From 9ba8cd9319bd99a5fd753eeb77fd5845990f89a0 Mon Sep 17 00:00:00 2001
From: Navaneet Villodi <11260095+nauaneed@users.noreply.github.com>
Date: Thu, 26 Sep 2024 23:38:55 +0530
Subject: [PATCH 1/5] ci(deps): install nothing separately

let pip handle all the dependencies while installing this package
---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6e26198..ab16e31 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -20,8 +20,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install -r requirements.txt
-          pip install .
+          pip install .[tests] -v
+          pip list
       - name: Run tests
         run: pytest -v --pyargs cyarray --benchmark-save benchmark-stats --benchmark-json benchmark-full.json --benchmark-histogram
 

From a97d0a9f6ea5af6929629fd234497410212d0a48 Mon Sep 17 00:00:00 2001
From: Navaneet Villodi <11260095+nauaneed@users.noreply.github.com>
Date: Thu, 26 Sep 2024 23:39:43 +0530
Subject: [PATCH 2/5] chore(deps): req in pyproject.toml, not setup.py

---
 pyproject.toml | 34 ++++++++++++++++++++++++++++++++++
 setup.py       | 13 -------------
 2 files changed, 34 insertions(+), 13 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5b68acd..5c90bee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,3 +6,37 @@ requires = [
     "Cython",
     "mako"
 ]
+
+[project]
+name = "cyarray"
+dynamic = ["version"]
+readme = "README.rst"
+license = {file = "LICENSE.txt"}
+dependencies = ['numpy']
+description = "A fast, typed, resizable, Cython array."
+authors = [
+  {name = "Cyarray Developers", email = "pysph-dev@googlegroups.com"}
+]
+keywords = ["Cython", "array", "resizable"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries",
+]
+
+[project.optional-dependencies]
+docs = ["sphinx"]
+tests = ["pytest", "pytest-benchmark[histogram]"]
+dev = ["sphinx", "pytest", "pytest-benchmark[histogram]", "cython"]
diff --git a/setup.py b/setup.py
index 3801e83..721a8c4 100644
--- a/setup.py
+++ b/setup.py
@@ -85,13 +85,6 @@ def setup_package():
     module = os.path.join('cyarray', '__init__.py')
     exec(compile(open(module).read(), module, 'exec'), info)
 
-    # The requirements.
-    install_requires = [
-        'numpy', 'mako', 'Cython', 'setuptools>=6.0'
-    ]
-    tests_require = ["pytest", "pytest-benchmark[histogram]"]
-    docs_require = ["sphinx"]
-
     ext_modules = get_basic_extensions()
     if MODE != 'info' and _is_cythonize_default():
         # Cython >= 0.25 uses cythonize to compile the extensions. This
@@ -128,12 +121,6 @@ def setup_package():
           ext_modules=ext_modules,
           include_package_data=True,
           cmdclass=cmdclass,
-          install_requires=install_requires,
-          extras_require={
-              "docs": docs_require,
-              "tests": tests_require,
-              "dev": docs_require + tests_require,
-          },
           zip_safe=False,
           platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
           classifiers=[c.strip() for c in """\

From e242bced0a076884869a3766f33afb7d2bdc84a7 Mon Sep 17 00:00:00 2001
From: Navaneet Villodi <11260095+nauaneed@users.noreply.github.com>
Date: Thu, 26 Sep 2024 23:48:53 +0530
Subject: [PATCH 3/5] chore: no more depend on pre-NumPy-1.7 C-API

Ref: https://cython.readthedocs.io/en/latest/src/userguide/migrating_to_cy30.html
---
 cyarray/carray.pyx      | 206 ++++++++++++++++++++++++----------------
 cyarray/carray.pyx.mako |  62 ++++++++----
 2 files changed, 166 insertions(+), 102 deletions(-)

diff --git a/cyarray/carray.pyx b/cyarray/carray.pyx
index 29cf108..dbf770f 100644
--- a/cyarray/carray.pyx
+++ b/cyarray/carray.pyx
@@ -3,6 +3,7 @@
 # To make changes modify the source templates (carray.pxd.mako) and regenerate
 # distutils: language=c++
 # cython: embedsignature=True, language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
 """
 Implementation of resizeable arrays of different types in Cython.
 
@@ -58,6 +59,10 @@ cdef extern from "numpy/arrayobject.h":
 
     np.ndarray PyArray_SimpleNewFromData(int, np.npy_intp*, int, void*)
 
+    void *PyArray_DATA(np.ndarray arr) noexcept nogil
+
+    np.npy_intp *PyArray_DIMS(np.ndarray arr) noexcept nogil
+
 
 # memcpy
 cdef extern from "stdlib.h":
@@ -68,7 +73,7 @@ cdef extern from "stdlib.h":
 cdef extern from *:
     """
     static void PyArray_SET_DATA(PyArrayObject *arr, char * data) {
-        arr->data = data;
+        ((PyArrayObject_fields *)arr)->data = data;
     }
     """
     void PyArray_SET_DATA(np.ndarray arr, char * data) noexcept nogil
@@ -161,9 +166,10 @@ cdef class BaseArray:
         pass
 
     cdef void c_reset(self) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *dims
         self.length = 0
-        arr.dimensions[0] = self.length
+        dims = PyArray_DIMS(self._npy_array)
+        dims[0] = self.length
 
     cdef void c_resize(self, long size) noexcept nogil:
         pass
@@ -203,11 +209,19 @@ cdef class BaseArray:
         """
         cdef PyArrayObject* sarr = <PyArrayObject*>nparr
         cdef PyArrayObject* darr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *s_dims, *d_dims
+        cdef void *s_data, *d_data
+    
+        s_data = PyArray_DATA(nparr)
+        d_data = PyArray_DATA(self._npy_array)
+
+        s_dims = PyArray_DIMS(nparr)
+        d_dims = PyArray_DIMS(self._npy_array)
 
-        if sarr.data == darr.data:
+        if s_data == d_data:
             return
-        elif sarr.dimensions[0] <= darr.dimensions[0]:
-            self._npy_array[:sarr.dimensions[0]] = nparr
+        elif s_dims[0] <= d_dims[0]:
+            self._npy_array[:s_dims[0]] = nparr
         else:
             raise ValueError, 'array size mismatch'
 
@@ -426,7 +440,7 @@ cdef class IntArray(BaseArray):
 
     cdef void c_append(self, int value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -434,10 +448,10 @@ cdef class IntArray(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <int*>aligned_realloc(
@@ -452,7 +466,7 @@ cdef class IntArray(BaseArray):
 
             self.data = <int*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -462,26 +476,29 @@ cdef class IntArray(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, int *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -500,7 +517,7 @@ cdef class IntArray(BaseArray):
 
         self.data = <int*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
 
     cpdef str get_c_type(self):
@@ -567,14 +584,16 @@ cdef class IntArray(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -617,7 +636,7 @@ cdef class IntArray(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -640,7 +659,8 @@ cdef class IntArray(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
@@ -931,7 +951,7 @@ cdef class UIntArray(BaseArray):
 
     cdef void c_append(self, unsigned int value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -939,10 +959,10 @@ cdef class UIntArray(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <unsigned int*>aligned_realloc(
@@ -957,7 +977,7 @@ cdef class UIntArray(BaseArray):
 
             self.data = <unsigned int*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -967,26 +987,29 @@ cdef class UIntArray(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, unsigned int *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -1005,7 +1028,7 @@ cdef class UIntArray(BaseArray):
 
         self.data = <unsigned int*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
 
     cpdef str get_c_type(self):
@@ -1072,14 +1095,16 @@ cdef class UIntArray(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -1122,7 +1147,7 @@ cdef class UIntArray(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -1145,7 +1170,8 @@ cdef class UIntArray(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
@@ -1436,7 +1462,7 @@ cdef class LongArray(BaseArray):
 
     cdef void c_append(self, long value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -1444,10 +1470,10 @@ cdef class LongArray(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <long*>aligned_realloc(
@@ -1462,7 +1488,7 @@ cdef class LongArray(BaseArray):
 
             self.data = <long*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -1472,26 +1498,29 @@ cdef class LongArray(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, long *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -1510,7 +1539,7 @@ cdef class LongArray(BaseArray):
 
         self.data = <long*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
 
     cpdef str get_c_type(self):
@@ -1577,14 +1606,16 @@ cdef class LongArray(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -1627,7 +1658,7 @@ cdef class LongArray(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -1650,7 +1681,8 @@ cdef class LongArray(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
@@ -1941,7 +1973,7 @@ cdef class FloatArray(BaseArray):
 
     cdef void c_append(self, float value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -1949,10 +1981,10 @@ cdef class FloatArray(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <float*>aligned_realloc(
@@ -1967,7 +1999,7 @@ cdef class FloatArray(BaseArray):
 
             self.data = <float*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -1977,26 +2009,29 @@ cdef class FloatArray(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, float *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -2015,7 +2050,7 @@ cdef class FloatArray(BaseArray):
 
         self.data = <float*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
 
     cpdef str get_c_type(self):
@@ -2082,14 +2117,16 @@ cdef class FloatArray(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -2132,7 +2169,7 @@ cdef class FloatArray(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -2155,7 +2192,8 @@ cdef class FloatArray(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
@@ -2446,7 +2484,7 @@ cdef class DoubleArray(BaseArray):
 
     cdef void c_append(self, double value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -2454,10 +2492,10 @@ cdef class DoubleArray(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <double*>aligned_realloc(
@@ -2472,7 +2510,7 @@ cdef class DoubleArray(BaseArray):
 
             self.data = <double*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -2482,26 +2520,29 @@ cdef class DoubleArray(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, double *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -2520,7 +2561,7 @@ cdef class DoubleArray(BaseArray):
 
         self.data = <double*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
 
     cpdef str get_c_type(self):
@@ -2587,14 +2628,16 @@ cdef class DoubleArray(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -2637,7 +2680,7 @@ cdef class DoubleArray(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -2660,7 +2703,8 @@ cdef class DoubleArray(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
diff --git a/cyarray/carray.pyx.mako b/cyarray/carray.pyx.mako
index cf75c31..5f44ebb 100644
--- a/cyarray/carray.pyx.mako
+++ b/cyarray/carray.pyx.mako
@@ -12,6 +12,7 @@ type_info = [
 # To make changes modify the source templates (carray.pxd.mako) and regenerate
 # distutils: language=c++
 # cython: embedsignature=True, language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
 """
 Implementation of resizeable arrays of different types in Cython.
 
@@ -67,6 +68,10 @@ cdef extern from "numpy/arrayobject.h":
 
     np.ndarray PyArray_SimpleNewFromData(int, np.npy_intp*, int, void*)
 
+    void *PyArray_DATA(np.ndarray arr) noexcept nogil
+
+    np.npy_intp *PyArray_DIMS(np.ndarray arr) noexcept nogil
+
 
 # memcpy
 cdef extern from "stdlib.h":
@@ -77,7 +82,7 @@ cdef extern from "stdlib.h":
 cdef extern from *:
     """
     static void PyArray_SET_DATA(PyArrayObject *arr, char * data) {
-        arr->data = data;
+        ((PyArrayObject_fields *)arr)->data = data;
     }
     """
     void PyArray_SET_DATA(np.ndarray arr, char * data) noexcept nogil
@@ -171,9 +176,10 @@ cdef class BaseArray:
         pass
 
     cdef void c_reset(self) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *dims
         self.length = 0
-        arr.dimensions[0] = self.length
+        dims = PyArray_DIMS(self._npy_array)
+        dims[0] = self.length
 
     cdef void c_resize(self, long size) noexcept nogil:
         pass
@@ -214,11 +220,19 @@ cdef class BaseArray:
         """
         cdef PyArrayObject* sarr = <PyArrayObject*>nparr
         cdef PyArrayObject* darr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *s_dims, *d_dims
+        cdef void *s_data, *d_data
+    
+        s_data = PyArray_DATA(nparr)
+        d_data = PyArray_DATA(self._npy_array)
+
+        s_dims = PyArray_DIMS(nparr)
+        d_dims = PyArray_DIMS(self._npy_array)
 
-        if sarr.data == darr.data:
+        if s_data == d_data:
             return
-        elif sarr.dimensions[0] <= darr.dimensions[0]:
-            self._npy_array[:sarr.dimensions[0]] = nparr
+        elif s_dims[0] <= d_dims[0]:
+            self._npy_array[:s_dims[0]] = nparr
         else:
             raise ValueError, 'array size mismatch'
 
@@ -439,7 +453,7 @@ cdef class ${CLASSNAME}(BaseArray):
 
     cdef void c_append(self, ${ARRAY_TYPE} value) noexcept nogil:
         cdef long l = self.length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if l >= self.alloc:
             self.c_reserve(l*2)
@@ -447,10 +461,10 @@ cdef class ${CLASSNAME}(BaseArray):
         self.length += 1
 
         # update the numpy arrays length
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_reserve(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
         cdef void* data = NULL
         if size > self.alloc:
             data = <${ARRAY_TYPE}*>aligned_realloc(
@@ -465,7 +479,7 @@ cdef class ${CLASSNAME}(BaseArray):
 
             self.data = <${ARRAY_TYPE}*>data
             self.alloc = size
-            arr.data = <char *>self.data
+            PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_reset(self) noexcept nogil:
         BaseArray.c_reset(self)
@@ -475,26 +489,29 @@ cdef class ${CLASSNAME}(BaseArray):
             PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     cdef void c_resize(self, long size) noexcept nogil:
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         # reserve memory
         self.c_reserve(size)
 
         # update the lengths
         self.length = size
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_set_view(self, ${ARRAY_TYPE} *array, long length) noexcept nogil:
         """Create a view of a given raw data pointer with given length.
         """
+        cdef np.npy_intp *arr_dims
+
         if self._old_data == NULL:
             self._old_data = self.data
 
         self.data = array
         self.length = length
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cdef void c_squeeze(self) noexcept nogil:
         cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
@@ -513,7 +530,7 @@ cdef class ${CLASSNAME}(BaseArray):
 
         self.data = <${ARRAY_TYPE}*>data
         self.alloc = size
-        arr.data = <char *>self.data
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
 
     ##### Python protocol ######################################
 
@@ -581,14 +598,16 @@ cdef class ${CLASSNAME}(BaseArray):
             itself.
 
         """
+        cdef np.npy_intp *arr_dims
+
         if self._parent is None:
             self._old_data = self.data
         self._parent = parent
         self.data = parent.data + start
         self.length = end - start
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
-        arr.data = <char *>self.data
-        arr.dimensions[0] = self.length
+        PyArray_SET_DATA(self._npy_array, <char *>self.data)
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef squeeze(self):
         """Release any unused memory.
@@ -631,7 +650,7 @@ cdef class ${CLASSNAME}(BaseArray):
         cdef long inlength = index_list.size
         cdef np.ndarray sorted_indices
         cdef long id
-        cdef PyArrayObject* arr = <PyArrayObject*>self._npy_array
+        cdef np.npy_intp *arr_dims
 
         if inlength > self.length:
             return
@@ -654,7 +673,8 @@ cdef class ${CLASSNAME}(BaseArray):
                     for j in range(stride):
                         self.data[id + j] = self.data[self.length - stride + j]
                     self.length = self.length - stride
-        arr.dimensions[0] = self.length
+        arr_dims = PyArray_DIMS(self._npy_array)
+        arr_dims[0] = self.length
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.

From 7aabc02730f1f169a19c0adc262814510c8a12b8 Mon Sep 17 00:00:00 2001
From: Navaneet Villodi <11260095+nauaneed@users.noreply.github.com>
Date: Fri, 27 Sep 2024 00:24:45 +0530
Subject: [PATCH 4/5] chore: update `raise` syntax

---
 cyarray/carray.pyx      |  2 +-
 cyarray/carray.pyx.mako | 22 +++++++++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/cyarray/carray.pyx b/cyarray/carray.pyx
index dbf770f..b6c7bc1 100644
--- a/cyarray/carray.pyx
+++ b/cyarray/carray.pyx
@@ -223,7 +223,7 @@ cdef class BaseArray:
         elif s_dims[0] <= d_dims[0]:
             self._npy_array[:s_dims[0]] = nparr
         else:
-            raise ValueError, 'array size mismatch'
+            raise ValueError('array size mismatch')
 
     cpdef squeeze(self):
         """Release any unused memory.
diff --git a/cyarray/carray.pyx.mako b/cyarray/carray.pyx.mako
index 5f44ebb..03f92f8 100644
--- a/cyarray/carray.pyx.mako
+++ b/cyarray/carray.pyx.mako
@@ -192,17 +192,17 @@ cdef class BaseArray:
     cpdef str get_c_type(self):
         """Return the c data type of this array.
         """
-        raise NotImplementedError, 'BaseArray::get_c_type'
+        raise NotImplementedError('BaseArray::get_c_type')
 
     cpdef reserve(self, long size):
         """Resizes the internal data to required size.
         """
-        raise NotImplementedError, 'BaseArray::reserve'
+        raise NotImplementedError(BaseArray::reserve')
 
     cpdef resize(self, long size):
         """Resizes the array to the new size.
         """
-        raise NotImplementedError, 'BaseArray::resize'
+        raise NotImplementedError(BaseArray::resize)
 
     cpdef np.ndarray get_npy_array(self):
         """Returns a numpy array of the data: do not keep its reference.
@@ -234,22 +234,22 @@ cdef class BaseArray:
         elif s_dims[0] <= d_dims[0]:
             self._npy_array[:s_dims[0]] = nparr
         else:
-            raise ValueError, 'array size mismatch'
+            raise ValueError('array size mismatch')
 
     cpdef squeeze(self):
         """Release any unused memory.
         """
-        raise NotImplementedError, 'BaseArray::squeeze'
+        raise NotImplementedError('BaseArray::squeeze')
 
     cpdef remove(self, np.ndarray index_list, bint input_sorted=0, int stride=1):
         """Remove the particles with indices in index_list.
         """
-        raise NotImplementedError, 'BaseArray::remove'
+        raise NotImplementedError('BaseArray::remove')
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
         """
-        raise NotImplementedError, 'BaseArray::extend'
+        raise NotImplementedError('BaseArray::extend')
 
     cpdef align_array(self, LongArray new_indices, int stride=1):
         """Rearrange the array contents according to the new indices.
@@ -261,23 +261,23 @@ cdef class BaseArray:
     cpdef reset(self):
         """Reset the length of the array to 0.
         """
-        raise NotImplementedError, 'BaseArray::reset'
+        raise NotImplementedError('BaseArray::reset')
 
     cpdef copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0):
         """Copy values of indexed particles from self to dest.
         """
-        raise NotImplementedError, 'BaseArray::copy_values'
+        raise NotImplementedError('BaseArray::copy_values')
 
     cpdef copy_subset(self, BaseArray source,
                       long start_index=-1, long end_index=-1, int stride=1):
         """Copy subset of values from source to self.
         """
-        raise NotImplementedError, 'BaseArray::copy_subset'
+        raise NotImplementedError('BaseArray::copy_subset')
 
     cpdef update_min_max(self):
         """Update the min and max values of the array.
         """
-        raise NotImplementedError, 'BaseArray::update_min_max'
+        raise NotImplementedError('BaseArray::update_min_max')
 
     def __len__(self):
         return self.length

From 54ae678e01b99ae7ffd069539160bddbc104726a Mon Sep 17 00:00:00 2001
From: navaneet <navaneet@acni>
Date: Fri, 13 Dec 2024 19:40:43 +0530
Subject: [PATCH 5/5] fix(carray.pyx): silly errors

---
 cyarray/carray.pyx      | 20 ++++++++++----------
 cyarray/carray.pyx.mako |  4 ++--
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/cyarray/carray.pyx b/cyarray/carray.pyx
index b6c7bc1..808764a 100644
--- a/cyarray/carray.pyx
+++ b/cyarray/carray.pyx
@@ -181,17 +181,17 @@ cdef class BaseArray:
     cpdef str get_c_type(self):
         """Return the c data type of this array.
         """
-        raise NotImplementedError, 'BaseArray::get_c_type'
+        raise NotImplementedError('BaseArray::get_c_type')
 
     cpdef reserve(self, long size):
         """Resizes the internal data to required size.
         """
-        raise NotImplementedError, 'BaseArray::reserve'
+        raise NotImplementedError('BaseArray::reserve')
 
     cpdef resize(self, long size):
         """Resizes the array to the new size.
         """
-        raise NotImplementedError, 'BaseArray::resize'
+        raise NotImplementedError('BaseArray::resize')
 
     cpdef np.ndarray get_npy_array(self):
         """Returns a numpy array of the data: do not keep its reference.
@@ -228,17 +228,17 @@ cdef class BaseArray:
     cpdef squeeze(self):
         """Release any unused memory.
         """
-        raise NotImplementedError, 'BaseArray::squeeze'
+        raise NotImplementedError('BaseArray::squeeze')
 
     cpdef remove(self, np.ndarray index_list, bint input_sorted=0, int stride=1):
         """Remove the particles with indices in index_list.
         """
-        raise NotImplementedError, 'BaseArray::remove'
+        raise NotImplementedError('BaseArray::remove')
 
     cpdef extend(self, np.ndarray in_array):
         """Extend the array with data from in_array.
         """
-        raise NotImplementedError, 'BaseArray::extend'
+        raise NotImplementedError('BaseArray::extend')
 
     cpdef align_array(self, LongArray new_indices, int stride=1):
         """Rearrange the array contents according to the new indices.
@@ -250,23 +250,23 @@ cdef class BaseArray:
     cpdef reset(self):
         """Reset the length of the array to 0.
         """
-        raise NotImplementedError, 'BaseArray::reset'
+        raise NotImplementedError('BaseArray::reset')
 
     cpdef copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0):
         """Copy values of indexed particles from self to dest.
         """
-        raise NotImplementedError, 'BaseArray::copy_values'
+        raise NotImplementedError('BaseArray::copy_values')
 
     cpdef copy_subset(self, BaseArray source,
                       long start_index=-1, long end_index=-1, int stride=1):
         """Copy subset of values from source to self.
         """
-        raise NotImplementedError, 'BaseArray::copy_subset'
+        raise NotImplementedError('BaseArray::copy_subset')
 
     cpdef update_min_max(self):
         """Update the min and max values of the array.
         """
-        raise NotImplementedError, 'BaseArray::update_min_max'
+        raise NotImplementedError('BaseArray::update_min_max')
 
     def __len__(self):
         return self.length
diff --git a/cyarray/carray.pyx.mako b/cyarray/carray.pyx.mako
index 03f92f8..058b377 100644
--- a/cyarray/carray.pyx.mako
+++ b/cyarray/carray.pyx.mako
@@ -197,12 +197,12 @@ cdef class BaseArray:
     cpdef reserve(self, long size):
         """Resizes the internal data to required size.
         """
-        raise NotImplementedError(BaseArray::reserve')
+        raise NotImplementedError('BaseArray::reserve')
 
     cpdef resize(self, long size):
         """Resizes the array to the new size.
         """
-        raise NotImplementedError(BaseArray::resize)
+        raise NotImplementedError('BaseArray::resize')
 
     cpdef np.ndarray get_npy_array(self):
         """Returns a numpy array of the data: do not keep its reference.