return False
+        if "404 Client Error" in str(err):  # Can't find image
+            return False
+        else:
+            raise err  # Unknown error.        
+
+
+cfg_file = data_folder / "config_file_docker.txt"
+vegetation_property_dir = (
+    data_folder / "directories" / "model_parameters" / "vegetation_property"
+)
+
+
+def write_config_file(cfg: dict, file: Path) -> None:
+    with file.open("w") as f:
+        for key, val in cfg.items():
+            f.write(f"{key}={val}\n")
+
+
+@pytest.fixture(scope="session")
+def prep_input_data():
+    optipar_path = (
+        vegetation_property_dir / "fluspect_parameters" / "Optipar2017_ProspectD.mat"
+    )
+    if not optipar_path.exists():
+        r = requests.get(  # Older version due to v2 compatibility issues
+            SCOPE_INPUTDATA_v1_7 + "fluspect_parameters/Optipar2017_ProspectD.mat"
+        )
+        assert r.status_code == 200
+        optipar_path.open("wb").write(r.content)
+
+    flex_s3_path = vegetation_property_dir / "radiationdata" / "FLEX-S3_std.atm"
+    if not flex_s3_path.exists():
+        r = requests.get(SCOPE_INPUTDATA_v2_1 + "radiationdata/FLEX-S3_std.atm")
+        assert r.status_code == 200
+        flex_s3_path.open("wb").write(r.content)
+
+    soil_path = vegetation_property_dir / "soil_spectrum" / "soilnew.txt"
+    if not soil_path.exists():
+        r = requests.get(SCOPE_INPUTDATA_v2_1 + "soil_spectra/soilnew.txt")
+        assert r.status_code == 200
+        soil_path.open("wb").write(r.content)
+
+
+@pytest.fixture(scope="session")
+def prepare_data_config(tmpdir_factory, prep_input_data) -> Path:
+    tempdir = Path(tmpdir_factory.mktemp("tempdir"))
+    output_dir = tempdir / "output_dir"
+    input_dir = tempdir / "input_dir"
+    output_dir.mkdir()
+    input_dir.mkdir()
+    config = config_io.read_config(cfg_file)
+    config["OutputPath"] = str(output_dir) + "/"
+    config["InputPath"] = str(input_dir) + "/"
+
+    forcing_io.prepare_forcing(config)
+    soil_io.prepare_soil_data(config)
+    soil_io.prepare_soil_init(config)
+
+    copy_tree(src=str(vegetation_property_dir), dst=str(input_dir))
+
+    config_dir = tempdir / "config.txt"
+    write_config_file(config, config_dir)
+
+    return config_dir
+
+
+@pytest.mark.skipif(not docker_available(), reason="Docker not available")
+def test_initialize(prepare_data_config):
+    model = StemmusScopeBmi()
+    model.initialize(str(prepare_data_config))
+    model.update()
+    model.finalize()