larch_select_paths: larch_select

annotate larch_select_paths.py @ 0:2e827836f0ad draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735

author	muon-spectroscopy-computational-project
date	Tue, 14 Nov 2023 15:35:52 +0000
parents
children	7fdca938d90c

rev	line source
0 2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	1 import csv
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	2 import json
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	3 import os
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	4 import re
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	5 import sys
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	6 from zipfile import ZIP_DEFLATED, ZipFile
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	7
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	8
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	9 class GDSWriter:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	10 def __init__(self, default_variables: "dict[str, dict]"):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	11 self.default_properties = {
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	12 "s02": {"name": "s02"},
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	13 "e0": {"name": "e0"},
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	14 "deltar": {"name": "alpha*reff"},
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	15 "sigma2": {"name": "sigma2"},
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	16 }
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	17 self.rows = [
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	18 f"{'id':>4s}, {'name':>24s}, {'value':>5s}, {'expr':>4s}, "
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	19 f"{'vary':>4s}\n"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	20 ]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	21 self.names = set()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	22
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	23 for property in self.default_properties:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	24 name = self.default_properties[property]["name"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	25 value = default_variables[property]["value"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	26 vary = default_variables[property]["vary"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	27 is_common = default_variables[property]["is_common"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	28
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	29 self.default_properties[property]["value"] = value
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	30 self.default_properties[property]["vary"] = vary
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	31 self.default_properties[property]["is_common"] = is_common
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	32
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	33 if is_common:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	34 self.append_gds(name=name, value=value, vary=vary)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	35
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	36 def append_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	37 self,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	38 name: str,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	39 value: float = 0.,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	40 expr: str = None,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	41 vary: bool = True,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	42 label: str = "",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	43 ):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	44 """Append a single GDS variable to the list of rows, later to be
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	45 written to file.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	46
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	47 Args:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	48 name (str): Name of the GDS variable.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	49 value (float, optional): Starting value for variable.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	50 Defaults to 0.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	51 expr (str, optional): Expression for setting the variable.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	52 Defaults to None.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	53 vary (bool, optional): Whether the variable is optimised during the
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	54 fit. Defaults to True.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	55 label (str, optional): Label to keep variables for different FEFF
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	56 directories distinct. Defaults to "".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	57 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	58 formatted_name = name if (label is None) else label + name
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	59 formatted_name = formatted_name.replace("*reff", "")
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	60 if not expr:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	61 expr = " "
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	62
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	63 if formatted_name in self.names:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	64 raise ValueError(f"{formatted_name} already used as variable name")
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	65 self.names.add(formatted_name)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	66
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	67 self.rows.append(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	68 f"{len(self.rows):4d}, {formatted_name:>24s}, {str(value):>5s}, "
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	69 f"{expr:>4s}, {str(vary):>4s}\n"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	70 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	71
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	72 def parse_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	73 self,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	74 property_name: str,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	75 variable_name: str = None,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	76 path_variable: dict = None,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	77 directory_label: str = None,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	78 path_label: str = None,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	79 ) -> str:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	80 """Parse and append a row defining a GDS variable for a particular
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	81 path.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	82
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	83 Args:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	84 property_name (str): The property to which the variable
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	85 corresponds. Should be a key in `self.default_properties`.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	86 variable_name (str, optional): Custom name for this variable.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	87 Defaults to None.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	88 path_variable (dict, optional): Dictionary defining the GDS
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	89 settings for this path's variable. Defaults to None.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	90 directory_label (str, optional): Label to indicate paths from a
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	91 separate directory. Defaults to None.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	92 path_label (str, optional): Label indicating the atoms involved in
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	93 this path. Defaults to None.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	94
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	95 Returns:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	96 str: Either `variable_name`, the name used as a default globally
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	97 for this `property_name`, or an automatically generated unique
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	98 name.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	99 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	100 if variable_name:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	101 self.append_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	102 name=variable_name,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	103 value=path_variable["value"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	104 expr=path_variable["expr"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	105 vary=path_variable["vary"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	106 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	107 return variable_name
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	108 elif self.default_properties[property_name]["is_common"]:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	109 return self.default_properties[property_name]["name"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	110 else:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	111 auto_name = self.default_properties[property_name]["name"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	112 if directory_label:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	113 auto_name += f"_{directory_label}"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	114 if path_label:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	115 auto_name += f"_{path_label.lower().replace('.', '')}"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	116
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	117 self.append_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	118 name=auto_name,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	119 value=self.default_properties[property_name]["value"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	120 vary=self.default_properties[property_name]["vary"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	121 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	122 return auto_name
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	123
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	124 def write(self):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	125 """Write GDS rows to file.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	126 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	127 with open("gds.csv", "w") as out:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	128 out.writelines(self.rows)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	129
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	130
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	131 class PathsWriter:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	132 def __init__(self, default_variables: "dict[str, dict]"):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	133 self.rows = [
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	134 f"{'id':>4s}, {'filename':>24s}, {'label':>24s}, {'s02':>3s}, "
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	135 f"{'e0':>4s}, {'sigma2':>24s}, {'deltar':>10s}\n"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	136 ]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	137 self.gds_writer = GDSWriter(default_variables=default_variables)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	138
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	139 def parse_feff_output(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	140 self,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	141 paths_file: str,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	142 selection: "dict[str, str\|list]",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	143 directory_label: str = "",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	144 ):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	145 """Parse selected paths from CSV summary and define GDS variables.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	146
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	147 Args:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	148 paths_file (str): CSV summary filename.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	149 selection (dict[str, str\|list]): Dictionary indicating which paths
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	150 to select, and how to define their variables.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	151 directory_label (str, optional): Label to indicate paths from a
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	152 separate directory. Defaults to "".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	153 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	154 paths = selection["paths"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	155 path_values_ids = [path_value["id"] for path_value in paths]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	156
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	157 with open(paths_file) as file:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	158 reader = csv.reader(file)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	159 for row in reader:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	160 id_match = re.search(r"\d+", row[0])
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	161 if id_match:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	162 path_id = int(id_match.group())
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	163 filename = row[0].strip()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	164 path_label = row[-2].strip()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	165 variables = {}
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	166
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	167 if path_id in path_values_ids:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	168 path_value = paths[path_values_ids.index(path_id)]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	169 for property in self.gds_writer.default_properties:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	170 variables[property] = self.gds_writer.parse_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	171 property_name=property,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	172 variable_name=path_value[property]["name"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	173 path_variable=path_value[property],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	174 directory_label=directory_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	175 path_label=path_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	176 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	177 self.parse_selected_path(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	178 filename=filename,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	179 path_label=path_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	180 directory_label=directory_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	181 **variables,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	182 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	183 elif selection["selection"] == "all" or int(row[-1]):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	184 path_value = None
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	185 for property in self.gds_writer.default_properties:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	186 variables[property] = self.gds_writer.parse_gds(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	187 property_name=property,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	188 directory_label=directory_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	189 path_label=path_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	190 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	191 self.parse_selected_path(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	192 filename=filename,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	193 path_label=path_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	194 directory_label=directory_label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	195 **variables,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	196 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	197
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	198 def parse_selected_path(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	199 self,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	200 filename: str,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	201 path_label: str,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	202 directory_label: str = "",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	203 s02: str = "s02",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	204 e0: str = "e0",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	205 sigma2: str = "sigma2",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	206 deltar: str = "alpha*reff",
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	207 ):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	208 """Format and append row representing a selected FEFF path.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	209
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	210 Args:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	211 filename (str): Name of the underlying FEFF path file, without
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	212 parent directory.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	213 path_label (str): Label indicating the atoms involved in this path.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	214 directory_label (str, optional): Label to indicate paths from a
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	215 separate directory. Defaults to "".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	216 s02 (str, optional): Electron screening factor variable name.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	217 Defaults to "s02".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	218 e0 (str, optional): Energy shift variable name. Defaults to "e0".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	219 sigma2 (str, optional): Mean squared displacement variable name.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	220 Defaults to "sigma2".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	221 deltar (str, optional): Change in path length variable.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	222 Defaults to "alpha*reff".
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	223 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	224 if directory_label:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	225 filename = os.path.join(directory_label, filename)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	226 label = f"{directory_label}.{path_label}"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	227 else:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	228 filename = os.path.join("feff", filename)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	229 label = path_label
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	230
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	231 self.rows.append(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	232 f"{len(self.rows):>4d}, {filename:>24s}, {label:>24s}, "
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	233 f"{s02:>3s}, {e0:>4s}, {sigma2:>24s}, {deltar:>10s}\n"
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	234 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	235
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	236 def write(self):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	237 """Write selected path and GDS rows to file.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	238 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	239 self.gds_writer.write()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	240 with open("sp.csv", "w") as out:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	241 out.writelines(self.rows)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	242
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	243
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	244 def main(input_values: dict):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	245 """Select paths and define GDS parameters.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	246
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	247 Args:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	248 input_values (dict): All input values from the Galaxy tool UI.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	249
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	250 Raises:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	251 ValueError: If a FEFF label is not unique.
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	252 """
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	253 default_variables = input_values["variables"]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	254
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	255 writer = PathsWriter(default_variables=default_variables)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	256
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	257 if len(input_values["feff_outputs"]) == 1:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	258 feff_output = input_values["feff_outputs"][0]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	259 writer.parse_feff_output(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	260 paths_file=feff_output["paths_file"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	261 selection=feff_output["selection"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	262 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	263 else:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	264 zfill_length = len(str(len(input_values["feff_outputs"])))
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	265 labels = set()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	266 with ZipFile("merged.zip", "x", ZIP_DEFLATED) as zipfile_out:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	267 for i, feff_output in enumerate(input_values["feff_outputs"]):
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	268 label = feff_output.pop("label") or str(i + 1).zfill(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	269 zfill_length
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	270 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	271 if label in labels:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	272 raise ValueError(f"Label '{label}' is not unique")
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	273 labels.add(label)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	274
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	275 writer.parse_feff_output(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	276 directory_label=label,
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	277 paths_file=feff_output["paths_file"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	278 selection=feff_output["selection"],
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	279 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	280
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	281 with ZipFile(feff_output["paths_zip"]) as z:
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	282 for zipinfo in z.infolist():
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	283 if zipinfo.filename != "feff/":
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	284 zipinfo.filename = zipinfo.filename[5:]
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	285 z.extract(member=zipinfo, path=label)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	286 zipfile_out.write(
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	287 os.path.join(label, zipinfo.filename)
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	288 )
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	289
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	290 writer.write()
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	291
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	292
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	293 if __name__ == "__main__":
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	294 input_values = json.load(open(sys.argv[1], "r", encoding="utf-8"))
2e827836f0ad planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	295 main(input_values)

Mercurial > repos > muon-spectroscopy-computational-project > larch_select_paths

annotate larch_select_paths.py @ 0:2e827836f0ad draft