Mercurial > repos > goeckslab > multimodal_learner

annotate multimodal_learner.py @ 6:871957823d0c draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 6e49ad44dd8572382ee203926690a30d7e888203
author goeckslab
date Mon, 26 Jan 2026 18:44:07 +0000
parents 975512caae22
children
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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1 #!/usr/bin/env python
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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2 """
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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3 Main entrypoint for AutoGluon multimodal training wrapper.
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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4 """
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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5
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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6 import argparse
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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7 import logging
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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8 import os
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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9 import sys
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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10 from typing import List, Optional
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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11
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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12 import pandas as pd
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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13 from metrics_logic import aggregate_metrics
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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14 from plot_logic import infer_problem_type
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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15 from report_utils import write_outputs
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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16 from sklearn.model_selection import KFold, StratifiedKFold
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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17 from split_logic import split_dataset
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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18 from test_pipeline import run_autogluon_test_experiment
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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19 from training_pipeline import autogluon_hyperparameters, handle_missing_images, run_autogluon_experiment
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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20 # ------------------------------------------------------------------
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21 # Local imports (your split utilities)
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22 # ------------------------------------------------------------------
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23 from utils import (
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24 absolute_path_expander,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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25 enable_deterministic_mode,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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26 enable_tensor_cores_if_available,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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27 ensure_local_tmp,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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28 load_file,
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29 prepare_image_search_dirs,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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30 set_seeds,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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31 str2bool,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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32 )
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33
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34 # ------------------------------------------------------------------
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35 # Logger setup
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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36 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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37 logger = logging.getLogger(__name__)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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38
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39
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40 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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41 # Argument parsing (unchanged from your original, only minor fixes)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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42 # ------------------------------------------------------------------
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43 def parse_args(argv=None):
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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44 parser = argparse.ArgumentParser(description="Train & report an AutoGluon model")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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45
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46 parser.add_argument("--input_csv_train", dest="train_dataset", required=True)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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47 parser.add_argument("--input_csv_test", dest="test_dataset", default=None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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48 parser.add_argument("--target_column", required=True)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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49 parser.add_argument("--output_json", default="results.json")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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50 parser.add_argument("--output_html", default="report.html")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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51 parser.add_argument("--output_config", default=None)
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52 parser.add_argument("--images_zip", nargs="*", default=None,
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53 help="One or more ZIP files that contain image assets")
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54 parser.add_argument("--missing_image_strategy", default="false",
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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55 help="true/false: remove rows with missing images or use placeholder")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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56 parser.add_argument("--threshold", type=float, default=None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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57 parser.add_argument("--time_limit", type=int, default=None)
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58 parser.add_argument("--deterministic", action="store_true", default=False,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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59 help="Enable deterministic algorithms to reduce run-to-run variance")
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60 parser.add_argument("--random_seed", type=int, default=42)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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61 parser.add_argument("--cross_validation", type=str, default="false")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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62 parser.add_argument("--num_folds", type=int, default=5)
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63 parser.add_argument("--epochs", type=int, default=None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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64 parser.add_argument("--learning_rate", type=float, default=None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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65 parser.add_argument("--batch_size", type=int, default=None)
6
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66 parser.add_argument("--num_workers", type=int, default=None,
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67 help="DataLoader worker count (0 disables multiprocessing).")
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68 parser.add_argument("--num_workers_eval", type=int, default=None,
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69 help="DataLoader workers for evaluation; defaults to --num_workers.")
0
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70 parser.add_argument("--backbone_image", type=str, default="swin_base_patch4_window7_224")
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71 parser.add_argument("--backbone_text", type=str, default="microsoft/deberta-v3-base")
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72 parser.add_argument("--validation_size", type=float, default=0.2)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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73 parser.add_argument("--split_probabilities", type=float, nargs=3,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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74 default=[0.7, 0.1, 0.2], metavar=("train", "val", "test"))
3
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75 parser.add_argument("--sample_id_column", default=None)
0
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76 parser.add_argument("--preset", choices=["medium_quality", "high_quality", "best_quality"],
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77 default="medium_quality")
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78 parser.add_argument("--eval_metric", default="roc_auc")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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79 parser.add_argument("--hyperparameters", default=None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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80
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81 args, unknown = parser.parse_known_args(argv)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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82 if unknown:
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83 logger.warning("Ignoring unknown CLI tokens: %s", unknown)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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84
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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85 # -------------------------- Validation --------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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86 if not (0.0 <= args.validation_size <= 1.0):
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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87 parser.error("--validation_size must be in [0, 1]")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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88 if len(args.split_probabilities) != 3 or abs(sum(args.split_probabilities) - 1.0) > 1e-6:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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89 parser.error("--split_probabilities must be three numbers summing to 1.0")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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90 if args.cross_validation.lower() == "true" and (args.num_folds < 2):
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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91 parser.error("--num_folds must be >= 2 when --cross_validation is true")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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92
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93 return args
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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94
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95
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96 def run_cross_validation(
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97 args,
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98 df_full: pd.DataFrame,
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99 test_dataset: Optional[pd.DataFrame],
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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100 image_cols: List[str],
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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101 ag_config: dict,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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102 ):
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103 """Cross-validation loop returning aggregated metrics and last predictor."""
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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104 df_full = df_full.drop(columns=["split"], errors="ignore")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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105 y = df_full[args.target_column]
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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106 try:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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107 use_stratified = y.dtype == object or y.nunique() <= 20
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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108 except Exception:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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109 use_stratified = False
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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110
3
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111 if args.sample_id_column and args.sample_id_column in df_full.columns:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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112 groups = df_full[args.sample_id_column]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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113 if use_stratified:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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114 try:
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115 from sklearn.model_selection import StratifiedGroupKFold
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116
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117 kf = StratifiedGroupKFold(
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118 n_splits=int(args.num_folds),
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119 shuffle=True,
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120 random_state=int(args.random_seed),
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121 )
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122 except Exception as exc:
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123 logger.warning(
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124 "StratifiedGroupKFold unavailable (%s); falling back to GroupKFold.",
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125 exc,
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126 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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127 from sklearn.model_selection import GroupKFold
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128
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129 kf = GroupKFold(n_splits=int(args.num_folds))
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130 use_stratified = False
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131 else:
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132 from sklearn.model_selection import GroupKFold
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133
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134 kf = GroupKFold(n_splits=int(args.num_folds))
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135 else:
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136 kf = StratifiedKFold(n_splits=int(args.num_folds), shuffle=True, random_state=int(args.random_seed)) if use_stratified else KFold(n_splits=int(args.num_folds), shuffle=True, random_state=int(args.random_seed))
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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137
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138 if args.sample_id_column and test_dataset is not None:
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139 test_dataset = test_dataset.drop(columns=[args.sample_id_column], errors="ignore")
0
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140
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141 raw_folds = []
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142 ag_folds = []
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143 folds_info = []
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144 last_predictor = None
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145 last_data_ctx = None
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146
3
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147 if args.sample_id_column and args.sample_id_column in df_full.columns:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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148 split_iter = kf.split(df_full, y if use_stratified else None, groups)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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149 else:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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150 split_iter = kf.split(df_full, y if use_stratified else None)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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151
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152 for fold_idx, (train_idx, val_idx) in enumerate(split_iter, start=1):
0
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153 logger.info(f"CV fold {fold_idx}/{args.num_folds}")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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154 df_tr = df_full.iloc[train_idx].copy()
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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155 df_va = df_full.iloc[val_idx].copy()
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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156 if args.sample_id_column:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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157 df_tr = df_tr.drop(columns=[args.sample_id_column], errors="ignore")
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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158 df_va = df_va.drop(columns=[args.sample_id_column], errors="ignore")
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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159
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160 df_tr["split"] = "train"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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161 df_va["split"] = "val"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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162 fold_dataset = pd.concat([df_tr, df_va], ignore_index=True)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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163
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164 predictor_fold, data_ctx = run_autogluon_experiment(
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165 train_dataset=fold_dataset,
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166 test_dataset=test_dataset,
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167 target_column=args.target_column,
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168 image_columns=image_cols,
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169 ag_config=ag_config,
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170 )
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171 last_predictor = predictor_fold
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172 last_data_ctx = data_ctx
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173 problem_type = infer_problem_type(predictor_fold, df_tr, args.target_column)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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174 eval_results = run_autogluon_test_experiment(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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175 predictor=predictor_fold,
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176 data_ctx=data_ctx,
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177 target_column=args.target_column,
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178 eval_metric=args.eval_metric,
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179 ag_config=ag_config,
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180 problem_type=problem_type,
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181 )
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182
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183 raw_metrics_fold = eval_results.get("raw_metrics", {})
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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184 ag_by_split_fold = eval_results.get("ag_eval", {})
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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185 raw_folds.append(raw_metrics_fold)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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186 ag_folds.append(ag_by_split_fold)
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187 folds_info.append(
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188 {
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189 "fold": int(fold_idx),
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190 "predictor_path": getattr(predictor_fold, "path", None),
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191 "raw_metrics": raw_metrics_fold,
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192 "ag_eval": ag_by_split_fold,
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193 }
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194 )
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195
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196 raw_metrics_mean, raw_metrics_std = aggregate_metrics(raw_folds)
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197 ag_by_split_mean, ag_by_split_std = aggregate_metrics(ag_folds)
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198 return (
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199 last_predictor,
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200 raw_metrics_mean,
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201 ag_by_split_mean,
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202 raw_folds,
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203 ag_folds,
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204 raw_metrics_std,
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205 ag_by_split_std,
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206 folds_info,
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207 last_data_ctx,
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208 )
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209
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210
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211 # ------------------------------------------------------------------
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212 # Main execution
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213 # ------------------------------------------------------------------
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214 def main():
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215 args = parse_args()
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216
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217 # ------------------------------------------------------------------
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218 # Debug output
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219 # ------------------------------------------------------------------
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220 logger.info("=== AutoGluon Training Wrapper Started ===")
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221 logger.info(f"Working directory: {os.getcwd()}")
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222 logger.info(f"Command line: {' '.join(sys.argv)}")
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223 logger.info(f"Parsed args: {vars(args)}")
4
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224 logger.info("Cache dirs: TORCH_HOME=%s HF_HOME=%s HUGGINGFACE_HUB_CACHE=%s",
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225 os.environ.get("TORCH_HOME"),
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226 os.environ.get("HF_HOME"),
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227 os.environ.get("HUGGINGFACE_HUB_CACHE"))
0
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228
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229 # ------------------------------------------------------------------
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230 # Reproducibility & performance
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231 # ------------------------------------------------------------------
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232 set_seeds(args.random_seed)
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233 if args.deterministic:
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234 enable_deterministic_mode(args.random_seed)
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235 logger.info("Deterministic mode enabled (seed=%s)", args.random_seed)
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236 ensure_local_tmp()
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237 enable_tensor_cores_if_available()
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238
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239 # ------------------------------------------------------------------
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240 # Load datasets
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241 # ------------------------------------------------------------------
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242 train_dataset = load_file(args.train_dataset)
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243 test_dataset = load_file(args.test_dataset) if args.test_dataset else None
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244
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245 logger.info(f"Train dataset loaded: {len(train_dataset)} rows")
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246 if test_dataset is not None:
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247 logger.info(f"Test dataset loaded: {len(test_dataset)} rows")
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248
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249 # ------------------------------------------------------------------
5
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250 # Resolve columns by name; if Galaxy passed a numeric index,
0
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251 # translate it to the corresponding header so downstream checks pass.
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252 # Galaxy's data_column widget is 1-based.
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253 # ------------------------------------------------------------------
5
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254 def resolve_column_name(value, columns, label):
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255 if value is None:
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256 return None
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257 if str(value).isdigit():
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258 idx = int(value) - 1
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259 if 0 <= idx < len(columns):
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260 resolved = columns[idx]
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261 if value in columns:
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262 logger.warning(
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263 "%s column value '%s' matches a header, but Galaxy data_column "
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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264 "inputs are interpreted as 1-based indices; using column #%s header '%s'.",
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265 label,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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266 value,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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267 idx + 1,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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268 resolved,
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269 )
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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270 logger.info(
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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271 "%s column '%s' not found; using column #%s header '%s' instead.",
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272 label,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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273 value,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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274 idx + 1,
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275 resolved,
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276 )
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277 return resolved
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278 logger.error(
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279 "Numeric %s index '%s' is out of range for dataset with %s columns.",
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280 label.lower(),
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281 value,
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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282 len(columns),
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283 )
0
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284 sys.exit(1)
5
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285 return value
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286
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287 args.target_column = resolve_column_name(args.target_column, train_dataset.columns, "Target")
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288 args.sample_id_column = resolve_column_name(
975512caae22 planemo upload for repository https://github.com/goeckslab/gleam.git commit e984bd965d46c5f9ee5c3beb7429f3fd4a91ee35
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289 args.sample_id_column, train_dataset.columns, "Sample ID"
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diff changeset
290 )
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
291
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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292 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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293 # Image handling (ZIP extraction + absolute path expansion)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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294 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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295 extracted_imgs_path = prepare_image_search_dirs(args)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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296
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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297 image_cols = absolute_path_expander(train_dataset, extracted_imgs_path, None)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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298 if test_dataset is not None:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
299 absolute_path_expander(test_dataset, extracted_imgs_path, image_cols)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
300
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
301 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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302 # Handle missing images
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
303 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
304 train_dataset = handle_missing_images(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
305 train_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
306 image_columns=image_cols,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
307 strategy=args.missing_image_strategy,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
308 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
309 if test_dataset is not None:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
310 test_dataset = handle_missing_images(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
311 test_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
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diff changeset
312 image_columns=image_cols,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
313 strategy=args.missing_image_strategy,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
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314 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
315
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
316 logger.info(f"After cleanup → train: {len(train_dataset)}, test: {len(test_dataset) if test_dataset is not None else 0}")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
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317
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
318 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
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319 # Dataset splitting logic (adds 'split' column to train_dataset)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
320 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
321 split_dataset(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
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322 train_dataset=train_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
323 test_dataset=test_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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diff changeset
324 target_column=args.target_column,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
325 split_probabilities=args.split_probabilities,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
326 validation_size=args.validation_size,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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parents:
diff changeset
327 random_seed=args.random_seed,
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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parents: 0
diff changeset
328 sample_id_column=args.sample_id_column,
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
329 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
330
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
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diff changeset
331 logger.info("Preprocessing complete — ready for AutoGluon training!")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
332 logger.info(f"Final split counts:\n{train_dataset['split'].value_counts().sort_index()}")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
333
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
334 # Verify target/image/text columns exist
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
335 if args.target_column not in train_dataset.columns:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
336 logger.error(f"Target column '{args.target_column}' not found in training data.")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
337 sys.exit(1)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
338 if test_dataset is not None and args.target_column not in test_dataset.columns:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
339 logger.error(f"Target column '{args.target_column}' not found in test data.")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
340 sys.exit(1)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
341
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
342 # Threshold is only meaningful for binary classification; ignore otherwise.
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
343 threshold_for_run = args.threshold
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
344 unique_labels = None
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
345 target_looks_binary = False
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
346 try:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
347 unique_labels = train_dataset[args.target_column].nunique(dropna=True)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
348 target_looks_binary = unique_labels == 2
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
349 except Exception:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
350 logger.warning("Could not inspect target column '%s' for threshold validation; proceeding without binary check.", args.target_column)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
351
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
352 if threshold_for_run is not None:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
353 if target_looks_binary:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
354 threshold_for_run = float(threshold_for_run)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
355 logger.info("Applying custom decision threshold %.4f for binary evaluation.", threshold_for_run)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
356 else:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
357 logger.warning(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
358 "Threshold %.3f provided but target '%s' does not appear binary (unique labels=%s); ignoring threshold.",
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
359 threshold_for_run,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
360 args.target_column,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
361 unique_labels if unique_labels is not None else "unknown",
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
362 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
363 threshold_for_run = None
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
364 args.threshold = threshold_for_run
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
365 # Image columns are auto-inferred; image_cols already resolved to absolute paths.
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
366 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
367 # Build AutoGluon configuration from CLI knobs
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
368 # ------------------------------------------------------------------
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
369 ag_config = autogluon_hyperparameters(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
370 threshold=args.threshold,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
371 time_limit=args.time_limit,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
372 random_seed=args.random_seed,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
373 epochs=args.epochs,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
374 learning_rate=args.learning_rate,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
375 batch_size=args.batch_size,
6
871957823d0c planemo upload for repository https://github.com/goeckslab/gleam.git commit 6e49ad44dd8572382ee203926690a30d7e888203
goeckslab
parents: 5
diff changeset
376 num_workers=args.num_workers,
871957823d0c planemo upload for repository https://github.com/goeckslab/gleam.git commit 6e49ad44dd8572382ee203926690a30d7e888203
goeckslab
parents: 5
diff changeset
377 num_workers_evaluation=args.num_workers_eval,
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
378 backbone_image=args.backbone_image,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
379 backbone_text=args.backbone_text,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
380 preset=args.preset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
381 eval_metric=args.eval_metric,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
382 hyperparameters=args.hyperparameters,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
383 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
384 logger.info(f"AutoGluon config prepared: fit={ag_config.get('fit')}, hyperparameters keys={list(ag_config.get('hyperparameters', {}).keys())}")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
385
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
386 cv_enabled = str2bool(args.cross_validation)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
387 if cv_enabled:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
388 (
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
389 predictor,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
390 raw_metrics,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
391 ag_by_split,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
392 raw_folds,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
393 ag_folds,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
394 raw_metrics_std,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
395 ag_by_split_std,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
396 folds_info,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
397 data_ctx,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
398 ) = run_cross_validation(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
399 args=args,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
400 df_full=train_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
401 test_dataset=test_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
402 image_cols=image_cols,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
403 ag_config=ag_config,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
404 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
405 if predictor is None:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
406 logger.error("All CV folds failed. Exiting.")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
407 sys.exit(1)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
408 eval_results = {
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
409 "raw_metrics": raw_metrics,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
410 "ag_eval": ag_by_split,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
411 "fit_summary": None,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
412 }
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
413 else:
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
parents: 0
diff changeset
414 # Drop sample-id column before training so it does not leak into modeling.
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
parents: 0
diff changeset
415 if args.sample_id_column:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
parents: 0
diff changeset
416 train_dataset = train_dataset.drop(columns=[args.sample_id_column], errors="ignore")
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
parents: 0
diff changeset
417 if test_dataset is not None:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
parents: 0
diff changeset
418 test_dataset = test_dataset.drop(columns=[args.sample_id_column], errors="ignore")
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
419 predictor, data_ctx = run_autogluon_experiment(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
420 train_dataset=train_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
421 test_dataset=test_dataset,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
422 target_column=args.target_column,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
423 image_columns=image_cols,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
424 ag_config=ag_config,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
425 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
426 logger.info("AutoGluon training finished. Model path: %s", getattr(predictor, "path", None))
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
427
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
428 # Evaluate predictor on Train/Val/Test splits
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
429 problem_type = infer_problem_type(predictor, train_dataset, args.target_column)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
430 eval_results = run_autogluon_test_experiment(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
431 predictor=predictor,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
432 data_ctx=data_ctx,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
433 target_column=args.target_column,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
434 eval_metric=args.eval_metric,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
435 ag_config=ag_config,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
436 problem_type=problem_type,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
437 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
438 raw_metrics = eval_results.get("raw_metrics", {})
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
439 ag_by_split = eval_results.get("ag_eval", {})
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
440 raw_folds = ag_folds = raw_metrics_std = ag_by_split_std = None
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
441
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
442 logger.info("Transparent metrics by split: %s", eval_results["raw_metrics"])
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
443 logger.info("AutoGluon evaluate() by split: %s", eval_results["ag_eval"])
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
444
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
445 if "problem_type" in eval_results:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
446 problem_type_final = eval_results["problem_type"]
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
447 else:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
448 problem_type_final = infer_problem_type(predictor, train_dataset, args.target_column)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
449
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
450 write_outputs(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
451 args=args,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
452 predictor=predictor,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
453 problem_type=problem_type_final,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
454 eval_results=eval_results,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
455 data_ctx=data_ctx,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
456 raw_folds=raw_folds,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
457 ag_folds=ag_folds,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
458 raw_metrics_std=raw_metrics_std,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
459 ag_by_split_std=ag_by_split_std,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
460 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
461
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
462
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
463 if __name__ == "__main__":
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
464 logging.basicConfig(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
465 level=logging.INFO,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
466 format="%(asctime)s | %(levelname)s | %(message)s",
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
467 datefmt="%H:%M:%S"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
468 )
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
469 # Quiet noisy image parsing logs (e.g., PIL.PngImagePlugin debug streams)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
470 logging.getLogger("PIL").setLevel(logging.WARNING)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
471 logging.getLogger("PIL.PngImagePlugin").setLevel(logging.WARNING)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
parents:
diff changeset
472 main()