Merge CMake,doxygen changes from develop,1.10 branches (#3578)

* Merge CMake,doxygen changes from develop,1.10 branches

* revert incorrect option in AT TS build

* Use variable for ignore-eol usage.

* Add last_test depends logic

* Just print status on CMake below 3.14

2 files changed, 77 insertions, 15 deletions

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e87b627..10b3a9c 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -336,30 +336,31 @@ jobs:
       - name: Dump matrix context
         run: echo '${{ toJSON(matrix) }}'
 
-      - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build doxygen graphviz
-        if: matrix.os == 'ubuntu-latest'
-
-      - name: Install Autotools Dependencies (Linux, serial)
+      # Only CMake need ninja-build, but we just install it unilaterally
+      # libssl, etc. are needed for the ros3 VFD
+      - name: Install Linux Dependencies
         run: |
            sudo apt update
-           sudo apt install automake autoconf libtool libtool-bin
-           sudo apt install gcc-12 g++-12 gfortran-12
+           sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+           sudo apt install gcc-12 g++-12 gfortran-12
            echo "CC=gcc-12" >> $GITHUB_ENV
            echo "CXX=g++-12" >> $GITHUB_ENV
            echo "FC=gfortran-12" >> $GITHUB_ENV
+        if: matrix.os == 'ubuntu-latest'
+
+      # CMake gets libaec from fetchcontent
+      - name: Install Autotools Dependencies (Linux)
+        run: |
+           sudo apt install automake autoconf libtool libtool-bin
            sudo apt install libaec0 libaec-dev
-        if: (matrix.generator == 'autogen') && (matrix.parallel != 'enable')
+        if: (matrix.generator == 'autogen')
 
       - name: Install Autotools Dependencies (Linux, parallel)
         run: |
-           sudo apt update
-           sudo apt install automake autoconf libtool libtool-bin
            sudo apt install openmpi-bin openmpi-common mpi-default-dev
            echo "CC=mpicc" >> $GITHUB_ENV
            echo "FC=mpif90" >> $GITHUB_ENV
-           sudo apt install libaec0 libaec-dev
         if: (matrix.generator == 'autogen') && (matrix.parallel == 'enable')
 
       - name: Install Dependencies (Windows)
@@ -390,7 +391,19 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --${{ matrix.deprec_sym }}-deprecated-symbols --with-default-api-version=${{ matrix.default_api }} --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --${{ matrix.ros3_vfd }}-ros3-vfd --with-szlib=${{ matrix.szip }}
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure \
+            --enable-build-mode=${{ matrix.build_mode.autotools }} \
+            --${{ matrix.deprec_sym }}-deprecated-symbols \
+            --with-default-api-version=${{ matrix.default_api }} \
+            --enable-shared \
+            --${{ matrix.parallel }}-parallel \
+            --${{ matrix.cpp }}-cxx \
+            --${{ matrix.fortran }}-fortran \
+            --${{ matrix.java }}-java \
+            --${{ matrix.mirror_vfd }}-mirror-vfd \
+            --${{ matrix.direct_vfd }}-direct-vfd \
+            --${{ matrix.ros3_vfd }}-ros3-vfd \
+            --with-szlib=${{ matrix.szip }}
         shell: bash
         if: (matrix.generator == 'autogen') && ! (matrix.thread_safety.enabled)
 
@@ -399,7 +412,15 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --enable-shared --enable-threadsafe --disable-hl --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --${{ matrix.ros3_vfd }}-ros3-vfd --with-szlib=${{ matrix.szip }}
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure \
+            --enable-build-mode=${{ matrix.build_mode.autotools }} \
+            --enable-shared \
+            --enable-threadsafe \
+            --disable-hl \
+            --${{ matrix.mirror_vfd }}-mirror-vfd \
+            --${{ matrix.direct_vfd }}-direct-vfd \
+            --${{ matrix.ros3_vfd }}-ros3-vfd \
+            --with-szlib=${{ matrix.szip }}
         shell: bash
         if: (matrix.generator == 'autogen') && (matrix.thread_safety.enabled)
 
@@ -411,7 +432,25 @@ jobs:
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_BUILD_DOC=${{ matrix.docs }} -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} $GITHUB_WORKSPACE
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            ${{ matrix.generator }} \
+            -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} \
+            -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} \
+            -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} \
+            -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} \
+            -DHDF5_BUILD_JAVA=${{ matrix.java }} \
+            -DHDF5_BUILD_DOC=${{ matrix.docs }} \
+            -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} \
+            -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} \
+            -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} \
+            -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} \
+            -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} \
+            -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} \
+            -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} \
+            $GITHUB_WORKSPACE
         shell: bash
         if: (matrix.generator != 'autogen') && ! (matrix.thread_safety.enabled)
 
@@ -420,7 +459,27 @@ jobs:
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_BUILD_DOC=OFF -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} $GITHUB_WORKSPACE
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            ${{ matrix.generator }} \
+            -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} \
+            -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_THREADSAFE:BOOL=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} \
+            -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
+            -DHDF5_BUILD_FORTRAN:BOOL=OFF \
+            -DHDF5_BUILD_JAVA:BOOL=OFF \
+            -DHDF5_BUILD_HL_LIB:BOOL=OFF \
+            -DHDF5_BUILD_DOC=OFF \
+            -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} \
+            -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} \
+            -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} \
+            -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} \
+            -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} \
+            -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} \
+            -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} \
+            $GITHUB_WORKSPACE
         shell: bash
         if: (matrix.generator != 'autogen') && (matrix.thread_safety.enabled)
 
diff --git a/.github/workflows/netcdf.yml b/.github/workflows/netcdf.yml
index 0ec7541..5b1ebf2 100644
--- a/.github/workflows/netcdf.yml
+++ b/.github/workflows/netcdf.yml
@@ -14,6 +14,9 @@ on:
       - 'COPYING**'
       - '**.md'
 
+permissions:
+  contents: read
+
 # Using concurrency to cancel any in-progress job or run
 concurrency:
   group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}