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annotate ebcsgen_generate_ts.py @ 0:3bdec3b22152 draft default tip

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
author sybila
date Fri, 09 Sep 2022 13:06:32 +0000
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
sybila
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diff changeset
1 import argparse
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3 from eBCSgen.Errors.ModelParsingError import ModelParsingError
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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4 from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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5 from eBCSgen.Parsing.ParseBCSL import Parser
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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6
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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7 import numpy as np
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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10 args_parser = argparse.ArgumentParser(description='Transition system generating')
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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12 args_parser._action_groups.pop()
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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13 required = args_parser.add_argument_group('required arguments')
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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14 optional = args_parser.add_argument_group('optional arguments')
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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16 required.add_argument('--model', type=str, required=True)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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17 required.add_argument('--output', type=str, required=True)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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18 required.add_argument('--direct', required=True)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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20 optional.add_argument('--max_time', type=float, default=np.inf)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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21 optional.add_argument('--max_size', type=float, default=np.inf)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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22 optional.add_argument('--bound', type=int, default=None)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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24 args = args_parser.parse_args()
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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26 model_parser = Parser("model")
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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27 model_str = open(args.model, "r").read()
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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29 model = model_parser.parse(model_str)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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30 if model.success:
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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31 if eval(args.direct):
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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32 ts = model.data.generate_direct_transition_system(args.max_time,
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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33 args.max_size,
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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34 args.bound)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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35 ts.change_to_vector_backend()
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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36 else:
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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37 vm = model.data.to_vector_model(args.bound)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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38 ts = vm.generate_transition_system(None, args.max_time, args.max_size)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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39 ts.save_to_json(args.output, model.data.params)
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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40 else:
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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41 if "error" in model.data:
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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42 raise UnspecifiedParsingError(model.data["error"])
3bdec3b22152 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
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43 raise ModelParsingError(model.data, model_str)