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

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This commit is contained in:
Anthony Scemama 2024-10-16 16:17:17 +02:00
commit b68fe5a18a
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76
.github/workflows/actions.yml vendored
View File

@ -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
runs-on: ubuntu-20.04
name: x86 Ubuntu
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 install libhdf5-dev emacs26
sudo apt-get update
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
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 .
@ -94,38 +100,42 @@ 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
- name: maintainer clean
run: make maintainer-clean
- 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
- name: recheck TREXIO for memory leaks
run: make -j2 check
- 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
runs-on: macos-12
name: x86 and arm64 MacOS
strategy:
# macos-13 = x86_64 ; macos-14 = aarch64
matrix:
os: [macos-13, macos-14]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@ -133,14 +143,16 @@ jobs:
- name: install dependencies
run: |
brew install emacs
brew install hdf5
brew install hdf5@1.14
brew install automake
brew install libtool
brew install swig
brew --prefix hdf5
- name: configure with autotools
run: |
./autogen.sh
./configure FC=gfortran-12 --enable-silent-rules
./configure CC=gcc-12 FC=gfortran-12 --enable-silent-rules
- name: compile TREXIO
run: make -j3
@ -148,20 +160,28 @@ jobs:
- name: check TREXIO
run: make -j3 check
- name: create venv
run: |
python3 -m venv trexio-venv
source trexio-venv/bin/activate
- name: compile Python API
run: |
export H5_CFLAGS="-I$(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

188
.github/workflows/build-wheels.yml vendored
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@ -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: ${{ github.event.pull_request.head.sha }}
@ -30,38 +30,135 @@ jobs:
run: |
set -xe
COMMIT_MSG=$(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
build_macos_wheels:
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'))
runs-on: ubuntu-20.04
(github.repository == 'trex-coe/trexio' && startswith(github.ref, 'refs/tags/v'))
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:
manylinux_tag: [2014_x86_64, 2_24_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: ["cp38", "cp39", "cp310", "cp311", "cp312"]
exclude:
- buildplat: [macos-14, macosx_arm64]
python: "cp38"
steps:
- name: Checkout the branch
uses: actions/checkout@v3
- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
- name: Set up Python
uses: actions/setup-python@v4
- uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
with:
python-version: '3.9'
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_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 ${{ env.PYTREXIO_VERSION }}
# Conventional download-artifact action does not work for artifact produced in a different workflow,
# which is the case here (TREXIO CI produced the Python API distribution tarball)
- name: Download the Python API distribution tarball
@ -72,12 +169,12 @@ jobs:
workflow_conclusion: success
name: pytrexio-source
path: python
# at the moment we have to pull the custom container with pre-installed HDF5
# the containers are built and stored in GitHub container registry ghcr.io/q-posev
- name: Pull the manylinux Docker container with HDF5
run: docker pull ghcr.io/q-posev/hdf5_1_12_on_${{ matrix.manylinux_tag }}:latest
- name: Build wheels for different versions of CPython inside the Docker container
run: >
docker run --rm
@ -87,36 +184,39 @@ jobs:
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@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]
runs-on: ubuntu-20.04
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
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
with:
@ -124,26 +224,24 @@ jobs:
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-*/
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
# uses: pypa/gh-action-pypi-publish@release/v1
# with:
# password: ${{ secrets.TEST_PYPI_API_TOKEN }}
# repository_url: https://test.pypi.org/legacy/
#verbose: true
# verbose: true
# ##verify-metadata: false
- 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')

2
CMakeLists.txt
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@ -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
)

49
README.md
View File

@ -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

2
configure.ac
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@ -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])

2
ocaml/trexio/trexio.opam
View File

@ -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."

11
python/README.md
View File

@ -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)

19
python/build_manylinux_wheels.sh
View File

@ -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

3
python/install_pytrexio.sh
View File

@ -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

2
python/pyproject.toml
View File

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

2
python/pytrexio/_version.py
View File

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

3
python/requirements.txt
View File

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

2
rust/trexio/Cargo.toml
View File

@ -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"]

297
src/numpy.i
View File

@ -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);

6
tools/prepare_python.sh
View File

@ -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."