Merge branch 'master' of github.com:TREX-CoE/trexio

.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: ${{ steps.commit_message.outputs.message }}
     steps:
@@ -29,11 +29,12 @@ jobs:
         run: |
           set -xe
           COMMIT_MSG=$(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
+    name: x86 Ubuntu
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: get_commit_message
 
     steps:
@@ -53,8 +54,8 @@ jobs:
 
       - name: install dependencies
         run: |
-          sudo add-apt-repository ppa:kelleyk/emacs
+          sudo apt-get update
-          sudo apt-get install libhdf5-dev emacs26
+          sudo apt-get install libhdf5-dev emacs
 
       - name: configure with autotools
         run: |
@@ -69,24 +70,29 @@ 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
 
-      - name: create virtual environment
+      - name: create venv
         run: |
-          python3 -m venv --clear pytrexio-venv
+          python3 -m venv trexio-venv
-          source pytrexio-venv/bin/activate
+          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 .
 
@@ -94,7 +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
@@ -105,7 +111,7 @@ 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
@@ -115,17 +121,21 @@ 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
         run: make maintainer-clean
 
   trexio_macos:
-    name: x86 MacOS 12
+    name: x86 and arm64 MacOS
-    runs-on: macos-12
+    strategy:
+      # macos-13 = x86_64 ; macos-14 = aarch64
+      matrix:
+        os: [macos-13, macos-14]
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -133,14 +143,16 @@ 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
           brew --prefix hdf5
 
       - 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
@@ -148,20 +160,28 @@ 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()
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6 
         with:
-          name: test-report-macos
+          name: test-report-${{ matrix.os }}
           path: test-suite.log
 
       - name: clean

.github/workflows/build-wheels.yml

@@ -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: ${{ github.event.pull_request.head.sha }}
@@ -30,28 +30,125 @@ jobs:
         run: |
           set -xe
           COMMIT_MSG=$(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:
+  build_macos_wheels:
-    name: Build Linux wheels for different versions of CPython on manylinux_x86_64
+    name: build 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'))
+      (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
-    runs-on: ubuntu-20.04
+    runs-on: ${{ matrix.buildplat[0] }}
+    env:
+      HDF5_INSTALLDIR: "/Users/runner/work/trexio/trexio/hdf5"
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        # 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: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+        exclude:
+          - buildplat: [macos-14, macosx_arm64]
+            python: "cp38"
+
+    steps:
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
+
+      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        with:
+          python-version: "3.x"
+
+      - name: install dependencies
+        run: |
+          brew install emacs
+          brew install automake
+          brew install libtool
+          brew install swig
+
+      - uses: actions/cache@v3
+        id: cache-hdf5
+        with:
+          path: $HDF5_INSTALLDIR
+          key: ${{ matrix.buildplat[0] }}-hdf5
+
+      - name: install hdf5
+        if: ${{ steps.cache-hdf5.outputs.cache-hit != 'true' }}
+        run: |
+          wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_3.tar.gz
+          tar -xzf hdf5-1_12_3.tar.gz
+          cd  hdf5-hdf5-1_12_3
+          if [[ "$ARCH" == "arm64" ]]; then
+            export MACOSX_DEPLOYMENT_TARGET="11.0"
+          else
+            export MACOSX_DEPLOYMENT_TARGET="10.9"
+          fi
+          ./autogen.sh
+          ./configure CC=gcc-12 --prefix $HDF5_INSTALLDIR --enable-build-mode=production --with-szlib
+          make -j3
+          make install
+
+      - name: configure with autotools
+        run: |
+          ./autogen.sh
+          export PATH=${PATH}:${HDF5_INSTALLDIR}/bin
+          ./configure FC=gfortran-12 --enable-silent-rules
+          make -j3
+          
+      - name: prepare python 
+        run: |
+          make python-install
+
+      - name: cleanup python 
+        run: |
+          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_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"
+        # 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
+        with:
+          name: pytrexio-${{ matrix.python }}-${{ matrix.buildplat[1] }}-wheels
+          path: ./wheelhouse/*.whl
+
+
+  build_linux_wheels:
+    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]') ||
+      (github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
+    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
@@ -89,31 +186,34 @@ jobs:
         working-directory: python
   
       - name: Upload produced wheels as artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
         with:
-          name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
+          name: pytrexio-manylinux-${{ matrix.manylinux_tag }}-wheels
           path: ./python/wheelhouse/*.whl
   
   
   publish_wheels:
     name: Publish all wheels on PyPI
-    needs: [build_linux_wheels]
+    needs: [build_linux_wheels, build_macos_wheels]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
   
     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
   
@@ -130,20 +230,18 @@ jobs:
       - name: Display and rearrange the downloaded artifacts
         run: |
           ls -R
-          mv pytrexio-manylinux-*/trexio-*.whl ./
+          mv pytrexio-*-wheels/trexio-*.whl ./
-          rm -rf -- pytrexio-manylinux-*/
+          rm -rf -- pytrexio-*-wheels/
           ls -sh -w 1
         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
+      #    ##verify-metadata: false
 
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
+        ##if: startsWith(github.ref, 'refs/tags')
-          password: ${{ secrets.PYPI_API_TOKEN }}
-        #if: startsWith(github.ref, 'refs/tags')

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
 	)

README.md

@@ -15,7 +15,6 @@ 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)

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])

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."

python/README.md

@@ -11,7 +11,7 @@ can be used to convert data from one input/output file format into another.
 
 ## Requirements
 
-- python3 	(>= 3.6)
+- 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)
 

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
+   CPYTHON="cp${PYVERSION}-cp${PYVERSION}"
-   if [[ ${PYVERSION} -eq 36 ]] || [[ ${PYVERSION} -eq 37 ]]; then
-       PYM="m"
-   else
-       PYM=""
-   fi
-
-   CPYTHON="cp${PYVERSION}-cp${PYVERSION}${PYM}"
 
    # create and activate a virtual environment based on CPython version ${PYVERSION}
    /opt/python/${CPYTHON}/bin/python3 -m venv --clear trexio-manylinux-py${PYVERSION}
@@ -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

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
 

python/pyproject.toml

@@ -3,6 +3,6 @@ requires = [
     "setuptools>=42",
     "wheel",
     "pkgconfig",
-    "oldest-supported-numpy"
+    "numpy",
 ]
 build-backend = "setuptools.build_meta"

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "2.5.0"
+__version__ = "2.5.1"

python/requirements.txt

@@ -1,4 +1,3 @@
 setuptools>=42
 pkgconfig
-numpy<1.27.0
+numpy
-numpy>=1.17.3

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"]

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 (PyBytes_Check(   py_obj)) return "string"      ;
-    if (PyInt_Check(     py_obj)) return "int"         ;
+    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* 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.
    */
@@ -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
 
-%#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*)(*$2), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
@@ -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
 
-%#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*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
@@ -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
 
-%#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*)(*$3), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
@@ -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
 
-%#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*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
@@ -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
 
-%#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*)(*$4), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
@@ -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
 
-%#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*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
-    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);
-%#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
   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
 
-%#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*)(*$5), SWIGPY_CAPSULE_NAME, free_cap);
-    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);

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."