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annotate split_logic.py @ 3:25bb80df7c0c draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
author goeckslab
date Sat, 17 Jan 2026 22:53:42 +0000
parents 375c36923da1
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
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diff changeset
1 import logging
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
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2 from typing import List, Optional
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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3
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
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4 import numpy as np
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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5 import pandas as pd
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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6 from sklearn.model_selection import train_test_split
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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8 logger = logging.getLogger(__name__)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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9 SPLIT_COL = "split"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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12 def _can_stratify(y: pd.Series) -> bool:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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13 return y.nunique() >= 2 and (y.value_counts() >= 2).all()
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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14
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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16 def split_dataset(
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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17 train_dataset: pd.DataFrame,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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18 test_dataset: Optional[pd.DataFrame],
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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19 target_column: str,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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20 split_probabilities: List[float],
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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21 validation_size: float,
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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22 random_seed: int = 42,
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25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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23 sample_id_column: Optional[str] = None,
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375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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24 ) -> None:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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25 if target_column not in train_dataset.columns:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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26 raise ValueError(f"Target column '{target_column}' not found")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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27
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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28 # Drop NaN labels early
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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29 before = len(train_dataset)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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30 train_dataset.dropna(subset=[target_column], inplace=True)
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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31 if len(train_dataset) == 0:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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32 raise ValueError("No rows remain after dropping NaN targets")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
goeckslab
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33 if before != len(train_dataset):
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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34 logger.warning(f"Dropped {before - len(train_dataset)} rows with NaN target")
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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35 y = train_dataset[target_column]
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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36
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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37 if sample_id_column and sample_id_column not in train_dataset.columns:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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38 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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39 "Sample ID column '%s' not found; proceeding without group-aware split.",
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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40 sample_id_column,
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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41 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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42 sample_id_column = None
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
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43 if sample_id_column and sample_id_column == target_column:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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44 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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45 "Sample ID column '%s' matches target column; proceeding without group-aware split.",
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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46 sample_id_column,
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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47 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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48 sample_id_column = None
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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49
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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50 # Respect existing valid split column
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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51 if SPLIT_COL in train_dataset.columns:
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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52 unique = set(train_dataset[SPLIT_COL].dropna().unique())
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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53 valid = {"train", "val", "validation", "test"}
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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54 if unique.issubset(valid):
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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55 train_dataset[SPLIT_COL] = train_dataset[SPLIT_COL].replace("validation", "val")
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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56 normalized = set(train_dataset[SPLIT_COL].dropna().unique())
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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57 required = {"train"} if test_dataset is not None else {"train", "test"}
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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58 missing = required - normalized
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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59 if missing:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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60 missing_list = ", ".join(sorted(missing))
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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61 if test_dataset is not None:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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62 raise ValueError(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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63 "Pre-existing 'split' column is missing required split(s): "
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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64 f"{missing_list}. Expected at least train when an external test set is provided, "
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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65 "or remove the 'split' column to let the tool create splits."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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66 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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67 raise ValueError(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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68 "Pre-existing 'split' column is missing required split(s): "
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
goeckslab
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69 f"{missing_list}. Expected at least train and test, "
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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70 "or remove the 'split' column to let the tool create splits."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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71 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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72 logger.info(f"Using pre-existing 'split' column: {sorted(normalized)}")
0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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73 return
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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74
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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75 train_dataset[SPLIT_COL] = "train"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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76
3
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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77 def _allocate_split_counts(n_total: int, probs: list) -> list:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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78 if n_total <= 0:
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79 return [0 for _ in probs]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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80 counts = [0 for _ in probs]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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81 active = [i for i, p in enumerate(probs) if p > 0]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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82 remainder = n_total
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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83 if active and n_total >= len(active):
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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84 for i in active:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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85 counts[i] = 1
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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86 remainder -= len(active)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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87 if remainder > 0:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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88 probs_arr = np.array(probs, dtype=float)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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89 probs_arr = probs_arr / probs_arr.sum()
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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90 raw = remainder * probs_arr
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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91 floors = np.floor(raw).astype(int)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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92 for i, value in enumerate(floors.tolist()):
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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93 counts[i] += value
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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94 leftover = remainder - int(floors.sum())
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95 if leftover > 0 and active:
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96 frac = raw - floors
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97 order = sorted(active, key=lambda i: (-frac[i], i))
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98 for i in range(leftover):
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99 counts[order[i % len(order)]] += 1
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100 return counts
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101
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102 def _choose_split(counts: list, targets: list, active: list) -> int:
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103 remaining = [targets[i] - counts[i] for i in range(len(targets))]
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104 best = max(active, key=lambda i: (remaining[i], -counts[i], -targets[i]))
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105 if remaining[best] <= 0:
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106 best = min(active, key=lambda i: counts[i])
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107 return best
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108
0
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109 if test_dataset is not None:
3
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110 if sample_id_column and sample_id_column in test_dataset.columns:
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111 train_ids = set(train_dataset[sample_id_column].dropna().astype(object).unique())
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112 test_ids = set(test_dataset[sample_id_column].dropna().astype(object).unique())
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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113 overlap = train_ids & test_ids
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114 if overlap:
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115 logger.warning(
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116 "Sample ID column '%s' has %d overlapping IDs between train and external test sets; "
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117 "consider removing overlaps to avoid leakage.",
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118 sample_id_column,
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119 len(overlap),
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120 )
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121 if sample_id_column:
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122 rng = np.random.RandomState(random_seed)
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123 group_series = train_dataset[sample_id_column].astype(object)
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124 missing_mask = group_series.isna()
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125 if missing_mask.any():
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126 group_series = group_series.copy()
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127 group_series.loc[missing_mask] = [
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128 f"__missing__{idx}" for idx in group_series.index[missing_mask]
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129 ]
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130 group_to_indices = {}
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131 for idx, group_id in group_series.items():
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132 group_to_indices.setdefault(group_id, []).append(idx)
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133 group_ids = sorted(group_to_indices.keys(), key=lambda x: str(x))
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134 rng.shuffle(group_ids)
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135 targets = _allocate_split_counts(len(train_dataset), [1.0 - validation_size, validation_size])
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136 counts = [0, 0]
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137 active = [0, 1]
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138 train_idx = []
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139 val_idx = []
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140 for group_id in group_ids:
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141 split_idx = _choose_split(counts, targets, active)
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142 counts[split_idx] += len(group_to_indices[group_id])
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143 if split_idx == 0:
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144 train_idx.extend(group_to_indices[group_id])
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145 else:
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146 val_idx.extend(group_to_indices[group_id])
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147 train_dataset.loc[val_idx, SPLIT_COL] = "val"
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148 else:
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149 if validation_size <= 0:
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150 logger.warning(
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151 "validation_size is %.3f; skipping validation split to avoid train_test_split errors.",
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152 validation_size,
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153 )
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154 elif validation_size >= 1:
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155 logger.warning(
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156 "validation_size is %.3f; assigning all rows to validation to avoid train_test_split errors.",
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157 validation_size,
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158 )
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159 train_dataset[SPLIT_COL] = "val"
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160 else:
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161 stratify = y if _can_stratify(y) else None
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162 train_idx, val_idx = train_test_split(
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163 train_dataset.index, test_size=validation_size,
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164 random_state=random_seed, stratify=stratify
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165 )
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166 train_dataset.loc[val_idx, SPLIT_COL] = "val"
0
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167 logger.info(f"External test set → created val split ({validation_size:.0%})")
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168
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169 else:
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170 p_train, p_val, p_test = split_probabilities
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171 if abs(p_train + p_val + p_test - 1.0) > 1e-6:
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172 raise ValueError("split_probabilities must sum to 1.0")
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173
3
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174 if sample_id_column:
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175 rng = np.random.RandomState(random_seed)
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176 group_series = train_dataset[sample_id_column].astype(object)
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177 missing_mask = group_series.isna()
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178 if missing_mask.any():
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179 group_series = group_series.copy()
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180 group_series.loc[missing_mask] = [
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181 f"__missing__{idx}" for idx in group_series.index[missing_mask]
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182 ]
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183 group_to_indices = {}
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184 for idx, group_id in group_series.items():
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185 group_to_indices.setdefault(group_id, []).append(idx)
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186 group_ids = sorted(group_to_indices.keys(), key=lambda x: str(x))
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187 rng.shuffle(group_ids)
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188 targets = _allocate_split_counts(len(train_dataset), [p_train, p_val, p_test])
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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189 counts = [0, 0, 0]
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190 active = [0, 1, 2]
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191 train_idx = []
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192 val_idx = []
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193 test_idx = []
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194 for group_id in group_ids:
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195 split_idx = _choose_split(counts, targets, active)
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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196 counts[split_idx] += len(group_to_indices[group_id])
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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197 if split_idx == 0:
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198 train_idx.extend(group_to_indices[group_id])
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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199 elif split_idx == 1:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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200 val_idx.extend(group_to_indices[group_id])
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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201 else:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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202 test_idx.extend(group_to_indices[group_id])
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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203 train_dataset.loc[val_idx, SPLIT_COL] = "val"
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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204 train_dataset.loc[test_idx, SPLIT_COL] = "test"
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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205 else:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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206 stratify = y if _can_stratify(y) else None
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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207 if p_test <= 0:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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208 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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209 "split_probabilities specify 0 test size; skipping test split to avoid train_test_split errors."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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210 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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211 tv_idx = train_dataset.index
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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212 test_idx = train_dataset.index[:0]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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213 elif p_test >= 1:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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214 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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215 "split_probabilities specify 100% test size; assigning all rows to test to avoid train_test_split errors."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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216 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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217 tv_idx = train_dataset.index[:0]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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218 test_idx = train_dataset.index
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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219 else:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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220 tv_idx, test_idx = train_test_split(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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221 train_dataset.index, test_size=p_test,
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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222 random_state=random_seed, stratify=stratify
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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223 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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224 rel_val = p_val / (p_train + p_val) if (p_train + p_val) > 0 else 0
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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225 train_idx = train_dataset.index[:0]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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226 val_idx = train_dataset.index[:0]
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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227 if len(tv_idx):
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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228 if rel_val <= 0:
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229 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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230 "split_probabilities specify 0 validation size; skipping validation split to avoid train_test_split errors."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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231 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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232 train_idx = tv_idx
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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233 elif rel_val >= 1:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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234 logger.warning(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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235 "split_probabilities specify 100% validation size; assigning all remaining rows to validation "
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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236 "to avoid train_test_split errors."
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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237 )
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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238 val_idx = tv_idx
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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239 else:
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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240 strat_tv = y.loc[tv_idx] if _can_stratify(y.loc[tv_idx]) else None
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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241 train_idx, val_idx = train_test_split(
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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242 tv_idx, test_size=rel_val,
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243 random_state=random_seed, stratify=strat_tv
25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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244 )
0
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245
3
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246 train_dataset.loc[val_idx, SPLIT_COL] = "val"
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247 train_dataset.loc[test_idx, SPLIT_COL] = "test"
0
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248 logger.info(f"3-way split → train:{len(train_idx)}, val:{len(val_idx)}, test:{len(test_idx)}")
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249
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250 logger.info(f"Final split distribution:\n{train_dataset[SPLIT_COL].value_counts().sort_index()}")