[JTH] cleaned wrappers and docu

Author: tausiaj

bluemath_tk/wrappers/_base_wrappers.py

@@ -34,36 +34,41 @@ class BaseModelWrapper(BlueMathModel):
 
     Methods
     -------
-    _check_parameters_type(default_parameters, model_parameters)
+    _check_parameters_type -> None
         Check if the parameters have the correct type.
-    _exec_bash_commands(str_cmd, out_file=None, err_file=None)
+    _exec_bash_commands -> None
         Execute bash commands.
-    list_available_launchers()
+    list_available_launchers -> dict
         List the available launchers.
-    set_cases_dirs_from_output_dir()
+    set_cases_dirs_from_output_dir -> None
         Set the cases directories from the output directory.
-    write_array_in_file(array, filename)
+    write_array_in_file -> None
         Write an array in a file.
-    copy_files(src, dst)
+    copy_files -> None
         Copy file(s) from source to destination.
-    render_file_from_template(template_name, context, output_filename=None)
+    render_file_from_template -> None
         Render a file from a template.
-    create_cases_context_one_by_one()
+    create_cases_context_one_by_one -> List[dict]
         Create an array of dictionaries with the combinations of values from the
         input dictionary, one by one.
-    create_cases_context_all_combinations()
+    create_cases_context_all_combinations -> List[dict]
         Create an array of dictionaries with each possible combination of values
         from the input dictionary.
-    build_cases(mode="one_by_one")
+    build_cases -> None
         Create the cases folders and render the input files.
-    run_cases(launcher=None, cases_to_run=None, parallel=False)
+    run_case -> None
+        Run the case based on the launcher specified.
+    run_cases -> None
         Run the cases based on the launcher specified.
         Parallel execution is optional.
-    postprocess_case(case_num, case_dir)
+        Cases to run can be specified.
+    run_cases_bulk -> None
+        Run the cases based on the launcher specified.
+    postprocess_case -> None
         Postprocess the model output for a specific case.
-    join_postprocessed_files(postprocessed_files)
+    join_postprocessed_files -> xr.Dataset
         Join the postprocessed files.
-    postprocess_cases(cases_to_postprocess=None)
+    postprocess_cases -> Union[xr.Dataset, List[xr.Dataset]]
         Postprocess the model output.
     """
 
@@ -348,7 +353,13 @@ def build_cases(self, mode: str = "one_by_one") -> None:
             f"{len(self.cases_dirs)} cases created in {mode} mode and saved in {self.output_dir}"
         )
 
-    def run_case(self, case_dir: str, launcher: str) -> None:
+    def run_case(
+        self,
+        case_dir: str,
+        launcher: str,
+        ouput_log_file: str = "wrapper_out.log",
+        error_log_file: str = "wrapper_error.log",
+    ) -> None:
         """
         Run the case based on the launcher specified.
 
@@ -358,14 +369,23 @@ def run_case(self, case_dir: str, launcher: str) -> None:
             The case directory.
         launcher : str
             The launcher to run the case.
+        ouput_log_file : str, optional
+            The name of the output log file. Default is "wrapper_out.log".
+        error_log_file : str, optional
+            The name of the error log file. Default is "wrapper_error.log".
         """
 
         # Get launcher command from the available launchers
         launcher = self.list_available_launchers().get(launcher, launcher)
 
+        # Run the case in the case directory
         self.logger.info(f"Running case in {case_dir} with launcher={launcher}.")
         os.chdir(case_dir)
-        self._exec_bash_commands(str_cmd=launcher)
+        self._exec_bash_commands(
+            str_cmd=launcher,
+            out_file=ouput_log_file,
+            err_file=error_log_file,
+        )
 
     def run_cases(
         self,

bluemath_tk/wrappers/cgwave/__init__.py bluemath_tk/wrappers/sfincs/__init__.pybluemath_tk/wrappers/cgwave/__init__.py renamed to bluemath_tk/wrappers/sfincs/__init__.py

@@ -1,4 +1,3 @@
-import sys
 from .._base_wrappers import BaseModelWrapper
 
 
@@ -9,17 +8,10 @@ class SwanModelWrapper(BaseModelWrapper):
 
     Attributes
     ----------
-    swan_exec : str
-        The SWAN executable path.
     default_parameters : dict
-        The default parameters type for the model.
-
-    Methods
-    -------
-    set_swan_exec(swan_exec: str) -> None
-        Set the SWAN executable path.
-    run_model(case_dir: str, log_file: str = "swan_exec.log") -> None
-        Run the SWAN model for the specified case.
+        The default parameters type for the wrapper.
+    available_launchers : dict
+        The available launchers for the wrapper.
     """
 
     default_parameters = {
@@ -29,71 +21,30 @@ class SwanModelWrapper(BaseModelWrapper):
         "spr": float,
     }
 
+    available_launchers = {
+        "bash": "swanrun -input input.sws",
+        "docker": "docker run --rm -v .:/case_dir -w /case_dir tausiaj/swan-geoocean:41.51 swanrun -input input.sws",
+    }
+
     def __init__(
         self,
         templates_dir: str,
-        templates_name: dict,
         model_parameters: dict,
         output_dir: str,
-    ):
+        templates_name: dict = "all",
+        debug: bool = True,
+    ) -> None:
         """
-        Initialize the SWAN model wrapper.
-
-        Parameters
-        ----------
-        templates_dir : str
-            The directory where the templates are stored.
-        templates_name : list
-            The names of the templates.
-        model_parameters : dict
-            The parameters to be used in the templates.
-        output_dir : str
-            The directory where the output files will be saved.
+        Initialize the SWASH model wrapper.
         """
 
         super().__init__(
             templates_dir=templates_dir,
-            templates_name=templates_name,
             model_parameters=model_parameters,
             output_dir=output_dir,
+            templates_name=templates_name,
             default_parameters=self.default_parameters,
         )
-        self.set_logger_name(self.__class__.__name__)
-        self._swan_exec: str = None
-
-    @property
-    def swan_exec(self) -> str:
-        return self._swan_exec
-
-    def set_swan_exec(self, swan_exec: str) -> None:
-        self._swan_exec = swan_exec
-
-    def run_model(self, case_dir: str, log_file: str = "swan_exec.log") -> None:
-        """
-        Run the SWAN model for the specified case.
-
-        Parameters
-        ----------
-        case_dir : str
-            The case directory.
-        log_file : str, optional
-            The log file name. Default is "swan_exec.log".
-
-        Raises
-        ------
-        ValueError
-            If the SWAN executable was not set.
-        """
-
-        if not self.swan_exec:
-            raise ValueError("The SWAN executable was not set.")
-        # check if windows OS
-        is_win = sys.platform.startswith("win")
-        if is_win:
-            cmd = "cd {0} && {1} input".format(case_dir, self.swan_exec)
-        else:
-            cmd = "cd {0} && {1} -input input.sws".format(case_dir, self.swan_exec)
-        # redirect output
-        cmd += f" 2>&1 > {log_file}"
-        # execute command
-        self._exec_bash_commands(str_cmd=cmd)
+        self.set_logger_name(
+            name=self.__class__.__name__, level="DEBUG" if debug else "INFO"
+        )

…ath_tk/wrappers/cgwave/cgwave_wrapper.py …ath_tk/wrappers/sfincs/sfincs_wrapper.pybluemath_tk/wrappers/cgwave/cgwave_wrapper.py renamed to bluemath_tk/wrappers/sfincs/sfincs_wrapper.py bluemath_tk/wrappers/cgwave/cgwave_wrapper.py renamed to bluemath_tk/wrappers/sfincs/sfincs_wrapper.py

@@ -92,18 +92,14 @@ def build_cases(
     model_parameters = mda.centroids.to_dict(orient="list")
     output_dir = "/home/tausiaj/GitHub-GeoOcean/BlueMath/test_cases/swash/"
     # Create an instance of the SWASH model wrapper
-    swash_model = VeggySwashModelWrapper(
+    swash_wrapper = VeggySwashModelWrapper(
         templates_dir=templates_dir,
         model_parameters=model_parameters,
         output_dir=output_dir,
     )
     # Build the input files
-    swash_model.build_cases(mode="one_by_one")
+    swash_wrapper.build_cases(mode="one_by_one")
     # List available launchers
-    print(swash_model.list_available_launchers())
-    # Set the SWASH executable (not used if docker is used)
-    swash_model.set_swash_exec(
-        "/home/tausiaj/GeoOcean-Execs/SWASH-10.05-Linux/bin/swashrun"
-    )
+    print(swash_wrapper.list_available_launchers())
     # Run the model
-    swash_model.run_cases(launcher="bash", parallel=True)
+    swash_wrapper.run_cases(launcher="bash", parallel=True)

bluemath_tk/wrappers/swan/swan_wrapper.py

@@ -22,13 +22,9 @@ class SwashModelWrapper(BaseModelWrapper):
         The available launchers for the wrapper.
     postprocess_functions : dict
         The postprocess functions for the wrapper.
-    swash_exec : str
-        The SWASH executable path.
 
     Methods
     -------
-    set_swash_exec -> None
-        Sets the SWASH executable path.
     list_available_postprocess_vars -> List[str]
         List available postprocess variables.
     _read_tabfile -> pd.DataFrame
@@ -94,14 +90,6 @@ def __init__(
         self.set_logger_name(
             name=self.__class__.__name__, level="DEBUG" if debug else "INFO"
         )
-        self._swash_exec: str = None
-
-    @property
-    def swash_exec(self) -> str:
-        return self._swash_exec
-
-    def set_swash_exec(self, swash_exec: str) -> None:
-        self._swash_exec = swash_exec
 
     def list_available_postprocess_vars(self) -> List[str]:
         """

bluemath_tk/wrappers/swash/swash_example.py

@@ -8,61 +8,39 @@ class XBeachModelWrapper(BaseModelWrapper):
 
     Attributes
     ----------
-    xbeach_exec : str
-        The XBeach executable path.
     default_parameters : dict
-        The default parameters type for the model.
-
-    Methods
-    -------
-    set_xbeach_exec(xbeach_exec: str) -> None
-        Set the XBeach executable path.
-    run_model() -> None
-        Run the XBeach model for the specified case.
+        The default parameters type for the wrapper.
+    available_launchers : dict
+        The available launchers for the wrapper.
     """
 
     default_parameters = {
         "spectra": str,
     }
 
+    available_launchers = {
+        "geoocean-cluster": "launchXbeach.sh",
+    }
+
     def __init__(
         self,
         templates_dir: str,
-        templates_name: dict,
         model_parameters: dict,
         output_dir: str,
+        templates_name: dict = "all",
+        debug: bool = True,
     ) -> None:
         """
         Initialize the SWASH model wrapper.
-
-        Parameters
-        ----------
-        templates_dir : str
-            The directory where the templates are stored.
-        templates_name : list
-            The names of the templates.
-        model_parameters : dict
-            The parameters to be used in the templates.
-        output_dir : str
-            The directory where the output files will be saved.
         """
 
         super().__init__(
             templates_dir=templates_dir,
-            templates_name=templates_name,
             model_parameters=model_parameters,
             output_dir=output_dir,
+            templates_name=templates_name,
             default_parameters=self.default_parameters,
         )
-        self.set_logger_name(self.__class__.__name__)
-        self._xbeach_exec = None
-
-    @property
-    def xbeach_exec(self) -> str:
-        return self._xbeach_exec
-
-    def set_xbeach_exec(self, xbeach_exec: str) -> None:
-        self._xbeach_exec = xbeach_exec
-
-    def run_model(self) -> None:
-        pass
+        self.set_logger_name(
+            name=self.__class__.__name__, level="DEBUG" if debug else "INFO"
+        )

bluemath_tk/wrappers/swash/swash_wrapper.py

@@ -0,0 +1 @@
+::: bluemath_tk.wrappers.delft3d.delft3d_wrapper