make bindings consistent with sparsediffengine folder refactor (#11)

dance858 · web-flow · commit d9b72e9141d3 · 2026-03-31T07:37:05.000-07:00
* reflect sparsediffengine refactor in bindings'

* update includes to reflect sparsediffengine structure

* bump version to 0.1.6 and update SparseDiffEngine submodule
diff --git 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
@@ -1 +1 @@
-Subproject commit 7e7875df92f92b0ef2ecd431d77174768aa22e01
+Subproject commit b9d282f04d4347af2420e64a48e00c2c2e5da882
diff --git 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"]
diff --git 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
@@ -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
@@ -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/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
@@ -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/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/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/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/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/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/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
@@ -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/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/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/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
@@ -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
@@ -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
@@ -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
@@ -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)
 {
diff --git 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"},

Original file line number	Diff line number	Diff line change
`@@ -20,6 +20,9 @@ python3_add_library(_sparsediffengine MODULE`
`20`	`20`
`21`	`21`	`target_include_directories(_sparsediffengine PRIVATE`
`22`	`22`	`${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include`
	`23`	`+ ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/atoms`
	`24`	`+ ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/utils`
	`25`	`+ ${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/include/old-code`
`23`	`26`	`${CMAKE_CURRENT_SOURCE_DIR}/SparseDiffEngine/src`
`24`	`27`	`${CMAKE_CURRENT_SOURCE_DIR}/sparsediffpy/_bindings`
`25`	`28`	`)`
Original file line number	Diff line number	Diff line change
`@@ -2,7 +2,7 @@`
`2`	`2`	`#define ATOM_ASINH_H`
`3`	`3`
`4`	`4`	`#include "common.h"`
`5`		`-#include "elementwise_univariate.h"`
	`5`	`+#include "elementwise_full_dom.h"`
`6`	`6`
`7`	`7`	`static PyObject py_make_asinh(PyObject self, PyObject *args)`
`8`	`8`	`{`
Original file line number	Diff line number	Diff line change
`@@ -2,7 +2,7 @@`
`2`	`2`	`#define ATOM_ATANH_H`
`3`	`3`
`4`	`4`	`#include "common.h"`
`5`		`-#include "elementwise_univariate.h"`
	`5`	`+#include "elementwise_restricted_dom.h"`
`6`	`6`
`7`	`7`	`static PyObject py_make_atanh(PyObject self, PyObject *args)`
`8`	`8`	`{`
Original file line number	Diff line number	Diff line change
`@@ -2,7 +2,7 @@`
`2`	`2`	`#define ATOM_COS_H`
`3`	`3`
`4`	`4`	`#include "common.h"`
`5`		`-#include "elementwise_univariate.h"`
	`5`	`+#include "elementwise_full_dom.h"`
`6`	`6`
`7`	`7`	`static PyObject py_make_cos(PyObject self, PyObject *args)`
`8`	`8`	`{`