Mercurial > repos > sybila > ebcsgen_generate_transition_system

annotate ebcsgen_generate_ts.py @ 0:9e58089710ea draft

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
author sybila
date Fri, 09 Sep 2022 13:22:19 +0000
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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diff changeset
1 import argparse
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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3 from eBCSgen.Errors.ModelParsingError import ModelParsingError
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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4 from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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5 from eBCSgen.Parsing.ParseBCSL import Parser
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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7 import numpy as np
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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10 args_parser = argparse.ArgumentParser(description='Transition system generating')
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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12 args_parser._action_groups.pop()
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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13 required = args_parser.add_argument_group('required arguments')
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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14 optional = args_parser.add_argument_group('optional arguments')
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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16 required.add_argument('--model', type=str, required=True)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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17 required.add_argument('--output', type=str, required=True)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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18 required.add_argument('--direct', required=True)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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20 optional.add_argument('--max_time', type=float, default=np.inf)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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21 optional.add_argument('--max_size', type=float, default=np.inf)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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22 optional.add_argument('--bound', type=int, default=None)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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24 args = args_parser.parse_args()
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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26 model_parser = Parser("model")
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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27 model_str = open(args.model, "r").read()
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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29 model = model_parser.parse(model_str)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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30 if model.success:
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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31 if eval(args.direct):
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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32 ts = model.data.generate_direct_transition_system(args.max_time,
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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33 args.max_size,
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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34 args.bound)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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35 ts.change_to_vector_backend()
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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36 else:
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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37 vm = model.data.to_vector_model(args.bound)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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38 ts = vm.generate_transition_system(None, args.max_time, args.max_size)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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39 ts.save_to_json(args.output, model.data.params)
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
sybila
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40 else:
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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41 if "error" in model.data:
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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42 raise UnspecifiedParsingError(model.data["error"])
9e58089710ea planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit e26adecc1caf5c8fe966a5c891cc7941324d73bb
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43 raise ModelParsingError(model.data, model_str)