Merge pull request #61 from TREX-CoE/fix-numpy-dependency

Pin minimal required numpy versions
2024-08-24 22:21:43 +02:00 · 2021-09-30 21:46:00 +02:00 · 2021-09-30 21:46:00 +02:00 · 0cba81fc38
commit 0cba81fc38
parent 1ba0876d81 35cb07d11b
6 changed files with 203 additions and 29 deletions
--- a/configure.ac
+++ b/configure.ac
@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.

 AC_PREREQ([2.69])
-AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio], [1.0.0], [https://github.com/TREX-CoE/trexio/issues])
 AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
 AM_MAINTAINER_MODE()
 LT_PREREQ([2.2])
--- a/docker/build_manylinux_wheels.sh
+++ b/docker/build_manylinux_wheels.sh
@ -58,7 +58,14 @@ function build_wheel_for_py()
   # upgrade pip, otherwise it complains that manylinux wheel is "...not supported wheel on this platform"
   pip install --upgrade pip 
   # install dependencies needed to build manylinux wheel
-   pip install --upgrade setuptools wheel auditwheel numpy
+   pip install --upgrade setuptools wheel auditwheel
+   if [ ${PYVERSION} -eq 36 ] || [ ${PYVERSION} -eq 37 ]; then
+       pip install numpy==1.17.3
+   elif [ ${PYVERSION} -eq 38 ]; then
+       pip install numpy==1.18.3
+   else
+       pip install numpy==1.19.3
+   fi

   # set an environment variable needed to locate numpy header files
   source tools/set_NUMPY_INCLUDEDIR.sh
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@ -2,6 +2,19 @@
 requires = [
    "setuptools>=42",
    "wheel",
-    "pkgconfig"
+    "pkgconfig",
+    # Numpy requirements for different OS/architectures
+    # Copied from https://github.com/scipy/scipy/blob/master/pyproject.toml (which is also licensed under BSD)
+    "numpy==1.17.3; python_version=='3.6' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64'",
+    "numpy==1.17.3; python_version=='3.7' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64'",
+    "numpy==1.18.3; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64'",
+    "numpy==1.19.3; python_version>='3.9' and (platform_machine!='arm64' or platform_system!='Darwin')",
+    # Aarch64(Python 3.9 requirements are the same as AMD64)
+    "numpy==1.19.2; python_version=='3.6' and platform_machine=='aarch64'",
+    "numpy==1.19.2; python_version=='3.7' and platform_machine=='aarch64'",
+    "numpy==1.19.2; python_version=='3.8' and platform_machine=='aarch64'",
+    # Darwin Arm64
+    "numpy>=1.20.0; python_version=='3.8' and platform_machine=='arm64' and platform_system=='Darwin'",
+    "numpy>=1.20.0; python_version=='3.9' and platform_machine=='arm64' and platform_system=='Darwin'"
 ]
 build-backend = "setuptools.build_meta"
--- a/python/requirements.txt
+++ b/python/requirements.txt
@ -1,3 +1,3 @@
 setuptools>=42
 pkgconfig
-numpy
+numpy>=1.17.3
--- a/python/setup.py
+++ b/python/setup.py
@ -113,7 +113,6 @@ setup(name             = 'trexio',
         "Operating System :: MacOS"
      ],
      python_requires = ">=3.6",
-      setup_requires = ['numpy', 'pkgconfig'],
-      install_requires = ['numpy']
+      install_requires = ['numpy>=1.17.3']
      )

--- a/src/numpy.i
+++ b/src/numpy.i
@ -114,12 +114,17 @@
    if (py_obj == NULL          ) return "C NULL value";
    if (py_obj == Py_None       ) return "Python None" ;
    if (PyCallable_Check(py_obj)) return "callable"    ;
-    if (PyBytes_Check(   py_obj)) return "string"      ;
-    if (PyLong_Check(    py_obj)) return "int"         ;
+    if (PyString_Check(  py_obj)) return "string"      ;
+    if (PyInt_Check(     py_obj)) return "int"         ;
    if (PyFloat_Check(   py_obj)) return "float"       ;
    if (PyDict_Check(    py_obj)) return "dict"        ;
    if (PyList_Check(    py_obj)) return "list"        ;
    if (PyTuple_Check(   py_obj)) return "tuple"       ;
+%#if PY_MAJOR_VERSION < 3
+    if (PyFile_Check(    py_obj)) return "file"        ;
+    if (PyModule_Check(  py_obj)) return "module"      ;
+    if (PyInstance_Check(py_obj)) return "instance"    ;
+%#endif

    return "unknown type";
  }
@ -540,7 +545,7 @@
    const npy_intp *dims = array_dimensions(ary);
    for (i=0; i < nd; ++i)
      n_non_one += (dims[i] != 1) ? 1 : 0;
-    if (n_non_one > 1)
+    if (n_non_one > 1)    
      array_clearflags(ary,NPY_ARRAY_CARRAY);
    array_enableflags(ary,NPY_ARRAY_FARRAY);
    /* Recompute the strides */
@ -2002,7 +2007,7 @@
  (PyObject* array = NULL)
 {
  npy_intp dims[1];
-  if (!PyLong_Check($input))
+  if (!PyInt_Check($input))
  {
    const char* typestring = pytype_string($input);
    PyErr_Format(PyExc_TypeError,
@ -2010,8 +2015,7 @@
                 typestring);
    SWIG_fail;
  }
-  $2 = (DIM_TYPE) PyLong_AsSsize_t($input);
-  if ($2 == -1 && PyErr_Occurred()) SWIG_fail;
+  $2 = (DIM_TYPE) PyInt_AsLong($input);
  dims[0] = (npy_intp) $2;
  array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
  if (!array) SWIG_fail;
@ -2031,7 +2035,7 @@
  (PyObject* array = NULL)
 {
  npy_intp dims[1];
-  if (!PyLong_Check($input))
+  if (!PyInt_Check($input))
  {
    const char* typestring = pytype_string($input);
    PyErr_Format(PyExc_TypeError,
@ -2039,8 +2043,7 @@
                 typestring);
    SWIG_fail;
  }
-  $1 = (DIM_TYPE) PyLong_AsSsize_t($input);
-  if ($1 == -1 && PyErr_Occurred()) SWIG_fail;
+  $1 = (DIM_TYPE) PyInt_AsLong($input);
  dims[0] = (npy_intp) $1;
  array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
  if (!array) SWIG_fail;
@ -2494,9 +2497,9 @@
  if (!array) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$2), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$2), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2564,9 +2567,9 @@
  if (!array) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$3), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2634,9 +2637,9 @@
  if (!array || !require_fortran(array)) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$3), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2708,9 +2711,9 @@
  if (!array) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$4), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2782,9 +2785,9 @@
  if (!array || !require_fortran(array)) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$4), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2858,9 +2861,161 @@
  if (!array) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$5), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+  PyArray_BASE(array) = cap;
+%#else
+  PyArray_SetBaseObject(array,cap);
+%#endif
+
+  $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+                      DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+  (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1    , DIM_TYPE* DIM2    , DIM_TYPE* DIM3    , DIM_TYPE* DIM4    )
+  (DATA_TYPE* data_temp = NULL    , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+  $1 = &data_temp;
+  $2 = &dim1_temp;
+  $3 = &dim2_temp;
+  $4 = &dim3_temp;
+  $5 = &dim4_temp;
+}
+%typemap(argout,
+         fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+  (DATA_TYPE** ARGOUTVIEWM_FARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3)
+{
+  npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+  PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+  PyArrayObject* array = (PyArrayObject*) obj;
+
+  if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+  PyArray_BASE(array) = cap;
+%#else
+  PyArray_SetBaseObject(array,cap);
+%#endif
+
+  $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+                      DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+ */
+%typemap(in,numinputs=0)
+  (DIM_TYPE* DIM1    , DIM_TYPE* DIM2    , DIM_TYPE* DIM3    , DIM_TYPE* DIM4    , DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+  (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL    )
+{
+  $1 = &dim1_temp;
+  $2 = &dim2_temp;
+  $3 = &dim3_temp;
+  $4 = &dim4_temp;
+  $5 = &data_temp;
+}
+%typemap(argout,
+         fragment="NumPy_Backward_Compatibility,NumPy_Array_Requirements,NumPy_Utilities")
+  (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_FARRAY4)
+{
+  npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+  PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+  PyArrayObject* array = (PyArrayObject*) obj;
+
+  if (!array || !require_fortran(array)) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+  PyArray_BASE(array) = cap;
+%#else
+  PyArray_SetBaseObject(array,cap);
+%#endif
+
+  $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2,
+                      DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+ */
+%typemap(in,numinputs=0)
+  (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1    , DIM_TYPE* DIM2    , DIM_TYPE* DIM3    , DIM_TYPE* DIM4    )
+  (DATA_TYPE* data_temp = NULL   , DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp)
+{
+  $1 = &data_temp;
+  $2 = &dim1_temp;
+  $3 = &dim2_temp;
+  $4 = &dim3_temp;
+  $5 = &dim4_temp;
+}
+%typemap(argout,
+         fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+  (DATA_TYPE** ARGOUTVIEWM_ARRAY4, DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4)
+{
+  npy_intp dims[4] = { *$2, *$3, *$4 , *$5 };
+  PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$1));
+  PyArrayObject* array = (PyArrayObject*) obj;
+
+  if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
+%#endif
+
+%#if NPY_API_VERSION < 0x00000007
+  PyArray_BASE(array) = cap;
+%#else
+  PyArray_SetBaseObject(array,cap);
+%#endif
+
+  $result = SWIG_Python_AppendOutput($result,obj);
+}
+
+/* Typemap suite for (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4,
+                      DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+ */
+%typemap(in,numinputs=0)
+  (DIM_TYPE* DIM1    , DIM_TYPE* DIM2    , DIM_TYPE* DIM3    , DIM_TYPE* DIM4    , DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+  (DIM_TYPE dim1_temp, DIM_TYPE dim2_temp, DIM_TYPE dim3_temp, DIM_TYPE dim4_temp, DATA_TYPE* data_temp = NULL   )
+{
+  $1 = &dim1_temp;
+  $2 = &dim2_temp;
+  $3 = &dim3_temp;
+  $4 = &dim4_temp;
+  $5 = &data_temp;
+}
+%typemap(argout,
+         fragment="NumPy_Backward_Compatibility,NumPy_Utilities")
+  (DIM_TYPE* DIM1, DIM_TYPE* DIM2, DIM_TYPE* DIM3, DIM_TYPE* DIM4, DATA_TYPE** ARGOUTVIEWM_ARRAY4)
+{
+  npy_intp dims[4] = { *$1, *$2, *$3 , *$4 };
+  PyObject* obj = PyArray_SimpleNewFromData(4, dims, DATA_TYPECODE, (void*)(*$5));
+  PyArrayObject* array = (PyArrayObject*) obj;
+
+  if (!array) SWIG_fail;
+
+%#ifdef SWIGPY_USE_CAPSULE
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
+%#else
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007
@ -2934,9 +3089,9 @@
  if (!array || !require_fortran(array)) SWIG_fail;

 %#ifdef SWIGPY_USE_CAPSULE
-    PyObject* cap = PyCapsule_New((void*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
+    PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 %#else
-    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$5), free);
+    PyObject* cap = PyCObject_FromVoidPtr((void*)(*$1), free);
 %#endif

 %#if NPY_API_VERSION < 0x00000007