muspinsim_config: build_file.py annotate

annotate build_file.py @ 0:c70012022f0f draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4

author	muon-spectroscopy-computational-project
date	Thu, 25 Aug 2022 16:16:47 +0000
parents
children	331d0776abb4

rev	line source
0 c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	1 import json
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	2 import re
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	3 import sys
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	4
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	5 from muspinsim import MuSpinInput
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	6
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	7
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	8 def write_file(file_name, content):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	9 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	10 Write muspinsim file
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	11 :param file_name: name of file
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	12 :param content: list of strings containing blocks to write
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	13 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	14 with open(file_name, "w") as f:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	15 f.write(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	16 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	17 #######################################################
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	18 #Muspinsim Input File
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	19 #Generated using Muon Galaxy Tool Muspinsim_Input
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	20 #######################################################\n\n"""
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	21 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	22 f.write("".join(content))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	23
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	24
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	25 def build_block(title, vals):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	26 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	27 Build keyword block
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	28 :param title: string - Keyword
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	29 :param vals: list of strings - lines containing values for keyword
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	30 :return: A string containing formatted keyword block
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	31 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	32 return "{0}\n {1}\n".format(title, "\n ".join(vals))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	33
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	34
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	35 def format_entry(entry):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	36 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	37 Helper function to remove whitespace between function parameters
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	38 and remove ',' or ';' inbetween parameters
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	39 :param entry: string - user entry
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	40 :return: string containing only valid parameters
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	41 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	42 stck = []
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	43 new_str = ""
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	44 for i, char in enumerate(entry):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	45 if char == "(":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	46 stck.append(i)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	47 elif char == ")":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	48 if len(stck) == 0:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	49 raise ValueError(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	50 "Could not parse entry {0}"
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	51 "brackets mismatch - unexpected ')' "
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	52 "found on char {1}".format(entry, i)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	53 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	54 stck.pop()
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	55 elif char == " " and len(stck) > 0:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	56 continue
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	57
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	58 # remove ',' between functions
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	59 elif char in [",", ";"] and len(stck) == 0:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	60 new_str += " "
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	61 continue
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	62 new_str += char
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	63
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	64 if len(stck) != 0:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	65 raise ValueError(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	66 "Could not parse entry {0}"
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	67 "brackets mismatch - unclosed '(' found on char(s): {1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	68 entry, stck
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	69 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	70 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	71 return new_str
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	72
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	73
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	74 def split_into_args(entry, nargs=1):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	75 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	76 Helper function to split input into a list of args
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	77 :param entry: a string containing a user inputted line
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	78 :param nargs: number of expected arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	79 :return: a list of arguments found
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	80 :exception: ValueError - if number of arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	81 found does not match expected (nargs)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	82 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	83
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	84 # remove square brackets and extra whitespace/newline
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	85 content = " ".join(entry.replace("[", "").replace("]", "").split())
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	86
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	87 # remove whitespace in between expressions/functions
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	88 # remove commas/semicolons in between expressions/functions
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	89 # split on whitespace to separate args
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	90
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	91 content = re.split(r"\s", format_entry(content))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	92 chars = [elem.strip() for elem in content if elem != ""]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	93 if len(chars) != nargs:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	94 raise ValueError(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	95 "Could not parse entry {0}"
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	96 " incorrect number of args"
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	97 " found {1}:\n({2})\nBut expected {3}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	98 entry, len(chars), chars, nargs
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	99 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	100 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	101 return chars
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	102
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	103
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	104 def parse_matrix(entry_string, size):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	105 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	106 Helper function to parse and format matrix/vector
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	107 to be readable by Muspinsim
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	108 :param entry_string: a user input string for a matrix/vector
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	109 :param size: (x, y) integer tuple: dimensions of matrix
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	110 :return: a list of strings of length y, each string
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	111 containing x elements (space separated)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	112 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	113 content = split_into_args(entry_string, nargs=size[0] * size[1])
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	114 return [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	115 " ".join(content[x: x + size[0]])
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	116 for x in range(0, len(content), size[0])
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	117 ]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	118
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	119
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	120 def parse_interactions(interaction):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	121 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	122 Helper function to build keyword blocks for all
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	123 interaction parameters entered
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	124 (hyperfine, zeeman, dipolar, quadrupolar and dissipation)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	125
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	126 :param interaction: a dictionary containing all interaction parameters
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	127 :return: a string containing several formatted blocks
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	128 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	129
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	130 options = interaction["interaction_options"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	131 interaction_type = options["interaction"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	132 try:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	133 return {
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	134 "zeeman": lambda options: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	135 "zeeman {0}".format(options["zeeman_index"]),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	136 parse_matrix(options["zeeman_vector"], (3, 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	137 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	138 "hyperfine": lambda options: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	139 "hyperfine {0} {1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	140 options["hfine_index"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	141 options["hfine_e_index"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	142 if options["hfine_e_index"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	143 else "",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	144 ).strip(),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	145 parse_matrix(options["hfine_matrix"], (3, 3)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	146 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	147 "dipolar": lambda options: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	148 "dipolar {0} {1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	149 options["di_index"], options["di_index_2"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	150 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	151 parse_matrix(options["di_vector"], (3, 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	152 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	153 "quadrupolar": lambda options: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	154 "quadrupolar {0}".format(options["quad_index"]),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	155 parse_matrix(options["quad_matrix"], (3, 3)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	156 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	157 "dissipation": lambda options: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	158 "dissipation {0}".format(options["dis_index"]),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	159 [options["dis_val"]],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	160 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	161 }.get(interaction_type)(options)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	162 except ValueError as e:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	163 raise ValueError("Error occurred when parsing {0}".format(e))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	164
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	165
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	166 def parse_orientation(orientation):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	167 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	168 Helper function to parse orientation keyword arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	169 :param orientation: a dictionary containing one set of
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	170 orientation arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	171 :return: a formatted string
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	172 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	173
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	174 options = orientation["orientation_options"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	175 preset = options["orientation_preset"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	176
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	177 return {
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	178 "zcw": lambda options: "zcw({0})".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	179 " ".join(split_into_args(options["zcw_n"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	180 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	181 "eulrange": lambda options: "eulrange({0})".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	182 " ".join(split_into_args(options["eul_n"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	183 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	184 "2_polar": lambda options: "{0} {1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	185 " ".join(split_into_args(options["theta"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	186 " ".join(split_into_args(options["phi"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	187 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	188 "3_euler": lambda options: "{0} {1} {2}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	189 " ".join(split_into_args(options["eul_1"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	190 " ".join(split_into_args(options["eul_2"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	191 " ".join(split_into_args(options["eul_3"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	192 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	193 "4_euler": lambda options: "{0} {1} {2} {3}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	194 " ".join(split_into_args(options["eul_1"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	195 " ".join(split_into_args(options["eul_2"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	196 " ".join(split_into_args(options["eul_3"], 1)),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	197 options["weight"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	198 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	199 }.get(preset)(options)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	200
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	201
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	202 def parse_polarization(polarization):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	203 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	204 Helper function to parse polarization keyword arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	205 :param polarization: a dictionary containing one set
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	206 of polarization arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	207 :return: a formatted string
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	208 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	209 options = polarization["polarization_options"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	210 preset = options["polarization_preset"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	211 if preset != "custom":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	212 return preset
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	213 else:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	214 try:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	215 return " ".join(split_into_args(options["polarization"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	216 except ValueError:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	217 return " ".join(split_into_args(options["polarization"], 3))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	218
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	219
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	220 def parse_field(field):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	221 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	222 Helper function to parse field keyword arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	223 :param field: a dictionary containing one set of field arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	224 :return: a formatted string
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	225 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	226 try:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	227 return " ".join(split_into_args(field["field"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	228 except ValueError:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	229 return " ".join(split_into_args(field["field"], 3))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	230
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	231
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	232 def parse_fitting_variables(fitting_variables):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	233 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	234 Helper function to parse field keyword fitting_variables
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	235 :param fitting_variables: a dictionary containing one set of
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	236 arguments
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	237 :return: a formatted string
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	238 """
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	239 return "{0} {1} {2} {3}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	240 fitting_variables["var_name"].strip().replace(" ", "_"),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	241 " ".join(split_into_args(fitting_variables["start_val"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	242 if fitting_variables["start_val"].strip() != ""
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	243 else "",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	244 " ".join(split_into_args(fitting_variables["min_bound"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	245 if fitting_variables["min_bound"].strip() != ""
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	246 else "",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	247 " ".join(split_into_args(fitting_variables["max_bound"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	248 if fitting_variables["max_bound"].strip() != ""
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	249 else "",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	250 ).strip()
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	251
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	252
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	253 def parse_spin(spin):
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	254 if spin["spin_preset"] != "custom":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	255 return spin["spin_preset"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	256 else:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	257 elem_name = spin["spin"].strip()
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	258 if elem_name not in ['e', 'mu']:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	259 elem_name = elem_name.capitalize()
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	260 return "{0}{1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	261 int(spin["atomic_mass"]) if spin["atomic_mass"] else "",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	262 elem_name
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	263 ).strip()
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	264
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	265
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	266 parse_func_dict = {
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	267 "spins": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	268 "spins",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	269 [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	270 " ".join(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	271 [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	272 parse_spin(entry["spin_options"])
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	273 for entry in values
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	274 ]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	275 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	276 ],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	277 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	278 # either 1x3 vector or scalar or function
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	279 "fields": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	280 "field", [parse_field(entry) for entry in values]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	281 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	282 # either scalar or single function
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	283 "times": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	284 "time",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	285 [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	286 " ".join(split_into_args(entry["time"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	287 for entry in values
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	288 ],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	289 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	290 # either scalar or single function
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	291 "temperatures": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	292 "temperature",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	293 [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	294 " ".join(split_into_args(entry["temperature"], 1))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	295 for entry in values
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	296 ],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	297 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	298 "x_axis": lambda value: build_block("x_axis", [value]),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	299 "y_axis": lambda value: build_block("y_axis", [value]),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	300 "average_axes": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	301 "average_axes", values
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	302 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	303 "experiment_preset": lambda value: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	304 "experiment", [value]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	305 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	306 "orientations": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	307 "orientation {0}".format(euler_convention),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	308 [parse_orientation(entry) for entry in values],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	309 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	310 "interactions": lambda values: "".join(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	311 [parse_interactions(entry) for entry in values]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	312 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	313 "polarizations": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	314 "polarization",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	315 [parse_polarization(entry) for entry in values],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	316 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	317 "fitting": lambda value: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	318 "fitting_data", ['load("fitting_data.dat")']
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	319 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	320 "fitting_method": lambda value: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	321 "fitting_method", [value]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	322 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	323 "fitting_variables": lambda values: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	324 "fitting_variables",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	325 [parse_fitting_variables(entry) for entry in values],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	326 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	327 "fitting_tolerance": lambda value: build_block(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	328 "fitting_tolerance",
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	329 [str(value)],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	330 ),
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	331 }
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	332 euler_convention = 'ZYZ'
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	333
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	334
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	335 def main():
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	336 input_json_path = sys.argv[1]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	337 mu_params = json.load(open(input_json_path, "r"))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	338
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	339 out_file_name = mu_params["out_file_prefix"].strip().replace(" ", "_")
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	340
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	341 # combine all sections
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	342 mu_params = {
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	343 **mu_params["spins"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	344 **mu_params["interaction_params"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	345 **mu_params["experiment_params"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	346 **mu_params["fitting_params"]["fitting_options"],
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	347 }
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	348
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	349 # get experiment parameters
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	350 experiment = mu_params["experiment"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	351 mu_params = {mu_params, experiment}
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	352
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	353 if experiment["experiment_preset"] == "custom":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	354 del mu_params["experiment_preset"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	355 del mu_params["experiment"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	356
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	357 global euler_convention
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	358 euler_convention = mu_params["euler_convention"]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	359
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	360 err_found = False
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	361 file_contents = [
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	362 build_block("name", [out_file_name.strip().replace(" ", "_")])
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	363 ]
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	364 for keyword, val in mu_params.items():
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	365 if val and val not in ["None"]:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	366 try:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	367 keyword_func = parse_func_dict.get(keyword)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	368 if keyword_func:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	369 file_contents.append(keyword_func(val))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	370
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	371 except ValueError as e:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	372 sys.stderr.write(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	373 "Error occurred when parsing {0}\n{1}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	374 keyword, str(e)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	375 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	376 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	377 err_found = True
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	378
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	379 if err_found:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	380 sys.exit(1)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	381
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	382 write_file("outfile.in", file_contents)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	383
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	384 try:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	385 MuSpinInput(open("outfile.in"))
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	386 except Exception as e:
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	387 sys.stdout.write(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	388 "Warning, This created file may not work properly. "
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	389 "Error(s) encountered when trying to parse the file : {0}".format(
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	390 str(e)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	391 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	392 )
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	393 sys.exit(1)
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	394
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	395
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	396 if __name__ == "__main__":
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	397 main()

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

annotate build_file.py @ 0:c70012022f0f draft