reformat docstring

src/odatse/_info.py

@@ -39,8 +39,10 @@ def __init__(self, d: Optional[MutableMapping] = None):
         """
         Initialize the Info object.
 
-        Parameters:
-        d (Optional[MutableMapping]): A dictionary to initialize the Info object.
+        Parameters
+        ----------
+        d : MutableMapping (optional)
+            A dictionary to initialize the Info object.
         """
         if d is not None:
             self.from_dict(d)
@@ -51,11 +53,15 @@ def from_dict(self, d: MutableMapping) -> None:
         """
         Initialize the Info object from a dictionary.
 
-        Parameters:
-        d (MutableMapping): A dictionary containing the information to initialize the Info object.
+        Parameters
+        ----------
+        d : MutableMapping
+            A dictionary containing the information to initialize the Info object.
 
-        Raises:
-        exception.InputError: If any required section is missing in the input dictionary.
+        Raises
+        ------
+        exception.InputError
+            If any required section is missing in the input dictionary.
         """
         for section in ["base", "algorithm", "solver"]:
             if section not in d:
@@ -92,16 +98,24 @@ def from_file(cls, file_name, fmt="", **kwargs):
         """
         Create an Info object from a file.
 
-        Parameters:
-        file_name (str): The name of the file to load the information from.
-        fmt (str): The format of the file (default is "").
-        **kwargs: Additional keyword arguments.
-
-        Returns:
-        Info: An Info object initialized with the data from the file.
-
-        Raises:
-        ValueError: If the file format is unsupported.
+        Parameters
+        ----------
+        file_name : str
+            The name of the file to load the information from.
+        fmt : str
+            The format of the file (default is "").
+        **kwargs
+            Additional keyword arguments.
+
+        Returns
+        -------
+        Info
+            An Info object initialized with the data from the file.
+
+        Raises
+        ------
+        ValueError
+            If the file format is unsupported.
         """
         if fmt == "toml" or fnmatch(file_name.lower(), "*.toml"):
             inp = {}
@@ -111,4 +125,4 @@ def from_file(cls, file_name, fmt="", **kwargs):
                 inp = mpi.comm().bcast(inp, root=0)
             return cls(inp)
         else:
-            raise ValueError("unsupported file format: {}".format(file_name))
+            raise ValueError("unsupported file format: {}".format(file_name))

src/odatse/_main.py

@@ -23,9 +23,9 @@
 
 def main():
     """
-        Main function to run the data-analysis software for quantum beam diffraction experiments
-        on 2D material structures. It parses command-line arguments, loads the input file,
-        selects the appropriate algorithm and solver, and executes the analysis.
+    Main function to run the data-analysis software for quantum beam diffraction experiments
+    on 2D material structures. It parses command-line arguments, loads the input file,
+    selects the appropriate algorithm and solver, and executes the analysis.
     """
     import argparse
 

src/odatse/algorithm/_algorithm.py

@@ -76,9 +76,14 @@ def __init__(
         """
         Initialize the algorithm with the given information and runner.
 
-        :param info: Information object containing algorithm and base parameters.
-        :param runner: Optional runner object to execute the algorithm.
-        :param run_mode: Mode in which the algorithm should run.
+        Parameters
+        ----------
+        info : Info
+            Information object containing algorithm and base parameters.
+        runner : Runner (optional)
+            Optional runner object to execute the algorithm.
+        run_mode : str
+            Mode in which the algorithm should run.
         """
         self.mpicomm = mpi.comm()
         self.mpisize = mpi.size()
@@ -132,7 +137,10 @@ def __init_rng(self, info: odatse.Info) -> None:
         """
         Initialize the random number generator.
 
-        :param info: Information object containing algorithm parameters.
+        Parameters
+        ----------
+        info : Info
+            Information object containing algorithm parameters.
         """
         seed = info.algorithm.get("seed", None)
         seed_delta = info.algorithm.get("seed_delta", 314159)
@@ -146,7 +154,10 @@ def set_runner(self, runner: odatse.Runner) -> None:
         """
         Set the runner for the algorithm.
 
-        :param runner: Runner object to execute the algorithm.
+        Parameters
+        ----------
+        runner : Runner
+            Runner object to execute the algorithm.
         """
         self.runner = runner
 
@@ -189,7 +200,10 @@ def post(self) -> Dict:
         """
         Perform post-processing after the algorithm has run.
 
-        :return: Dictionary containing post-processing results.
+        Returns
+        -------
+        Dict
+            Dictionary containing post-processing results.
         """
         if self.status < AlgorithmStatus.RUN:
             msg = "algorithm has not run yet"
@@ -237,7 +251,10 @@ def write_timer(self, filename: Path):
         """
         Write the timing information to a file.
 
-        :param filename: Path to the file where timing information will be written.
+        Parameters
+        ----------
+        filename : Path
+            Path to the file where timing information will be written.
         """
         with open(filename, "w") as fw:
             fw.write("#in units of seconds\n")
@@ -259,9 +276,14 @@ def _save_data(self, data, filename="state.pickle", ngen=3) -> None:
         """
         Save data to a file with versioning.
 
-        :param data: Data to be saved.
-        :param filename: Name of the file to save the data.
-        :param ngen: Number of generations for versioning.
+        Parameters
+        ----------
+        data
+            Data to be saved.
+        filename
+            Name of the file to save the data.
+        ngen : int, default: 3
+            Number of generations for versioning.
         """
         try:
             fn = Path(filename + ".tmp")
@@ -287,8 +309,15 @@ def _load_data(self, filename="state.pickle") -> Dict:
         """
         Load data from a file.
 
-        :param filename: Name of the file to load the data from.
-        :return: Dictionary containing the loaded data.
+        Parameters
+        ----------
+        filename
+            Name of the file to load the data from.
+
+        Returns
+        -------
+        Dict
+            Dictionary containing the loaded data.
         """
         if Path(filename).exists():
             try:
@@ -317,7 +346,10 @@ def _check_parameters(self, param=None):
         """
         Check the parameters of the algorithm against previous parameters.
 
-        :param param: Previous parameters to check against.
+        Parameters
+        ----------
+        param (optional)
+            Previous parameters to check against.
         """
         info = flatten_dict(self.info)
         info_prev = flatten_dict(param)
@@ -335,10 +367,19 @@ def flatten_dict(d, parent_key="", separator="."):
     """
     Flatten a nested dictionary.
 
-    :param d: Dictionary to flatten.
-    :param parent_key: Key for the parent dictionary.
-    :param separator: Separator to use between keys.
-    :return: Flattened dictionary.
+    Parameters
+    ----------
+    d
+        Dictionary to flatten.
+    parent_key : str, default : ""
+        Key for the parent dictionary.
+    separator : str, default : "."
+        Separator to use between keys.
+
+    Returns
+    -------
+    dict
+        Flattened dictionary.
     """
     items = []
     if d:
@@ -348,4 +389,4 @@ def flatten_dict(d, parent_key="", separator="."):
                 items.extend(flatten_dict(val, key, separator=separator).items())
             else:
                 items.append((key, val))
-    return dict(items)
+    return dict(items)

src/odatse/algorithm/mapper_mpi.py

@@ -40,10 +40,16 @@ def __init__(self, info: odatse.Info,
         """
         Initialize the Algorithm instance.
 
-        :param info: Information object containing algorithm parameters.
-        :param runner: Optional runner object for submitting tasks.
-        :param domain: Optional domain object, defaults to MeshGrid.
-        :param run_mode: Mode to run the algorithm, defaults to "initial".
+        Parameters
+        ----------
+        info : Info
+            Information object containing algorithm parameters.
+        runner : Runner
+            Optional runner object for submitting tasks.
+        domain :
+            Optional domain object, defaults to MeshGrid.
+        run_mode : str
+            Mode to run the algorithm, defaults to "initial".
         """
         super().__init__(info=info, runner=runner, run_mode=run_mode)
 
@@ -174,7 +180,10 @@ def _post(self) -> Dict:
         """
         Post-process the results and gather data from all MPI ranks.
 
-        :return: Dictionary of results.
+        Returns
+        -------
+        Dict
+            Dictionary of results.
         """
         if self.mpisize > 1:
             fx_lists = self.mpicomm.allgather(self.fx_list)
@@ -196,7 +205,10 @@ def _save_state(self, filename) -> None:
         """
         Save the current state of the algorithm to a file.
 
-        :param filename: The name of the file to save the state to.
+        Parameters
+        ----------
+        filename
+            The name of the file to save the state to.
         """
         data = {
             "mpisize": self.mpisize,
@@ -212,8 +224,12 @@ def _load_state(self, filename, restore_rng=True):
         """
         Load the state of the algorithm from a file.
 
-        :param filename: The name of the file to load the state from.
-        :param restore_rng: Whether to restore the random number generator state.
+        Parameters
+        ----------
+        filename
+            The name of the file to load the state from.
+        restore_rng : bool
+            Whether to restore the random number generator state.
         """
         data = self._load_data(filename)
         if not data:
@@ -230,4 +246,4 @@ def _load_state(self, filename, restore_rng=True):
 
         self.fx_list = data["fx_list"]
 
-        assert len(self.mesh_list) == data["mesh_size"]
+        assert len(self.mesh_list) == data["mesh_size"]

src/odatse/algorithm/min_search.py

@@ -60,10 +60,16 @@ def __init__(self, info: odatse.Info,
         """
         Initialize the Algorithm class.
 
-        :param info: Information object containing algorithm settings.
-        :param runner: Runner object for submitting jobs.
-        :param domain: Domain object defining the search space.
-        :param run_mode: Mode of running the algorithm.
+        Parameters
+        ----------
+        info : Info
+            Information object containing algorithm settings.
+        runner : Runner
+            Runner object for submitting jobs.
+        domain :
+            Domain object defining the search space.
+        run_mode : str
+            Mode of running the algorithm.
         """
         super().__init__(info=info, runner=runner, run_mode=run_mode)
 
@@ -132,9 +138,17 @@ def _f_calc(x_list: np.ndarray, iset) -> float:
             """
             Calculate the objective function value.
 
-            :param x_list: List of variables.
-            :param iset: Set index.
-            :return: Objective function value.
+            Parameters
+            ----------
+            x_list : np.ndarray
+                List of variables.
+            iset :
+                Set index.
+
+            Returns
+            -------
+            float
+                Objective function value.
             """
             # check if within region -> boundary option in minimize
             # note: 'bounds' option supported in scipy >= 1.7.0
@@ -259,4 +273,4 @@ def _post(self):
                     for x, y in zip(label_list, x0s[idx]):
                         fp.write(f"initial {x} = {y}\n")
 
-        return {"x": xs[idx], "fx": fxs[idx], "x0": x0s[idx]}
+        return {"x": xs[idx], "fx": fxs[idx], "x0": x0s[idx]}