orca-sdk 0.1.3__tar.gz → 0.1.5__tar.gz

{orca_sdk-0.1.3 → orca_sdk-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orca_sdk
-Version: 0.1.3
+Version: 0.1.5
 Summary: SDK for interacting with Orca Services
 License-Expression: Apache-2.0
 Author: Orca DB Inc.

{orca_sdk-0.1.3 → orca_sdk-0.1.5}/orca_sdk/_shared/metrics.py

@@ -9,7 +9,7 @@ IMPORTANT:
 """
 
 from dataclasses import dataclass
-from typing import Any, Literal, TypedDict, cast
+from typing import Any, Literal, Sequence, TypedDict, cast
 
 import numpy as np
 import sklearn.metrics
@@ -39,6 +39,66 @@ def transform_eval_pred(eval_pred: Any) -> tuple[NDArray, NDArray[np.float32]]:
     return (references, logits)
 
 
+def convert_to_float32_array(
+    data: (
+        Sequence[float | None]
+        | NDArray[np.float32]
+        | Sequence[Sequence[float]]
+        | Sequence[NDArray[np.float32]]
+        | NDArray[np.float32]
+    ),
+) -> NDArray[np.float32]:
+    """
+    Convert a list or array that may contain None values to a float32 numpy array.
+    None values are converted to NaN.
+
+    Args:
+        data: Input data that may contain None values
+
+    Returns:
+        A float32 numpy array with None values converted to NaN
+    """
+    array = np.array(data)
+    # Convert None values to NaN to handle missing values
+    if array.dtype == object:
+
+        def convert_value(x):
+            return np.nan if x is None else float(x)
+
+        array = np.vectorize(convert_value, otypes=[np.float32])(array)
+    else:
+        array = np.asarray(array, dtype=np.float32)
+    return cast(NDArray[np.float32], array)
+
+
+def calculate_anomaly_score_stats(
+    anomaly_scores: NDArray[np.float32] | Sequence[float] | None,
+) -> tuple[float | None, float | None, float | None]:
+    """
+    Calculate statistics (mean, median, variance) for anomaly scores.
+
+    Args:
+        anomaly_scores: Anomaly scores as a list, numpy array, or None
+
+    Returns:
+        A tuple of (mean, median, variance). All values are None if anomaly_scores is None.
+    """
+    if anomaly_scores is None:
+        return (None, None, None)
+
+    # Convert to numpy array if needed
+    if isinstance(anomaly_scores, list):
+        anomalies = np.array(anomaly_scores, dtype=np.float32)
+    else:
+        anomalies = anomaly_scores
+
+    return (
+        float(np.mean(anomalies)),
+        float(np.median(anomalies)),
+        float(np.var(anomalies)),
+    )
+
+
 class PRCurve(TypedDict):
     thresholds: list[float]
     precisions: list[float]
@@ -196,37 +256,93 @@ class ClassificationMetrics:
         )
 
 
-def calculate_classification_metrics(
-    expected_labels: list[int] | NDArray[np.int64],
-    logits: list[list[float]] | list[NDArray[np.float32]] | NDArray[np.float32],
-    anomaly_scores: list[float] | None = None,
-    average: Literal["micro", "macro", "weighted", "binary"] | None = None,
-    multi_class: Literal["ovr", "ovo"] = "ovr",
-    include_curves: bool = False,
-) -> ClassificationMetrics:
-    references = np.array(expected_labels)
+def convert_logits_to_probabilities(logits: NDArray[np.float32]) -> NDArray[np.float32]:
+    """
+    Convert logits to probability distributions.
+
+    This function handles multiple input formats:
+    - 1D arrays: Binary classification probabilities (must be between 0 and 1)
+    - 2D arrays: Multi-class logits or probabilities
+
+    For 2D inputs, the function automatically detects the format:
+    - If any values are <= 0: applies softmax (raw logits)
+    - If rows don't sum to 1: normalizes to probabilities
+    - If rows sum to 1: treats as already normalized probabilities
 
-    logits = np.array(logits)
+    Args:
+        logits: Input logits or probabilities as a float32 numpy array.
+            Can be 1D (binary) or 2D (multi-class). May contain NaN values.
+
+    Returns:
+        A 2D float32 numpy array of probabilities with shape (n_samples, n_classes).
+        Each row sums to 1.0 (except for rows with all NaN values).
+
+    Raises:
+        ValueError: If logits are not 1D or 2D
+        ValueError: If 1D logits are not between 0 and 1 (for binary classification)
+        ValueError: If 2D logits have fewer than 2 classes (use regression metrics instead)
+    """
     if logits.ndim == 1:
-        if (logits > 1).any() or (logits < 0).any():
+        # Binary classification: 1D probabilities
+        # Check non-NaN values only
+        valid_logits = logits[~np.isnan(logits)]
+        if len(valid_logits) > 0 and ((valid_logits > 1).any() or (valid_logits < 0).any()):
             raise ValueError("Logits must be between 0 and 1 for binary classification")
-        # convert 1D probabilities (binary) to 2D logits
-        logits = np.column_stack([1 - logits, logits])
-        probabilities = logits  # no need to convert to probabilities
+        # Convert 1D probabilities to 2D format: [1-p, p]
+        probabilities = cast(NDArray[np.float32], np.column_stack([1 - logits, logits]))
     elif logits.ndim == 2:
         if logits.shape[1] < 2:
             raise ValueError("Use a different metric function for regression tasks")
-        if not (logits > 0).all():
-            # convert logits to probabilities with softmax if necessary
-            probabilities = softmax(logits)
+        # Check if any non-NaN values are <= 0 (NaN-aware comparison)
+        valid_logits = logits[~np.isnan(logits)]
+        if len(valid_logits) > 0 and not (valid_logits > 0).all():
+            # Contains negative values or zeros: apply softmax (raw logits)
+            probabilities = cast(NDArray[np.float32], softmax(logits))
         elif not np.allclose(logits.sum(-1, keepdims=True), 1.0):
-            # convert logits to probabilities through normalization if necessary
-            probabilities = logits / logits.sum(-1, keepdims=True)
+            # Rows don't sum to 1: normalize to probabilities
+            probabilities = cast(NDArray[np.float32], logits / logits.sum(-1, keepdims=True))
         else:
+            # Already normalized probabilities
             probabilities = logits
     else:
         raise ValueError("Logits must be 1 or 2 dimensional")
 
+    return probabilities
+
+
+def calculate_classification_metrics(
+    expected_labels: list[int] | NDArray[np.int64],
+    logits: list[list[float]] | list[NDArray[np.float32]] | NDArray[np.float32],
+    anomaly_scores: list[float] | None = None,
+    average: Literal["micro", "macro", "weighted", "binary"] | None = None,
+    multi_class: Literal["ovr", "ovo"] = "ovr",
+    include_curves: bool = False,
+) -> ClassificationMetrics:
+    references = np.array(expected_labels)
+
+    # Convert to numpy array, handling None values
+    logits = convert_to_float32_array(logits)
+
+    # Check if all logits are NaN (all predictions are None/NaN)
+    if np.all(np.isnan(logits)):
+        # Return placeholder metrics when all logits are invalid
+        return ClassificationMetrics(
+            coverage=0.0,
+            f1_score=0.0,
+            accuracy=0.0,
+            loss=None,
+            anomaly_score_mean=None,
+            anomaly_score_median=None,
+            anomaly_score_variance=None,
+            roc_auc=None,
+            pr_auc=None,
+            pr_curve=None,
+            roc_curve=None,
+        )
+
+    # Convert logits to probabilities
+    probabilities = convert_logits_to_probabilities(logits)
+
     predictions = np.argmax(probabilities, axis=-1)
     predictions[np.isnan(probabilities).all(axis=-1)] = -1  # set predictions to -1 for all nan logits
 
@@ -238,10 +354,6 @@ def calculate_classification_metrics(
     if average is None:
         average = "binary" if num_classes_references == 2 and num_none_predictions == 0 else "weighted"
 
-    anomaly_score_mean = float(np.mean(anomaly_scores)) if anomaly_scores else None
-    anomaly_score_median = float(np.median(anomaly_scores)) if anomaly_scores else None
-    anomaly_score_variance = float(np.var(anomaly_scores)) if anomaly_scores else None
-
     accuracy = sklearn.metrics.accuracy_score(references, predictions)
     f1 = sklearn.metrics.f1_score(references, predictions, average=average)
     # Ensure sklearn sees the full class set corresponding to probability columns
@@ -259,10 +371,12 @@ def calculate_classification_metrics(
     if num_classes_references == num_classes_predictions and num_none_predictions == 0:
         # special case for binary classification: https://github.com/scikit-learn/scikit-learn/issues/20186
         if num_classes_references == 2:
-            roc_auc = sklearn.metrics.roc_auc_score(references, logits[:, 1])
-            roc_curve = calculate_roc_curve(references, logits[:, 1]) if include_curves else None
-            pr_auc = sklearn.metrics.average_precision_score(references, logits[:, 1])
-            pr_curve = calculate_pr_curve(references, logits[:, 1]) if include_curves else None
+            # Use probabilities[:, 1] which is guaranteed to be 2D
+            probabilities_positive = probabilities[:, 1]
+            roc_auc = sklearn.metrics.roc_auc_score(references, probabilities_positive)
+            roc_curve = calculate_roc_curve(references, probabilities_positive) if include_curves else None
+            pr_auc = sklearn.metrics.average_precision_score(references, probabilities_positive)
+            pr_curve = calculate_pr_curve(references, probabilities_positive) if include_curves else None
         else:
             roc_auc = sklearn.metrics.roc_auc_score(references, probabilities, multi_class=multi_class)
             roc_curve = None
@@ -274,6 +388,9 @@ def calculate_classification_metrics(
         pr_curve = None
         roc_curve = None
 
+    # Calculate anomaly score statistics
+    anomaly_score_mean, anomaly_score_median, anomaly_score_variance = calculate_anomaly_score_stats(anomaly_scores)
+
     return ClassificationMetrics(
         coverage=coverage,
         accuracy=float(accuracy),
@@ -337,9 +454,9 @@ class RegressionMetrics:
 
 
 def calculate_regression_metrics(
-    expected_scores: NDArray[np.float32] | list[float],
-    predicted_scores: NDArray[np.float32] | list[float],
-    anomaly_scores: list[float] | None = None,
+    expected_scores: NDArray[np.float32] | Sequence[float],
+    predicted_scores: NDArray[np.float32] | Sequence[float | None],
+    anomaly_scores: NDArray[np.float32] | Sequence[float] | None = None,
 ) -> RegressionMetrics:
     """
     Calculate regression metrics for model evaluation.
@@ -354,23 +471,42 @@ def calculate_regression_metrics(
 
     Raises:
         ValueError: If predictions and references have different lengths
+        ValueError: If expected_scores contains None or NaN values
     """
-    references = np.array(expected_scores)
-    predictions = np.array(predicted_scores)
+    # Convert to numpy arrays, handling None values
+    references = convert_to_float32_array(expected_scores)
+    predictions = convert_to_float32_array(predicted_scores)
 
     if len(predictions) != len(references):
         raise ValueError("Predictions and references must have the same length")
 
-    anomaly_score_mean = float(np.mean(anomaly_scores)) if anomaly_scores else None
-    anomaly_score_median = float(np.median(anomaly_scores)) if anomaly_scores else None
-    anomaly_score_variance = float(np.var(anomaly_scores)) if anomaly_scores else None
+    # Validate that all expected_scores are non-None and non-NaN
+    if np.any(np.isnan(references)):
+        raise ValueError("expected_scores must not contain None or NaN values")
+
+    # If all of the predictions are None or NaN, return None for all metrics
+    if np.all(np.isnan(predictions)):
+        anomaly_score_mean, anomaly_score_median, anomaly_score_variance = calculate_anomaly_score_stats(anomaly_scores)
+        return RegressionMetrics(
+            coverage=0.0,
+            mse=0.0,
+            rmse=0.0,
+            mae=0.0,
+            r2=0.0,
+            explained_variance=0.0,
+            loss=0.0,
+            anomaly_score_mean=anomaly_score_mean,
+            anomaly_score_median=anomaly_score_median,
+            anomaly_score_variance=anomaly_score_variance,
+        )
 
-    none_prediction_mask = np.isnan(predictions)
-    num_none_predictions = none_prediction_mask.sum()
+    # Filter out NaN values from predictions (expected_scores are already validated to be non-NaN)
+    valid_mask = ~np.isnan(predictions)
+    num_none_predictions = (~valid_mask).sum()
     coverage = 1 - num_none_predictions / len(predictions)
     if num_none_predictions > 0:
-        references = references[~none_prediction_mask]
-        predictions = predictions[~none_prediction_mask]
+        references = references[valid_mask]
+        predictions = predictions[valid_mask]
 
     # Calculate core regression metrics
     mse = float(sklearn.metrics.mean_squared_error(references, predictions))
@@ -379,6 +515,9 @@ def calculate_regression_metrics(
     r2 = float(sklearn.metrics.r2_score(references, predictions))
     explained_var = float(sklearn.metrics.explained_variance_score(references, predictions))
 
+    # Calculate anomaly score statistics
+    anomaly_score_mean, anomaly_score_median, anomaly_score_variance = calculate_anomaly_score_stats(anomaly_scores)
+
     return RegressionMetrics(
         coverage=coverage,
         mse=mse,

{orca_sdk-0.1.3 → orca_sdk-0.1.5}/orca_sdk/_shared/metrics_test.py

@@ -80,24 +80,36 @@ def test_multiclass_metrics_with_3_classes(
 def test_does_not_modify_logits_unless_necessary():
     logits = np.array([[0.1, 0.9], [0.2, 0.8], [0.7, 0.3], [0.8, 0.2]])
     expected_labels = [0, 1, 0, 1]
-    assert calculate_classification_metrics(expected_labels, logits).loss == sklearn.metrics.log_loss(
-        expected_labels, logits
+    loss = calculate_classification_metrics(expected_labels, logits).loss
+    assert loss is not None
+    assert np.allclose(
+        loss,
+        sklearn.metrics.log_loss(expected_labels, logits),
+        atol=1e-6,
     )
 
 
 def test_normalizes_logits_if_necessary():
     logits = np.array([[1.2, 3.9], [1.2, 5.8], [1.2, 2.7], [1.2, 1.3]])
     expected_labels = [0, 1, 0, 1]
-    assert calculate_classification_metrics(expected_labels, logits).loss == sklearn.metrics.log_loss(
-        expected_labels, logits / logits.sum(axis=1, keepdims=True)
+    loss = calculate_classification_metrics(expected_labels, logits).loss
+    assert loss is not None
+    assert np.allclose(
+        loss,
+        sklearn.metrics.log_loss(expected_labels, logits / logits.sum(axis=1, keepdims=True)),
+        atol=1e-6,
     )
 
 
 def test_softmaxes_logits_if_necessary():
     logits = np.array([[-1.2, 3.9], [1.2, -5.8], [1.2, 2.7], [1.2, 1.3]])
     expected_labels = [0, 1, 0, 1]
-    assert calculate_classification_metrics(expected_labels, logits).loss == sklearn.metrics.log_loss(
-        expected_labels, softmax(logits)
+    loss = calculate_classification_metrics(expected_labels, logits).loss
+    assert loss is not None
+    assert np.allclose(
+        loss,
+        sklearn.metrics.log_loss(expected_labels, softmax(logits)),
+        atol=1e-6,
     )
 
 
@@ -271,3 +283,84 @@ def test_regression_metrics_handles_nans():
     assert metrics.mae > 0.0
     assert 0.0 <= metrics.r2 <= 1.0
     assert 0.0 <= metrics.explained_variance <= 1.0
+
+
+def test_regression_metrics_handles_none_values():
+    # Test with lists containing None values
+    y_true = [1.0, 2.0, 3.0, 4.0, 5.0]
+    y_pred = [1.1, 1.9, None, 3.8, np.nan]
+
+    metrics = calculate_regression_metrics(y_true, y_pred)
+
+    # Coverage should be 0.6 (3 out of 5 predictions are valid)
+    # Positions with None/NaN predictions (indices 2 and 4) are filtered out
+    assert np.allclose(metrics.coverage, 0.6)
+
+    # Metrics should be calculated only on valid pairs (indices 0, 1, 3)
+    # Valid pairs: (1.0, 1.1), (2.0, 1.9), and (4.0, 3.8)
+    expected_mse = np.mean([(1.0 - 1.1) ** 2, (2.0 - 1.9) ** 2, (4.0 - 3.8) ** 2])
+    expected_mae = np.mean([abs(1.0 - 1.1), abs(2.0 - 1.9), abs(4.0 - 3.8)])
+
+    assert metrics.mse == pytest.approx(expected_mse)
+    assert metrics.mae == pytest.approx(expected_mae)
+    assert metrics.rmse == pytest.approx(np.sqrt(expected_mse))
+    assert 0.0 <= metrics.r2 <= 1.0
+    assert 0.0 <= metrics.explained_variance <= 1.0
+
+
+def test_regression_metrics_rejects_none_expected_scores():
+    # Test that None values in expected_scores are rejected
+    y_true = [1.0, 2.0, None, 4.0, 5.0]
+    y_pred = [1.1, 1.9, 3.2, 3.8, 5.1]
+
+    with pytest.raises(ValueError, match="expected_scores must not contain None or NaN values"):
+        calculate_regression_metrics(y_true, y_pred)
+
+
+def test_regression_metrics_rejects_nan_expected_scores():
+    # Test that NaN values in expected_scores are rejected
+    y_true = np.array([1.0, 2.0, np.nan, 4.0, 5.0], dtype=np.float32)
+    y_pred = np.array([1.1, 1.9, 3.2, 3.8, 5.1], dtype=np.float32)
+
+    with pytest.raises(ValueError, match="expected_scores must not contain None or NaN values"):
+        calculate_regression_metrics(y_true, y_pred)
+
+
+def test_regression_metrics_all_predictions_none():
+    # Test with all predictions being None
+    y_true = [1.0, 2.0, 3.0, 4.0, 5.0]
+    y_pred = [None, None, None, None, None]
+
+    metrics = calculate_regression_metrics(y_true, y_pred)
+
+    # When all predictions are None, coverage should be 0.0 and all metrics should be 0.0
+    assert metrics.coverage == 0.0
+    assert metrics.mse == 0.0
+    assert metrics.rmse == 0.0
+    assert metrics.mae == 0.0
+    assert metrics.r2 == 0.0
+    assert metrics.explained_variance == 0.0
+    assert metrics.loss == 0.0
+    assert metrics.anomaly_score_mean is None
+    assert metrics.anomaly_score_median is None
+    assert metrics.anomaly_score_variance is None
+
+
+def test_regression_metrics_all_predictions_nan():
+    # Test with all predictions being NaN
+    y_true = np.array([1.0, 2.0, 3.0, 4.0, 5.0], dtype=np.float32)
+    y_pred = np.array([np.nan, np.nan, np.nan, np.nan, np.nan], dtype=np.float32)
+
+    metrics = calculate_regression_metrics(y_true, y_pred)
+
+    # When all predictions are NaN, coverage should be 0.0 and all metrics should be 0.0
+    assert metrics.coverage == 0.0
+    assert metrics.mse == 0.0
+    assert metrics.rmse == 0.0
+    assert metrics.mae == 0.0
+    assert metrics.r2 == 0.0
+    assert metrics.explained_variance == 0.0
+    assert metrics.loss == 0.0
+    assert metrics.anomaly_score_mean is None
+    assert metrics.anomaly_score_median is None
+    assert metrics.anomaly_score_variance is None

{orca_sdk-0.1.3 → orca_sdk-0.1.5}/orca_sdk/_utils/data_parsing_test.py

@@ -33,7 +33,7 @@ def test_hf_dataset_from_torch_dict():
     # Then the HF dataset should be created successfully
     assert isinstance(hf_dataset, Dataset)
     assert len(hf_dataset) == len(dataset)
-    assert set(hf_dataset.column_names) == {"value", "label", "key", "score", "source_id"}
+    assert set(hf_dataset.column_names) == {"value", "label", "key", "score", "source_id", "partition_id"}
 
 
 class PytorchTupleDataset(TorchDataset):