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annotate test.py @ 0:7cc026583189 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
author rv43
date Mon, 20 Mar 2023 17:54:33 +0000
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children 07647d52d7d3
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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1 #!/usr/bin/env python3
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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3 import logging
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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5 import sys
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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6 import argparse
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7 import numpy as np
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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9 def __main__():
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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11 # Parse command line arguments
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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12 parser = argparse.ArgumentParser(
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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13 description='Test')
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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14 parser.add_argument('-l', '--log',
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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15 type=argparse.FileType('w'),
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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16 default=sys.stdout,
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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17 help='Log file')
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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18 args = parser.parse_args()
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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20 # Set basic log configuration
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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21 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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22 log_level = 'INFO'
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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23 level = getattr(logging, log_level.upper(), None)
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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24 if not isinstance(level, int):
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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25 raise ValueError(f'Invalid log_level: {log_level}')
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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26 logging.basicConfig(format=logging_format, level=level, force=True,
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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27 handlers=[logging.StreamHandler()])
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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29 logging.info(f'log = {args.log}')
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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30 logging.info(f'is log stdout? {args.log is sys.stdout}')
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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32 if __name__ == "__main__":
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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33 __main__()
7cc026583189 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d
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