comparison larch_select_paths.py @ 4:204c4afe2f1e draft default tip

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 4814f53888643f1d3667789050914675fffb7d59

3:1d08395c1a9f

class GDSWriter:
    def __init__(self, default_variables: "dict[str, dict]"):
        self.default_properties = {
            "s02": {"name": "s02"},
            "e0": {"name": "e0"},
            "deltar": {"name": "alpha*reff"},
            "sigma2": {"name": "sigma2"},
        }
        self.rows = [
            f"{'id':>4s}, {'name':>24s}, {'value':>5s}, {'expr':>4s}, "
            f"{'vary':>4s}\n"

        if formatted_name in self.names:
            raise ValueError(f"{formatted_name} already used as variable name")
        self.names.add(formatted_name)

        self.rows.append(
            f"{len(self.rows):4d}, {formatted_name:>24s}, {str(value):>5s}, "
            f"{expr:>4s}, {str(vary):>4s}\n"
        )

    def parse_gds(
        self,
        property_name: str,

class PathsWriter:
    def __init__(self, default_variables: "dict[str, dict]"):
        self.rows = [
            f"{'id':>4s}, {'filename':>24s}, {'label':>24s}, {'s02':>3s}, "
            f"{'e0':>4s}, {'sigma2':>24s}, {'deltar':>10s}\n"
        ]
        self.gds_writer = GDSWriter(default_variables=default_variables)
        self.all_combinations = [[0]]  # 0 corresponds to the header row

    def parse_feff_output(

    def parse_selected_path(
        self,
        filename: str,
        path_label: str,
        directory_label: str = "",
        s02: str = "s02",
        e0: str = "e0",
        sigma2: str = "sigma2",
        deltar: str = "alpha*reff",
    ) -> int:
        """Format and append row representing a selected FEFF path.

        Args:
            filename (str): Name of the underlying FEFF path file, without
                parent directory.
            path_label (str): Label indicating the atoms involved in this path.
            directory_label (str, optional): Label to indicate paths from a
                separate directory. Defaults to "".
            s02 (str, optional): Electron screening factor variable name.
                Defaults to "s02".
            e0 (str, optional): Energy shift variable name. Defaults to "e0".
            sigma2 (str, optional): Mean squared displacement variable name.
                Defaults to "sigma2".
            deltar (str, optional): Change in path length variable.
                Defaults to "alpha*reff".

        Returns:
            int: The id of the added row.
        """
        if directory_label:

            filename = os.path.join("feff", filename)
            label = path_label

        row_id = len(self.rows)
        self.rows.append(
            f"{row_id:>4d}, {filename:>24s}, {label:>24s}, "
            f"{s02:>3s}, {e0:>4s}, {sigma2:>24s}, {deltar:>10s}\n"
        )

        return row_id

    def write(self):

4:204c4afe2f1e

class GDSWriter:
    def __init__(self, default_variables: "dict[str, dict]"):
        self.default_properties = {
            "degen": {"name": "degen"},
            "s02": {"name": "s02"},
            "e0": {"name": "e0"},
            "deltar": {"name": "alpha"},
            "sigma2": {"name": "sigma2"},
        }
        self.rows = [
            f"{'id':>4s}, {'name':>24s}, {'value':>5s}, {'expr':>4s}, "
            f"{'vary':>4s}\n"

        if formatted_name in self.names:
            raise ValueError(f"{formatted_name} already used as variable name")
        self.names.add(formatted_name)

        if value is not None:
            formatted_value = str(value)
        else:
            formatted_value = ""

        self.rows.append(
            f"{len(self.rows):4d}, {formatted_name:>24s}, "
            f"{formatted_value:>5s}, {expr:>4s}, {str(vary):>4s}\n"
        )

    def parse_gds(
        self,
        property_name: str,

class PathsWriter:
    def __init__(self, default_variables: "dict[str, dict]"):
        self.rows = [
            f"{'id':>4s}, {'filename':>24s}, {'label':>24s}, {'degen':>5s}, "
            f"{'s02':>3s}, {'e0':>4s}, {'sigma2':>24s}, {'deltar':>10s}\n"
        ]
        self.gds_writer = GDSWriter(default_variables=default_variables)
        self.all_combinations = [[0]]  # 0 corresponds to the header row

    def parse_feff_output(

    def parse_selected_path(
        self,
        filename: str,
        path_label: str,
        directory_label: str = "",
        degen: str = "degen",
        s02: str = "s02",
        e0: str = "e0",
        sigma2: str = "sigma2",
        deltar: str = "alpha",
    ) -> int:
        """Format and append row representing a selected FEFF path.

        Args:
            filename (str): Name of the underlying FEFF path file, without
                parent directory.
            path_label (str): Label indicating the atoms involved in this path.
            directory_label (str, optional): Label to indicate paths from a
                separate directory. Defaults to "".
            degen (str, optional): Path degeneracy variable name.
                Defaults to "degen".
            s02 (str, optional): Electron screening factor variable name.
                Defaults to "s02".
            e0 (str, optional): Energy shift variable name. Defaults to "e0".
            sigma2 (str, optional): Mean squared displacement variable name.
                Defaults to "sigma2".
            deltar (str, optional): Change in path length variable.
                Defaults to "alpha".

        Returns:
            int: The id of the added row.
        """
        if directory_label:

            filename = os.path.join("feff", filename)
            label = path_label

        row_id = len(self.rows)
        self.rows.append(
            f"{row_id:>4d}, {filename:>24s}, {label:>24s}, {degen:>5s}, "
            f"{s02:>3s}, {e0:>4s}, {sigma2:>24s}, {deltar + '*reff':>10s}\n"
        )

        return row_id

    def write(self):