Increase timeout (#250)

* Set timeout to 300 second

* Fix some linter issues

src/ewatercycle/models/lisflood.py

@@ -1,4 +1,5 @@
-"""Module with Lisflood model."""
+"""eWaterCycle wrapper around Lisflood BMI."""
+
 import datetime
 import logging
 import xml.etree.ElementTree as ET
@@ -37,13 +38,12 @@ class Lisflood(AbstractModel[LisfloodForcing]):
     available_versions = ("20.10",)
     """Versions for which ewatercycle grpc4bmi docker images are available."""
 
-    def __init__(
+    def __init__(  # noqa: D107
         self,
         version: str,
         parameter_set: ParameterSet,
         forcing: LisfloodForcing,
     ):
-        """Construct Lisflood model with initial values."""
         super().__init__(version, parameter_set, forcing)
         self._check_forcing(forcing)
         self.cfg = XmlConfig(parameter_set.config)
@@ -96,7 +96,10 @@ def setup(  # type: ignore
             Path to config file and path to config directory
         """
         # TODO forcing can be a part of parameter_set
-        cfg_dir_as_path = to_absolute_path(cfg_dir) if cfg_dir else None
+        cfg_dir_as_path = None
+        if cfg_dir:
+            cfg_dir_as_path = to_absolute_path(cfg_dir)
+
         cfg_dir_as_path = _generate_workdir(cfg_dir_as_path)
         config_file = self._create_lisflood_config(
             cfg_dir_as_path,
@@ -122,6 +125,7 @@ def setup(  # type: ignore
                 image=str(self.singularity_image),
                 input_dirs=input_dirs,
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         elif CFG["container_engine"].lower() == "docker":
             self._set_docker_image()
@@ -130,6 +134,7 @@ def setup(  # type: ignore
                 image_port=55555,
                 input_dirs=input_dirs,
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         else:
             raise ValueError(
@@ -138,7 +143,7 @@ def setup(  # type: ignore
         return str(config_file), str(cfg_dir_as_path)
 
     def _check_forcing(self, forcing):
-        """Checks forcing argument and get path, start/end time of forcing data."""
+        """Check forcing argument and get path, start/end time of forcing data."""
         # TODO check if mask has same grid as forcing files,
         # if not warn users to run reindex_forcings
         if isinstance(forcing, LisfloodForcing):
@@ -341,7 +346,7 @@ def parameters(self) -> Iterable[Tuple[str, Any]]:
 
 
 def _generate_workdir(cfg_dir: Path = None) -> Path:
-    """Creates or makes sure workdir exists.
+    """Create or make sure workdir exists.
 
     Args:
         cfg_dir: If cfg dir is None then create sub-directory in CFG['output_dir']

src/ewatercycle/models/marrmot.py

@@ -1,3 +1,5 @@
+"""eWaterCycle wrapper around Marrmot BMI."""
+
 import datetime
 import logging
 from dataclasses import asdict, dataclass
@@ -21,7 +23,9 @@
 
 @dataclass
 class Solver:
-    """Solver, for current implementations see `here
+    """Container for properties of the solver.
+
+    For current implementations see `here
     <https://github.com/wknoben/MARRMoT/tree/master/MARRMoT/Functions/Time%20stepping>`_.
     """
 
@@ -31,7 +35,8 @@ class Solver:
 
 
 def _generate_cfg_dir(cfg_dir: Path = None) -> Path:
-    """
+    """Make sure there is a working directory.
+
     Args:
         cfg_dir: If cfg dir is None or does not exist then create sub-directory
             in CFG['output_dir']
@@ -70,8 +75,7 @@ class MarrmotM01(AbstractModel[MarrmotForcing]):
     available_versions = ("2020.11",)
     """Versions for which ewatercycle grpc4bmi docker images are available."""
 
-    def __init__(self, version: str, forcing: MarrmotForcing):
-        """Construct MarrmotM01 with initial values."""
+    def __init__(self, version: str, forcing: MarrmotForcing):  # noqa: D107
         super().__init__(version, forcing=forcing)
         self._parameters = [1000.0]
         self.store_ini = [900.0]
@@ -128,7 +132,10 @@ def setup(  # type: ignore
             self.store_ini = [initial_soil_moisture_storage]
         if solver:
             self.solver = solver
-        cfg_dir_as_path = to_absolute_path(cfg_dir) if cfg_dir else None
+
+        cfg_dir_as_path = None
+        if cfg_dir:
+            cfg_dir_as_path = to_absolute_path(cfg_dir)
 
         cfg_dir_as_path = _generate_cfg_dir(cfg_dir_as_path)
         config_file = self._create_marrmot_config(cfg_dir_as_path, start_time, end_time)
@@ -139,12 +146,14 @@ def setup(  # type: ignore
             self.bmi = BmiClientSingularity(
                 image=str(self.singularity_image),
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         elif CFG["container_engine"].lower() == "docker":
             self.bmi = BmiClientDocker(
                 image=self.docker_image,
                 image_port=55555,
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         else:
             raise ValueError(
@@ -153,7 +162,7 @@ def setup(  # type: ignore
         return str(config_file), str(cfg_dir_as_path)
 
     def _check_forcing(self, forcing):
-        """ "Check forcing argument and get path, start and end time of forcing data."""
+        """Check forcing argument and get path, start and end time of forcing data."""
         if isinstance(forcing, MarrmotForcing):
             forcing_dir = to_absolute_path(forcing.directory)
             self.forcing_file = str(forcing_dir / forcing.forcing_file)
@@ -270,14 +279,13 @@ def get_value_as_xarray(self, name: str) -> xr.DataArray:
     @property
     def parameters(self) -> Iterable[Tuple[str, Any]]:
         """List the parameters for this model."""
-        p = [
+        return [
             ("maximum_soil_moisture_storage", self._parameters[0]),
             ("initial_soil_moisture_storage", self.store_ini[0]),
             ("solver", self.solver),
             ("start time", self.forcing_start_time.strftime("%Y-%m-%dT%H:%M:%SZ")),
             ("end time", self.forcing_end_time.strftime("%Y-%m-%dT%H:%M:%SZ")),
         ]
-        return p
 
 
 M14_PARAMS = (
@@ -315,8 +323,7 @@ class MarrmotM14(AbstractModel[MarrmotForcing]):
     available_versions = ("2020.11",)
     """Versions for which ewatercycle grpc4bmi docker images are available."""
 
-    def __init__(self, version: str, forcing: MarrmotForcing):
-        """Construct MarrmotM14 with initial values."""
+    def __init__(self, version: str, forcing: MarrmotForcing):  # noqa: D107
         super().__init__(version, forcing=forcing)
         self._parameters = [1000.0, 0.5, 0.5, 100.0, 0.5, 4.25, 2.5]
         self.store_ini = [900.0, 900.0]
@@ -392,7 +399,10 @@ def setup(  # type: ignore
             self.store_ini[1] = initial_saturated_zone_storage
         if solver:
             self.solver = solver
-        cfg_dir_as_path = to_absolute_path(cfg_dir) if cfg_dir else None
+
+        cfg_dir_as_path = None
+        if cfg_dir:
+            cfg_dir_as_path = to_absolute_path(cfg_dir)
 
         cfg_dir_as_path = _generate_cfg_dir(cfg_dir_as_path)
         config_file = self._create_marrmot_config(cfg_dir_as_path, start_time, end_time)
@@ -403,12 +413,14 @@ def setup(  # type: ignore
             self.bmi = BmiClientSingularity(
                 image=str(self.singularity_image),
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         elif CFG["container_engine"].lower() == "docker":
             self.bmi = BmiClientDocker(
                 image=self.docker_image,
                 image_port=55555,
                 work_dir=str(cfg_dir_as_path),
+                timeout=300,
             )
         else:
             raise ValueError(

src/ewatercycle/models/pcrglobwb.py

@@ -1,3 +1,5 @@
+"""eWaterCycle wrapper around PCRGlobWB BMI."""
+
 import datetime
 import logging
 from os import PathLike
@@ -24,7 +26,6 @@ class PCRGlobWB(AbstractModel[PCRGlobWBForcing]):
     """eWaterCycle implementation of PCRGlobWB hydrological model.
 
     Args:
-
         version: pick a version from :py:attr:`~available_versions`
         parameter_set: instance of
             :py:class:`~ewatercycle.parameter_sets.default.ParameterSet`.
@@ -35,7 +36,7 @@ class PCRGlobWB(AbstractModel[PCRGlobWBForcing]):
 
     available_versions = ("setters",)
 
-    def __init__(
+    def __init__(  # noqa: D107
         self,
         version: str,
         parameter_set: ParameterSet,
@@ -94,7 +95,8 @@ def _setup_default_config(self):
                 "temperatureNC",
                 str(
                     to_absolute_path(
-                        self.forcing.temperatureNC, parent=self.forcing.directory
+                        self.forcing.temperatureNC,
+                        parent=self.forcing.directory,
                     )
                 ),
             )
@@ -103,7 +105,8 @@ def _setup_default_config(self):
                 "precipitationNC",
                 str(
                     to_absolute_path(
-                        self.forcing.precipitationNC, parent=self.forcing.directory
+                        self.forcing.precipitationNC,
+                        parent=self.forcing.directory,
                     )
                 ),
             )
@@ -129,17 +132,17 @@ def setup(self, cfg_dir: str = None, **kwargs) -> Tuple[str, str]:  # type: igno
 
         try:
             self._start_container()
-        except FutureTimeoutError:
+        except FutureTimeoutError as exc:
             # https://github.com/eWaterCycle/grpc4bmi/issues/95
             # https://github.com/eWaterCycle/grpc4bmi/issues/100
             raise ValueError(
                 "Couldn't spawn container within allocated time limit "
-                "(15 seconds). You may try pulling the docker image with"
+                "(300 seconds). You may try pulling the docker image with"
                 f" `docker pull {self.docker_image}` or call `singularity "
                 f"build {self._singularity_image(CFG['singularity_dir'])} "
                 f"docker://{self.docker_image}` if you're using singularity,"
                 " and then try again."
-            )
+            ) from exc
 
         return str(cfg_file), str(work_dir)
 
@@ -199,14 +202,14 @@ def _start_container(self):
                 image_port=55555,
                 work_dir=str(self.work_dir),
                 input_dirs=additional_input_dirs,
-                timeout=15,
+                timeout=300,
             )
         elif CFG["container_engine"] == "singularity":
             self.bmi = BmiClientSingularity(
                 image=self._singularity_image(CFG["singularity_dir"]),
                 work_dir=str(self.work_dir),
                 input_dirs=additional_input_dirs,
-                timeout=15,
+                timeout=300,
             )
         else:
             raise ValueError(
@@ -216,7 +219,7 @@ def _start_container(self):
     def _coords_to_indices(
         self, name: str, lat: Iterable[float], lon: Iterable[float]
     ) -> Iterable[int]:
-        """Converts lat/lon values to index.
+        """Convert lat/lon values to index.
 
         Args:
             lat: Latitudinal value

src/ewatercycle/models/wflow.py

@@ -1,3 +1,5 @@
+"""eWaterCycle wrapper around WFlow BMI."""
+
 import datetime
 import logging
 import shutil
@@ -35,13 +37,12 @@ class Wflow(AbstractModel[WflowForcing]):
     available_versions = ("2020.1.1",)
     """Show supported WFlow versions in eWaterCycle"""
 
-    def __init__(
+    def __init__(  # noqa: D107
         self,
         version: str,
         parameter_set: ParameterSet,
         forcing: Optional[WflowForcing] = None,
     ):
-
         super().__init__(version, parameter_set, forcing)
         self._set_docker_image()
         self._setup_default_config()
@@ -121,17 +122,17 @@ def setup(self, cfg_dir: str = None, **kwargs) -> Tuple[str, str]:  # type: igno
 
         try:
             self._start_container()
-        except FutureTimeoutError:
+        except FutureTimeoutError as exc:
             # https://github.com/eWaterCycle/grpc4bmi/issues/95
             # https://github.com/eWaterCycle/grpc4bmi/issues/100
             raise ValueError(
                 "Couldn't spawn container within allocated time limit "
-                "(15 seconds). You may try pulling the docker image with"
+                "(300 seconds). You may try pulling the docker image with"
                 f" `docker pull {self.docker_image}` or call `singularity "
                 f"build {self._singularity_image(CFG['singularity_dir'])} "
                 f"docker://{self.docker_image}` if you're using singularity,"
                 " and then try again."
-            )
+            ) from exc
 
         return (
             str(updated_cfg_file),
@@ -165,21 +166,21 @@ def _start_container(self):
                 image=self.docker_image,
                 image_port=55555,
                 work_dir=str(self.work_dir),
-                timeout=10,
+                timeout=300,
             )
         elif CFG["container_engine"] == "singularity":
             self.bmi = BmiClientSingularity(
                 image=self._singularity_image(CFG["singularity_dir"]),
                 work_dir=str(self.work_dir),
-                timeout=15,
+                timeout=300,
             )
         else:
             raise ValueError(f"Unknown container technology: {CFG['container_engine']}")
 
     def _coords_to_indices(
         self, name: str, lat: Iterable[float], lon: Iterable[float]
     ) -> Iterable[int]:
-        """Converts lat/lon values to index.
+        """Convert lat/lon values to index.
 
         Args:
             lat: Latitudinal value
@@ -240,11 +241,11 @@ def parameters(self) -> Iterable[Tuple[str, Any]]:
         ]
 
 
-def _wflow_to_iso(t):
-    dt = datetime.datetime.fromisoformat(t)
+def _wflow_to_iso(time):
+    dt = datetime.datetime.fromisoformat(time)
     return dt.strftime("%Y-%m-%dT%H:%M:%SZ")
 
 
-def _iso_to_wflow(t):
-    dt = get_time(t)
+def _iso_to_wflow(time):
+    dt = get_time(time)
     return dt.strftime("%Y-%m-%d %H:%M:%S")

tests/models/test_lisflood.py

@@ -108,6 +108,7 @@ def test_setup(self, model_with_setup, tmp_path):
                 f"{tmp_path}/forcing",
             ],
             work_dir=f"{tmp_path}/lisflood_20210102_030405",
+            timeout=300,
         )
 
         # Check content config file
@@ -207,6 +208,7 @@ def test_setup(self, model_with_setup, tmp_path):
                     f"{tmp_path}/custommask",
                 ],
                 work_dir=f"{tmp_path}/lisflood_20210102_030405",
+                timeout=300,
             )
 
             # Check content config file