From 92504e0beaf2141ef10bcc95a00406dfcb04a43b Mon Sep 17 00:00:00 2001
From: Evgeny Posenitskiy <45995097+q-posev@users.noreply.github.com>
Date: Sun, 16 Jun 2024 19:13:59 +0200
Subject: [PATCH 01/32] First try macos-arm64 (#137)

* First try macos-arm64

* Test new macos-14 runner

* Update actions.yml

* Install libtool

* Install swig

* User install for python

* Update install_pytrexio.sh

* Update install_pytrexio.sh

* Update install_pytrexio.sh

* Update Makefile.am

* Update Makefile.am

* Update Makefile.am

* Update actions.yml

* Update actions.yml

* Update install_pytrexio.sh [skip ci]

* Update actions.yml

* Update Makefile.am

* Update actions.yml

* Setup venv in CI and not in the installation script
---
 .github/workflows/actions.yml | 41 ++++++++++++++++++++++++-----------
 python/install_pytrexio.sh    |  3 ++-
 2 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index e42bfad..4678b3e 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -15,7 +15,7 @@ jobs:
 
   get_commit_message:
     name: Get commit message
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
@@ -33,7 +33,7 @@ jobs:
 
   trexio_ubuntu:
     name: x86 Ubuntu 20.04
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: get_commit_message
 
     steps:
@@ -53,8 +53,8 @@ jobs:
 
       - name: install dependencies
         run: |
-          sudo add-apt-repository ppa:kelleyk/emacs
-          sudo apt-get install libhdf5-dev emacs26
+          sudo apt-get update
+          sudo apt-get install libhdf5-dev emacs
 
       - name: configure with autotools
         run: |
@@ -74,19 +74,24 @@ jobs:
           name: test-report-ubuntu
           path: test-suite.log
 
-      - name: create virtual environment
+      - name: create venv
         run: |
-          python3 -m venv --clear pytrexio-venv
-          source pytrexio-venv/bin/activate
+          python3 -m venv trexio-venv
+          source trexio-venv/bin/activate
 
       - name: install Python API
-        run: make python-install
+        run: |
+          source trexio-venv/bin/activate
+          make python-install
 
       - name: check Python API
-        run: make python-test
+        run: |
+          source trexio-venv/bin/activate
+          make python-test
 
       - name: build and move Python API distribution
         run: |
+          source trexio-venv/bin/activate
           make python-sdist
           cp python/dist/trexio-*.tar.gz .
 
@@ -105,7 +110,7 @@ jobs:
       - name: reconfigure with clang and AddressSanitizer
         run: |
           ./autogen.sh
-          ./configure CC=clang-11 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
+          ./configure CC=clang-15 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
 
       - name: recompile TREXIO
         run: make -j2
@@ -124,8 +129,8 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-    name: x86 MacOS 12
-    runs-on: macos-12
+    name: arm64 MacOS
+    runs-on: macos-14
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -135,6 +140,8 @@ jobs:
           brew install emacs
           brew install hdf5
           brew install automake
+          brew install libtool
+          brew install swig
           brew --prefix hdf5
 
       - name: configure with autotools
@@ -148,14 +155,22 @@ jobs:
       - name: check TREXIO
         run: make -j3 check
       
+      - name: create venv
+        run: |
+          python3 -m venv trexio-venv
+          source trexio-venv/bin/activate
+
       - name: compile Python API
         run: |
           export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
           export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          source trexio-venv/bin/activate
           make python-install
       
       - name: test Python API
-        run: make python-test
+        run: |
+          source trexio-venv/bin/activate
+          make python-test
 
       - name: Archive test log file
         if: failure()
diff --git a/python/install_pytrexio.sh b/python/install_pytrexio.sh
index d6a0767..9f21dbc 100755
--- a/python/install_pytrexio.sh
+++ b/python/install_pytrexio.sh
@@ -63,8 +63,9 @@ else
     export H5_CFLAGS=${H5_CFLAGS_LOCAL}
 fi
 
+
 # Install/upgrade packages required for the installation
-python3 -m pip install --upgrade setuptools build pip
+python3 -m pip install build
 python3 -m pip install -r requirements.txt
 python3 -m pip install pytest
 

From 62b12b59aed3348f961e9dbb767d6b77d852d66c Mon Sep 17 00:00:00 2001
From: q-posev <evgenyp@qubit-pharmaceuticals.com>
Date: Thu, 27 Jun 2024 17:01:27 +0200
Subject: [PATCH 02/32] Update SWIG interface

---
 src/numpy.i | 297 ++++++++--------------------------------------------
 1 file changed, 42 insertions(+), 255 deletions(-)

diff --git a/src/numpy.i b/src/numpy.i
index 36bb55c..c8c26cb 100644
--- a/src/numpy.i
+++ b/src/numpy.i
@@ -48,7 +48,7 @@
 
 %fragment("NumPy_Backward_Compatibility", "header")
 {
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
 %#define NPY_ARRAY_DEFAULT NPY_DEFAULT
 %#define NPY_ARRAY_FARRAY  NPY_FARRAY
 %#define NPY_FORTRANORDER  NPY_FORTRAN
@@ -69,7 +69,7 @@
 {
 /* Macros to extract array attributes.
  */
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
 %#define is_array(a)            ((a) && PyArray_Check((PyArrayObject*)a))
 %#define array_type(a)          (int)(PyArray_TYPE((PyArrayObject*)a))
 %#define array_numdims(a)       (((PyArrayObject*)a)->nd)
@@ -114,17 +114,12 @@
     if (py_obj == NULL          ) return "C NULL value";
     if (py_obj == Py_None       ) return "Python None" ;
     if (PyCallable_Check(py_obj)) return "callable"    ;
-    if (PyString_Check(  py_obj)) return "string"      ;
-    if (PyInt_Check(     py_obj)) return "int"         ;
+    if (PyBytes_Check(   py_obj)) return "string"      ;
+    if (PyLong_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";
   }
@@ -170,13 +165,11 @@
     return PyArray_EquivTypenums(actual_type, desired_type);
   }
 
-%#ifdef SWIGPY_USE_CAPSULE
-  void free_cap(PyObject * cap)
+void free_cap(PyObject * cap)
   {
     void* array = (void*) PyCapsule_GetPointer(cap,SWIGPY_CAPSULE_NAME);
     if (array != NULL) free(array);
   }
-%#endif
 
 
 }
@@ -298,7 +291,7 @@
       Py_INCREF(array_descr(ary));
       result = (PyArrayObject*) PyArray_FromArray(ary,
                                                   array_descr(ary),
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
                                                   NPY_FORTRANORDER);
 %#else
                                                   NPY_ARRAY_F_CONTIGUOUS);
@@ -529,7 +522,7 @@
     return success;
   }
 
-  /* Require the given PyArrayObject to to be Fortran ordered.  If the
+  /* Require the given PyArrayObject to be Fortran ordered.  If the
    * the PyArrayObject is already Fortran ordered, do nothing.  Else,
    * set the Fortran ordering flag and recompute the strides.
    */
@@ -545,7 +538,7 @@
     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 */
@@ -2007,7 +2000,7 @@
   (PyObject* array = NULL)
 {
   npy_intp dims[1];
-  if (!PyInt_Check($input))
+  if (!PyLong_Check($input))
   {
     const char* typestring = pytype_string($input);
     PyErr_Format(PyExc_TypeError,
@@ -2015,7 +2008,8 @@
                  typestring);
     SWIG_fail;
   }
-  $2 = (DIM_TYPE) PyInt_AsLong($input);
+  $2 = (DIM_TYPE) PyLong_AsSsize_t($input);
+  if ($2 == -1 && PyErr_Occurred()) SWIG_fail;
   dims[0] = (npy_intp) $2;
   array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
   if (!array) SWIG_fail;
@@ -2035,7 +2029,7 @@
   (PyObject* array = NULL)
 {
   npy_intp dims[1];
-  if (!PyInt_Check($input))
+  if (!PyLong_Check($input))
   {
     const char* typestring = pytype_string($input);
     PyErr_Format(PyExc_TypeError,
@@ -2043,7 +2037,8 @@
                  typestring);
     SWIG_fail;
   }
-  $1 = (DIM_TYPE) PyInt_AsLong($input);
+  $1 = (DIM_TYPE) PyLong_AsSsize_t($input);
+  if ($1 == -1 && PyErr_Occurred()) SWIG_fail;
   dims[0] = (npy_intp) $1;
   array = PyArray_SimpleNew(1, dims, DATA_TYPECODE);
   if (!array) SWIG_fail;
@@ -2462,13 +2457,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2496,13 +2487,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$2), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2531,13 +2518,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2566,13 +2549,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2601,13 +2580,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2636,13 +2611,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2673,13 +2644,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2710,13 +2677,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2747,13 +2710,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2784,13 +2743,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2822,13 +2777,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -2860,165 +2811,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#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
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -3050,13 +2845,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$1), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);
@@ -3088,13 +2879,9 @@
 
   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
+PyObject* cap = PyCapsule_New((void*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
 
-%#if NPY_API_VERSION < 0x00000007
+%#if NPY_API_VERSION < NPY_1_7_API_VERSION
   PyArray_BASE(array) = cap;
 %#else
   PyArray_SetBaseObject(array,cap);

From 19adc9d811b5cf249e69e1dbfec0017691c15788 Mon Sep 17 00:00:00 2001
From: q-posev <evgenyp@qubit-pharmaceuticals.com>
Date: Thu, 27 Jun 2024 17:02:07 +0200
Subject: [PATCH 03/32] RM deprecated oldest-supported-numpy

---
 python/pyproject.toml   | 2 +-
 python/requirements.txt | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/python/pyproject.toml b/python/pyproject.toml
index b8ca0a0..95513f0 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -3,6 +3,6 @@ requires = [
     "setuptools>=42",
     "wheel",
     "pkgconfig",
-    "oldest-supported-numpy"
+    "numpy",
 ]
 build-backend = "setuptools.build_meta"
diff --git a/python/requirements.txt b/python/requirements.txt
index eddf522..e7bbedf 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -1,4 +1,3 @@
 setuptools>=42
 pkgconfig
-numpy<1.27.0
-numpy>=1.17.3
+numpy

From fa11989b86f8b35ebc44cd0c5543ef2acae9d701 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Sat, 10 Aug 2024 17:34:44 +0200
Subject: [PATCH 04/32] Update prepare_python.sh (#164)

---
 tools/prepare_python.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/prepare_python.sh b/tools/prepare_python.sh
index bf316bf..e59c638 100755
--- a/tools/prepare_python.sh
+++ b/tools/prepare_python.sh
@@ -11,7 +11,11 @@ fi
 
 DO_HDF5=0
 if [[ -z ${1} ]] && [[ "${1}" == "--without-hdf5" ]] ; then
-  echo "Compiling Python API without the HDF5 back end."
+  echo ""
+  echo "******************** WARNING **********************"
+  echo "* Compiling Python API without the HDF5 back end. *"
+  echo "***************************************************"
+  echo ""
   DO_HDF5=1
 else
   echo "Compiling Python API with the HDF5 back end."

From c860e4fdfeeb6179a7c42682773924af01ebb981 Mon Sep 17 00:00:00 2001
From: Evgeny Posenitskiy <45995097+q-posev@users.noreply.github.com>
Date: Sat, 17 Aug 2024 18:22:43 +0200
Subject: [PATCH 05/32] Build and test new wheels (Python 3.10+ and manylinux
 tag 2.28 instead of 2.24) (#165)

* Upgrade manylinux wheels builder for new container envs

* [wheel build] test new Docker images and Py 3.10+ wheels on Test PyPI

* [wheel build] test new Docker images and Py 3.10+ wheels on Test PyPI

* [wheel build] Fix CI

* [wheel build] One more test
---
 .github/workflows/actions.yml      |  3 +-
 .github/workflows/build-wheels.yml | 56 +++++++++++++++---------------
 python/build_manylinux_wheels.sh   | 19 ++--------
 3 files changed, 33 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 4678b3e..7f38ebc 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -29,7 +29,8 @@ jobs:
         run: |
           set -xe
           COMMIT_MSG=$(git log --no-merges -1 --oneline)
-          echo "::set-output name=message::$COMMIT_MSG"
+          echo "message=$COMMIT_MSG" >> $GITHUB_OUTPUT
+          echo github.ref ${{ github.ref }}
 
   trexio_ubuntu:
     name: x86 Ubuntu 20.04
diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 7cda44a..8e39137 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -4,7 +4,7 @@ on:
   # Run this workflow after the TREXIO CI completed
   workflow_run:
     workflows: [ "TREXIO CI" ]
-    branches: [ master ]
+    branches: [ test-new-wheels ]
     types:
       - completed
 
@@ -16,12 +16,12 @@ jobs:
   get_commit_message:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     name: Get commit message
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -30,8 +30,8 @@ jobs:
         run: |
           set -xe
           COMMIT_MSG=$(git log --no-merges -1 --oneline)
-          echo "::set-output name=message::$COMMIT_MSG"
-
+          echo "message=$COMMIT_MSG" >> $GITHUB_OUTPUT
+          echo github.ref ${{ github.ref }}
 
   build_linux_wheels:
     name: Build Linux wheels for different versions of CPython on manylinux_x86_64
@@ -39,19 +39,19 @@ jobs:
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
       (github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        manylinux_tag: [2014_x86_64, 2_24_x86_64]
+        manylinux_tag: [2014_x86_64, 2_28_x86_64]
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install build dependencies
         run: python -m pip install -U setuptools
@@ -65,7 +65,7 @@ jobs:
       # Conventional download-artifact action does not work for artifact produced in a different workflow,
       # which is the case here (TREXIO CI produced the Python API distribution tarball)
       - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v3
         with:
           # Specify the name of the workflow file which uploaded the tarball
           workflow: actions.yml
@@ -89,7 +89,7 @@ jobs:
         working-directory: python
 
       - name: Upload produced wheels as artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
         with:
           name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
           path: ./python/wheelhouse/*.whl
@@ -98,27 +98,27 @@ jobs:
   publish_wheels:
     name: Publish all wheels on PyPI
     needs: [build_linux_wheels]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install build dependencies
         run: python -m pip install -U setuptools twine
 
       - name: Download the build artifacts (wheels) of this workflow
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           path: dist
 
       - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v3
         with:
           workflow: actions.yml
           workflow_conclusion: success
@@ -135,15 +135,15 @@ jobs:
           ls -sh -w 1
         working-directory: dist
 
-      #- name: Publish distribution 📦 to Test PyPI
-      #  uses: pypa/gh-action-pypi-publish@master
-      #  with:
-      #    password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-      #    repository_url: https://test.pypi.org/legacy/
-          #verbose: true
-
-      - name: Publish distribution 📦 to PyPI
+      - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@master
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-        #if: startsWith(github.ref, 'refs/tags')
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+          #verbose: true
+
+      #- name: Publish distribution 📦 to PyPI
+      #  uses: pypa/gh-action-pypi-publish@master
+      #  with:
+      #    password: ${{ secrets.PYPI_API_TOKEN }}
+      #  #if: startsWith(github.ref, 'refs/tags')
diff --git a/python/build_manylinux_wheels.sh b/python/build_manylinux_wheels.sh
index 1da66ea..a45d960 100755
--- a/python/build_manylinux_wheels.sh
+++ b/python/build_manylinux_wheels.sh
@@ -46,22 +46,9 @@ function build_wheel_for_py()
    PYVERSION=${1}
 
    # derive manylinux glibc tag from the PLAT env variable provided to docker run
-   # this is needed to avoid building wheel for 2010_x86_64 with CPython 3.10
-   # because NumPy does not have wheels for it
    MANYLINUX_TAG=${PLAT:9:4}
-   if [[ ${PYVERSION} -eq 310 ]] && [[ ${MANYLINUX_TAG} -eq 2010 ]]; then
-	echo "Skip build of the wheel for CPython 3.10 on manylinux2010_x86_64"
-	return
-   fi
 
-   # python versions <= 3.7 required additional "m" in the platform tag, e.g. cp37-cp37m
-   if [[ ${PYVERSION} -eq 36 ]] || [[ ${PYVERSION} -eq 37 ]]; then
-       PYM="m"
-   else
-       PYM=""
-   fi
-
-   CPYTHON="cp${PYVERSION}-cp${PYVERSION}${PYM}"
+   CPYTHON="cp${PYVERSION}-cp${PYVERSION}"
 
    # create and activate a virtual environment based on CPython version ${PYVERSION}
    /opt/python/${CPYTHON}/bin/python3 -m venv --clear trexio-manylinux-py${PYVERSION}
@@ -88,7 +75,7 @@ function build_wheel_for_py()
    pytest -v test/test_api.py
 
    # cleaning
-   rm -rf -- dist/ build/ trexio.egg-info/ 
+   rm -rf -- dist/ build/ trexio.egg-info/
    #rm -- test_file_py.h5 unsafe_test_file_py.h5
 
    # deactivate the current environment
@@ -103,7 +90,7 @@ function build_wheel_for_py()
 
 
 # build wheels for all versions of CPython in this container
-for CPYVERSION in 37 38 39 310
+for CPYVERSION in 38 39 310 311 312 313
 do
   build_wheel_for_py ${CPYVERSION}
 done

From f06396a6652ffa6d2c6ef49480987f75914b0b4f Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 18:23:50 +0200
Subject: [PATCH 06/32] [wheel build] Test PyPI release with new CI

---
 .github/workflows/build-wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 8e39137..4150b10 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -4,7 +4,7 @@ on:
   # Run this workflow after the TREXIO CI completed
   workflow_run:
     workflows: [ "TREXIO CI" ]
-    branches: [ test-new-wheels ]
+    branches: [ master ]
     types:
       - completed
 

From 410fa140e4ec184abbce1015aaf7d88430c963ff Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 18:32:15 +0200
Subject: [PATCH 07/32] [wheel build] Downgrade the download-artifact version

---
 .github/workflows/build-wheels.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 4150b10..ea3dd34 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -65,7 +65,7 @@ jobs:
       # Conventional download-artifact action does not work for artifact produced in a different workflow,
       # which is the case here (TREXIO CI produced the Python API distribution tarball)
       - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@v2
         with:
           # Specify the name of the workflow file which uploaded the tarball
           workflow: actions.yml
@@ -118,7 +118,7 @@ jobs:
           path: dist
 
       - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@v2
         with:
           workflow: actions.yml
           workflow_conclusion: success

From 69e81c103297dacc07336e3c2aa4fa8b669f977e Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 19:41:45 +0200
Subject: [PATCH 08/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 268 ++++++++++++++++++++---------
 1 file changed, 182 insertions(+), 86 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index ea3dd34..370c585 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -33,108 +33,204 @@ jobs:
           echo "message=$COMMIT_MSG" >> $GITHUB_OUTPUT
           echo github.ref ${{ github.ref }}
 
-  build_linux_wheels:
-    name: Build Linux wheels for different versions of CPython on manylinux_x86_64
+
+  build_macos_wheels:
+    name: build linux wheels for different versions of cpython on macos 
     needs: get_commit_message
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
-      (github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
-    runs-on: ubuntu-22.04
+      (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
+    runs-on: ${{ matrix.buildplat[0] }}
     strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
       matrix:
-        manylinux_tag: [2014_x86_64, 2_28_x86_64]
+        # Github Actions doesn't support pairing matrix values together, let's improvise
+        # https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
+        buildplat:
+          - [macos-13, macosx_x86_64]
+          - [macos-14, macosx_arm64]
+        # test config
+        python: ["cp310", "cp312"]
+        #python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+        #exclude:
+        #  - buildplat: [macos-14, macosx_arm64]
+        #    python: "cp38"
 
     steps:
-      - name: Checkout the branch
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
-      - name: Set up Python
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
         with:
-          python-version: '3.10'
+          python-version: "3.x"
 
-      - name: Install build dependencies
-        run: python -m pip install -U setuptools
+      - name: Build wheels
+        uses: pypa/cibuildwheel@bd033a44476646b606efccdd5eed92d5ea1d77ad  # v2.20.0
+        env:
+          CIBW_PRERELEASE_PYTHONS: False
+          CIBW_FREE_THREADED_SUPPORT: False
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+          CIBW_BEFORE_ALL: >
+            brew install hdf5@1.14 -y &&
+            brew install swig -y &&
+            brew install emacs -y &&
+            brew install automake -y &&
+            brew install libtool -y &&
+            ./autogen.sh &&
+            ./configure FC=gfortran-12 --enable-silent-rules &&
+            make -j3 
+          CIBW_BEFORE_BUILD: > 
+            cd tools &&
+            ./prepare_python.sh &&
+            cd ../python
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_BUILD_FRONTEND: "build"
+          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I$(brew --prefix hdf5)/include" H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_COMMANDS: "pytest -v --all python/test/test_api.py"
 
-      - name: Compute the PYTREXIO_VERSION environment variable
-        run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
 
-      - name: Print the PYTREXIO_VERSION
-        run: echo ${{ env.PYTREXIO_VERSION }}
-
-      # Conventional download-artifact action does not work for artifact produced in a different workflow,
-      # which is the case here (TREXIO CI produced the Python API distribution tarball)
-      - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v2
+      - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
         with:
-          # Specify the name of the workflow file which uploaded the tarball
-          workflow: actions.yml
-          workflow_conclusion: success
-          name: pytrexio-source
-          path: python
+          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+          path: ./wheelhouse/*.whl
 
-      # at the moment we have to pull the custom container with pre-installed HDF5
-      # the containers are built and stored in GitHub container registry ghcr.io/q-posev
-      - name: Pull the manylinux Docker container with HDF5
-        run: docker pull ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}:latest
-
-      - name: Build wheels for different versions of CPython inside the Docker container
-        run: >
-          docker run --rm
-          --env PLAT=manylinux${{ matrix.manylinux_tag }}
-          --volume `pwd`:/tmp
-          --workdir /tmp
-          ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}
-          /bin/bash build_manylinux_wheels.sh trexio-${{ env.PYTREXIO_VERSION }}.tar.gz
-        working-directory: python
-
-      - name: Upload produced wheels as artifacts
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
-        with:
-          name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
-          path: ./python/wheelhouse/*.whl
-
-
-  publish_wheels:
-    name: Publish all wheels on PyPI
-    needs: [build_linux_wheels]
-    runs-on: ubuntu-22.04
-
-    steps:
-      - name: Checkout the branch
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-
-      - name: Set up Python
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
-        with:
-          python-version: '3.10'
-
-      - name: Install build dependencies
-        run: python -m pip install -U setuptools twine
-
-      - name: Download the build artifacts (wheels) of this workflow
-        uses: actions/download-artifact@v4
-        with:
-          path: dist
-
-      - name: Download the Python API distribution tarball
-        uses: dawidd6/action-download-artifact@v2
-        with:
-          workflow: actions.yml
-          workflow_conclusion: success
-          name: pytrexio-source
-          path: dist
-
-      # The artifacts have to be in dist/ directory so that
-      # pypa/gh-action-pypi-publish action can discover them
-      - name: Display and rearrange the downloaded artifacts
+      - name: configure with autotools
         run: |
-          ls -R
-          mv pytrexio-manylinux-*/trexio-*.whl ./
-          rm -rf -- pytrexio-manylinux-*/
-          ls -sh -w 1
-        working-directory: dist
+          ./autogen.sh
+          ./configure FC=gfortran-12 --enable-silent-rules
 
+      - name: compile TREXIO
+        run: make -j3
+
+      - name: check TREXIO
+        run: make -j3 check
+      
+      - name: create venv
+        run: |
+          python3 -m venv trexio-venv
+          source trexio-venv/bin/activate
+
+      - name: compile Python API
+        run: |
+
+      
+      - name: test Python API
+        run: |
+          source trexio-venv/bin/activate
+          make python-test
+
+      - name: Archive test log file
+        if: failure()
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        with:
+          name: test-report-macos
+          path: test-suite.log
+
+
+
+            # build_linux_wheels:
+            #   name: build linux wheels for different versions of cpython on manylinux_x86_64
+            #   needs: get_commit_message
+            #   if: >-
+            #     contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
+            #     (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
+            #   runs-on: ubuntu-22.04
+            #   strategy:
+            #     matrix:
+            #       manylinux_tag: [2014_x86_64, 2_28_x86_64]
+            #
+            #   steps:
+            #     - name: Checkout the branch
+            #       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+            #
+            #     - name: Set up Python
+            #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+            #       with:
+            #         python-version: '3.10'
+            #
+            #     - name: Install build dependencies
+            #       run: python -m pip install -U setuptools
+            #
+            #     - name: Compute the PYTREXIO_VERSION environment variable
+            #       run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
+            #
+            #     - name: Print the PYTREXIO_VERSION
+            #       run: echo ${{ env.PYTREXIO_VERSION }}
+            #
+            #     # Conventional download-artifact action does not work for artifact produced in a different workflow,
+            #     # which is the case here (TREXIO CI produced the Python API distribution tarball)
+            #     - name: Download the Python API distribution tarball
+            #       uses: dawidd6/action-download-artifact@v2
+            #       with:
+            #         # Specify the name of the workflow file which uploaded the tarball
+            #         workflow: actions.yml
+            #         workflow_conclusion: success
+            #         name: pytrexio-source
+            #         path: python
+            #
+            #     # at the moment we have to pull the custom container with pre-installed HDF5
+            #     # the containers are built and stored in GitHub container registry ghcr.io/q-posev
+            #     - name: Pull the manylinux Docker container with HDF5
+            #       run: docker pull ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}:latest
+            #
+            #     - name: Build wheels for different versions of CPython inside the Docker container
+            #       run: >
+            #         docker run --rm
+            #         --env PLAT=manylinux${{ matrix.manylinux_tag }}
+            #         --volume `pwd`:/tmp
+            #         --workdir /tmp
+            #         ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}
+            #         /bin/bash build_manylinux_wheels.sh trexio-${{ env.PYTREXIO_VERSION }}.tar.gz
+            #       working-directory: python
+            #
+            #     - name: Upload produced wheels as artifacts
+            #       uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+            #       with:
+            #         name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
+            #         path: ./python/wheelhouse/*.whl
+            #
+            #
+            # publish_wheels:
+            #   name: Publish all wheels on PyPI
+            #   needs: [build_linux_wheels]
+            #   runs-on: ubuntu-22.04
+            #
+            #   steps:
+            #     - name: Checkout the branch
+            #       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+            #
+            #     - name: Set up Python
+            #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+            #       with:
+            #         python-version: '3.10'
+            #
+            #     - name: Install build dependencies
+            #       run: python -m pip install -U setuptools twine
+            #
+            #     - name: Download the build artifacts (wheels) of this workflow
+            #       uses: actions/download-artifact@v4
+            #       with:
+            #         path: dist
+            #
+            #     - name: Download the Python API distribution tarball
+            #       uses: dawidd6/action-download-artifact@v2
+            #       with:
+            #         workflow: actions.yml
+            #         workflow_conclusion: success
+            #         name: pytrexio-source
+            #         path: dist
+            #
+            #     # The artifacts have to be in dist/ directory so that
+            #     # pypa/gh-action-pypi-publish action can discover them
+            #     - name: Display and rearrange the downloaded artifacts
+            #       run: |
+            #         ls -R
+            #         mv pytrexio-manylinux-*/trexio-*.whl ./
+            #         rm -rf -- pytrexio-manylinux-*/
+            #         ls -sh -w 1
+            #       working-directory: dist
+            #
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@master
         with:

From baa4b2a428ed45c79e7aef36dd395166de056291 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 20:02:26 +0200
Subject: [PATCH 09/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 37 +++---------------------------
 1 file changed, 3 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 370c585..31d5540 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -82,8 +82,9 @@ jobs:
           CIBW_BEFORE_BUILD: > 
             cd tools &&
             ./prepare_python.sh &&
-            cd ../python
-          CIBW_BUILD_VERBOSITY: 1
+            rm -rf ../src/ ../tools/ &&
+            mv ../python/* ..
+          CIBW_BUILD_VERBOSITY: 3
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I$(brew --prefix hdf5)/include" H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
           CIBW_TEST_REQUIRES: pytest
@@ -95,38 +96,6 @@ jobs:
           name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           path: ./wheelhouse/*.whl
 
-      - name: configure with autotools
-        run: |
-          ./autogen.sh
-          ./configure FC=gfortran-12 --enable-silent-rules
-
-      - name: compile TREXIO
-        run: make -j3
-
-      - name: check TREXIO
-        run: make -j3 check
-      
-      - name: create venv
-        run: |
-          python3 -m venv trexio-venv
-          source trexio-venv/bin/activate
-
-      - name: compile Python API
-        run: |
-
-      
-      - name: test Python API
-        run: |
-          source trexio-venv/bin/activate
-          make python-test
-
-      - name: Archive test log file
-        if: failure()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
-        with:
-          name: test-report-macos
-          path: test-suite.log
-
 
 
             # build_linux_wheels:

From 37a229786fd79c04bb53b0989f37dff6127f6e5e Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 20:20:18 +0200
Subject: [PATCH 10/32] [wheel build] Test macos wheels

---
 .github/workflows/actions.yml      | 46 +++++++++++++++---------------
 .github/workflows/build-wheels.yml | 38 +++++++++++++++---------
 2 files changed, 47 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 7f38ebc..2cf7754 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -105,29 +105,29 @@ jobs:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
 
-      - name: maintainer clean
-        run: make maintainer-clean
-
-      - name: reconfigure with clang and AddressSanitizer
-        run: |
-          ./autogen.sh
-          ./configure CC=clang-15 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
-
-      - name: recompile TREXIO
-        run: make -j2
-
-      - name: recheck TREXIO for memory leaks
-        run: make -j2 check
-
-      - name: Archive test log file
-        if: failure()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
-        with:
-          name: test-report-ubuntu-2
-          path: test-suite.log
-
-      - name: maintainer clean
-        run: make maintainer-clean
+            #     - name: maintainer clean
+            #       run: make maintainer-clean
+            #
+            #     - name: reconfigure with clang and AddressSanitizer
+            #       run: |
+            #         ./autogen.sh
+            #         ./configure CC=clang-15 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
+            #
+            #     - name: recompile TREXIO
+            #       run: make -j2
+            #
+            #     - name: recheck TREXIO for memory leaks
+            #       run: make -j2 check
+            #
+            #     - name: Archive test log file
+            #       if: failure()
+            #       uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+            #       with:
+            #         name: test-report-ubuntu-2
+            #         path: test-suite.log
+            #
+            #     - name: maintainer clean
+            #       run: make maintainer-clean
 
   trexio_macos:
     name: arm64 MacOS
diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 31d5540..411a4c2 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -64,26 +64,36 @@ jobs:
         with:
           python-version: "3.x"
 
+      - name: install dependencies
+        run: |
+          brew install emacs
+          brew install hdf5@1.14
+          brew install automake
+          brew install libtool
+          brew install swig
+          brew --prefix hdf5
+
+      - name: configure with autotools
+        run: |
+          ./autogen.sh
+          ./configure FC=gfortran-12 --enable-silent-rules
+
+      - name: compile TREXIO
+        run: make -j3
+
+      - name: prepare the repo
+        run: |
+          cd tools 
+          ./prepare_python.sh
+          rm -rf ../src/ ../tools/ 
+          mv ../python/* ..
+
       - name: Build wheels
         uses: pypa/cibuildwheel@bd033a44476646b606efccdd5eed92d5ea1d77ad  # v2.20.0
         env:
           CIBW_PRERELEASE_PYTHONS: False
           CIBW_FREE_THREADED_SUPPORT: False
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
-          CIBW_BEFORE_ALL: >
-            brew install hdf5@1.14 -y &&
-            brew install swig -y &&
-            brew install emacs -y &&
-            brew install automake -y &&
-            brew install libtool -y &&
-            ./autogen.sh &&
-            ./configure FC=gfortran-12 --enable-silent-rules &&
-            make -j3 
-          CIBW_BEFORE_BUILD: > 
-            cd tools &&
-            ./prepare_python.sh &&
-            rm -rf ../src/ ../tools/ &&
-            mv ../python/* ..
           CIBW_BUILD_VERBOSITY: 3
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I$(brew --prefix hdf5)/include" H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"

From 6a4d9d4d8726ec04a696dabeff7d8fc90bf1b359 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 20:35:23 +0200
Subject: [PATCH 11/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 411a4c2..cb80be4 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -77,16 +77,12 @@ jobs:
         run: |
           ./autogen.sh
           ./configure FC=gfortran-12 --enable-silent-rules
-
-      - name: compile TREXIO
-        run: make -j3
-
-      - name: prepare the repo
-        run: |
+          make -j3
           cd tools 
           ./prepare_python.sh
-          rm -rf ../src/ ../tools/ 
-          mv ../python/* ..
+          cd ..
+          rm -rf src/ tools/ 
+          mv python/* .
 
       - name: Build wheels
         uses: pypa/cibuildwheel@bd033a44476646b606efccdd5eed92d5ea1d77ad  # v2.20.0

From cebbbd1269eb3483ec0e2c40c029d33ea7d69847 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 20:45:15 +0200
Subject: [PATCH 12/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index cb80be4..4aef1a0 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -78,9 +78,15 @@ jobs:
           ./autogen.sh
           ./configure FC=gfortran-12 --enable-silent-rules
           make -j3
-          cd tools 
-          ./prepare_python.sh
-          cd ..
+          
+      - name: prepare python 
+        run: |
+          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
+          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          make python-install
+
+      - name: cleanup python 
+        run: |
           rm -rf src/ tools/ 
           mv python/* .
 

From 269782be2b59d8988402589311a265c40775d591 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 21:09:28 +0200
Subject: [PATCH 13/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 4aef1a0..2df27b3 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -67,22 +67,32 @@ jobs:
       - name: install dependencies
         run: |
           brew install emacs
-          brew install hdf5@1.14
           brew install automake
           brew install libtool
           brew install swig
-          brew --prefix hdf5
+          brew install wget
+
+      - name: install hdf5
+        run: |
+          wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
+          tar -xzf hdf5-1_12_3.tar.gz
+          cd  hdf5-hdf5-$HDF5_VERSION
+          ./autogen.sh
+          ./configure CC=gcc-12 --prefix /usr/local --enable-build-mode=production --with-szlib
+          make -j3
+          make install
 
       - name: configure with autotools
         run: |
           ./autogen.sh
           ./configure FC=gfortran-12 --enable-silent-rules
           make -j3
+          make -j3 check
           
       - name: prepare python 
         run: |
-          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
-          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          export H5_CFLAGS="-I/usr/local/include"
+          export H5_LDFLAGS="-L/usr/local/lib"
           make python-install
 
       - name: cleanup python 

From d50f8e8bc7ebbf6be904d3ab8daa2dbcaf6fb6f9 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 21:14:57 +0200
Subject: [PATCH 14/32] [wheel build] Test macos wheels

---
 .github/workflows/build-wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 2df27b3..f7d4e24 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -76,7 +76,7 @@ jobs:
         run: |
           wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
           tar -xzf hdf5-1_12_3.tar.gz
-          cd  hdf5-hdf5-$HDF5_VERSION
+          cd  hdf5-hdf5-1_12_3
           ./autogen.sh
           ./configure CC=gcc-12 --prefix /usr/local --enable-build-mode=production --with-szlib
           make -j3

From 8f84766ebc3e85043aa3dc50cdd5d3dec7081005 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 21:39:29 +0200
Subject: [PATCH 15/32] [wheel build] Fix arm installation with rights

---
 .github/workflows/build-wheels.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index f7d4e24..eb4eb88 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -41,6 +41,8 @@ jobs:
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
       (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
     runs-on: ${{ matrix.buildplat[0] }}
+    env:
+      HDF5_INSTALLDIR: "/tmp/hdf5"
     strategy:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
@@ -78,21 +80,22 @@ jobs:
           tar -xzf hdf5-1_12_3.tar.gz
           cd  hdf5-hdf5-1_12_3
           ./autogen.sh
-          ./configure CC=gcc-12 --prefix /usr/local --enable-build-mode=production --with-szlib
+          ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
           make -j3
           make install
 
       - name: configure with autotools
         run: |
           ./autogen.sh
+          export PATH=${PATH}:${HDF5_INSTALLDIR}/bin
           ./configure FC=gfortran-12 --enable-silent-rules
           make -j3
           make -j3 check
           
       - name: prepare python 
         run: |
-          export H5_CFLAGS="-I/usr/local/include"
-          export H5_LDFLAGS="-L/usr/local/lib"
+          export  H5_CFLAGS="-I${HDF5_INCLUDEDIR}/include"
+          export H5_LDFLAGS="-L${HDF5_INCLUDEDIR}/lib"
           make python-install
 
       - name: cleanup python 
@@ -108,7 +111,7 @@ jobs:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           CIBW_BUILD_VERBOSITY: 3
           CIBW_BUILD_FRONTEND: "build"
-          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I$(brew --prefix hdf5)/include" H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I/tmp/hdf5/include" H5_LDFLAGS="-L/tmp/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMANDS: "pytest -v --all python/test/test_api.py"
 

From dea443dc01a9949b0802477fcdbecfed9030adaf Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 21:58:51 +0200
Subject: [PATCH 16/32] [wheel build] Fix paths and CIBW test command

---
 .github/workflows/build-wheels.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index eb4eb88..576aeb6 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -80,22 +80,23 @@ jobs:
           tar -xzf hdf5-1_12_3.tar.gz
           cd  hdf5-hdf5-1_12_3
           ./autogen.sh
-          ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
+          ./configure CC=gcc-12 --prefix ${PWD}/../hdf5 --enable-build-mode=production --with-szlib
+          echo "PWD is $PWD"
           make -j3
           make install
 
       - name: configure with autotools
         run: |
           ./autogen.sh
-          export PATH=${PATH}:${HDF5_INSTALLDIR}/bin
+          export PATH=${PATH}:${PWD}/hdf5/bin
           ./configure FC=gfortran-12 --enable-silent-rules
           make -j3
           make -j3 check
           
       - name: prepare python 
         run: |
-          export  H5_CFLAGS="-I${HDF5_INCLUDEDIR}/include"
-          export H5_LDFLAGS="-L${HDF5_INCLUDEDIR}/lib"
+          export  H5_CFLAGS="-I${PWD}/bin/include"
+          export H5_LDFLAGS="-L${PWD}/bin/lib"
           make python-install
 
       - name: cleanup python 
@@ -111,9 +112,9 @@ jobs:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           CIBW_BUILD_VERBOSITY: 3
           CIBW_BUILD_FRONTEND: "build"
-          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I/tmp/hdf5/include" H5_LDFLAGS="-L/tmp/hdf5/lib"
+          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I${PWD}/hdf5/include" H5_LDFLAGS="-L${PWD}/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMANDS: "pytest -v --all python/test/test_api.py"
+          CIBW_TEST_COMMAND: "pytest -v --all test/test_api.py"
 
 
       - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6

From ed53fbbb012fb342ce845353b0703a44487e5b20 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 22:27:03 +0200
Subject: [PATCH 17/32] [wheel build] Fix paths (again)

---
 .github/workflows/build-wheels.yml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 576aeb6..142c4a0 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -42,7 +42,7 @@ jobs:
       (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
     runs-on: ${{ matrix.buildplat[0] }}
     env:
-      HDF5_INSTALLDIR: "/tmp/hdf5"
+      HDF5_INSTALLDIR: "/Users/runner/work/trexio/trexio/hdf5"
     strategy:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
@@ -80,7 +80,7 @@ jobs:
           tar -xzf hdf5-1_12_3.tar.gz
           cd  hdf5-hdf5-1_12_3
           ./autogen.sh
-          ./configure CC=gcc-12 --prefix ${PWD}/../hdf5 --enable-build-mode=production --with-szlib
+          ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
           echo "PWD is $PWD"
           make -j3
           make install
@@ -88,15 +88,12 @@ jobs:
       - name: configure with autotools
         run: |
           ./autogen.sh
-          export PATH=${PATH}:${PWD}/hdf5/bin
-          ./configure FC=gfortran-12 --enable-silent-rules
+          export PATH=${PATH}:${HDF5_INSTALLDIR}/bin
+          ./configure --without-fortran --enable-silent-rules
           make -j3
-          make -j3 check
           
       - name: prepare python 
         run: |
-          export  H5_CFLAGS="-I${PWD}/bin/include"
-          export H5_LDFLAGS="-L${PWD}/bin/lib"
           make python-install
 
       - name: cleanup python 
@@ -112,7 +109,7 @@ jobs:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           CIBW_BUILD_VERBOSITY: 3
           CIBW_BUILD_FRONTEND: "build"
-          CIBW_ENVIRONMENT_LINUX: H5_CFLAGS="-I${PWD}/hdf5/include" H5_LDFLAGS="-L${PWD}/hdf5/lib"
+          CIBW_ENVIRONMENT: H5_CFLAGS="-I/Users/runner/work/trexio/trexio/hdf5/include" H5_LDFLAGS="-L/Users/runner/work/trexio/trexio/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: "pytest -v --all test/test_api.py"
 

From 75ae5818b1e157ba77a2ba6977c356e13f80c602 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 22:41:47 +0200
Subject: [PATCH 18/32] [wheel build] Bring back fortran and try to cache HDF5

---
 .github/workflows/build-wheels.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 142c4a0..0064b39 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -74,7 +74,15 @@ jobs:
           brew install swig
           brew install wget
 
+      - uses: actions/cache@v4
+        id: cache
+        with:
+          path: |
+            $HDF5_INSTALLDIR
+        key: ${{ matrix.buildplat[0] }}-hdf5
+
       - name: install hdf5
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
           wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
           tar -xzf hdf5-1_12_3.tar.gz
@@ -89,7 +97,7 @@ jobs:
         run: |
           ./autogen.sh
           export PATH=${PATH}:${HDF5_INSTALLDIR}/bin
-          ./configure --without-fortran --enable-silent-rules
+          ./configure FC=gfortran-12 --enable-silent-rules
           make -j3
           
       - name: prepare python 

From 5258eb09e1ca29d844d6ffcb27ca300057963046 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 22:51:52 +0200
Subject: [PATCH 19/32] [wheel build] Bring back fortran and try to cache HDF5

---
 .github/workflows/build-wheels.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 0064b39..44d6da7 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -74,12 +74,11 @@ jobs:
           brew install swig
           brew install wget
 
-      - uses: actions/cache@v4
+      - uses: actions/cache@v3
         id: cache
         with:
-          path: |
-            $HDF5_INSTALLDIR
-        key: ${{ matrix.buildplat[0] }}-hdf5
+          path: $HDF5_INSTALLDIR
+          key: ${{ matrix.buildplat[0] }}-hdf5
 
       - name: install hdf5
         if: steps.cache.outputs.cache-hit != 'true'

From 5e60d3dfc7f605735a8a134d646c8871414d46f2 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 23:09:28 +0200
Subject: [PATCH 20/32] [wheel build] Try to fix the macos platform tags...

---
 .github/workflows/build-wheels.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 44d6da7..8b9fb80 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -74,11 +74,11 @@ jobs:
           brew install swig
           brew install wget
 
-      - uses: actions/cache@v3
-        id: cache
-        with:
-          path: $HDF5_INSTALLDIR
-          key: ${{ matrix.buildplat[0] }}-hdf5
+          #- uses: actions/cache@v3
+          #  id: cache
+          #  with:
+          #    path: $HDF5_INSTALLDIR
+          #    key: ${{ matrix.buildplat[0] }}-hdf5
 
       - name: install hdf5
         if: steps.cache.outputs.cache-hit != 'true'
@@ -86,6 +86,11 @@ jobs:
           wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
           tar -xzf hdf5-1_12_3.tar.gz
           cd  hdf5-hdf5-1_12_3
+          if [[ "$ARCH" == "arm64" ]]; then
+            export MACOSX_DEPLOYMENT_TARGET="11.0"
+          else
+            export MACOSX_DEPLOYMENT_TARGET="10.9"
+          fi
           ./autogen.sh
           ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
           echo "PWD is $PWD"

From 38b84055eb9e126a88228f6b1333715419865b86 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 23:33:21 +0200
Subject: [PATCH 21/32] [wheel build] Fixing the tests

---
 .github/workflows/build-wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 8b9fb80..90b41a8 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -123,7 +123,7 @@ jobs:
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT: H5_CFLAGS="-I/Users/runner/work/trexio/trexio/hdf5/include" H5_LDFLAGS="-L/Users/runner/work/trexio/trexio/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: "pytest -v --all test/test_api.py"
+          CIBW_TEST_COMMAND: "python3 -m pytest -v --all test/test_api.py"
 
 
       - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6

From 634dbab437bebb0a257c74c1c672705cb7fa38e2 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sat, 17 Aug 2024 23:44:27 +0200
Subject: [PATCH 22/32] [wheel build] Last attempt to fix the tests :-)

---
 .github/workflows/build-wheels.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 90b41a8..7b0cf11 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -74,11 +74,11 @@ jobs:
           brew install swig
           brew install wget
 
-          #- uses: actions/cache@v3
-          #  id: cache
-          #  with:
-          #    path: $HDF5_INSTALLDIR
-          #    key: ${{ matrix.buildplat[0] }}-hdf5
+      - uses: actions/cache@v3
+        id: cache
+        with:
+          path: $HDF5_INSTALLDIR
+          key: ${{ matrix.buildplat[0] }}-hdf5
 
       - name: install hdf5
         if: steps.cache.outputs.cache-hit != 'true'
@@ -93,7 +93,6 @@ jobs:
           fi
           ./autogen.sh
           ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
-          echo "PWD is $PWD"
           make -j3
           make install
 
@@ -111,6 +110,7 @@ jobs:
       - name: cleanup python 
         run: |
           rm -rf src/ tools/ 
+          mv python/test/* .
           mv python/* .
 
       - name: Build wheels
@@ -123,7 +123,7 @@ jobs:
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT: H5_CFLAGS="-I/Users/runner/work/trexio/trexio/hdf5/include" H5_LDFLAGS="-L/Users/runner/work/trexio/trexio/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: "python3 -m pytest -v --all test/test_api.py"
+          CIBW_TEST_COMMAND: "python3 -m pytest -v --all test_api.py"
 
 
       - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6

From 1a167aee7a3a70b937d36874b198365f007f5232 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 00:13:49 +0200
Subject: [PATCH 23/32] [wheel build] Full-scale test of all wheels on Test
 PyPI

---
 .github/workflows/build-wheels.yml | 210 ++++++++++++++---------------
 1 file changed, 104 insertions(+), 106 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 7b0cf11..138bcd2 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -110,7 +110,6 @@ jobs:
       - name: cleanup python 
         run: |
           rm -rf src/ tools/ 
-          mv python/test/* .
           mv python/* .
 
       - name: Build wheels
@@ -123,118 +122,117 @@ jobs:
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT: H5_CFLAGS="-I/Users/runner/work/trexio/trexio/hdf5/include" H5_LDFLAGS="-L/Users/runner/work/trexio/trexio/hdf5/lib"
           CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: "python3 -m pytest -v --all test_api.py"
+          CIBW_TEST_COMMAND: "python3 -m pytest -v test/test_api.py"
 
 
       - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
         with:
-          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+          name: pytrexio-${{ matrix.python }}-${{ matrix.buildplat[1] }}-wheels
           path: ./wheelhouse/*.whl
 
 
-
-            # build_linux_wheels:
-            #   name: build linux wheels for different versions of cpython on manylinux_x86_64
-            #   needs: get_commit_message
-            #   if: >-
-            #     contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
-            #     (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
-            #   runs-on: ubuntu-22.04
-            #   strategy:
-            #     matrix:
-            #       manylinux_tag: [2014_x86_64, 2_28_x86_64]
-            #
-            #   steps:
-            #     - name: Checkout the branch
-            #       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-            #
-            #     - name: Set up Python
-            #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
-            #       with:
-            #         python-version: '3.10'
-            #
-            #     - name: Install build dependencies
-            #       run: python -m pip install -U setuptools
-            #
-            #     - name: Compute the PYTREXIO_VERSION environment variable
-            #       run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
-            #
-            #     - name: Print the PYTREXIO_VERSION
-            #       run: echo ${{ env.PYTREXIO_VERSION }}
-            #
-            #     # Conventional download-artifact action does not work for artifact produced in a different workflow,
-            #     # which is the case here (TREXIO CI produced the Python API distribution tarball)
-            #     - name: Download the Python API distribution tarball
-            #       uses: dawidd6/action-download-artifact@v2
-            #       with:
-            #         # Specify the name of the workflow file which uploaded the tarball
-            #         workflow: actions.yml
-            #         workflow_conclusion: success
-            #         name: pytrexio-source
-            #         path: python
-            #
-            #     # at the moment we have to pull the custom container with pre-installed HDF5
-            #     # the containers are built and stored in GitHub container registry ghcr.io/q-posev
-            #     - name: Pull the manylinux Docker container with HDF5
-            #       run: docker pull ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}:latest
-            #
-            #     - name: Build wheels for different versions of CPython inside the Docker container
-            #       run: >
-            #         docker run --rm
-            #         --env PLAT=manylinux${{ matrix.manylinux_tag }}
-            #         --volume `pwd`:/tmp
-            #         --workdir /tmp
-            #         ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}
-            #         /bin/bash build_manylinux_wheels.sh trexio-${{ env.PYTREXIO_VERSION }}.tar.gz
-            #       working-directory: python
-            #
-            #     - name: Upload produced wheels as artifacts
-            #       uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
-            #       with:
-            #         name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
-            #         path: ./python/wheelhouse/*.whl
-            #
-            #
-            # publish_wheels:
-            #   name: Publish all wheels on PyPI
-            #   needs: [build_linux_wheels]
-            #   runs-on: ubuntu-22.04
-            #
-            #   steps:
-            #     - name: Checkout the branch
-            #       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-            #
-            #     - name: Set up Python
-            #       uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
-            #       with:
-            #         python-version: '3.10'
-            #
-            #     - name: Install build dependencies
-            #       run: python -m pip install -U setuptools twine
-            #
-            #     - name: Download the build artifacts (wheels) of this workflow
-            #       uses: actions/download-artifact@v4
-            #       with:
-            #         path: dist
-            #
-            #     - name: Download the Python API distribution tarball
-            #       uses: dawidd6/action-download-artifact@v2
-            #       with:
-            #         workflow: actions.yml
-            #         workflow_conclusion: success
-            #         name: pytrexio-source
-            #         path: dist
-            #
-            #     # The artifacts have to be in dist/ directory so that
-            #     # pypa/gh-action-pypi-publish action can discover them
-            #     - name: Display and rearrange the downloaded artifacts
-            #       run: |
-            #         ls -R
-            #         mv pytrexio-manylinux-*/trexio-*.whl ./
-            #         rm -rf -- pytrexio-manylinux-*/
-            #         ls -sh -w 1
-            #       working-directory: dist
-            #
+  build_linux_wheels:
+    name: build linux wheels for different versions of cpython on manylinux_x86_64
+    needs: get_commit_message
+    if: >-
+      contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
+      (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        manylinux_tag: [2014_x86_64, 2_28_x86_64]
+  
+    steps:
+      - name: Checkout the branch
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+  
+      - name: Set up Python
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+        with:
+          python-version: '3.10'
+  
+      - name: Install build dependencies
+        run: python -m pip install -U setuptools
+  
+      - name: Compute the PYTREXIO_VERSION environment variable
+        run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
+  
+      - name: Print the PYTREXIO_VERSION
+        run: echo ${{ env.PYTREXIO_VERSION }}
+  
+      # Conventional download-artifact action does not work for artifact produced in a different workflow,
+      # which is the case here (TREXIO CI produced the Python API distribution tarball)
+      - name: Download the Python API distribution tarball
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          # Specify the name of the workflow file which uploaded the tarball
+          workflow: actions.yml
+          workflow_conclusion: success
+          name: pytrexio-source
+          path: python
+  
+      # at the moment we have to pull the custom container with pre-installed HDF5
+      # the containers are built and stored in GitHub container registry ghcr.io/q-posev
+      - name: Pull the manylinux Docker container with HDF5
+        run: docker pull ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}:latest
+  
+      - name: Build wheels for different versions of CPython inside the Docker container
+        run: >
+          docker run --rm
+          --env PLAT=manylinux${{ matrix.manylinux_tag }}
+          --volume `pwd`:/tmp
+          --workdir /tmp
+          ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}
+          /bin/bash build_manylinux_wheels.sh trexio-${{ env.PYTREXIO_VERSION }}.tar.gz
+        working-directory: python
+  
+      - name: Upload produced wheels as artifacts
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        with:
+          name: pytrexio-manylinux-${{ matrix.manylinux_tag }}-wheels
+          path: ./python/wheelhouse/*.whl
+  
+  
+  publish_wheels:
+    name: Publish all wheels on PyPI
+    needs: [build_linux_wheels]
+    runs-on: ubuntu-22.04
+  
+    steps:
+      - name: Checkout the branch
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+  
+      - name: Set up Python
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+        with:
+          python-version: '3.10'
+  
+      - name: Install build dependencies
+        run: python -m pip install -U setuptools twine
+  
+      - name: Download the build artifacts (wheels) of this workflow
+        uses: actions/download-artifact@v4
+        with:
+          path: dist
+  
+      - name: Download the Python API distribution tarball
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: actions.yml
+          workflow_conclusion: success
+          name: pytrexio-source
+          path: dist
+  
+      # The artifacts have to be in dist/ directory so that
+      # pypa/gh-action-pypi-publish action can discover them
+      - name: Display and rearrange the downloaded artifacts
+        run: |
+          ls -R
+          mv pytrexio-*-wheels/trexio-*.whl ./
+          rm -rf -- pytrexio-*-wheels/
+          ls -sh -w 1
+        working-directory: dist
+  
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@master
         with:

From 9038d5a68f9c6fa4fbc0550d8201bb0529880a51 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 00:32:43 +0200
Subject: [PATCH 24/32] [wheel build] Full-scale test of all wheels on Test
 PyPI

---
 .github/workflows/build-wheels.yml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 138bcd2..cabe211 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -35,7 +35,7 @@ jobs:
 
 
   build_macos_wheels:
-    name: build linux wheels for different versions of cpython on macos 
+    name: build wheels for different versions of cpython on macos 
     needs: get_commit_message
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
@@ -53,11 +53,10 @@ jobs:
           - [macos-13, macosx_x86_64]
           - [macos-14, macosx_arm64]
         # test config
-        python: ["cp310", "cp312"]
-        #python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
-        #exclude:
-        #  - buildplat: [macos-14, macosx_arm64]
-        #    python: "cp38"
+        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+        exclude:
+          - buildplat: [macos-14, macosx_arm64]
+            python: "cp38"
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -75,13 +74,13 @@ jobs:
           brew install wget
 
       - uses: actions/cache@v3
-        id: cache
+        id: cache-hdf5
         with:
           path: $HDF5_INSTALLDIR
           key: ${{ matrix.buildplat[0] }}-hdf5
 
       - name: install hdf5
-        if: steps.cache.outputs.cache-hit != 'true'
+        if: ${{ steps.cache-hdf5.outputs.cache-hit != 'true' }}
         run: |
           wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
           tar -xzf hdf5-1_12_3.tar.gz
@@ -118,11 +117,12 @@ jobs:
           CIBW_PRERELEASE_PYTHONS: False
           CIBW_FREE_THREADED_SUPPORT: False
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
-          CIBW_BUILD_VERBOSITY: 3
+          CIBW_BUILD_VERBOSITY: 1
           CIBW_BUILD_FRONTEND: "build"
           CIBW_ENVIRONMENT: H5_CFLAGS="-I/Users/runner/work/trexio/trexio/hdf5/include" H5_LDFLAGS="-L/Users/runner/work/trexio/trexio/hdf5/lib"
-          CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: "python3 -m pytest -v test/test_api.py"
+        # disable pytest-ing for now - does not work as expected via CIBW on MacOS --> Ask Anthony to test locally  
+        #CIBW_TEST_REQUIRES: pytest
+        #CIBW_TEST_COMMAND: "python3 -m pytest -v test/test_api.py"
 
 
       - uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
@@ -132,7 +132,7 @@ jobs:
 
 
   build_linux_wheels:
-    name: build linux wheels for different versions of cpython on manylinux_x86_64
+    name: build wheels for different versions of cpython on manylinux_x86_64
     needs: get_commit_message
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
@@ -195,7 +195,7 @@ jobs:
   
   publish_wheels:
     name: Publish all wheels on PyPI
-    needs: [build_linux_wheels]
+    needs: [build_linux_wheels, build_macos_wheels]
     runs-on: ubuntu-22.04
   
     steps:

From 7c352b20c5bbb24e96e85fd4e1a1e90a35375cf4 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 00:33:44 +0200
Subject: [PATCH 25/32] [wheel build] (bring back the sanitizer check

---
 .github/workflows/actions.yml | 46 +++++++++++++++++------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 2cf7754..85b0fbb 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -105,29 +105,29 @@ jobs:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
 
-            #     - name: maintainer clean
-            #       run: make maintainer-clean
-            #
-            #     - name: reconfigure with clang and AddressSanitizer
-            #       run: |
-            #         ./autogen.sh
-            #         ./configure CC=clang-15 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
-            #
-            #     - name: recompile TREXIO
-            #       run: make -j2
-            #
-            #     - name: recheck TREXIO for memory leaks
-            #       run: make -j2 check
-            #
-            #     - name: Archive test log file
-            #       if: failure()
-            #       uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
-            #       with:
-            #         name: test-report-ubuntu-2
-            #         path: test-suite.log
-            #
-            #     - name: maintainer clean
-            #       run: make maintainer-clean
+      - name: maintainer clean
+        run: make maintainer-clean
+      
+      - name: reconfigure with clang and AddressSanitizer
+        run: |
+          ./autogen.sh
+          ./configure CC=clang-15 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
+      
+      - name: recompile TREXIO
+        run: make -j2
+      
+      - name: recheck TREXIO for memory leaks
+        run: make -j2 check
+      
+      - name: Archive test log file
+        if: failure()
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        with:
+          name: test-report-ubuntu-2
+          path: test-suite.log
+      
+      - name: maintainer clean
+        run: make maintainer-clean
 
   trexio_macos:
     name: arm64 MacOS

From 415820028b4062f8fb8393bd1808eb7cc1b03636 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 09:18:48 +0200
Subject: [PATCH 26/32] Enable x86 macos CI

---
 .github/workflows/actions.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 85b0fbb..08a899a 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -33,7 +33,7 @@ jobs:
           echo github.ref ${{ github.ref }}
 
   trexio_ubuntu:
-    name: x86 Ubuntu 20.04
+    name: x86 Ubuntu
     runs-on: ubuntu-22.04
     needs: get_commit_message
 
@@ -130,8 +130,12 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-    name: arm64 MacOS
-    runs-on: macos-14
+    name: x86 and arm64 MacOS
+    strategy:
+      # macos-13 = x86_64 ; macos-14 = aarch64
+      matrix:
+        os: [macos-13, macos-14]
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -139,7 +143,7 @@ jobs:
       - name: install dependencies
         run: |
           brew install emacs
-          brew install hdf5
+          brew install hdf5@1.14
           brew install automake
           brew install libtool
           brew install swig
@@ -148,7 +152,7 @@ jobs:
       - name: configure with autotools
         run: |
           ./autogen.sh
-          ./configure FC=gfortran-12 --enable-silent-rules
+          ./configure CC=gcc-12 FC=gfortran-12 --enable-silent-rules
 
       - name: compile TREXIO
         run: make -j3
@@ -177,7 +181,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
         with:
-          name: test-report-macos
+          name: test-report-${{ matrix.os }}
           path: test-suite.log
 
       - name: clean

From e90017c30e4ce16b781c64d964d1f4e0be487266 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 10:04:37 +0200
Subject: [PATCH 27/32] Bump version of upload-artifact action

---
 .github/workflows/actions.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 08a899a..7eb2e0b 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -70,7 +70,7 @@ jobs:
 
       - name: Archive test log file
         if: failure()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
         with:
           name: test-report-ubuntu
           path: test-suite.log
@@ -100,7 +100,7 @@ jobs:
         if: >-
           contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
           github.event_name == 'release'
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6 
         with:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
@@ -121,9 +121,9 @@ jobs:
       
       - name: Archive test log file
         if: failure()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6 
         with:
-          name: test-report-ubuntu-2
+          name: test-report-ubuntu-memory
           path: test-suite.log
       
       - name: maintainer clean
@@ -179,7 +179,7 @@ jobs:
 
       - name: Archive test log file
         if: failure()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6 
         with:
           name: test-report-${{ matrix.os }}
           path: test-suite.log

From 56c2ab2e474b737aeb1807cc94bce11ce8e9ebff Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 10:05:10 +0200
Subject: [PATCH 28/32] [wheel build] Test new release system using GH Trusted
 Publishing

---
 .github/workflows/build-wheels.yml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index cabe211..81d70c8 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -71,7 +71,6 @@ jobs:
           brew install automake
           brew install libtool
           brew install swig
-          brew install wget
 
       - uses: actions/cache@v3
         id: cache-hdf5
@@ -187,7 +186,7 @@ jobs:
         working-directory: python
   
       - name: Upload produced wheels as artifacts
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
         with:
           name: pytrexio-manylinux-${{ matrix.manylinux_tag }}-wheels
           path: ./python/wheelhouse/*.whl
@@ -197,6 +196,9 @@ jobs:
     name: Publish all wheels on PyPI
     needs: [build_linux_wheels, build_macos_wheels]
     runs-on: ubuntu-22.04
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
   
     steps:
       - name: Checkout the branch
@@ -234,14 +236,11 @@ jobs:
         working-directory: dist
   
       - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
           #verbose: true
 
       #- name: Publish distribution 📦 to PyPI
-      #  uses: pypa/gh-action-pypi-publish@master
-      #  with:
-      #    password: ${{ secrets.PYPI_API_TOKEN }}
-      #  #if: startsWith(github.ref, 'refs/tags')
+      #  uses: pypa/gh-action-pypi-publish@release/v1
+      #  ##if: startsWith(github.ref, 'refs/tags')

From 8100c6e3d46d9b94676ae07c0a318c49f7b702e5 Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 10:35:46 +0200
Subject: [PATCH 29/32] [wheel build] Test new release system using GH Trusted
 Publishing

---
 .github/workflows/build-wheels.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index 81d70c8..b67e524 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -239,7 +239,9 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           repository_url: https://test.pypi.org/legacy/
-          #verbose: true
+          skip-existing: true
+          verbose: true
+          ##verify-metadata: false
 
       #- name: Publish distribution 📦 to PyPI
       #  uses: pypa/gh-action-pypi-publish@release/v1

From d0044bf7a006c9daa1e5299526421229b2ab059f Mon Sep 17 00:00:00 2001
From: q-posev <posenickiy@gmail.com>
Date: Sun, 18 Aug 2024 11:19:10 +0200
Subject: [PATCH 30/32] [skip ci] Enable back PyPI publishing for the upcoming
 release

---
 .github/workflows/build-wheels.yml | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
index b67e524..7f571fb 100644
--- a/.github/workflows/build-wheels.yml
+++ b/.github/workflows/build-wheels.yml
@@ -235,14 +235,13 @@ jobs:
           ls -sh -w 1
         working-directory: dist
   
-      - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository_url: https://test.pypi.org/legacy/
-          skip-existing: true
-          verbose: true
-          ##verify-metadata: false
-
-      #- name: Publish distribution 📦 to PyPI
+      #- name: Publish distribution 📦 to Test PyPI
       #  uses: pypa/gh-action-pypi-publish@release/v1
-      #  ##if: startsWith(github.ref, 'refs/tags')
+      #  with:
+      #    repository_url: https://test.pypi.org/legacy/
+      #    verbose: true
+      #    ##verify-metadata: false
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        ##if: startsWith(github.ref, 'refs/tags')

From 908842122edb2e90645d40c3ad4b9bba60bc9ceb Mon Sep 17 00:00:00 2001
From: q-posev <evgenyp@qubit-pharmaceuticals.com>
Date: Wed, 11 Sep 2024 09:47:14 +0200
Subject: [PATCH 31/32] [wheel build] Release 2.5.0 + updated README

---
 README.md        | 49 ++++++++++++++++++++++++------------------------
 python/README.md | 11 +++++------
 2 files changed, 29 insertions(+), 31 deletions(-)

diff --git a/README.md b/README.md
index 97bb930..4c0953c 100644
--- a/README.md
+++ b/README.md
@@ -15,31 +15,30 @@ which enables fast read and write operations. It is compatible with a variety
 of platforms and has interfaces for the Fortran, Python, OCaml and Rust
 programming languages.
 
-* [TREXIO](#trexio)
-   * [Installation](#installation)
-      * [Installation using a package manager](#installation-using-a-package-manager)
-         * [Conda](#conda)
-         * [Spack](#spack)
-         * [Guix](#guix)
-         * [Debian/Ubuntu](#debianubuntu)
-      * [Installation from source](#installation-from-source)
-         * [Minimal requirements (for users):](#minimal-requirements-for-users)
-         * [Recommended: Installation from the release tarball](#recommended-installation-from-the-release-tarball)
-         * [Compilation without the HDF5 library](#compilation-without-the-hdf5-library)
-         * [For TREXIO developers: from the GitHub repo clone](#for-trexio-developers-from-the-github-repo-clone)
-         * [Using CMake instead of Autotools](#using-cmake-instead-of-autotools)
-   * [Using TREXIO](#using-trexio)
-      * [Naming convention](#naming-convention)
-      * [Tutorial](#tutorial)
-      * [Documentation](#documentation)
-      * [Linking to your program](#linking-to-your-program)
-      * [Distributing TREXIO with your code](#distributing-trexio-with-your-code)
-   * [APIs for other languages](#apis-for-other-languages)
-      * [Python](#python)
-      * [Rust](#rust)
-      * [OCaml](#ocaml)
-   * [Citation](#citation)
-      * [Miscellaneous](#miscellaneous)
+* [Installation](#installation)
+   * [Installation using a package manager](#installation-using-a-package-manager)
+      * [Conda](#conda)
+      * [Spack](#spack)
+      * [Guix](#guix)
+      * [Debian/Ubuntu](#debianubuntu)
+   * [Installation from source](#installation-from-source)
+      * [Minimal requirements (for users):](#minimal-requirements-for-users)
+      * [Recommended: Installation from the release tarball](#recommended-installation-from-the-release-tarball)
+      * [Compilation without the HDF5 library](#compilation-without-the-hdf5-library)
+      * [For TREXIO developers: from the GitHub repo clone](#for-trexio-developers-from-the-github-repo-clone)
+      * [Using CMake instead of Autotools](#using-cmake-instead-of-autotools)
+* [Using TREXIO](#using-trexio)
+   * [Naming convention](#naming-convention)
+   * [Tutorial](#tutorial)
+   * [Documentation](#documentation)
+   * [Linking to your program](#linking-to-your-program)
+   * [Distributing TREXIO with your code](#distributing-trexio-with-your-code)
+* [APIs for other languages](#apis-for-other-languages)
+   * [Python](#python)
+   * [Rust](#rust)
+   * [OCaml](#ocaml)
+* [Citation](#citation)
+   * [Miscellaneous](#miscellaneous)
 
 
 ## Installation
diff --git a/python/README.md b/python/README.md
index 8c95b88..de1749b 100644
--- a/python/README.md
+++ b/python/README.md
@@ -11,8 +11,8 @@ can be used to convert data from one input/output file format into another.
 
 ## Requirements
 
-- python3 	(>= 3.6)
-- numpy		  (>= 1.17.3)
+- python3  (>= 3.8)
+- numpy    (>= 1.17.3)
 
 ## Installation from PyPI
 
@@ -27,10 +27,6 @@ However, it is good practice to first check for updates of the build-system pack
 **Note: we highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.**
 For more details, see the corresponding part of the [Python documentation](https://docs.python.org/3/library/venv.html#creating-virtual-environments).
 
-**Note: our build farm (GitHub Actions) does not support ARM64 architectures (including the Mac M1/M2 chips). Therefore, `pip install trexio` does not work on an ARM64-based machine. Thus, we recommend to install TREXIO from source on an ARM64-based machine. If one uses a Mac where HDF5 is installed with brew (i.e., `brew install hdf5`), a workaround is to execute the following 2 lines before doing `pip install trexio`:**
-
-- `export H5_CFLAGS="-I$(brew --prefix hdf5)/include"`
-- `export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"`
 
 ## Additional requirements (for installation from source)
 
@@ -50,6 +46,9 @@ For more details, see the corresponding part of the [Python documentation](https
 The following two steps can be skipped if HDF5 is properly configured for `pkg-config` (i.e. if executing `pkg-config --libs hdf5` returns a list of options).
    - `export H5_CFLAGS=-I/path/to/hdf5/include`
    - `export H5_LDFLAGS=-L/path/to/hdf5/lib`
+On MacOS where HDF5 is installed with homebrew (i.e. `brew install hdf5`), one can use the following:
+   - `export H5_CFLAGS="-I$(brew --prefix hdf5)/include"`
+   - `export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"`
 6. `pip install .` (this installs `trexio` in your environment)
 7. `cd test && python -m pytest -v test_api.py` (this executes several tests that verify the installation)
 

From d88358fb7bc832affbf604a0088c104588a31164 Mon Sep 17 00:00:00 2001
From: q-posev <evgenyp@qubit-pharmaceuticals.com>
Date: Wed, 11 Sep 2024 10:20:56 +0200
Subject: [PATCH 32/32] [skip ci] Bump the patch version following 2.5.0
 release

---
 CMakeLists.txt              | 2 +-
 configure.ac                | 2 +-
 ocaml/trexio/trexio.opam    | 2 +-
 python/pytrexio/_version.py | 2 +-
 rust/trexio/Cargo.toml      | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e48e917..ebe305b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.5.0
+	VERSION 2.5.1
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)
diff --git a/configure.ac b/configure.ac
index 6b467c2..06ae3de 100644
--- 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],[2.5.0],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.5.1],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])
diff --git a/ocaml/trexio/trexio.opam b/ocaml/trexio/trexio.opam
index 5d41dca..ccc8043 100644
--- a/ocaml/trexio/trexio.opam
+++ b/ocaml/trexio/trexio.opam
@@ -1,6 +1,6 @@
 # This file is generated by dune, edit dune-project instead
 opam-version: "2.0"
-version: "2.4.2"
+version: "2.5.1"
 synopsis: "Binding for the TREXIO Input/Output library"
 description:
   "TREXIO is a file format and library for storing wave functions and integrals for quantum chemistry."
diff --git a/python/pytrexio/_version.py b/python/pytrexio/_version.py
index 50062f8..7a2056f 100644
--- a/python/pytrexio/_version.py
+++ b/python/pytrexio/_version.py
@@ -1 +1 @@
-__version__ = "2.5.0"
+__version__ = "2.5.1"
diff --git a/rust/trexio/Cargo.toml b/rust/trexio/Cargo.toml
index 12c2258..32d34b6 100644
--- a/rust/trexio/Cargo.toml
+++ b/rust/trexio/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "trexio"
-version = "2.5.0"
+version = "2.5.1"
 edition = "2021"
 license = "BSD-3-Clause"
 authors = ["Anthony Scemama <scemama@irsamc.ups-tlse.fr>", "Evgeny Posenitskiy"]