Bindings for diag_mat, upper_tri, and vstack atoms (#7)

* Bindings for diag_mat, kron_left, upper_tri, and vstack atoms

Add Python C extension bindings for four new SparseDiffEngine atoms:
- diag_mat: extract diagonal from square matrix
- upper_tri: extract strict upper triangular elements
- kron_left: Kronecker product kron(C, X) with constant sparse C
- vstack: vertical stack of expressions (via transpose-hstack composition)

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

* Update SparseDiffEngine submodule with main merge

Merges SparseDiffEngine main into adds-more-affine-atoms branch to
pick up folder restructuring and parameter support while preserving
diag_mat, upper_tri, and vstack atoms.

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

* pin diffengine to tag

---------

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

Author: Transurgeon

SparseDiffEngine

@@ -0,0 +1,32 @@
+#ifndef ATOM_DIAG_MAT_H
+#define ATOM_DIAG_MAT_H
+
+#include "common.h"
+
+static PyObject *py_make_diag_mat(PyObject *self, PyObject *args)
+{
+    PyObject *child_capsule;
+
+    if (!PyArg_ParseTuple(args, "O", &child_capsule))
+    {
+        return NULL;
+    }
+
+    expr *child = (expr *) PyCapsule_GetPointer(child_capsule, EXPR_CAPSULE_NAME);
+    if (!child)
+    {
+        return NULL;
+    }
+
+    expr *node = new_diag_mat(child);
+    if (!node)
+    {
+        PyErr_SetString(PyExc_RuntimeError, "failed to create diag_mat node");
+        return NULL;
+    }
+
+    expr_retain(node);
+    return PyCapsule_New(node, EXPR_CAPSULE_NAME, expr_capsule_destructor);
+}
+
+#endif /* ATOM_DIAG_MAT_H */

sparsediffpy/_bindings/atoms/diag_mat.h

@@ -0,0 +1,32 @@
+#ifndef ATOM_UPPER_TRI_H
+#define ATOM_UPPER_TRI_H
+
+#include "common.h"
+
+static PyObject *py_make_upper_tri(PyObject *self, PyObject *args)
+{
+    PyObject *child_capsule;
+
+    if (!PyArg_ParseTuple(args, "O", &child_capsule))
+    {
+        return NULL;
+    }
+
+    expr *child = (expr *) PyCapsule_GetPointer(child_capsule, EXPR_CAPSULE_NAME);
+    if (!child)
+    {
+        return NULL;
+    }
+
+    expr *node = new_upper_tri(child);
+    if (!node)
+    {
+        PyErr_SetString(PyExc_RuntimeError, "failed to create upper_tri node");
+        return NULL;
+    }
+
+    expr_retain(node);
+    return PyCapsule_New(node, EXPR_CAPSULE_NAME, expr_capsule_destructor);
+}
+
+#endif /* ATOM_UPPER_TRI_H */

sparsediffpy/_bindings/atoms/upper_tri.h

@@ -0,0 +1,51 @@
+#ifndef ATOM_VSTACK_H
+#define ATOM_VSTACK_H
+
+#include "common.h"
+
+static PyObject *py_make_vstack(PyObject *self, PyObject *args)
+{
+    (void) self;
+    PyObject *list_obj;
+    if (!PyArg_ParseTuple(args, "O", &list_obj))
+    {
+        return NULL;
+    }
+    if (!PyList_Check(list_obj))
+    {
+        PyErr_SetString(PyExc_TypeError,
+                        "First argument must be a list of expr capsules");
+        return NULL;
+    }
+    Py_ssize_t n_args = PyList_Size(list_obj);
+    if (n_args == 0)
+    {
+        PyErr_SetString(PyExc_ValueError, "List of expr capsules cannot be empty");
+        return NULL;
+    }
+    expr **expr_args = (expr **) calloc(n_args, sizeof(expr *));
+    for (Py_ssize_t i = 0; i < n_args; ++i)
+    {
+        PyObject *item = PyList_GetItem(list_obj, i);
+        expr *e = (expr *) PyCapsule_GetPointer(item, EXPR_CAPSULE_NAME);
+        if (!e)
+        {
+            free(expr_args);
+            PyErr_SetString(PyExc_ValueError, "Invalid expr capsule in list");
+            return NULL;
+        }
+        expr_args[i] = e;
+    }
+    int n_vars = expr_args[0]->n_vars;
+    expr *node = new_vstack(expr_args, (int) n_args, n_vars);
+    free(expr_args);
+    if (!node)
+    {
+        PyErr_SetString(PyExc_RuntimeError, "failed to create vstack node");
+        return NULL;
+    }
+    expr_retain(node);
+    return PyCapsule_New(node, EXPR_CAPSULE_NAME, expr_capsule_destructor);
+}
+
+#endif // ATOM_VSTACK_H

sparsediffpy/_bindings/atoms/vstack.h

@@ -8,6 +8,7 @@
 #include "atoms/atanh.h"
 #include "atoms/broadcast.h"
 #include "atoms/cos.h"
+#include "atoms/diag_mat.h"
 #include "atoms/diag_vec.h"
 #include "atoms/entr.h"
 #include "atoms/exp.h"
@@ -40,8 +41,10 @@
 #include "atoms/tanh.h"
 #include "atoms/trace.h"
 #include "atoms/transpose.h"
+#include "atoms/upper_tri.h"
 #include "atoms/variable.h"
 #include "atoms/vector_mult.h"
+#include "atoms/vstack.h"
 #include "atoms/xexp.h"
 
 /* Include problem bindings */
@@ -80,6 +83,8 @@ static PyMethodDef DNLPMethods[] = {
     {"make_hstack", py_make_hstack, METH_VARARGS,
      "Create hstack node from list of expr capsules and n_vars (make_hstack([e1, "
      "e2, ...], n_vars))"},
+    {"make_vstack", py_make_vstack, METH_VARARGS,
+     "Create vstack node from list of expr capsules (make_vstack([e1, e2, ...]))"},
     {"make_sum", py_make_sum, METH_VARARGS, "Create sum node"},
     {"make_neg", py_make_neg, METH_VARARGS, "Create neg node"},
     {"make_normal_cdf", py_make_normal_cdf, METH_VARARGS, "Create normal_cdf node"},
@@ -100,12 +105,14 @@ static PyMethodDef DNLPMethods[] = {
      "Create prod_axis_one node"},
     {"make_sin", py_make_sin, METH_VARARGS, "Create sin node"},
     {"make_cos", py_make_cos, METH_VARARGS, "Create cos node"},
+    {"make_diag_mat", py_make_diag_mat, METH_VARARGS, "Create diag_mat node"},
     {"make_diag_vec", py_make_diag_vec, METH_VARARGS, "Create diag_vec node"},
     {"make_tan", py_make_tan, METH_VARARGS, "Create tan node"},
     {"make_sinh", py_make_sinh, METH_VARARGS, "Create sinh node"},
     {"make_tanh", py_make_tanh, METH_VARARGS, "Create tanh node"},
     {"make_asinh", py_make_asinh, METH_VARARGS, "Create asinh node"},
     {"make_atanh", py_make_atanh, METH_VARARGS, "Create atanh node"},
+    {"make_upper_tri", py_make_upper_tri, METH_VARARGS, "Create upper_tri node"},
     {"make_broadcast", py_make_broadcast, METH_VARARGS, "Create broadcast node"},
     {"make_entr", py_make_entr, METH_VARARGS, "Create entr node"},
     {"make_logistic", py_make_logistic, METH_VARARGS, "Create logistic node"},