Mercurial > repos > goeckslab > ludwig_train

annotate ludwig_hyperopt.py @ 0:f0be10937f5c 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 22:44:09 +0000
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0
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
1 import logging
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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2 import os
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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3 import pickle
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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4 import sys
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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5
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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6 from ludwig.globals import (
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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7 HYPEROPT_STATISTICS_FILE_NAME,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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8 )
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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9 from ludwig.hyperopt_cli import cli
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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10 from ludwig.visualize import get_visualizations_registry
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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11
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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12 from model_unpickler import SafeUnpickler
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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13
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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14 from utils import (
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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15 encode_image_to_base64,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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16 get_html_closing,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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17 get_html_template
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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18 )
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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19
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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20 logging.basicConfig(level=logging.DEBUG)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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21
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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22 LOG = logging.getLogger(__name__)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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23
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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24 setattr(pickle, 'Unpickler', SafeUnpickler)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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26 cli(sys.argv[1:])
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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27
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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29 def generate_html_report(title):
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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30
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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31 # Read test statistics JSON and convert to HTML table
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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32 # try:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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33 # test_statistics_path = hyperopt_stats_path
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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34 # with open(test_statistics_path, "r") as f:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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35 # test_statistics = json.load(f)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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36 # test_statistics_html = "<h2>Hyperopt Statistics</h2>"
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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37 # test_statistics_html += json_to_html_table(test_statistics)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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38 # except Exception as e:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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39 # LOG.info(f"Error reading hyperopt statistics: {e}")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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40
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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41 plots_html = ""
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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42 # Convert visualizations to HTML
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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43 hyperopt_hiplot_path = os.path.join(
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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44 viz_output_directory, "hyperopt_hiplot.html")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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45 if os.path.isfile(hyperopt_hiplot_path):
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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46 with open(hyperopt_hiplot_path, "r", encoding="utf-8") as file:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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47 hyperopt_hiplot_html = file.read()
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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48 plots_html += f'<div class="hiplot">{hyperopt_hiplot_html}</div>'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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49 plots_html += "uid is the identifier for different hyperopt runs"
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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50 plots_html += "<br><br>"
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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51
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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52 # Iterate through other files in viz_output_directory
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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53 for plot_file in sorted(os.listdir(viz_output_directory)):
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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54 plot_path = os.path.join(viz_output_directory, plot_file)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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55 if os.path.isfile(plot_path) and plot_file.endswith((".png", ".jpg")):
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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56 encoded_image = encode_image_to_base64(plot_path)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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57 plots_html += (
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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58 f'<div class="plot">'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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59 f'<h3>{os.path.splitext(plot_file)[0]}</h3>'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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60 '<img src="data:image/png;base64,'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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61 f'{encoded_image}" alt="{plot_file}">'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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62 f'</div>'
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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63 )
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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64
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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65 # Generate the full HTML content
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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66 html_content = f"""
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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67 {get_html_template()}
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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68 <h1>{title}</h1>
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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69 <h2>Visualizations</h2>
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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70 {plots_html}
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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71 {get_html_closing()}
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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72 """
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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73
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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74 # Save the HTML report
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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75 report_name = title.lower().replace(" ", "_")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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76 report_path = os.path.join(output_directory, f"{report_name}_report.html")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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77 with open(report_path, "w") as report_file:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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78 report_file.write(html_content)
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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79
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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80 LOG.info(f"HTML report generated at: {report_path}")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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81
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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82
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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83 # visualization
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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84 output_directory = None
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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85 for ix, arg in enumerate(sys.argv):
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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86 if arg == "--output_directory":
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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87 output_directory = sys.argv[ix+1]
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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88 break
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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89
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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90 hyperopt_stats_path = os.path.join(
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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91 output_directory,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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92 "hyperopt", HYPEROPT_STATISTICS_FILE_NAME
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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93 )
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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parents:
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94
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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parents:
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95 visualizations = ["hyperopt_report", "hyperopt_hiplot"]
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
96
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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97 viz_output_directory = os.path.join(output_directory, "visualizations")
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
98 for viz in visualizations:
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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99 viz_func = get_visualizations_registry()[viz]
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
100 viz_func(
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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101 hyperopt_stats_path=hyperopt_stats_path,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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102 output_directory=viz_output_directory,
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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103 file_format="png",
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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104 )
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff changeset
105
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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106 # report
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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107 title = "Ludwig Hyperopt"
f0be10937f5c planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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108 generate_html_report(title)