Mercurial > repos > goeckslab > ludwig_render_config

annotate ludwig_render_config.py @ 6:dd663701df49 draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 59a0f37fed961b3ba4c55f8205e7cf4ebd551767
author goeckslab
date Sat, 06 Sep 2025 01:52:15 +0000
parents e3c63770083d
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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1 import json
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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3 import sys
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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4
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e3c63770083d planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 4dc221b2fa9717552787f0985ad3fc3df4460158
goeckslab
parents: 0
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5 import yaml
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ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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6 from ludwig.constants import (
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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7 COMBINER,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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8 HYPEROPT,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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9 INPUT_FEATURES,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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10 MODEL_TYPE,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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11 OUTPUT_FEATURES,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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12 PROC_COLUMN,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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13 TRAINER,
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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14 )
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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15 from ludwig.schema.model_types.utils import merge_with_defaults
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
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18 logging.basicConfig(level=logging.DEBUG)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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19 LOG = logging.getLogger(__name__)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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20 inputs = sys.argv[1]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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21 with open(inputs, 'r') as handler:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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22 params = json.load(handler)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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23
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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24 config = {}
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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25 # input features
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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26 config[INPUT_FEATURES] = []
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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27 for ftr in params[INPUT_FEATURES]['input_feature']:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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28 config[INPUT_FEATURES].append(ftr['input_feature_selector'])
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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30 # output features
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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31 config[OUTPUT_FEATURES] = []
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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32 for ftr in params[OUTPUT_FEATURES]['output_feature']:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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33 config[OUTPUT_FEATURES].append(ftr['output_feature_selector'])
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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35 # combiner
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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36 config[COMBINER] = params[COMBINER]
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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38 # training
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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39 config[TRAINER] = params[TRAINER][TRAINER]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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40 config[MODEL_TYPE] = config[TRAINER].pop(MODEL_TYPE)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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41
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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42 # hyperopt
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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43 if params[HYPEROPT]['do_hyperopt'] == 'true':
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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44 config[HYPEROPT] = params[HYPEROPT][HYPEROPT]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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45
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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46 with open('./pre_config.yml', 'w') as f:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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47 yaml.safe_dump(config, f, allow_unicode=True, default_flow_style=False)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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49 output = sys.argv[2]
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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50 output_config = merge_with_defaults(config)
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
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53 def clean_proc_column(config: dict) -> None:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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54 for ftr in config[INPUT_FEATURES]:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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55 ftr.pop(PROC_COLUMN, None)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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56 for ftr in config[OUTPUT_FEATURES]:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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57 ftr.pop(PROC_COLUMN, None)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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58
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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59
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60 clean_proc_column(output_config)
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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61
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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62 with open(output, "w") as f:
ed8a9ea5bc73 planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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63 yaml.safe_dump(output_config, f, sort_keys=False)