Merge origin/main into parameter-support-v2

Resolves conflicts from folder structure refactor (#63) and more tests (#62).
Moves scalar_mult/vector_mult to src/affine/ and test files to new
subdirectory structure. Updates affine.h declarations with parameter support
signatures.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Transurgeon

include/affine.h

@@ -41,6 +41,28 @@ expr *new_reshape(expr *child, int d1, int d2);
 expr *new_broadcast(expr *child, int target_d1, int target_d2);
 expr *new_diag_vec(expr *child);
 expr *new_transpose(expr *child);
-expr *new_diag_vec(expr *child);
+
+/* Left matrix multiplication: A @ f(x) where A is a constant or parameter
+ * sparse matrix. param_node is NULL for fixed constants. */
+expr *new_left_matmul(expr *param_node, expr *u, const CSR_Matrix *A);
+
+/* Left matrix multiplication: A @ f(x) where A is a constant or parameter
+ * dense matrix (row-major, m x n). Uses CBLAS for efficient computation. */
+expr *new_left_matmul_dense(expr *param_node, expr *u, int m, int n,
+                            const double *data);
+
+/* Right matrix multiplication: f(x) @ A where A is a constant or parameter
+ * matrix. */
+expr *new_right_matmul(expr *param_node, expr *u, const CSR_Matrix *A);
+
+expr *new_right_matmul_dense(expr *param_node, expr *u, int m, int n,
+                             const double *data);
+
+/* Scalar multiplication: a * f(x) where a comes from param_node */
+expr *new_scalar_mult(expr *param_node, expr *child);
+
+/* Vector elementwise multiplication: a . f(x) where a comes from
+ * param_node */
+expr *new_vector_mult(expr *param_node, expr *child);
 
 #endif /* AFFINE_H */

include/bivariate.h

@@ -18,38 +18,11 @@
 #ifndef BIVARIATE_H
 #define BIVARIATE_H
 
-#include "expr.h"
-
-expr *new_elementwise_mult(expr *left, expr *right);
-expr *new_rel_entr_vector_args(expr *left, expr *right);
-expr *new_quad_over_lin(expr *left, expr *right);
-
-expr *new_rel_entr_first_arg_scalar(expr *left, expr *right);
-expr *new_rel_entr_second_arg_scalar(expr *left, expr *right);
-
-/* Matrix multiplication: Z = X @ Y */
-expr *new_matmul(expr *x, expr *y);
-
-/* Left matrix multiplication: A @ f(x) where A is a constant or parameter
- * sparse matrix. param_node is NULL for fixed constants. */
-expr *new_left_matmul(expr *param_node, expr *u, const CSR_Matrix *A);
-
-/* Left matrix multiplication: A @ f(x) where A is a constant or parameter
- * dense matrix (row-major, m x n). Uses CBLAS for efficient computation. */
-expr *new_left_matmul_dense(expr *param_node, expr *u, int m, int n,
-                            const double *data);
-
-/* Right matrix multiplication: f(x) @ A where A is a constant or parameter
- * matrix. */
-expr *new_right_matmul(expr *param_node, expr *u, const CSR_Matrix *A);
-
-expr *new_right_matmul_dense(expr *param_node, expr *u, int m, int n,
-                             const double *data);
-
-/* Scalar multiplication: a * f(x) where a comes from param_node */
-expr *new_scalar_mult(expr *param_node, expr *child);
-
-/* Vector elementwise multiplication: a ∘ f(x) where a comes from param_node */
-expr *new_vector_mult(expr *param_node, expr *child);
+/* Compatibility header — includes all bivariate-related declarations.
+ * Prefer including the specific header directly:
+ *   affine.h, bivariate_full_dom.h, bivariate_restricted_dom.h */
+#include "affine.h"
+#include "bivariate_full_dom.h"
+#include "bivariate_restricted_dom.h"
 
 #endif /* BIVARIATE_H */

include/bivariate_full_dom.h

@@ -0,0 +1,11 @@
+#ifndef BIVARIATE_FULL_DOM_H
+#define BIVARIATE_FULL_DOM_H
+
+#include "expr.h"
+
+expr *new_elementwise_mult(expr *left, expr *right);
+
+/* Matrix multiplication: Z = X @ Y */
+expr *new_matmul(expr *x, expr *y);
+
+#endif /* BIVARIATE_FULL_DOM_H */

include/bivariate_restricted_dom.h

@@ -0,0 +1,11 @@
+#ifndef BIVARIATE_RESTRICTED_DOM_H
+#define BIVARIATE_RESTRICTED_DOM_H
+
+#include "expr.h"
+
+expr *new_quad_over_lin(expr *left, expr *right);
+expr *new_rel_entr_vector_args(expr *left, expr *right);
+expr *new_rel_entr_first_arg_scalar(expr *left, expr *right);
+expr *new_rel_entr_second_arg_scalar(expr *left, expr *right);
+
+#endif /* BIVARIATE_RESTRICTED_DOM_H */

src/affine/diag_vec.c

@@ -34,7 +34,7 @@ static void forward(expr *node, const double *u)
     /* child's forward pass */
     x->forward(x, u);
 
-    /* zero-initialize output */
+    /* zero-initialize output, TODO: do we need to do this? */
     memset(node->value, 0, node->size * sizeof(double));
 
     /* place input elements on the diagonal */

src/bivariate/left_matmul.c src/affine/left_matmul.csrc/bivariate/left_matmul.c renamed to src/affine/left_matmul.c

@@ -15,7 +15,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-#include "bivariate.h"
+#include "affine.h"
 #include "subexpr.h"
 #include "utils/matrix.h"
 #include <assert.h>

src/bivariate/right_matmul.c src/affine/right_matmul.csrc/bivariate/right_matmul.c renamed to src/affine/right_matmul.c

@@ -16,7 +16,6 @@
  * limitations under the License.
  */
 #include "affine.h"
-#include "bivariate.h"
 #include "subexpr.h"
 #include "utils/CSR_Matrix.h"
 #include <stdlib.h>

src/bivariate/scalar_mult.c src/affine/scalar_mult.csrc/bivariate/scalar_mult.c renamed to src/affine/scalar_mult.c

@@ -15,7 +15,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "subexpr.h"
 #include "utils/mini_numpy.h"
 #include <assert.h>