Add Manylinux wheel generation workflow

.github/workflows/bundle_with_dakota.yml

@@ -0,0 +1,162 @@
+name: 🏎️ Make & Test Wheels 🏎️
+
+on: [pull_request]
+
+env:
+  ERT_SHOW_BACKTRACE: 1
+  NO_PROJECT_RES: 1
+  BOOST_VERSION: 1.83.0
+  BOOST_VERSION_UNDERSCORES: 1_83_0
+  DAKOTA_VERSION: 6.18.0
+  SEBA_TAG: 6.12.0
+  INSTALL_DIR: local
+  FORCE_REBUILD: false
+
+jobs:
+  build_wheels:
+    name: 🛞 Build Wheels 🛞
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8','3.9','3.10'] # Versions > 3.10 excluded. Reason: not supported by Everest.
+        os: [ubuntu-latest]
+        ert-version: ['main']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/cache@v3
+      id: cache-package-check
+      with:
+        key: carolina_dist_${{ matrix.os }}_python-${{ matrix.python-version }}_boost-${{ env.BOOST_VERSION }}_dakota-${{ env.DAKOTA_VERSION }}
+        path: ./carolina_dist
+
+    - uses: actions/checkout@v3
+      if: env.FORCE_REBUILD == 'true' || steps.cache-package-check.outputs.cache-hit != 'true'
+      with:
+        fetch-depth: 0
+
+    - name: Build Linux Wheel
+      if: env.FORCE_REBUILD == 'true' || steps.cache-package-check.outputs.cache-hit != 'true'
+      uses: docker://quay.io/pypa/manylinux2014_x86_64
+      env:
+        PYTHON_VERSION: ${{ matrix.python-version }}
+        BOOST_VERSION: ${{ env.BOOST_VERSION }}
+        BOOST_VERSION_UNDERSCORES: ${{ env.BOOST_VERSION_UNDERSCORES }}
+        DAKOTA_VERSION: ${{ env.DAKOTA_VERSION }}
+      with:
+        entrypoint: /bin/bash
+        args: '-c "sh dakota_manylinux_install_files/build_wheels_gha.sh ${{ matrix.python-version }}"'
+
+    - uses: actions/cache/save@v3
+      if: env.FORCE_REBUILD == 'true' || steps.cache-package-check.outputs.cache-hit != 'true'
+      id: cache-package-store
+      with:
+        key: carolina_dist_${{ matrix.os }}_python-${{ matrix.python-version }}_boost-${{ env.BOOST_VERSION }}_dakota-${{ env.DAKOTA_VERSION }}
+        path: ./carolina_dist
+
+    - name: Get Carolina wheel from cache
+      uses: actions/cache/restore@v3
+      id: restore-cached-package
+      with:
+        key: carolina_dist_${{ matrix.os }}_python-${{ matrix.python-version }}_boost-${{ env.BOOST_VERSION }}_dakota-${{ env.DAKOTA_VERSION }}
+        path: /local/carolina_dist
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up python venv
+      run: |
+        python -m venv myvenv
+
+    - name: Install Carolina from wheel
+      run: |
+        source myvenv/bin/activate
+        pyv=$(echo ${{matrix.python-version}} | sed 's/\.//g')
+        pip install carolina_dist/carolina-1.0-cp$pyv-cp$pyv-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+
+    - name: Install other Everest dependencies
+      run: |
+        source myvenv/bin/activate
+        pip install git+https://${{ secrets.DEPENDENCY_ACCESS_TOKEN }}@github.com/equinor/spinningjenny.git
+        pip install git+https://${{ secrets.DEPENDENCY_ACCESS_TOKEN }}@github.com/TNO-Everest/seba.git@${{ env.SEBA_TAG }}
+      
+    - name: Install Everest
+      run: |
+        source myvenv/bin/activate
+        git clone https://${{ secrets.DEPENDENCY_ACCESS_TOKEN }}@github.com/equinor/everest.git
+        cd everest
+        pip install .[test,docs]
+
+    - name: Install latest ert main
+      if: matrix.ert-version == 'main'
+      run: |
+        source myvenv/bin/activate
+        sudo apt-get install build-essential
+        pip install git+https://github.com/equinor/ert.git
+
+    - name: Run Tests
+      run: |
+        source myvenv/bin/activate
+        cd everest
+        pytest tests -n 4 -m "not ui_test and not integration_test" --dist loadgroup -sv
+
+    - name: Run Integration Tests
+      run: |
+        source myvenv/bin/activate
+        cd everest
+        pytest tests -n 4 -m "integration_test" --dist loadgroup
+
+    - name: Build Documentation
+      run: |
+        source myvenv/bin/activate
+        cd everest
+        mkdir tmp
+        sphinx-build -W -b html -d tmp/doctrees docs/source {envtmpdir}/html
+
+    - name: Run UI Tests
+      env:
+        QT_QPA_PLATFORM: 'minimal'
+      run: |
+        source myvenv/bin/activate
+        cd everest
+        python -m pytest  -m "ui_test"
+ 
+    - name: Upload wheel as artifact
+      if: always()
+      uses: actions/upload-artifact@v3
+      with:
+        name: ${{ matrix.os }} Python ${{ matrix.python-version }} wheel
+        path: |
+          carolina_dist/*
+          trace/*
+
+  publish:
+    name: 👾 Publish 👾
+    runs-on: ubuntu-latest
+    needs: [ build_wheels ]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    steps:
+      - name: Get wheels
+        uses: actions/download-artifact@v3
+        with:
+          path: artifacts
+
+      - name: Create dist/ folder with all python wheels
+        run: |
+          mkdir dist
+          find artifacts -name "carolina*.whl" -exec mv '{}' dist/ \;
+
+      - name: Upload dist/ folder as artifact (debug)
+        uses: actions/upload-artifact@v3
+        with:
+          path: dist/*
+
+      - name: Publish to pypi
+        uses: pypa/gh-action-pypi-publish@v1.8.10
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -1,11 +1,15 @@
 # Carolina
 
-Carolina is a [pyDAKOTA](https://github.com/wisdem/pyDAKOTA) fork maintained by Equinor.  Its raison d'être is to have easier building of a Python [Dakota](https://dakota.sandia.gov/) wrapper, without any MPI support.
+Carolina is a [pyDAKOTA](https://github.com/wisdem/pyDAKOTA) fork maintained by Equinor.  Its raison d'être is to have easier building of a Python [Dakota](https://dakota.sandia.gov/) wrapper, without any MPI support. Carolina supports Python version 3.8, 3.9, 3.10
 
 ## Installation
+For Linux: 
 
-Python version: Carolina supports Python version 3.6, 3.7, 3.8, 3.10
+```pip install carolina```
 
+If not on Linux, build Carolina youself as described below.
+
+## Building and installing Carolina
 In order to build Carolina, [Boost](https://www.boost.org/), including Boost.Python, and [Dakota](https://dakota.sandia.gov/) must be installed. This requires [CMake](https://cmake.org/) and a C/C++ compiler.
 
 The `BOOST_ROOT` environment variable can be set to the location of the boost library, if not in a default location.

dakota_manylinux_install_files/CMakeLists.txt.patch

@@ -0,0 +1,31 @@
+--- a/dakota-6.18.0-public-src-cli/CMakeLists.txt	2023-05-11 03:08:25
++++ b/dakota-6.18.0-public-src-cli/CMakeLists.txt	2023-10-26 08:43:44
+@@ -150,10 +150,20 @@
+ # Perl is required for examples, docs, and system tests
+ find_package(Perl REQUIRED)
+
++set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wall -lpthread -lutil")
+ # Python is optionally required by Dakota, Teuchos, and Acro; probe
+ # for components here at top-level:
++include_directories(${PYTHON_INCLUDE_DIRS})
++include_directories(/usr/include)
++include_directories(/usr/lib64)
++include_directories(/tmp/INSTALL_DIR/dakota-6.18.0-public-src-cli/packages/external/eigen3/include/)
++find_package(Threads REQUIRED)
++
++set (PYBIND11_PYTHON_VERSION "3.10")
++
+ include(DakotaFindPython)
+ dakota_find_python()
++add_link_options()
+
+ # Conditionally find Java JDK needed for input spec, docs, Java API
+ include(DakotaFindJava)
+@@ -186,6 +196,7 @@
+       "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS} -undefined dynamic_lookup")
+ endif()
+
++link_directories(/usr/lib64)
+
+ include(DakotaFindSystemTPLs)
+ # Unconditionally find BLAS/LAPACK or equivalent

dakota_manylinux_install_files/DakotaFindPython.cmake.patch

@@ -0,0 +1,11 @@
+--- a/dakota-6.18.0-public-src-cli/cmake/DakotaFindPython.cmake	2023-05-11 03:08:25
++++ b/dakota-6.18.0-public-src-cli/cmake/DakotaFindPython.cmake	2023-10-26 08:43:44
+@@ -17,7 +17,7 @@
+
+     endif()
+
+-    find_package(Python REQUIRED ${dakota_python_components})
++    find_package(Python COMPONENTS ${dakota_python_components} REQUIRED)
+
+     # pybind11, C3, Acro, etc., use older CMake FindPythonInterp, so we
+     # coerce it to use same as Dakota; more complex situations may

dakota_manylinux_install_files/build_wheels_gha.sh

@@ -0,0 +1,159 @@
+#!/bin/bash
+set -e
+
+if [ -z "$1" ]; then
+  echo "Please provide a Python version as an argument (e.g., 3.10)"
+  exit 1
+fi
+
+cd /tmp
+INSTALL_DIR=/tmp/INSTALL_DIR
+
+mkdir -p $INSTALL_DIR
+mkdir /github/workspace/trace
+touch /github/workspace/trace/boost_bootstrap.log
+touch /github/workspace/trace/boost_install.log
+touch /github/workspace/trace/dakota_bootstrap.log
+touch /github/workspace/trace/dakota_install.log
+touch /github/workspace/trace/env
+
+# VERY IMPORTANT: extract python dev headers,
+# more info: https://github.com/pypa/manylinux/pull/1250
+pushd /opt/_internal && tar -xJf static-libs-for-embedding-only.tar.xz && popd
+
+echo "pushd /opt/_internal && tar -xJf static-libs-for-embedding-only.tar.xz && popd" >> /github/workspace/trace/env
+echo "INSTALL_DIR=$INSTALL_DIR" >> /github/workspace/trace/env
+
+yum install lapack-devel -y
+yum install python3-devel.x86_64 -y
+yum install -y wget
+cd /tmp
+
+wget https://boostorg.jfrog.io/artifactory/main/release/$BOOST_VERSION/source/boost_$BOOST_VERSION_UNDERSCORES.tar.bz2 --no-check-certificate > /dev/null
+python_exec=$(which python$1)
+$python_exec -m venv myvenv
+source ./myvenv/bin/activate
+pip install numpy
+pip install pybind11[global]
+
+PYTHON_DEV_HEADERS_DIR=$(rpm -ql python3-devel.x86_64 | grep '\.h$' | head -n 1 | xargs dirname)
+NUMPY_INCLUDE_PATH=$(find /tmp -type d -path "*site-packages/numpy/core/include")
+PYTHON_INCLUDE_PATH=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")
+python_root=$(python -c "import sys; print(sys.prefix)")
+python_version=$(python --version | sed -E 's/.*([0-9]+\.[0-9]+)\.([0-9]+).*/\1/')
+python_version_no_dots="$(echo "${python_version//\./}")"
+python_bin_include_lib="    using python : $python_version : $(python -c "from sysconfig import get_paths as gp; g=gp(); print(f\"$python_exec : {g['include']} : {g['stdlib']} ;\")")"
+
+echo "Found dev headers $PYTHON_DEV_HEADERS_DIR"
+echo "Found numpy include path $NUMPY_INCLUDE_PATH"
+echo "Found python include path $PYTHON_INCLUDE_PATH"
+echo "Found python root $python_root"
+
+tar xf boost_$BOOST_VERSION_UNDERSCORES.tar.bz2
+cd boost_$BOOST_VERSION_UNDERSCORES
+
+echo "python_exec=$python_exec" >> /github/workspace/trace/env
+echo "PYTHON_DEV_HEADERS_DIR=$PYTHON_DEV_HEADERS_DIR" >> /github/workspace/trace/env
+echo "NUMPY_INCLUDE_PATH=$NUMPY_INCLUDE_PATH" >> /github/workspace/trace/env
+echo "PYTHON_INCLUDE_PATH=$PYTHON_INCLUDE_PATH" >> /github/workspace/trace/env
+echo "python_root=$python_root" >> /github/workspace/trace/env
+echo "python_version=$python_version" >> /github/workspace/trace/env
+echo "python_version_no_dots=$python_version_no_dots" >> /github/workspace/trace/env
+echo "python_bin_include_lib=$python_bin_include_lib" >> /github/workspace/trace/env
+echo "bootstrap_cmd=./bootstrap.sh --with-libraries=python,filesystem,program_options,regex,serialization,system --with-python=$(which python) --with-python-root=$python_root &> "$INSTALL_DIR/boost_bootstrap.log"" >> /github/workspace/trace/env
+
+./bootstrap.sh --with-libraries=python,filesystem,program_options,regex,serialization,system --with-python=$(which python) --with-python-root="$python_root" &> "$INSTALL_DIR/boost_bootstrap.log"
+sed -i -e "s|.*using python.*|$python_bin_include_lib|" project-config.jam
+echo "# sed -i -e \"s|.*using python.*|$python_bin_include_lib|\" project-config.jam" >> /github/workspace/trace/env
+
+./b2 install -j8 -a cxxflags="-std=c++17" --prefix="$INSTALL_DIR" &> /github/workspace/trace/boost_install.log
+echo "# ./b2 install -j8 -a cxxflags="-std=c++17" --prefix="$INSTALL_DIR" &> /github/workspace/trace/boost_install.log" >> /github/workspace/trace/env
+
+cd $INSTALL_DIR
+DAKOTA_INSTALL_DIR=/tmp/INSTALL_DIR/dakota
+mkdir -p $DAKOTA_INSTALL_DIR
+echo "DAKOTA_INSTALL_DIR=$DAKOTA_INSTALL_DIR" >> /github/workspace/trace/env
+
+wget https://github.com/snl-dakota/dakota/releases/download/v$DAKOTA_VERSION/dakota-$DAKOTA_VERSION-public-src-cli.tar.gz > /dev/null
+tar xf dakota-$DAKOTA_VERSION-public-src-cli.tar.gz
+
+CAROLINA_DIR=/github/workspace
+
+cd dakota-$DAKOTA_VERSION-public-src-cli
+patch -s -p2 < $CAROLINA_DIR/dakota_manylinux_install_files/CMakeLists.txt.patch
+patch -s -p2 < $CAROLINA_DIR/dakota_manylinux_install_files/DakotaFindPython.cmake.patch
+
+mkdir build
+cd build
+
+export PATH=/tmp/INSTALL_DIR/bin:$PATH
+export PYTHON_INCLUDE_DIRS="$PYTHON_INCLUDE_PATH $PYTHON_DEV_HEADERS_DIR /tmp/INSTALL_DIR/lib"
+export PYTHON_EXECUTABLE=$(which python)
+export LD_LIBRARY_PATH="$INSTALL_DIR/lib:/usr/local/lib:$PYTHON_INCLUDE_PATH:$NUMPY_INCLUDE_PATH:$NUMPY_INCLUDE_PATH/numpy:$PYTHON_DEV_HEADERS_DIR:/tmp/INSTALL_DIR/lib:$LD_LIBRARY_PATH"
+
+echo "export PATH=$PATH" >> /github/workspace/trace/env
+echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> /github/workspace/trace/env
+echo "export PYTHON_INCLUDE_DIRS=$PYTHON_INCLUDE_DIRS" >> /github/workspace/trace/env
+echo "export PYTHON_EXECUTABLE=$PYTHON_EXECUTABLE" >> /github/workspace/trace/env
+
+export BOOST_PYTHON="boost_python$python_version_no_dots"
+export BOOST_ROOT=$INSTALL_DIR
+export PATH="$PATH:$INSTALL_DIR/bin"
+
+# More stable approach: Go via python
+numpy_lib_dir=$(find /tmp/myvenv/ -name numpy.libs)
+export LD_LIBRARY_PATH="/usr/lib:/usr/lib64:$INSTALL_DIR/lib:$INSTALL_DIR/bin:$numpy_lib_dir:$NUMPY_INCLUDE_PATH"
+export CMAKE_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | sed 's/::/:/g' | sed 's/:/;/g')
+export PYTHON_LIBRARIES="/usr/lib64/"
+export PYTHON_INCLUDE_DIR="/opt/_internal/cpython-3.7.17/include/python3.7m"
+export CMAKE_LINK_OPTS="-Wl,--copy-dt-needed-entries,-l pthread"
+
+echo "export BOOST_PYTHON=$BOOST_PYTHON" >> /github/workspace/trace/env
+echo "export BOOST_ROOT=$BOOST_ROOT" >> /github/workspace/trace/env
+echo "export PATH=$PATH" >> /github/workspace/trace/env
+echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> /github/workspace/trace/env
+echo "export CMAKE_LIBRARY_PATH=\"$CMAKE_LIBRARY_PATH\"" >> /github/workspace/trace/env
+echo "export PYTHON_LIBRARIES=\"$PYTHON_LIBRARIES\"" >> /github/workspace/trace/env
+echo "export PYTHON_INCLUDE_DIR=\"$PYTHON_INCLUDE_DIR\"" >> /github/workspace/trace/env
+
+cmake_command="""
+cmake \
+      -DCMAKE_CXX_STANDARD=14 \
+      -DBUILD_SHARED_LIBS=ON \
+      -DDAKOTA_PYTHON=ON \
+      -DDAKOTA_PYTHON_DIRECT_INTERFACE=ON \
+      -DDAKOTA_PYTHON_DIRECT_INTERFACE_NUMPY=ON \
+      -DDAKOTA_DLL_API=OFF \
+      -DHAVE_X_GRAPHICS=OFF \
+      -DDAKOTA_ENABLE_TESTS=OFF \
+      -DDAKOTA_ENABLE_TPL_TESTS=OFF \
+      -DCMAKE_BUILD_TYPE="Release" \
+      -DDAKOTA_NO_FIND_TRILINOS:BOOL=TRUE \
+      -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \
+      -DPYTHON_LIBRARIES=$PYTHON_LIBRARIES \
+      -DCMAKE_LINK_OPTIONS=\"$CMAKE_LINK_OPTS\" \
+      .. &> "$INSTALL_DIR/dakota_bootstrap.log"
+
+"""
+echo "# $cmake_command" >> /github/workspace/trace/env
+
+echo "Boostrapping Dakota ..."
+$($cmake_command &> /github/workspace/trace/dakota_bootstrap.log)
+
+echo "# make --debug=b -j8 install" >> /github/workspace/trace/env
+echo "Building Dakota ..."
+make --debug=b -j8 install &> /github/workspace/trace/dakota_install.log
+
+cd $INSTALL_DIR/..
+
+git clone https://github.com/equinor/Carolina.git
+cd Carolina
+pip install . &> $INSTALL_DIR/carolina_install.log
+
+pip install pytest
+pytest tests
+
+pip wheel . -w wheelhouse &> $INSTALL_DIR/carolina_pipwheel.log
+auditwheel repair wheelhouse/* -w /github/workspace/carolina_dist &> $INSTALL_DIR/carolina_auditwheel_repair.log
+
+echo "Copied distributables and installation trace"