Restore PositiveDefinite link with deprecation warning

Author: han-ol

bayesflow/links/__init__.py

@@ -3,6 +3,7 @@
 from .ordered import Ordered
 from .ordered_quantiles import OrderedQuantiles
 from .cholesky_factor import CholeskyFactor
+from .positive_definite import PositiveDefinite
 
 from ..utils._docs import _add_imports_to_all
 

bayesflow/links/positive_definite.py

@@ -0,0 +1,53 @@
+import keras
+
+from bayesflow.types import Tensor
+from bayesflow.utils import layer_kwargs, fill_triangular_matrix
+from bayesflow.utils.serialization import serializable
+
+from warnings import warn
+
+
+@serializable("bayesflow.links")
+class PositiveDefinite(keras.Layer):
+    """Activation function to link from flat elements of a lower triangular matrix to a positive definite matrix."""
+
+    def __init__(self, **kwargs):
+        super().__init__(**layer_kwargs(kwargs))
+        self.built = True
+
+        warn(
+            "This class is deprecated. It was replaced by bayesflow.links.CholeskyFactor.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
+    def call(self, inputs: Tensor) -> Tensor:
+        # Build cholesky factor from inputs
+        L = fill_triangular_matrix(inputs, positive_diag=True)
+
+        # calculate positive definite matrix from cholesky factors
+        psd = keras.ops.matmul(
+            L,
+            keras.ops.moveaxis(L, -2, -1),  # L transposed
+        )
+        return psd
+
+    def compute_output_shape(self, input_shape):
+        m = input_shape[-1]
+        n = int((0.25 + 2.0 * m) ** 0.5 - 0.5)
+        return input_shape[:-1] + (n, n)
+
+    def compute_input_shape(self, output_shape):
+        """
+        Returns the shape of parameterization of a cholesky factor triangular matrix.
+
+        There are m nonzero elements of a lower triangular nxn matrix with m = n * (n + 1) / 2.
+
+        Example
+        -------
+        >>> PositiveDefinite().compute_output_shape((None, 3, 3))
+        6
+        """
+        n = output_shape[-1]
+        m = int(n * (n + 1) / 2)
+        return output_shape[:-2] + (m,)