Mercurial > repos > goeckslab > ludwig_render_config

annotate ludwig_autogenconfig.py @ 4:e3c63770083d draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
author goeckslab
date Sat, 21 Jun 2025 15:04:30 +0000
parents ed8a9ea5bc73
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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diff changeset
1 import argparse
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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2 import logging
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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4 from ludwig import automl
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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5 from ludwig.utils import defaults
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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6 from pandas import read_csv
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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8 logging.basicConfig(level=logging.DEBUG)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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9 LOG = logging.getLogger(__name__)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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12 def main():
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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13 parser = argparse.ArgumentParser(
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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14 description='Render a Ludwig config')
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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15 parser.add_argument(
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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16 '--dataset',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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17 type=str,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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18 help='Path to the dataset file',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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19 required=True)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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20 parser.add_argument(
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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21 '--output_feature',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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22 type=int,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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23 help='Name for the output feature',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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24 required=True)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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25 parser.add_argument(
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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26 '--output',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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27 type=str,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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28 help='Path for the output file',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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29 required=True)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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30 parser.add_argument(
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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31 '--renderconfig',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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32 action='store_true',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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33 help='Render the config',
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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34 required=False,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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35 default=False)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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36 args = parser.parse_args()
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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37
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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38 # get the output feature name
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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39 df = read_csv(args.dataset, nrows=2, sep=None, engine='python')
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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40 names = df.columns.tolist()
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e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
goeckslab
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41 target = names[args.output_feature - 1]
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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42
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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43 args_init = ["--dataset", args.dataset,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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44 "--target", target,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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45 "--output", args.output]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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46 automl.cli_init_config(args_init)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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47
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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48 if args.renderconfig:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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49 args_render = ["--config", args.output, "--output", args.output]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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50 defaults.cli_render_config(args_render)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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51
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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52
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53 if __name__ == "__main__":
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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54 main()