Merge pull request #22 from profminton/master

Addition of continuous integration using cibuildwheels, scikit-build-core, and GitHub Actions
MintonGroup · Sep 7, 2023 · ef89afd · ef89afd
2 parents e7c27a4 + 741bfef
commit ef89afd
Show file tree

Hide file tree

Showing 43 changed files with 2,947 additions and 847 deletions.
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -0,0 +1,42 @@
+name: swiftest
+
+on: push
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, macos-12, macos-13]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.15.0
+        env:
+          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_ARCHS_LINUX: x86_64 aarch64
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+          config-file: "{package}/pyproject.toml"
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
diff --git a/.gitignore b/.gitignore
@@ -18,13 +18,15 @@ swiftest_driver.sh
 !README.swifter 
 dump*
 !**/.gitignore
+!.github/workflows/build_wheels.yml
 !setup.py
 !examples/**
 !swiftest/**
 !tests/**
 *ipynb_checkpoints
 **/.DS_Store
 !version.txt
+!LICENSE.txt
 !requirements.txt
 !pyproject.toml
 **/_skbuild

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -15,7 +15,15 @@ CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
 
 # Get version stored in text file
 FILE(READ "version.txt" VERSION)
-PROJECT(swiftest VERSION ${VERSION} LANGUAGES C Fortran)
+PROJECT(${SKBUILD_PROJECT_NAME} LANGUAGES C Fortran VERSION ${VERSION})
+
+IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
+    SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
+ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+    SET(COMPILER_OPTIONS "GNU" CACHE STRING "Compiler identified as gfortran")
+ELSE ()
+    MESSAGE(FATAL_ERROR "Compiler ${CMAKE_Fortran_COMPILER_ID} not recognized!") 
+ENDIF ()
 
 # Set some options the user may choose
 OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
@@ -29,28 +37,7 @@ IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
 ENDIF()
 
 # Ensure scikit-build modules
-FIND_PACKAGE(Python3 COMPONENTS Interpreter Development.Module REQUIRED)
-IF (NOT SKBUILD)
-  EXECUTE_PROCESS(
-    COMMAND "${Python3_EXECUTABLE}"
-    -c "import os, skbuild; print(os.path.dirname(skbuild.__file__))"
-    OUTPUT_VARIABLE SKBLD_DIR
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-  )
-  FILE(TO_CMAKE_PATH ${SKBLD_DIR} SKBLD_DIR)
-  LIST(APPEND CMAKE_MODULE_PATH "${SKBLD_DIR}/resources/cmake")
-  MESSAGE(STATUS "Looking in ${SKBLD_DIR}/resources/cmake for CMake modules")
-ENDIF()
-
-# Detect when building against a conda environment set the _using_conda variable
-# for use both in this file and in the parent
-GET_FILENAME_COMPONENT(_python_bin_dir ${Python3_EXECUTABLE} DIRECTORY)
-IF(EXISTS "${_python_bin_dir}/../conda-meta")
-  MESSAGE("-- Detected conda environment, setting INSTALL_RPATH_USE_LINK_PATH")
-  SET(_using_conda On)
-ELSE()
-  SET(_using_conda Off)
-ENDIF()
+FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
 # Add our local modules to the module path
 FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
@@ -77,6 +64,9 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${BIN})
 # Have the .mod files placed in the lib folder
 SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
 
+# Set the name of the swiftest library
+SET(SWIFTEST_LIBRARY swiftest)
+
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${BIN})
 

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,10 @@
+Copyright 2023 - David Minton 
+The Swiftest development team: David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, Dana Singh, & Kaustub Anand
+
+This file is part of Swiftest.
+Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with Swiftest. 
+If not, see: https://www.gnu.org/licenses. 
diff --git a/buildscripts/_build_getopts.sh b/buildscripts/_build_getopts.sh
@@ -14,10 +14,9 @@ SCRIPT_DIR=$(realpath $(dirname $0))
 ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
 
 # Parse arguments
-USTMT="Usage: ${0} <-d /path/to/dependency/source> [-p /prefix/path|{/usr/local}] [-m MACOSX_DEPLOYMENT_TARGET|{11.0}]"
-PREFIX=/usr/local
-DEPENDENCY_DIR="${ROOT_DIR}/_dependencies"
-MACOSX_DEPLOYMENT_TARGET="13.0"
+USTMT="Usage: ${0} [-d /path/to/dependency/source] [-p /prefix/path] [-m MACOSX_DEPLOYMENT_TARGET]"
+MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET:-"$(sw_vers --ProductVersion)"}
+
 while getopts ":d:p:m:h" ARG; do
     case "${ARG}" in
     d)
@@ -46,26 +45,9 @@ while getopts ":d:p:m:h" ARG; do
 done
 
 read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
-
-if [ -z ${DEPENDENCY_ENV_VARS+x} ]; then
-    . ${SCRIPT_DIR}/set_compilers.sh 
-
-    LD_LIBRARY_PATH="${PREFIX}/lib:${LD_LIBRARY_PATH}"
-    CPPFLAGS="${CPPFLAGS} -isystem ${PREFIX}/include"
-    LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-    CPATH="${CPATH} ${PREFIX}/include}"
-
-    HDF5_ROOT="${PREFIX}"
-    HDF5_LIBDIR="${HDF5_ROOT}/lib"
-    HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
-    HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
-    NCDIR="${PREFIX}"
-    NFDIR="${PREFIX}"
-    NETCDF_FORTRAN_HOME=${NFDIR}
-    NETCDF_HOME=${NCDIR}
-
-    DEPENDENCY_ENV_VARS=true
-fi
+BUILD_DIR=${BUILD_DIR:-$(mktemp -ut swiftest_build.XXXXXXXX)}
+PREFIX=${PREFIX:-${ROOT_DIR}}
+DEPENDENCY_DIR=${DEPENDENCY_DIR:-${BUILD_DIR}}
 
 mkdir -p ${DEPENDENCY_DIR}
 mkdir -p ${PREFIX}/lib

diff --git a/buildscripts/build_all.sh b/buildscripts/build_all.sh
diff --git a/buildscripts/build_dependencies.sh b/buildscripts/build_dependencies.sh
@@ -17,47 +17,6 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 
-ZLIB_VER="1.3"
-HDF5_VER="1_14_2"
-NC_VER="4.9.2"
-NF_VER="4.6.1"
-
-printf "*********************************************************\n"
-printf "*          FETCHING DEPENCENCY SOURCES                  *\n"
-printf "*********************************************************\n"
-printf "Copying files to ${DEPENDENCY_DIR}\n"
-mkdir -p ${DEPENDENCY_DIR}
-if [ ! -d ${DEPENDENCY_DIR}/zlib-${ZLIB_VER} ]; then
-    [ -d ${DEPENDENCY_DIR}/zlib-* ] && rm -rf ${DEPENDENCY_DIR}/zlib-*
-    curl -L https://github.com/madler/zlib/releases/download/v${ZLIB_VER}/zlib-${ZLIB_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
-fi
-
-printf "Checking if HDF5 source exists\n"
-if [[ (-d ${DEPENDENCY_DIR}/hdfsrc) && (-f ${DEPENDENCY_DIR}/hdfsrc/README.md) ]]; then
-    OLDVER=$(grep version ${DEPENDENCY_DIR}/hdfsrc/README.md | awk '{print $3}' | sed 's/\./_/g')
-    printf "Existing copy of HDF5 source detected\n"
-    printf "Existing version : ${OLDVER}\n"
-    printf "Requested version: ${HDF5_VER}\n"
-    if [ "$OLDVER" != "${HDF5_VER}" ]; then
-        printf "Existing version of HDF5 source doesn't match requested. Deleting\n"
-        rm -rf ${DEPENDENCY_DIR}/hdfsrc
-    fi
-fi
-
-if [ ! -d ${DEPENDENCY_DIR}/hdfsrc ]; then
-    curl -s -L https://github.com/HDFGroup/hdf5/releases/download/hdf5-${HDF5_VER}/hdf5-${HDF5_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
-fi
-
-if [ ! -d ${DEPENDENCY_DIR}/netcdf-c-${NC_VER} ]; then
-    [ -d ${DEPENDENCY_DIR}/netcdf-c-* ] && rm -rf ${DEPENDENCY_DIR}/netcdf-c-*
-    curl -s -L https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NC_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
-fi
-
-if [ ! -d ${DEPENDENCY_DIR}/netcdf-fortran-${NF_VER} ]; then
-    [ -d ${DEPENDENCY_DIR}/netcdf-fortran-* ] && rm -rf ${DEPENDENCY_DIR}/netcdf-fortran-*
-    curl -s -L https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${NF_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
-fi 
-
 cd $ROOT_DIR
 printf "*********************************************************\n"
 printf "*          STARTING DEPENDENCY BUILD                    *\n"
@@ -66,34 +25,21 @@ printf "Using ${OS} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
 printf "Installing to ${PREFIX}\n"
 printf "\n"
 
-set -e
-if [ ! -f ${PREFIX}/lib/libz.a ]; then
-    ${SCRIPT_DIR}/build_zlib.sh ${ARGS}
-else
-    echo "Found: ${PREFIX}/lib/libz.a"
-fi
-
-if [ ! -f ${PREFIX}/lib/libhdf5.a ]; then
-    ${SCRIPT_DIR}/build_hdf5.sh ${ARGS}
-else
-    echo "Found: ${PREFIX}/lib/libhdf5.a"
+# Get the OpenMP Libraries
+if [ $OS = "MacOSX" ]; then
+    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
 fi
 
-
-if [ ! -f ${PREFIX}/lib/libnetcdf.a ]; then
-    ${SCRIPT_DIR}/build_netcdf-c.sh ${ARGS}
-else
-    echo "Found: ${PREFIX}/lib/libnetcdf.a" 
-fi
-
-if [ ! -f ${PREFIX}/lib/libnetcdff.a ]; then
-    ${SCRIPT_DIR}/build_netcdf-fortran.sh ${ARGS}
-else
-    echo "Found: ${PREFIX}/lib/libnetcdff.a"
-fi
+set -e
+${SCRIPT_DIR}/build_zlib.sh ${ARGS}
+${SCRIPT_DIR}/build_hdf5.sh ${ARGS}
+${SCRIPT_DIR}/build_netcdf-c.sh ${ARGS}
+${SCRIPT_DIR}/build_netcdf-fortran.sh ${ARGS}
 
 printf "\n"
 printf "*********************************************************\n"
 printf "*             DEPENDENCIES ARE BUILT                    *\n"
 printf "*********************************************************\n"
 printf "Dependencys are installed to: ${PREFIX}\n\n"
+
+
diff --git a/buildscripts/build_hdf5.sh b/buildscripts/build_hdf5.sh
@@ -15,9 +15,32 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 
+HDF5_VER="1_14_2"
+printf "*********************************************************\n"
+printf "*             FETCHING HDF5 SOURCE                      *\n"
+printf "*********************************************************\n"
+printf "Copying files to ${DEPENDENCY_DIR}\n"
+
+printf "Checking if HDF5 source exists\n"
+if [[ (-d ${DEPENDENCY_DIR}/hdfsrc) && (-f ${DEPENDENCY_DIR}/hdfsrc/README.md) ]]; then
+    OLDVER=$(grep version ${DEPENDENCY_DIR}/hdfsrc/README.md | awk '{print $3}' | sed 's/\./_/g')
+    printf "Existing copy of HDF5 source detected\n"
+    printf "Existing version : ${OLDVER}\n"
+    printf "Requested version: ${HDF5_VER}\n"
+    if [ "$OLDVER" != "${HDF5_VER}" ]; then
+        printf "Existing version of HDF5 source doesn't match requested. Deleting\n"
+        rm -rf ${DEPENDENCY_DIR}/hdfsrc
+    fi
+fi
+
+if [ ! -d ${DEPENDENCY_DIR}/hdfsrc ]; then
+    curl -s -L https://github.com/HDFGroup/hdf5/releases/download/hdf5-${HDF5_VER}/hdf5-${HDF5_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
+fi
+
+
 printf "\n"
 printf "*********************************************************\n"
-printf "*            BUILDING HDF5 STATIC LIBRARY               *\n"
+printf "*               BUILDING HDF5 LIBRARY                   *\n"
 printf "*********************************************************\n"
 printf "LIBS: ${LIBS}\n"
 printf "CFLAGS: ${CFLAGS}\n"
@@ -35,7 +58,7 @@ if [ $OS = "MacOSX" ]; then
       printf "echo arm-apple-darwin" > bin/config.sub 
    fi
 fi
-COPTS="--disable-shared --enable-build-mode=production --enable-tests=no --enable-tools=no --disable-fortran --disable-java --disable-cxx --prefix=${PREFIX} --with-zlib=${PREFIX}"
+COPTS="--enable-build-mode=production --enable-tests=no --enable-tools=no --disable-fortran --disable-java --disable-cxx --prefix=${PREFIX} --with-zlib=${PREFIX}"
 ./configure ${COPTS}
 make 
 if [ -w ${PREFIX} ]; then
@@ -48,6 +71,3 @@ if [ $? -ne 0 ]; then
    printf "hdf5 could not be compiled.\n"
    exit 1
 fi
-
-make distclean
-
diff --git a/buildscripts/build_netcdf-c.sh b/buildscripts/build_netcdf-c.sh
@@ -16,9 +16,22 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 
+
+NC_VER="4.9.2"
+
+printf "*********************************************************\n"
+printf "*            FETCHING NETCDF-C SOURCE                   *\n"
+printf "*********************************************************\n"
+printf "Copying files to ${DEPENDENCY_DIR}\n"
+
+if [ ! -d ${DEPENDENCY_DIR}/netcdf-c-${NC_VER} ]; then
+    [ -d ${DEPENDENCY_DIR}/netcdf-c-* ] && rm -rf ${DEPENDENCY_DIR}/netcdf-c-*
+    curl -s -L https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NC_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
+fi
+
 printf "\n"
 printf "*********************************************************\n"
-printf "*          BUILDING NETCDF-C STATIC LIBRARY             *\n"
+printf "*              BUILDING NETCDF-C LIBRARY                *\n"
 printf "*********************************************************\n"
 printf "LIBS: ${LIBS}\n"
 printf "CFLAGS: ${CFLAGS}\n"
@@ -30,10 +43,7 @@ printf "HDF5_ROOT: ${HDF5_ROOT}\n"
 printf "*********************************************************\n"
 
 cd ${DEPENDENCY_DIR}/netcdf-c-*
-COPTS="--disable-shared --disable-dap --disable-byterange --disable-testsets --prefix=${PREFIX}"
-if [ !  $OS = "MacOSX" ]; then
-    COPTS="${COPTS} --disable-libxml2"
-fi
+COPTS="--disable-testsets --disable-nczarr --prefix=${PREFIX}"
 printf "COPTS: ${COPTS}\n"
 ./configure $COPTS
 make && make check 
@@ -47,6 +57,4 @@ fi
 if [ $? -ne 0 ]; then
    printf "netcdf-c could not be compiled."\n
    exit 1
-fi
-
-make distclean
+fi