From bec476fb472732b1e2d0502f65dcab675b31e7f4 Mon Sep 17 00:00:00 2001
From: dance858 <danielcederberg1@gmail.com>
Date: Mon, 9 Mar 2026 17:04:19 -0700
Subject: [PATCH 01/10] new bindings

---
 sparsediffpy/_bindings/atoms/dense_matmul.h | 101 ++++++++++++++++++++
 sparsediffpy/_bindings/atoms/left_matmul.h  |   2 +-
 sparsediffpy/_bindings/atoms/right_matmul.h |   2 +-
 sparsediffpy/_bindings/bindings.c           |  13 ++-
 4 files changed, 112 insertions(+), 6 deletions(-)
 create mode 100644 sparsediffpy/_bindings/atoms/dense_matmul.h

diff --git a/sparsediffpy/_bindings/atoms/dense_matmul.h b/sparsediffpy/_bindings/atoms/dense_matmul.h
new file mode 100644
index 0000000..d8aef8f
--- /dev/null
+++ b/sparsediffpy/_bindings/atoms/dense_matmul.h
@@ -0,0 +1,101 @@
+#ifndef ATOM_DENSE_MATMUL_H
+#define ATOM_DENSE_MATMUL_H
+
+#include "bivariate.h"
+#include "common.h"
+
+/* Dense left matrix multiplication: A @ f(x) where A is a dense matrix.
+ *
+ * Python signature:
+ *   make_dense_left_matmul(child, A_data_flat, m, n)
+ *
+ * - child: the child expression capsule f(x).
+ * - A_data_flat: contiguous row-major numpy float64 array of size m*n.
+ * - m, n: dimensions of matrix A. */
+static PyObject *py_make_dense_left_matmul(PyObject *self, PyObject *args)
+{
+    PyObject *child_capsule;
+    PyObject *data_obj;
+    int m, n;
+    if (!PyArg_ParseTuple(args, "OOii", &child_capsule, &data_obj, &m, &n))
+    {
+        return NULL;
+    }
+
+    expr *child = (expr *) PyCapsule_GetPointer(child_capsule, EXPR_CAPSULE_NAME);
+    if (!child)
+    {
+        PyErr_SetString(PyExc_ValueError, "invalid child capsule");
+        return NULL;
+    }
+
+    PyArrayObject *data_array =
+        (PyArrayObject *) PyArray_FROM_OTF(data_obj, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!data_array)
+    {
+        return NULL;
+    }
+
+    double *A_data = (double *) PyArray_DATA(data_array);
+
+    expr *node = new_left_matmul_dense(child, m, n, A_data);
+    Py_DECREF(data_array);
+
+    if (!node)
+    {
+        PyErr_SetString(PyExc_RuntimeError,
+                        "failed to create dense_left_matmul node");
+        return NULL;
+    }
+    expr_retain(node);
+    return PyCapsule_New(node, EXPR_CAPSULE_NAME, expr_capsule_destructor);
+}
+
+/* Dense right matrix multiplication: f(x) @ A where A is a dense matrix.
+ *
+ * Python signature:
+ *   make_dense_right_matmul(child, A_data_flat, m, n)
+ *
+ * - child: the child expression capsule f(x).
+ * - A_data_flat: contiguous row-major numpy float64 array of size m*n.
+ * - m, n: dimensions of matrix A. */
+static PyObject *py_make_dense_right_matmul(PyObject *self, PyObject *args)
+{
+    PyObject *child_capsule;
+    PyObject *data_obj;
+    int m, n;
+    if (!PyArg_ParseTuple(args, "OOii", &child_capsule, &data_obj, &m, &n))
+    {
+        return NULL;
+    }
+
+    expr *child = (expr *) PyCapsule_GetPointer(child_capsule, EXPR_CAPSULE_NAME);
+    if (!child)
+    {
+        PyErr_SetString(PyExc_ValueError, "invalid child capsule");
+        return NULL;
+    }
+
+    PyArrayObject *data_array =
+        (PyArrayObject *) PyArray_FROM_OTF(data_obj, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!data_array)
+    {
+        return NULL;
+    }
+
+    double *A_data = (double *) PyArray_DATA(data_array);
+
+    expr *node = new_right_matmul_dense(child, m, n, A_data);
+    Py_DECREF(data_array);
+
+    if (!node)
+    {
+        PyErr_SetString(PyExc_RuntimeError,
+                        "failed to create dense_right_matmul node");
+        return NULL;
+    }
+    expr_retain(node);
+    return PyCapsule_New(node, EXPR_CAPSULE_NAME, expr_capsule_destructor);
+}
+
+#endif /* ATOM_DENSE_MATMUL_H */
\ No newline at end of file
diff --git a/sparsediffpy/_bindings/atoms/left_matmul.h b/sparsediffpy/_bindings/atoms/left_matmul.h
index 27fe3a4..09fa985 100644
--- a/sparsediffpy/_bindings/atoms/left_matmul.h
+++ b/sparsediffpy/_bindings/atoms/left_matmul.h
@@ -5,7 +5,7 @@
 #include "common.h"
 
 /* Left matrix multiplication: A @ f(x) where A is a constant matrix */
-static PyObject *py_make_left_matmul(PyObject *self, PyObject *args)
+static PyObject *py_make_sparse_left_matmul(PyObject *self, PyObject *args)
 {
     PyObject *child_capsule;
     PyObject *data_obj, *indices_obj, *indptr_obj;
diff --git a/sparsediffpy/_bindings/atoms/right_matmul.h b/sparsediffpy/_bindings/atoms/right_matmul.h
index c1c3481..f808058 100644
--- a/sparsediffpy/_bindings/atoms/right_matmul.h
+++ b/sparsediffpy/_bindings/atoms/right_matmul.h
@@ -5,7 +5,7 @@
 #include "common.h"
 
 /* Right matrix multiplication: f(x) @ A where A is a constant matrix */
-static PyObject *py_make_right_matmul(PyObject *self, PyObject *args)
+static PyObject *py_make_sparse_right_matmul(PyObject *self, PyObject *args)
 {
     PyObject *child_capsule;
     PyObject *data_obj, *indices_obj, *indptr_obj;
diff --git a/sparsediffpy/_bindings/bindings.c b/sparsediffpy/_bindings/bindings.c
index 2e51960..9f3c4b0 100644
--- a/sparsediffpy/_bindings/bindings.c
+++ b/sparsediffpy/_bindings/bindings.c
@@ -11,6 +11,7 @@
 #include "atoms/const_vector_mult.h"
 #include "atoms/constant.h"
 #include "atoms/cos.h"
+#include "atoms/dense_matmul.h"
 #include "atoms/diag_vec.h"
 #include "atoms/entr.h"
 #include "atoms/exp.h"
@@ -109,10 +110,14 @@ static PyMethodDef DNLPMethods[] = {
     {"make_entr", py_make_entr, METH_VARARGS, "Create entr node"},
     {"make_logistic", py_make_logistic, METH_VARARGS, "Create logistic node"},
     {"make_xexp", py_make_xexp, METH_VARARGS, "Create xexp node"},
-    {"make_left_matmul", py_make_left_matmul, METH_VARARGS,
-     "Create left matmul node (A @ f(x))"},
-    {"make_right_matmul", py_make_right_matmul, METH_VARARGS,
-     "Create right matmul node (f(x) @ A)"},
+    {"make_sparse_left_matmul", py_make_sparse_left_matmul, METH_VARARGS,
+     "Create sparse left matmul node (A @ f(x))"},
+    {"make_dense_left_matmul", py_make_dense_left_matmul, METH_VARARGS,
+     "Create dense left matmul node (A @ f(x)) where A is dense"},
+    {"make_sparse_right_matmul", py_make_sparse_right_matmul, METH_VARARGS,
+     "Create sparse right matmul node (f(x) @ A)"},
+    {"make_dense_right_matmul", py_make_dense_right_matmul, METH_VARARGS,
+     "Create dense right matmul node (f(x) @ A) where A is dense"},
     {"make_quad_form", py_make_quad_form, METH_VARARGS,
      "Create quadratic form node (x' * Q * x)"},
     {"make_quad_over_lin", py_make_quad_over_lin, METH_VARARGS,

From 3fec61a605222f221b4332e00e7abf8fef369784 Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 18:55:47 -0400
Subject: [PATCH 02/10] update SparseDiffEngine to latest main

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 SparseDiffEngine | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SparseDiffEngine b/SparseDiffEngine
index 7c84b13..9480159 160000
--- a/SparseDiffEngine
+++ b/SparseDiffEngine
@@ -1 +1 @@
-Subproject commit 7c84b137ea7ac51846eaa5a30fe3ea707bc9d7aa
+Subproject commit 94801591f2f059ed3de6d68ab3db5a370bf3d667

From fdfd21fd4c0e0320051879965d3fbfb891888e30 Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 19:06:32 -0400
Subject: [PATCH 03/10] add BLAS linking for all platforms
 (Accelerate/OpenBLAS/vcpkg)

The updated SparseDiffEngine submodule introduces dense_matrix.c which
requires CBLAS. Link Accelerate on macOS, OpenBLAS on Linux, and
OpenBLAS via vcpkg on Windows. Install BLAS dev packages in CI
via CIBW_BEFORE_BUILD for Linux and Windows.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml |  3 ++
 setup.py                                | 40 +++++++++++++++++--------
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index d1b3a38..d2ec3a5 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -64,6 +64,9 @@ jobs:
           CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
           CIBW_ARCHS_MACOS: "x86_64 universal2"
           CIBW_ARCHS_LINUX: "auto aarch64"
+          CIBW_BEFORE_BUILD_LINUX: "yum install -y openblas-devel || apt-get install -y libopenblas-dev"
+          CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows"
+          CIBW_ENVIRONMENT_WINDOWS: "VCPKG_INSTALLED_DIR=C:\\vcpkg\\installed\\x64-windows"
 
       - name: Check wheels
         shell: bash
diff --git a/setup.py b/setup.py
index 3b572ad..e02b24f 100644
--- a/setup.py
+++ b/setup.py
@@ -16,14 +16,13 @@
 
 import builtins
 import glob
+import os
 import platform
 
 from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
-
-def not_on_windows(s: str) -> str:
-    return s if platform.system().lower() != "windows" else ""
+system = platform.system().lower()
 
 
 class build_ext_numpy(build_ext):
@@ -44,9 +43,25 @@ def finalize_options(self) -> None:
 
 # Define _POSIX_C_SOURCE on Linux for clock_gettime and struct timespec
 defines = []
-if platform.system().lower() == "linux":
+if system == "linux":
     defines.append(("_POSIX_C_SOURCE", "200809L"))
 
+# Platform-specific BLAS configuration
+if system == "darwin":
+    blas_link_args = ["-framework", "Accelerate"]
+    blas_include_dirs = []
+elif system == "linux":
+    blas_link_args = ["-lopenblas"]
+    blas_include_dirs = []
+else:
+    # Windows: OpenBLAS via vcpkg
+    vcpkg_root = os.environ.get(
+        "VCPKG_INSTALLED_DIR",
+        r"C:\vcpkg\installed\x64-windows",
+    )
+    blas_link_args = [os.path.join(vcpkg_root, "lib", "openblas.lib")]
+    blas_include_dirs = [os.path.join(vcpkg_root, "include")]
+
 sparsediffengine = Extension(
     "sparsediffpy._sparsediffengine",
     sources=diff_engine_sources,
@@ -54,16 +69,15 @@ def finalize_options(self) -> None:
         "SparseDiffEngine/include/",
         "SparseDiffEngine/src/",
         "sparsediffpy/_bindings/",
-    ],
+    ] + blas_include_dirs,
     define_macros=defines,
-    extra_compile_args=[
-        "-O3",
-        "-std=c99",
-        "-Wall",
-        not_on_windows("-Wextra"),
-        '-DDIFF_ENGINE_VERSION="0.1.3"',
-    ],
-    extra_link_args=["-lm"] if platform.system().lower() != "windows" else [],
+    extra_compile_args=(
+        ["-O3", "-std=c99", "-Wall", "-Wextra",
+         '-DDIFF_ENGINE_VERSION="0.1.3"']
+        if system != "windows" else
+        ['/O2', '/DDIFF_ENGINE_VERSION="0.1.3"']
+    ),
+    extra_link_args=(["-lm"] if system != "windows" else []) + blas_link_args,
 )
 
 setup(

From f5ee2a029712476eec45d50d6ee0d9f60be417ab Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 19:34:15 -0400
Subject: [PATCH 04/10] fix Linux BLAS include path for manylinux containers

Add /usr/include/openblas to include_dirs on Linux so cblas.h resolves
in manylinux (CentOS-based) containers where openblas-devel installs
headers to /usr/include/openblas/ instead of /usr/include/.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index e02b24f..42b9e39 100644
--- a/setup.py
+++ b/setup.py
@@ -52,7 +52,7 @@ def finalize_options(self) -> None:
     blas_include_dirs = []
 elif system == "linux":
     blas_link_args = ["-lopenblas"]
-    blas_include_dirs = []
+    blas_include_dirs = ["/usr/include/openblas"]
 else:
     # Windows: OpenBLAS via vcpkg
     vcpkg_root = os.environ.get(

From 449589780d8c0dc8ea84189b9f9a36e2b80856f3 Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 19:45:58 -0400
Subject: [PATCH 05/10] fix Windows vcpkg path in CI (backslash escaping issue)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CIBW_ENVIRONMENT_WINDOWS values are parsed by shlex, which treats
backslashes as escape characters. Use forward slashes instead —
Windows accepts them and they survive shlex parsing.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index d2ec3a5..d9ecfac 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -66,7 +66,7 @@ jobs:
           CIBW_ARCHS_LINUX: "auto aarch64"
           CIBW_BEFORE_BUILD_LINUX: "yum install -y openblas-devel || apt-get install -y libopenblas-dev"
           CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows"
-          CIBW_ENVIRONMENT_WINDOWS: "VCPKG_INSTALLED_DIR=C:\\vcpkg\\installed\\x64-windows"
+          CIBW_ENVIRONMENT_WINDOWS: "VCPKG_INSTALLED_DIR=C:/vcpkg/installed/x64-windows"
 
       - name: Check wheels
         shell: bash

From d96fcc95eb6d842f4ad79f49b7840d2faf8e473a Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 19:53:27 -0400
Subject: [PATCH 06/10] cache vcpkg on Windows CI to skip OpenBLAS rebuild

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index d9ecfac..f63198b 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -57,6 +57,13 @@ jobs:
         with:
           platforms: all
 
+      - name: Cache vcpkg packages
+        if: runner.os == 'Windows'
+        uses: actions/cache@v4
+        with:
+          path: C:\vcpkg\installed
+          key: vcpkg-windows-openblas-v1
+
       - name: Build wheels
         uses: pypa/cibuildwheel@v3.3.0
         env:

From 32c0c67b953690cb97107a0705fd1a70f1dc6e19 Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 20:05:56 -0400
Subject: [PATCH 07/10] debug Windows cblas.h: add dir listing and openblas
 include fallback

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml | 2 +-
 setup.py                                | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index f63198b..1db67ff 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           CIBW_ARCHS_MACOS: "x86_64 universal2"
           CIBW_ARCHS_LINUX: "auto aarch64"
           CIBW_BEFORE_BUILD_LINUX: "yum install -y openblas-devel || apt-get install -y libopenblas-dev"
-          CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows"
+          CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows && dir C:\\vcpkg\\installed\\x64-windows\\include\\ && dir C:\\vcpkg\\installed\\x64-windows\\lib\\"
           CIBW_ENVIRONMENT_WINDOWS: "VCPKG_INSTALLED_DIR=C:/vcpkg/installed/x64-windows"
 
       - name: Check wheels
diff --git a/setup.py b/setup.py
index 42b9e39..67ab935 100644
--- a/setup.py
+++ b/setup.py
@@ -60,7 +60,10 @@ def finalize_options(self) -> None:
         r"C:\vcpkg\installed\x64-windows",
     )
     blas_link_args = [os.path.join(vcpkg_root, "lib", "openblas.lib")]
-    blas_include_dirs = [os.path.join(vcpkg_root, "include")]
+    blas_include_dirs = [
+        os.path.join(vcpkg_root, "include"),
+        os.path.join(vcpkg_root, "include", "openblas"),
+    ]
 
 sparsediffengine = Extension(
     "sparsediffpy._sparsediffengine",

From 9667d490ea862211e48169cb1d1733a16616cb5f Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 20:07:32 -0400
Subject: [PATCH 08/10] skip BLAS and dense_matrix on Windows (matches C
 engine)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml | 10 ----------
 setup.py                                | 19 ++++++++-----------
 2 files changed, 8 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index 1db67ff..cd28c2a 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -57,13 +57,6 @@ jobs:
         with:
           platforms: all
 
-      - name: Cache vcpkg packages
-        if: runner.os == 'Windows'
-        uses: actions/cache@v4
-        with:
-          path: C:\vcpkg\installed
-          key: vcpkg-windows-openblas-v1
-
       - name: Build wheels
         uses: pypa/cibuildwheel@v3.3.0
         env:
@@ -72,9 +65,6 @@ jobs:
           CIBW_ARCHS_MACOS: "x86_64 universal2"
           CIBW_ARCHS_LINUX: "auto aarch64"
           CIBW_BEFORE_BUILD_LINUX: "yum install -y openblas-devel || apt-get install -y libopenblas-dev"
-          CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows && dir C:\\vcpkg\\installed\\x64-windows\\include\\ && dir C:\\vcpkg\\installed\\x64-windows\\lib\\"
-          CIBW_ENVIRONMENT_WINDOWS: "VCPKG_INSTALLED_DIR=C:/vcpkg/installed/x64-windows"
-
       - name: Check wheels
         shell: bash
         run: |
diff --git a/setup.py b/setup.py
index 67ab935..497631b 100644
--- a/setup.py
+++ b/setup.py
@@ -36,9 +36,13 @@ def finalize_options(self) -> None:
 
 
 # Collect all C source files from SparseDiffEngine
+_exclude = {"dnlp_diff_engine"}
+if system == "windows":
+    _exclude.add("dense_matrix")
+
 diff_engine_sources = [
     s for s in glob.glob("SparseDiffEngine/src/**/*.c", recursive=True)
-    if "dnlp_diff_engine" not in s
+    if not any(ex in s for ex in _exclude)
 ] + ["sparsediffpy/_bindings/bindings.c"]
 
 # Define _POSIX_C_SOURCE on Linux for clock_gettime and struct timespec
@@ -54,16 +58,9 @@ def finalize_options(self) -> None:
     blas_link_args = ["-lopenblas"]
     blas_include_dirs = ["/usr/include/openblas"]
 else:
-    # Windows: OpenBLAS via vcpkg
-    vcpkg_root = os.environ.get(
-        "VCPKG_INSTALLED_DIR",
-        r"C:\vcpkg\installed\x64-windows",
-    )
-    blas_link_args = [os.path.join(vcpkg_root, "lib", "openblas.lib")]
-    blas_include_dirs = [
-        os.path.join(vcpkg_root, "include"),
-        os.path.join(vcpkg_root, "include", "openblas"),
-    ]
+    # Windows: no BLAS available
+    blas_link_args = []
+    blas_include_dirs = []
 
 sparsediffengine = Extension(
     "sparsediffpy._sparsediffengine",

From f07a23c680aeaefc4be2ffafbe2e4caeee840f27 Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Wed, 11 Mar 2026 20:20:31 -0400
Subject: [PATCH 09/10] fix Windows build: stub dense_matrix symbols and guard
 dense bindings

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 setup.py                                   |  3 +++
 sparsediffpy/_bindings/bindings.c          |  6 ++++++
 sparsediffpy/_bindings/dense_matrix_stub.c | 25 ++++++++++++++++++++++
 3 files changed, 34 insertions(+)
 create mode 100644 sparsediffpy/_bindings/dense_matrix_stub.c

diff --git a/setup.py b/setup.py
index 497631b..dc7bae9 100644
--- a/setup.py
+++ b/setup.py
@@ -45,6 +45,9 @@ def finalize_options(self) -> None:
     if not any(ex in s for ex in _exclude)
 ] + ["sparsediffpy/_bindings/bindings.c"]
 
+if system == "windows":
+    diff_engine_sources.append("sparsediffpy/_bindings/dense_matrix_stub.c")
+
 # Define _POSIX_C_SOURCE on Linux for clock_gettime and struct timespec
 defines = []
 if system == "linux":
diff --git a/sparsediffpy/_bindings/bindings.c b/sparsediffpy/_bindings/bindings.c
index 9f3c4b0..02a0c37 100644
--- a/sparsediffpy/_bindings/bindings.c
+++ b/sparsediffpy/_bindings/bindings.c
@@ -11,7 +11,9 @@
 #include "atoms/const_vector_mult.h"
 #include "atoms/constant.h"
 #include "atoms/cos.h"
+#ifndef _MSC_VER
 #include "atoms/dense_matmul.h"
+#endif
 #include "atoms/diag_vec.h"
 #include "atoms/entr.h"
 #include "atoms/exp.h"
@@ -112,12 +114,16 @@ static PyMethodDef DNLPMethods[] = {
     {"make_xexp", py_make_xexp, METH_VARARGS, "Create xexp node"},
     {"make_sparse_left_matmul", py_make_sparse_left_matmul, METH_VARARGS,
      "Create sparse left matmul node (A @ f(x))"},
+#ifndef _MSC_VER
     {"make_dense_left_matmul", py_make_dense_left_matmul, METH_VARARGS,
      "Create dense left matmul node (A @ f(x)) where A is dense"},
+#endif
     {"make_sparse_right_matmul", py_make_sparse_right_matmul, METH_VARARGS,
      "Create sparse right matmul node (f(x) @ A)"},
+#ifndef _MSC_VER
     {"make_dense_right_matmul", py_make_dense_right_matmul, METH_VARARGS,
      "Create dense right matmul node (f(x) @ A) where A is dense"},
+#endif
     {"make_quad_form", py_make_quad_form, METH_VARARGS,
      "Create quadratic form node (x' * Q * x)"},
     {"make_quad_over_lin", py_make_quad_over_lin, METH_VARARGS,
diff --git a/sparsediffpy/_bindings/dense_matrix_stub.c b/sparsediffpy/_bindings/dense_matrix_stub.c
new file mode 100644
index 0000000..d7e3fe5
--- /dev/null
+++ b/sparsediffpy/_bindings/dense_matrix_stub.c
@@ -0,0 +1,25 @@
+/*
+ * Stub implementations for dense matrix functions on Windows,
+ * where BLAS is not available. These satisfy the linker for
+ * left_matmul.c which references them, but the dense matmul
+ * bindings are excluded via #ifndef _MSC_VER so they are
+ * never actually called.
+ */
+#ifdef _MSC_VER
+#include "utils/matrix.h"
+#include <stdlib.h>
+
+Matrix *new_dense_matrix(int m, int n, const double *data)
+{
+    (void) m;
+    (void) n;
+    (void) data;
+    return NULL;
+}
+
+Matrix *dense_matrix_trans(const Dense_Matrix *self)
+{
+    (void) self;
+    return NULL;
+}
+#endif

From 0646432184fa595453b2886963930a35ab20e2ef Mon Sep 17 00:00:00 2001
From: William Zijie Zhang <william@gridmatic.com>
Date: Thu, 12 Mar 2026 00:39:07 -0400
Subject: [PATCH 10/10] migrate build system from setuptools to
 scikit-build-core

Replace the manual setup.py (which compiled ~49 C files with per-platform
BLAS logic and Windows workarounds) with a top-level CMakeLists.txt that
delegates to the submodule's existing CMake build. This eliminates the
dense_matrix_stub.c, the #ifdef _MSC_VER guards in bindings.c, and enables
dense matmul support on Windows via vcpkg OpenBLAS.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/build-and-publish.yml    |  2 +
 CMakeLists.txt                             | 29 +++++++
 pyproject.toml                             | 12 ++-
 setup.py                                   | 89 ----------------------
 sparsediffpy/_bindings/bindings.c          |  6 --
 sparsediffpy/_bindings/dense_matrix_stub.c | 25 ------
 6 files changed, 36 insertions(+), 127 deletions(-)
 create mode 100644 CMakeLists.txt
 delete mode 100644 setup.py
 delete mode 100644 sparsediffpy/_bindings/dense_matrix_stub.c

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index cd28c2a..2e27fa1 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -65,6 +65,8 @@ jobs:
           CIBW_ARCHS_MACOS: "x86_64 universal2"
           CIBW_ARCHS_LINUX: "auto aarch64"
           CIBW_BEFORE_BUILD_LINUX: "yum install -y openblas-devel || apt-get install -y libopenblas-dev"
+          CIBW_BEFORE_BUILD_WINDOWS: "vcpkg install openblas:x64-windows"
+          CIBW_ENVIRONMENT_WINDOWS: "CMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake"
       - name: Check wheels
         shell: bash
         run: |
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..c391e91
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,29 @@
+cmake_minimum_required(VERSION 3.15)
+project(SparseDiffPy LANGUAGES C)
+
+add_subdirectory(SparseDiffEngine)
+
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module NumPy)
+
+# Linux: CMake find_package(BLAS) doesn't set include dirs;
+# openblas puts cblas.h in /usr/include/openblas/
+if(UNIX AND NOT APPLE)
+    find_path(OPENBLAS_INCLUDE_DIR cblas.h PATHS /usr/include/openblas /usr/include)
+    if(OPENBLAS_INCLUDE_DIR)
+        target_include_directories(dnlp_diff PRIVATE ${OPENBLAS_INCLUDE_DIR})
+    endif()
+endif()
+
+python3_add_library(_sparsediffengine MODULE
+    sparsediffpy/_bindings/bindings.c
+)
+
+target_include_directories(_sparsediffengine PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include
+    ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/src
+    ${CMAKE_CURRENT_SOURCE_DIR}/sparsediffpy/_bindings
+)
+
+target_link_libraries(_sparsediffengine PRIVATE dnlp_diff Python3::NumPy)
+
+install(TARGETS _sparsediffengine DESTINATION sparsediffpy)
diff --git a/pyproject.toml b/pyproject.toml
index f40d0e7..10465ff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
-requires = ["numpy >= 2.0.0", "setuptools >= 68.1.0", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core >= 0.10", "numpy >= 2.0.0"]
+build-backend = "scikit_build_core.build"
 
 [project]
 name = "sparsediffpy"
@@ -14,8 +14,6 @@ license = "Apache-2.0"
 file = "README.md"
 content-type = "text/markdown"
 
-[tool.setuptools]
-include-package-data = false
-
-[tool.setuptools.packages.find]
-include = ["sparsediffpy*"]
+[tool.scikit-build]
+cmake.minimum-version = "3.15"
+wheel.packages = ["sparsediffpy"]
diff --git a/setup.py b/setup.py
deleted file mode 100644
index dc7bae9..0000000
--- a/setup.py
+++ /dev/null
@@ -1,89 +0,0 @@
-"""
-Copyright 2025, the SparseDiffPy developers
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-"""
-
-import builtins
-import glob
-import os
-import platform
-
-from setuptools import Extension, setup
-from setuptools.command.build_ext import build_ext
-
-system = platform.system().lower()
-
-
-class build_ext_numpy(build_ext):
-    """Custom build_ext that injects NumPy headers."""
-
-    def finalize_options(self) -> None:
-        build_ext.finalize_options(self)
-        builtins.__NUMPY_SETUP__ = False
-        import numpy
-        self.include_dirs.append(numpy.get_include())
-
-
-# Collect all C source files from SparseDiffEngine
-_exclude = {"dnlp_diff_engine"}
-if system == "windows":
-    _exclude.add("dense_matrix")
-
-diff_engine_sources = [
-    s for s in glob.glob("SparseDiffEngine/src/**/*.c", recursive=True)
-    if not any(ex in s for ex in _exclude)
-] + ["sparsediffpy/_bindings/bindings.c"]
-
-if system == "windows":
-    diff_engine_sources.append("sparsediffpy/_bindings/dense_matrix_stub.c")
-
-# Define _POSIX_C_SOURCE on Linux for clock_gettime and struct timespec
-defines = []
-if system == "linux":
-    defines.append(("_POSIX_C_SOURCE", "200809L"))
-
-# Platform-specific BLAS configuration
-if system == "darwin":
-    blas_link_args = ["-framework", "Accelerate"]
-    blas_include_dirs = []
-elif system == "linux":
-    blas_link_args = ["-lopenblas"]
-    blas_include_dirs = ["/usr/include/openblas"]
-else:
-    # Windows: no BLAS available
-    blas_link_args = []
-    blas_include_dirs = []
-
-sparsediffengine = Extension(
-    "sparsediffpy._sparsediffengine",
-    sources=diff_engine_sources,
-    include_dirs=[
-        "SparseDiffEngine/include/",
-        "SparseDiffEngine/src/",
-        "sparsediffpy/_bindings/",
-    ] + blas_include_dirs,
-    define_macros=defines,
-    extra_compile_args=(
-        ["-O3", "-std=c99", "-Wall", "-Wextra",
-         '-DDIFF_ENGINE_VERSION="0.1.3"']
-        if system != "windows" else
-        ['/O2', '/DDIFF_ENGINE_VERSION="0.1.3"']
-    ),
-    extra_link_args=(["-lm"] if system != "windows" else []) + blas_link_args,
-)
-
-setup(
-    cmdclass={"build_ext": build_ext_numpy},
-    ext_modules=[sparsediffengine],
-)
diff --git a/sparsediffpy/_bindings/bindings.c b/sparsediffpy/_bindings/bindings.c
index 02a0c37..9f3c4b0 100644
--- a/sparsediffpy/_bindings/bindings.c
+++ b/sparsediffpy/_bindings/bindings.c
@@ -11,9 +11,7 @@
 #include "atoms/const_vector_mult.h"
 #include "atoms/constant.h"
 #include "atoms/cos.h"
-#ifndef _MSC_VER
 #include "atoms/dense_matmul.h"
-#endif
 #include "atoms/diag_vec.h"
 #include "atoms/entr.h"
 #include "atoms/exp.h"
@@ -114,16 +112,12 @@ static PyMethodDef DNLPMethods[] = {
     {"make_xexp", py_make_xexp, METH_VARARGS, "Create xexp node"},
     {"make_sparse_left_matmul", py_make_sparse_left_matmul, METH_VARARGS,
      "Create sparse left matmul node (A @ f(x))"},
-#ifndef _MSC_VER
     {"make_dense_left_matmul", py_make_dense_left_matmul, METH_VARARGS,
      "Create dense left matmul node (A @ f(x)) where A is dense"},
-#endif
     {"make_sparse_right_matmul", py_make_sparse_right_matmul, METH_VARARGS,
      "Create sparse right matmul node (f(x) @ A)"},
-#ifndef _MSC_VER
     {"make_dense_right_matmul", py_make_dense_right_matmul, METH_VARARGS,
      "Create dense right matmul node (f(x) @ A) where A is dense"},
-#endif
     {"make_quad_form", py_make_quad_form, METH_VARARGS,
      "Create quadratic form node (x' * Q * x)"},
     {"make_quad_over_lin", py_make_quad_over_lin, METH_VARARGS,
diff --git a/sparsediffpy/_bindings/dense_matrix_stub.c b/sparsediffpy/_bindings/dense_matrix_stub.c
deleted file mode 100644
index d7e3fe5..0000000
--- a/sparsediffpy/_bindings/dense_matrix_stub.c
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Stub implementations for dense matrix functions on Windows,
- * where BLAS is not available. These satisfy the linker for
- * left_matmul.c which references them, but the dense matmul
- * bindings are excluded via #ifndef _MSC_VER so they are
- * never actually called.
- */
-#ifdef _MSC_VER
-#include "utils/matrix.h"
-#include <stdlib.h>
-
-Matrix *new_dense_matrix(int m, int n, const double *data)
-{
-    (void) m;
-    (void) n;
-    (void) data;
-    return NULL;
-}
-
-Matrix *dense_matrix_trans(const Dense_Matrix *self)
-{
-    (void) self;
-    return NULL;
-}
-#endif