Upgrade CI to HDF5 2.0.0 and AVRO 1.12.1

philippeVerney · philippeVerney · commit e5ae6b9e0e58 · 2026-02-14T22:52:08.000+01:00
diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml
@@ -7,20 +7,16 @@ jobs:
       - uses: actions/checkout@v5
       - name: Boost install
         run: |
-          (New-Object System.Net.WebClient).DownloadFile("https://archives.boost.io/release/1.88.0/binaries/boost_1_88_0-msvc-14.2-64.exe", "${{ runner.temp }}\boost.exe")
+          (New-Object System.Net.WebClient).DownloadFile("https://archives.boost.io/release/1.90.0/binaries/boost_1_90_0-msvc-14.2-64.exe", "${{ runner.temp }}\boost.exe")
           Start-Process -Wait -FilePath "${{ runner.temp }}\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES","/DIR=${{ runner.temp }}\boost-install"
       - name: AVRO install
         run: |
-          (New-Object System.Net.WebClient).DownloadFile("https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz", "${{ runner.temp }}\avro-cpp-1.11.3.tar.gz")
-          7z x ${{ runner.temp }}\avro-cpp-1.11.3.tar.gz -o${{ runner.temp }}
-          7z x ${{ runner.temp }}\avro-cpp-1.11.3.tar -o${{ runner.temp }}
-          ((Get-Content -path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt -Raw) -replace 'install \(TARGETS avrocpp avrocpp_s','install (TARGETS avrocpp_s') | Set-Content -Path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt
-          ((Get-Content -path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt -Raw) -replace 'install \(TARGETS avrogencpp RUNTIME DESTINATION bin\)','') | Set-Content -Path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt
           cd ${{ runner.temp }}
-          mkdir avro-cpp-build
-          cd avro-cpp-build
-          cmake -G"Visual Studio 17 2022" -A x64 -T host=x64 -Wno-dev -Wno-deprecated -DBoost_INCLUDE_DIR=${{ runner.temp }}\boost-install -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro-cpp-1.11.3
-          cmake --build . --config Release --target avrocpp_s -j2
+          git clone -b release-1.12.1 https://github.com/apache/avro.git avro
+          mkdir avro-build
+          cd avro-build
+          cmake -G"Visual Studio 17 2022" -A x64 -T host=x64 -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro/lang/c++
+          cmake --build . -j2
           cmake --install .
       - name: CMake build and install
         run: |
@@ -35,20 +31,16 @@ jobs:
       - uses: actions/checkout@v5
       - name: Boost install
         run: |
-          (New-Object System.Net.WebClient).DownloadFile("https://archives.boost.io/release/1.88.0/binaries/boost_1_88_0-msvc-14.2-64.exe", "${{ runner.temp }}\boost.exe")
+          (New-Object System.Net.WebClient).DownloadFile("https://archives.boost.io/release/1.90.0/binaries/boost_1_90_0-msvc-14.2-64.exe", "${{ runner.temp }}\boost.exe")
           Start-Process -Wait -FilePath "${{ runner.temp }}\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES","/DIR=${{ runner.temp }}\boost-install"
       - name: AVRO install
         run: |
-          (New-Object System.Net.WebClient).DownloadFile("https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz", "${{ runner.temp }}\avro-cpp-1.11.3.tar.gz")
-          7z x ${{ runner.temp }}\avro-cpp-1.11.3.tar.gz -o${{ runner.temp }}
-          7z x ${{ runner.temp }}\avro-cpp-1.11.3.tar -o${{ runner.temp }}
-          ((Get-Content -path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt -Raw) -replace 'install \(TARGETS avrocpp avrocpp_s','install (TARGETS avrocpp_s') | Set-Content -Path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt
-          ((Get-Content -path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt -Raw) -replace 'install \(TARGETS avrogencpp RUNTIME DESTINATION bin\)','') | Set-Content -Path ${{ runner.temp }}/avro-cpp-1.11.3/CMakeLists.txt
           cd ${{ runner.temp }}
-          mkdir avro-cpp-build
-          cd avro-cpp-build
-          cmake -G"Visual Studio 17 2022" -A x64 -T host=x64 -Wno-dev -Wno-deprecated -DBoost_INCLUDE_DIR=${{ runner.temp }}\boost-install -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro-cpp-1.11.3
-          cmake --build . --config Release --target avrocpp_s -j2
+          git clone -b release-1.12.1 https://github.com/apache/avro.git avro
+          mkdir avro-build
+          cd avro-build
+          cmake -G"Visual Studio 17 2022" -A x64 -T host=x64 -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro/lang/c++
+          cmake --build . -j2
           cmake --install .
       - name: FESAPI install
         run: |
@@ -71,15 +63,12 @@ jobs:
           sudo apt install -y libboost-all-dev
       - name: AVRO INSTALL
         run: |
-          curl https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz -o ${{ runner.temp }}/avro-cpp-1.11.3.tar.gz
           cd ${{ runner.temp }}
-          tar xzf avro-cpp-1.11.3.tar.gz
-          sed -i 's/install (TARGETS avrocpp avrocpp_s/install (TARGETS avrocpp_s/' avro-cpp-1.11.3/CMakeLists.txt
-          sed -i 's/install (TARGETS avrogencpp RUNTIME DESTINATION bin)//' avro-cpp-1.11.3/CMakeLists.txt
-          mkdir avro-cpp-build
-          cd avro-cpp-build
-          cmake -Wno-dev -Wno-deprecated -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro-cpp-1.11.3
-          cmake --build . -j2 --target avrocpp_s
+          git clone -b release-1.12.1 https://github.com/apache/avro.git avro
+          mkdir avro-build
+          cd avro-build
+          cmake -Wno-dev -Wno-deprecated -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro/lang/c++
+          cmake --build . -j2
           cmake --install .
       - name: CMake build and install
         run: |
@@ -102,15 +91,12 @@ jobs:
           sudo apt install -y libboost-all-dev
       - name: AVRO INSTALL
         run: |
-          curl https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz -o ${{ runner.temp }}/avro-cpp-1.11.3.tar.gz
           cd ${{ runner.temp }}
-          tar xzf avro-cpp-1.11.3.tar.gz
-          sed -i 's/install (TARGETS avrocpp avrocpp_s/install (TARGETS avrocpp_s/' avro-cpp-1.11.3/CMakeLists.txt
-          sed -i 's/install (TARGETS avrogencpp RUNTIME DESTINATION bin)//' avro-cpp-1.11.3/CMakeLists.txt
-          mkdir avro-cpp-build
-          cd avro-cpp-build
-          cmake -Wno-dev -Wno-deprecated -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro-cpp-1.11.3
-          cmake --build . -j2 --target avrocpp_s
+          git clone -b release-1.12.1 https://github.com/apache/avro.git avro
+          mkdir avro-build
+          cd avro-build
+          cmake -Wno-dev -Wno-deprecated -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install ${{ runner.temp }}/avro/lang/c++
+          cmake --build . -j2
           cmake --install .
       - name: CMake build and install
         run: |
@@ -160,15 +146,12 @@ jobs:
           find . -name "*.h" -exec cp --parents \{\} ${{ runner.temp }}/fesapi-install/include/fesapi/ \;
       - name: AVRO INSTALL
         run: |
-          curl https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz -o ${{ runner.temp }}/avro-cpp-1.11.3.tar.gz
           cd ${{ runner.temp }}
-          tar xzf avro-cpp-1.11.3.tar.gz
-          sed -i 's/install (TARGETS avrocpp avrocpp_s/install (TARGETS avrocpp_s/' avro-cpp-1.11.3/CMakeLists.txt
-          sed -i 's/install (TARGETS avrogencpp RUNTIME DESTINATION bin)//' avro-cpp-1.11.3/CMakeLists.txt
-          mkdir avro-cpp-build
-          cd avro-cpp-build
-          cmake -Wno-dev -Wno-deprecated -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install -DCMAKE_C_COMPILER=${{ matrix.cc }} -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} ${{ runner.temp }}/avro-cpp-1.11.3
-          cmake --build . -j2 --target avrocpp_s
+          git clone -b release-1.12.1 https://github.com/apache/avro.git avro
+          mkdir avro-build
+          cd avro-build
+          cmake -Wno-dev -Wno-deprecated -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/avro-cpp-install /avro/lang/c++
+          cmake --build . -j2
           cmake --install .
       - name: CMake build and install
         run: |
@@ -230,8 +213,8 @@ jobs:
         # https://github.com/pypa/cibuildwheel/issues/1139
         run: touch python/setup.py
       - name: Build wheels
-        # Above cibuildwheel@v2.22.0, GNU 14 is most likely used instead of GNU 12 or 13 which makes AVRO 1.11.3 not compiling
-        uses: pypa/cibuildwheel@v2.22.0
+        uses: pypa/cibuildwheel@v3.2.1
+        # RedHat nor Debian maintain security patches for hdf5. We consequently build the latest HDF5 version.
         env:
           CIBW_BUILD: cp38-manylinux_* cp39-manylinux_* cp310-manylinux_* cp311-manylinux_* cp312-manylinux_* cp313-manylinux_*
           CIBW_ARCHS: auto64
@@ -241,30 +224,35 @@ jobs:
             yum search epel-release &&
             yum info epel-release &&
             yum install -y epel-release &&
-            yum --enablerepo=epel install -y minizip1.2-devel hdf5-devel cmake3 &&
+            yum --enablerepo=epel install -y minizip1.2-devel cmake3 &&
+            cd / &&
+            wget --no-verbose https://support.hdfgroup.org/releases/hdf5/v2_0/v2_0_0/downloads/hdf5-2.0.0.tar.gz && 
+            tar -xzf hdf5-2.0.0.tar.gz &&
+            mkdir hdf5-build &&
+            cd hdf5-build &&
+            cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DHDF5_BUILD_GENERATORS:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=OFF -DHDF5_BUILD_UTILS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DCMAKE_INSTALL_PREFIX:STRING=/hdf5-install /hdf5-2.0.0 &&
+            cmake --build . -j2 &&
+            cmake3 --install . &&
             cd / &&
             wget https://github.com/F2I-Consulting/fesapi/archive/refs/tags/v2.14.0.0.zip &&
             unzip v2.14.0.0.zip &&
             mkdir fesapi-build &&
             cd fesapi-build &&
-            cmake3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:STRING=/fesapi-install /fesapi-2.14.0.0 &&
-            cmake3 --build . -j2 --config Release &&
+            cmake3 -DCMAKE_BUILD_TYPE=Release -DHDF5_ROOT=/hdf5-install -DHDF5_USE_STATIC_LIBRARIES=TRUE -DCMAKE_INSTALL_PREFIX:STRING=/fesapi-install /fesapi-2.14.0.0 &&
+            cmake3 --build . -j2 &&
             cmake3 --install . &&
             cd / &&
-            wget https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz &&
-            tar xf avro-cpp-1.11.3.tar.gz &&
-            sed -i 's/install (TARGETS avrocpp avrocpp_s/install (TARGETS avrocpp_s/' avro-cpp-1.11.3/CMakeLists.txt &&
-            sed -i 's/install (TARGETS avrogencpp RUNTIME DESTINATION bin)//' avro-cpp-1.11.3/CMakeLists.txt &&
+            git clone -b release-1.12.1 https://github.com/apache/avro.git avro &&
             mkdir avro-build &&
             cd avro-build &&
-            cmake3 -Wno-dev -Wno-deprecated -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=/avro-install /avro-cpp-1.11.3 &&
-            cmake3 --build . -j2 --target avrocpp_s --config Release &&
+            cmake3 -Wno-dev -Wno-deprecated -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DAVRO_BUILD_SHARED=FALSE -DCMAKE_INSTALL_PREFIX=/avro-install /avro/lang/c++ &&
+            cmake3 --build . -j2 &&
             cmake3 --install . &&
             cd / &&
             mkdir build &&
             cd build &&
             cmake3 -DCMAKE_BUILD_TYPE=Release -DAVRO_ROOT=/avro-install -DAVRO_USE_STATIC_LIBS=TRUE -DWITH_FESAPI=TRUE -DFESAPI_ROOT=/fesapi-install -DWITH_PYTHON_WRAPPING=TRUE -DCMAKE_INSTALL_PREFIX:STRING=/fetpapi-install {project} &&
-            cmake3 --build . -j2 --config Release &&
+            cmake3 --build . -j2 &&
             cmake3 --install .
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: >
             export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/fesapi-install/lib64:/fetpapi-install/lib64 &&
@@ -296,9 +284,9 @@ jobs:
           # Dont use brew for dependencies https://github.com/pypa/cibuildwheel/issues/1251#issuecomment-1234553537
           CIBW_BEFORE_ALL: >
             cd ${{ github.workspace }}/.. &&
-            wget --no-verbose https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.gz &&
-            tar xf boost_1_87_0.tar.gz &&
-            cd boost_1_87_0 &&
+            wget --no-verbose https://archives.boost.io/release/1.90.0/source/boost_1_90_0.tar.gz &&
+            tar xf boost_1_90_0.tar.gz &&
+            cd boost_1_90_0 &&
             ./bootstrap.sh --prefix=${{ github.workspace }}/../boost-install --with-libraries=filesystem,iostreams,program_options,regex,system &&
             ./b2 -d0 install &&
             git clone https://github.com/F2I-Consulting/Minizip.git ${{ github.workspace }}/../minizip &&
@@ -308,12 +296,12 @@ jobs:
             cmake --build . -j2 --config Release &&
             cmake --install . &&
             cd ${{ github.workspace }}/.. &&
-            wget --no-verbose https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.5/hdf5-1.14.5.tar.gz &&
-            tar xf hdf5-1.14.5.tar.gz &&
+            wget --no-verbose https://support.hdfgroup.org/releases/hdf5/v2_0/v2_0_0/downloads/hdf5-2.0.0.tar.gz && 
+            tar -xzf hdf5-2.0.0.tar.gz &&
             mkdir hdf5-build &&
             cd hdf5-build &&
-            cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=OFF -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DCMAKE_INSTALL_PREFIX:STRING=${{ github.workspace }}/../hdf5-install ${{ github.workspace }}/../hdf5-1.14.5 &&
-            cmake --build . -j2 --config Release &&
+            cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DHDF5_BUILD_GENERATORS:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=OFF -DHDF5_BUILD_UTILS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DCMAKE_INSTALL_PREFIX:STRING=${{ github.workspace }}/../hdf5-install ${{ github.workspace }}/../hdf5-2.0.0 &&
+            cmake --build . -j2 &&
             cmake --install . &&
             cd ${{ github.workspace }}/.. &&
             wget --no-verbose https://github.com/F2I-Consulting/fesapi/archive/refs/tags/v2.14.0.0.zip &&
@@ -331,16 +319,11 @@ jobs:
             make &&
             make install &&
             cd ${{ github.workspace }}/.. &&
-            wget --no-verbose https://archive.apache.org/dist/avro/avro-1.11.3/cpp/avro-cpp-1.11.3.tar.gz &&
-            tar xf avro-cpp-1.11.3.tar.gz &&
-            sed -i '' 's/cmake_minimum_required (VERSION 3.1)/cmake_minimum_required (VERSION 3.5)/' avro-cpp-1.11.3/CMakeLists.txt &&
-            sed -i '' 's/if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.0)/if (APPLE)/' avro-cpp-1.11.3/CMakeLists.txt &&
-            sed -i '' 's/install (TARGETS avrocpp avrocpp_s/install (TARGETS avrocpp_s/' avro-cpp-1.11.3/CMakeLists.txt &&
-            sed -i '' 's/install (TARGETS avrogencpp RUNTIME DESTINATION bin)//' avro-cpp-1.11.3/CMakeLists.txt &&
+            git clone -b release-1.12.1 https://github.com/apache/avro.git avro &&
             mkdir avro-build &&
             cd avro-build &&
-            cmake -Wno-dev -Wno-deprecated -DCMAKE_CXX_STANDARD=17 -DCMAKE_CXX_STANDARD_REQUIRED=ON -DCMAKE_CXX_EXTENSIONS=OFF -DBOOST_ROOT=${{ github.workspace }}/../boost-install -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=${{ github.workspace }}/../avro-install ${{ github.workspace }}/../avro-cpp-1.11.3 &&
-            cmake --build . -j2 --target avrocpp_s --config Release &&
+            cmake -Wno-dev -Wno-deprecated -DCMAKE_BUILD_TYPE=Release -DAVRO_BUILD_EXECUTABLES=FALSE -DAVRO_BUILD_TESTS=FALSE -DCMAKE_INSTALL_PREFIX=${{ github.workspace }}/../avro-install ${{ github.workspace }}/../avro/lang/c++ &&
+            cmake --build . -j2 &&
             cmake --install . &&
             brew install swig &&
             mkdir ${{ github.workspace }}/../build &&
