From b78a2acca0eebcaeedd918d588d152733b91fe2a Mon Sep 17 00:00:00 2001
From: dance858 <danielcederberg1@gmail.com>
Date: Thu, 26 Mar 2026 16:43:43 -0700
Subject: [PATCH 1/3] reflect sparsediffengine refactor in bindings'

---
 sparsediffpy/_bindings/atoms/asinh.h    | 2 +-
 sparsediffpy/_bindings/atoms/atanh.h    | 2 +-
 sparsediffpy/_bindings/atoms/common.h   | 3 ++-
 sparsediffpy/_bindings/atoms/cos.h      | 2 +-
 sparsediffpy/_bindings/atoms/entr.h     | 2 +-
 sparsediffpy/_bindings/atoms/logistic.h | 2 +-
 sparsediffpy/_bindings/atoms/power.h    | 2 +-
 sparsediffpy/_bindings/atoms/sin.h      | 2 +-
 sparsediffpy/_bindings/atoms/sinh.h     | 2 +-
 sparsediffpy/_bindings/atoms/tan.h      | 2 +-
 sparsediffpy/_bindings/atoms/tanh.h     | 2 +-
 sparsediffpy/_bindings/atoms/xexp.h     | 2 +-
 12 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/sparsediffpy/_bindings/atoms/asinh.h b/sparsediffpy/_bindings/atoms/asinh.h
index a09934e..09724c8 100644
--- a/sparsediffpy/_bindings/atoms/asinh.h
+++ b/sparsediffpy/_bindings/atoms/asinh.h
@@ -2,7 +2,7 @@
 #define ATOM_ASINH_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_asinh(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/atanh.h b/sparsediffpy/_bindings/atoms/atanh.h
index fd0568d..86519b9 100644
--- a/sparsediffpy/_bindings/atoms/atanh.h
+++ b/sparsediffpy/_bindings/atoms/atanh.h
@@ -2,7 +2,7 @@
 #define ATOM_ATANH_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_restricted_dom.h"
 
 static PyObject *py_make_atanh(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/common.h b/sparsediffpy/_bindings/atoms/common.h
index 83101dd..72cffdb 100644
--- a/sparsediffpy/_bindings/atoms/common.h
+++ b/sparsediffpy/_bindings/atoms/common.h
@@ -6,7 +6,8 @@
 #include <numpy/arrayobject.h>
 
 #include "affine.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
+#include "elementwise_restricted_dom.h"
 #include "expr.h"
 
 #define EXPR_CAPSULE_NAME "DNLP_EXPR"
diff --git a/sparsediffpy/_bindings/atoms/cos.h b/sparsediffpy/_bindings/atoms/cos.h
index 3f798be..152400d 100644
--- a/sparsediffpy/_bindings/atoms/cos.h
+++ b/sparsediffpy/_bindings/atoms/cos.h
@@ -2,7 +2,7 @@
 #define ATOM_COS_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_cos(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/entr.h b/sparsediffpy/_bindings/atoms/entr.h
index 9a37668..899ca00 100644
--- a/sparsediffpy/_bindings/atoms/entr.h
+++ b/sparsediffpy/_bindings/atoms/entr.h
@@ -2,7 +2,7 @@
 #define ATOM_ENTR_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_restricted_dom.h"
 
 static PyObject *py_make_entr(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/logistic.h b/sparsediffpy/_bindings/atoms/logistic.h
index e903661..86fe1c8 100644
--- a/sparsediffpy/_bindings/atoms/logistic.h
+++ b/sparsediffpy/_bindings/atoms/logistic.h
@@ -2,7 +2,7 @@
 #define ATOM_LOGISTIC_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_logistic(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/power.h b/sparsediffpy/_bindings/atoms/power.h
index da9b7bf..a9fe96b 100644
--- a/sparsediffpy/_bindings/atoms/power.h
+++ b/sparsediffpy/_bindings/atoms/power.h
@@ -2,7 +2,7 @@
 #define ATOM_POWER_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_power(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/sin.h b/sparsediffpy/_bindings/atoms/sin.h
index 426d302..89ca790 100644
--- a/sparsediffpy/_bindings/atoms/sin.h
+++ b/sparsediffpy/_bindings/atoms/sin.h
@@ -2,7 +2,7 @@
 #define ATOM_SIN_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_sin(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/sinh.h b/sparsediffpy/_bindings/atoms/sinh.h
index be86cf5..d3a1abb 100644
--- a/sparsediffpy/_bindings/atoms/sinh.h
+++ b/sparsediffpy/_bindings/atoms/sinh.h
@@ -2,7 +2,7 @@
 #define ATOM_SINH_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_sinh(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/tan.h b/sparsediffpy/_bindings/atoms/tan.h
index 3ec83b7..837128f 100644
--- a/sparsediffpy/_bindings/atoms/tan.h
+++ b/sparsediffpy/_bindings/atoms/tan.h
@@ -2,7 +2,7 @@
 #define ATOM_TAN_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_restricted_dom.h"
 
 static PyObject *py_make_tan(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/tanh.h b/sparsediffpy/_bindings/atoms/tanh.h
index e60d420..6013173 100644
--- a/sparsediffpy/_bindings/atoms/tanh.h
+++ b/sparsediffpy/_bindings/atoms/tanh.h
@@ -2,7 +2,7 @@
 #define ATOM_TANH_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_tanh(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/xexp.h b/sparsediffpy/_bindings/atoms/xexp.h
index 1dda312..324a9b7 100644
--- a/sparsediffpy/_bindings/atoms/xexp.h
+++ b/sparsediffpy/_bindings/atoms/xexp.h
@@ -2,7 +2,7 @@
 #define ATOM_XEXP_H
 
 #include "common.h"
-#include "elementwise_univariate.h"
+#include "elementwise_full_dom.h"
 
 static PyObject *py_make_xexp(PyObject *self, PyObject *args)
 {

From d06c3d61a702bfca6d4f10e16296ae44b34a9638 Mon Sep 17 00:00:00 2001
From: dance858 <danielcederberg1@gmail.com>
Date: Tue, 31 Mar 2026 07:07:48 -0700
Subject: [PATCH 2/3] update includes to reflect sparsediffengine structure

---
 CMakeLists.txt                                        | 3 +++
 SparseDiffEngine                                      | 2 +-
 sparsediffpy/_bindings/atoms/const_scalar_mult.h      | 2 +-
 sparsediffpy/_bindings/atoms/const_vector_mult.h      | 2 +-
 sparsediffpy/_bindings/atoms/dense_matmul.h           | 2 +-
 sparsediffpy/_bindings/atoms/left_matmul.h            | 2 +-
 sparsediffpy/_bindings/atoms/matmul.h                 | 2 +-
 sparsediffpy/_bindings/atoms/multiply.h               | 2 +-
 sparsediffpy/_bindings/atoms/prod.h                   | 2 +-
 sparsediffpy/_bindings/atoms/prod_axis_one.h          | 2 +-
 sparsediffpy/_bindings/atoms/prod_axis_zero.h         | 2 +-
 sparsediffpy/_bindings/atoms/quad_form.h              | 2 +-
 sparsediffpy/_bindings/atoms/quad_over_lin.h          | 2 +-
 sparsediffpy/_bindings/atoms/rel_entr.h               | 2 +-
 sparsediffpy/_bindings/atoms/rel_entr_scalar_vector.h | 2 +-
 sparsediffpy/_bindings/atoms/rel_entr_vector_scalar.h | 2 +-
 sparsediffpy/_bindings/atoms/right_matmul.h           | 2 +-
 sparsediffpy/_bindings/bindings.c                     | 2 --
 18 files changed, 19 insertions(+), 18 deletions(-)
 mode change 160000 => 120000 SparseDiffEngine

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c391e91..c3525ba 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -20,6 +20,9 @@ python3_add_library(_sparsediffengine MODULE
 
 target_include_directories(_sparsediffengine PRIVATE
     ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include
+    ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/atoms
+    ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/utils
+    ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/old-code
     ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/src
     ${CMAKE_CURRENT_SOURCE_DIR}/sparsediffpy/_bindings
 )
diff --git a/SparseDiffEngine b/SparseDiffEngine
deleted file mode 160000
index 7e7875d..0000000
--- a/SparseDiffEngine
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7e7875df92f92b0ef2ecd431d77174768aa22e01
diff --git a/SparseDiffEngine b/SparseDiffEngine
new file mode 120000
index 0000000..848f405
--- /dev/null
+++ b/SparseDiffEngine
@@ -0,0 +1 @@
+../SparseDiffEngine
\ No newline at end of file
diff --git a/sparsediffpy/_bindings/atoms/const_scalar_mult.h b/sparsediffpy/_bindings/atoms/const_scalar_mult.h
index 1a83e5a..121e0c7 100644
--- a/sparsediffpy/_bindings/atoms/const_scalar_mult.h
+++ b/sparsediffpy/_bindings/atoms/const_scalar_mult.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_CONST_SCALAR_MULT_H
 #define ATOM_CONST_SCALAR_MULT_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Constant scalar multiplication: a * f(x) where a is a constant double */
diff --git a/sparsediffpy/_bindings/atoms/const_vector_mult.h b/sparsediffpy/_bindings/atoms/const_vector_mult.h
index aa1f83e..ddb34f7 100644
--- a/sparsediffpy/_bindings/atoms/const_vector_mult.h
+++ b/sparsediffpy/_bindings/atoms/const_vector_mult.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_CONST_VECTOR_MULT_H
 #define ATOM_CONST_VECTOR_MULT_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Constant vector elementwise multiplication: a ∘ f(x) where a is a constant vector
diff --git a/sparsediffpy/_bindings/atoms/dense_matmul.h b/sparsediffpy/_bindings/atoms/dense_matmul.h
index d8aef8f..48a8ba9 100644
--- a/sparsediffpy/_bindings/atoms/dense_matmul.h
+++ b/sparsediffpy/_bindings/atoms/dense_matmul.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_DENSE_MATMUL_H
 #define ATOM_DENSE_MATMUL_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Dense left matrix multiplication: A @ f(x) where A is a dense matrix.
diff --git a/sparsediffpy/_bindings/atoms/left_matmul.h b/sparsediffpy/_bindings/atoms/left_matmul.h
index 09fa985..1e013c9 100644
--- a/sparsediffpy/_bindings/atoms/left_matmul.h
+++ b/sparsediffpy/_bindings/atoms/left_matmul.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_LEFT_MATMUL_H
 #define ATOM_LEFT_MATMUL_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Left matrix multiplication: A @ f(x) where A is a constant matrix */
diff --git a/sparsediffpy/_bindings/atoms/matmul.h b/sparsediffpy/_bindings/atoms/matmul.h
index 9bfe859..f6f589d 100644
--- a/sparsediffpy/_bindings/atoms/matmul.h
+++ b/sparsediffpy/_bindings/atoms/matmul.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_MATMUL_H
 #define ATOM_MATMUL_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Matrix multiplication: Z = X @ Y */
diff --git a/sparsediffpy/_bindings/atoms/multiply.h b/sparsediffpy/_bindings/atoms/multiply.h
index 5403b38..20db37b 100644
--- a/sparsediffpy/_bindings/atoms/multiply.h
+++ b/sparsediffpy/_bindings/atoms/multiply.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_MULTIPLY_H
 #define ATOM_MULTIPLY_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 static PyObject *py_make_multiply(PyObject *self, PyObject *args)
diff --git a/sparsediffpy/_bindings/atoms/prod.h b/sparsediffpy/_bindings/atoms/prod.h
index 9e15818..120d9ba 100644
--- a/sparsediffpy/_bindings/atoms/prod.h
+++ b/sparsediffpy/_bindings/atoms/prod.h
@@ -3,7 +3,7 @@
 #define ATOM_PROD_H
 
 #include "common.h"
-#include "other.h"
+#include "non_elementwise_full_dom.h"
 
 static PyObject *py_make_prod(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/prod_axis_one.h b/sparsediffpy/_bindings/atoms/prod_axis_one.h
index d9c3b8a..c532f6b 100644
--- a/sparsediffpy/_bindings/atoms/prod_axis_one.h
+++ b/sparsediffpy/_bindings/atoms/prod_axis_one.h
@@ -2,7 +2,7 @@
 #define ATOM_PROD_AXIS_ONE_H
 
 #include "common.h"
-#include "other.h"
+#include "non_elementwise_full_dom.h"
 
 static PyObject *py_make_prod_axis_one(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/prod_axis_zero.h b/sparsediffpy/_bindings/atoms/prod_axis_zero.h
index 02b30f0..e726076 100644
--- a/sparsediffpy/_bindings/atoms/prod_axis_zero.h
+++ b/sparsediffpy/_bindings/atoms/prod_axis_zero.h
@@ -3,7 +3,7 @@
 #define ATOM_PROD_AXIS_ZERO_H
 
 #include "common.h"
-#include "other.h"
+#include "non_elementwise_full_dom.h"
 
 static PyObject *py_make_prod_axis_zero(PyObject *self, PyObject *args)
 {
diff --git a/sparsediffpy/_bindings/atoms/quad_form.h b/sparsediffpy/_bindings/atoms/quad_form.h
index 036640a..de7fe89 100644
--- a/sparsediffpy/_bindings/atoms/quad_form.h
+++ b/sparsediffpy/_bindings/atoms/quad_form.h
@@ -2,7 +2,7 @@
 #define ATOM_QUAD_FORM_H
 
 #include "common.h"
-#include "other.h"
+#include "non_elementwise_full_dom.h"
 
 /* Quadratic form: y = x' * Q * x where Q is a constant matrix */
 static PyObject *py_make_quad_form(PyObject *self, PyObject *args)
diff --git a/sparsediffpy/_bindings/atoms/quad_over_lin.h b/sparsediffpy/_bindings/atoms/quad_over_lin.h
index d063c8a..a7047e8 100644
--- a/sparsediffpy/_bindings/atoms/quad_over_lin.h
+++ b/sparsediffpy/_bindings/atoms/quad_over_lin.h
@@ -3,7 +3,7 @@
 #ifndef ATOM_QUAD_OVER_LIN_H
 #define ATOM_QUAD_OVER_LIN_H
 
-#include "bivariate.h"
+#include "bivariate_restricted_dom.h"
 #include "common.h"
 
 /* quad_over_lin: y = sum(x^2) / z where x is left, z is right (scalar) */
diff --git a/sparsediffpy/_bindings/atoms/rel_entr.h b/sparsediffpy/_bindings/atoms/rel_entr.h
index 1b74318..d7e8cc5 100644
--- a/sparsediffpy/_bindings/atoms/rel_entr.h
+++ b/sparsediffpy/_bindings/atoms/rel_entr.h
@@ -3,7 +3,7 @@
 #ifndef ATOM_REL_ENTR_H
 #define ATOM_REL_ENTR_H
 
-#include "bivariate.h"
+#include "bivariate_restricted_dom.h"
 #include "common.h"
 
 /* rel_entr: rel_entr(x, y) = x * log(x/y) elementwise */
diff --git a/sparsediffpy/_bindings/atoms/rel_entr_scalar_vector.h b/sparsediffpy/_bindings/atoms/rel_entr_scalar_vector.h
index 85bcfe7..65d1708 100644
--- a/sparsediffpy/_bindings/atoms/rel_entr_scalar_vector.h
+++ b/sparsediffpy/_bindings/atoms/rel_entr_scalar_vector.h
@@ -3,7 +3,7 @@
 #ifndef ATOM_REL_ENTR_SCALAR_VECTOR_H
 #define ATOM_REL_ENTR_SCALAR_VECTOR_H
 
-#include "bivariate.h"
+#include "bivariate_restricted_dom.h"
 #include "common.h"
 
 /* rel_entr_scalar_vector: rel_entr(x, y) where x is scalar, y is vector */
diff --git a/sparsediffpy/_bindings/atoms/rel_entr_vector_scalar.h b/sparsediffpy/_bindings/atoms/rel_entr_vector_scalar.h
index d671646..eb05c15 100644
--- a/sparsediffpy/_bindings/atoms/rel_entr_vector_scalar.h
+++ b/sparsediffpy/_bindings/atoms/rel_entr_vector_scalar.h
@@ -3,7 +3,7 @@
 #ifndef ATOM_REL_ENTR_VECTOR_SCALAR_H
 #define ATOM_REL_ENTR_VECTOR_SCALAR_H
 
-#include "bivariate.h"
+#include "bivariate_restricted_dom.h"
 #include "common.h"
 
 /* rel_entr_vector_scalar: rel_entr(x, y) where x is vector, y is scalar */
diff --git a/sparsediffpy/_bindings/atoms/right_matmul.h b/sparsediffpy/_bindings/atoms/right_matmul.h
index f808058..3547837 100644
--- a/sparsediffpy/_bindings/atoms/right_matmul.h
+++ b/sparsediffpy/_bindings/atoms/right_matmul.h
@@ -1,7 +1,7 @@
 #ifndef ATOM_RIGHT_MATMUL_H
 #define ATOM_RIGHT_MATMUL_H
 
-#include "bivariate.h"
+#include "bivariate_full_dom.h"
 #include "common.h"
 
 /* Right matrix multiplication: f(x) @ A where A is a constant matrix */
diff --git a/sparsediffpy/_bindings/bindings.c b/sparsediffpy/_bindings/bindings.c
index cbda8e0..e7b30f5 100644
--- a/sparsediffpy/_bindings/bindings.c
+++ b/sparsediffpy/_bindings/bindings.c
@@ -19,7 +19,6 @@
 #include "atoms/hstack.h"
 #include "atoms/index.h"
 #include "atoms/left_matmul.h"
-#include "atoms/linear.h"
 #include "atoms/log.h"
 #include "atoms/logistic.h"
 #include "atoms/matmul.h"
@@ -72,7 +71,6 @@ static int ensure_numpy(void)
 static PyMethodDef DNLPMethods[] = {
     {"make_variable", py_make_variable, METH_VARARGS, "Create variable node"},
     {"make_constant", py_make_constant, METH_VARARGS, "Create constant node"},
-    {"make_linear", py_make_linear, METH_VARARGS, "Create linear op node"},
     {"make_log", py_make_log, METH_VARARGS, "Create log node"},
     {"make_exp", py_make_exp, METH_VARARGS, "Create exp node"},
     {"make_index", py_make_index, METH_VARARGS, "Create index node"},

From 796196c3beaf886a0f40fe3d1a6254f74439ba77 Mon Sep 17 00:00:00 2001
From: dance858 <danielcederberg1@gmail.com>
Date: Tue, 31 Mar 2026 07:16:43 -0700
Subject: [PATCH 3/3] bump version to 0.1.6 and update SparseDiffEngine
 submodule

---
 SparseDiffEngine | 2 +-
 pyproject.toml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 mode change 120000 => 160000 SparseDiffEngine

diff --git a/SparseDiffEngine b/SparseDiffEngine
deleted file mode 120000
index 848f405..0000000
--- a/SparseDiffEngine
+++ /dev/null
@@ -1 +0,0 @@
-../SparseDiffEngine
\ No newline at end of file
diff --git a/SparseDiffEngine b/SparseDiffEngine
new file mode 160000
index 0000000..b9d282f
--- /dev/null
+++ b/SparseDiffEngine
@@ -0,0 +1 @@
+Subproject commit b9d282f04d4347af2420e64a48e00c2c2e5da882
diff --git a/pyproject.toml b/pyproject.toml
index bcd5837..9edacec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "sparsediffpy"
-version = "0.1.5"
+version = "0.1.6"
 description = "Python bindings for SparseDiffEngine automatic differentiation"
 requires-python = ">=3.11"
 dependencies = ["numpy >= 2.0.0"]