Mercurial > repos > goeckslab > ludwig_evaluate

annotate ludwig_render_config.py @ 0:70a4d910f09a draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
author goeckslab
date Tue, 07 Jan 2025 22:46:16 +0000
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70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
1 import json
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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2 import logging
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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3 import sys
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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4
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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5 from ludwig.constants import (
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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6 COMBINER,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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7 HYPEROPT,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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8 INPUT_FEATURES,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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9 MODEL_TYPE,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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10 OUTPUT_FEATURES,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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11 PROC_COLUMN,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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12 TRAINER,
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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13 )
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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14 from ludwig.schema.model_types.utils import merge_with_defaults
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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15
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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16 import yaml
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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17
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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18 logging.basicConfig(level=logging.DEBUG)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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19 LOG = logging.getLogger(__name__)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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20 inputs = sys.argv[1]
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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21 with open(inputs, 'r') as handler:
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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22 params = json.load(handler)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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23
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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24 config = {}
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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25 # input features
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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26 config[INPUT_FEATURES] = []
70a4d910f09a 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']:
70a4d910f09a 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'])
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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29
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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30 # output features
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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31 config[OUTPUT_FEATURES] = []
70a4d910f09a 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']:
70a4d910f09a 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'])
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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34
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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35 # combiner
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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36 config[COMBINER] = params[COMBINER]
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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37
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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38 # training
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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39 config[TRAINER] = params[TRAINER][TRAINER]
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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40 config[MODEL_TYPE] = config[TRAINER].pop(MODEL_TYPE)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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41
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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42 # hyperopt
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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43 if params[HYPEROPT]['do_hyperopt'] == 'true':
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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44 config[HYPEROPT] = params[HYPEROPT][HYPEROPT]
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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45
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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46 with open('./pre_config.yml', 'w') as f:
70a4d910f09a 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)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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48
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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49 output = sys.argv[2]
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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50 output_config = merge_with_defaults(config)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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51
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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52
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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53 def clean_proc_column(config: dict) -> None:
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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54 for ftr in config[INPUT_FEATURES]:
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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55 ftr.pop(PROC_COLUMN, None)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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56 for ftr in config[OUTPUT_FEATURES]:
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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57 ftr.pop(PROC_COLUMN, None)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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58
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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59
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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60 clean_proc_column(output_config)
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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61
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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62 with open(output, "w") as f:
70a4d910f09a planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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63 yaml.safe_dump(output_config, f, sort_keys=False)