Merge remote-tracking branch 'Unidata/master'

2025-02-05 16:20:10 +08:00 · 2020-12-05 12:59:34 -07:00 · 2020-12-05 12:59:34 -07:00 · 731d9bbb0b
commit 731d9bbb0b
parent 2c71bf5d06 4cf290dc0b
9 changed files with 239 additions and 323 deletions
--- a/.github/workflows/automake-dmh.old
+++ b/.github/workflows/automake-dmh.old
@ -1,129 +0,0 @@
-name: automake
-
-on:
-  workflow_dispatch:
-  repository_dispatch:
-    types: buildandtest
-
-jobs:
-  autotools:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        hdf5: [ 1.8.20, 1.10.7 ]
-        use_nc4: [ nc3, nc4 ]
-        use_dap: [ dap_off, dap_on ]
-    steps:
-    - name: Set up Included Actions
-      uses: actions/checkout@v2
-    - name: Install Conda ${{ matrix.hdf5 }}
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ${{ matrix.hdf5 }}
-        environment-file: .github/workflows/conda-env/${{ matrix.hdf5 }}.txt
-
-###
-# Set environmental variables (for configuring)
-###
-
-    - run: echo "ENABLE_NC4=--disable-netcdf-4" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc3'
-    - run: echo "ENABLE_NC4=--enable-netcdf-4" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc4'
-
-    - run: echo "ENABLE_DAP=--disable-dap" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_off'
-    - run: echo "ENABLE_DAP=--enable-dap" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_on'
-
-###
-# Configure and Build and Run Tests
-###
-
-    - name: Autoreconf
-      shell: bash -l {0}
-      run: autoreconf -if
-    - name: Configure
-      shell: bash -l {0}
-      run: ./configure ${ENABLE_NC4_AC} ${ENABLE_DAP}
-    - name: Build
-      shell: bash -l {0}
-      run: make -j && make check TESTS="" -j
-    - name: Test
-      shell: bash -l {0}
-      run: make check -j
-
-#####
-# End Autotools Testing
-#####
-
-#####
-# CMake Testing
-#####
-
-  cmake:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        hdf5: [ 1.8.20, 1.10.7 ]
-        use_nc4: [ nc3, nc4 ]
-        use_dap: [ dap_off, dap_on ]
-    steps:
-    - name: Set up Included Actions
-      uses: actions/checkout@v2
-    - name: Install Conda ${{ matrix.hdf5 }}
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ${{ matrix.hdf5 }}
-        environment-file: .github/workflows/conda-env/${{ matrix.hdf5 }}.txt
-
-    #- name: Query User
-    #  run: whoami
-    #- name: Query System
-    #  run: uname -a
-    #- name: Directory Info
-    #  run: pwd && ls
-    #- name: Query Conda
-    #  shell: bash -l {0}
-    #  run: conda list
-    #- name: Query HDF5
-    #  shell: bash -l {0}
-    #  run: which h5dump
-    #- name: Run autoreconf
-    #  shell: bash -l {0}
-    #  run: autoreconf -if
-
-###
-# Set environmental variables (for configuring)
-###
-    - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
-
-    - run: echo "ENABLE_NC_NC4=OFF" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc3'
-    - run: echo "ENABLE_NC_NC4=ON" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc4'
-
-    - run: echo "ENABLE_NC_DAP=OFF" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_off'
-    - run: echo "ENABLE_NC_DAP=ON" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_on'
-
-###
-# Configure and Build and Run Tests
-###
-
-    - name: Create build directory.
-      shell: bash -l {0}
-      run: mkdir build && cd build && pwd
-    #- name: Sanity Check
-    #  shell: bash -l {0}
-    #  run: pwd && ls && ls ..
-    - name: cmake
-      shell: bash -l {0}
-      run: cd build && cmake .. -DENABLE_NETCDF_4=${ENABLE_NC_NC4} -DENABLE_DAP=${ENABLE_NC_DAP}
-    - name: build
-      shell: bash -l {0}
-      run: cd build && make -j
-    - name: Test
-      shell: bash -l {0}
-      run: cd build && make test -j
--- a/.github/workflows/automake-dmh.yml
+++ b/.github/workflows/automake-dmh.yml
@ -1,129 +0,0 @@
-name: automake
-
-on:
-  workflow_dispatch:
-  repository_dispatch:
-    types: buildandtest
-
-jobs:
-  autotools:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        hdf5: [ 1.8.20, 1.10.7 ]
-        use_nc4: [ nc3, nc4 ]
-        use_dap: [ dap_off, dap_on ]
-    steps:
-    - name: Set up Included Actions
-      uses: actions/checkout@v2
-    - name: Install Conda ${{ matrix.hdf5 }}
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ${{ matrix.hdf5 }}
-        environment-file: .github/workflows/conda-env/${{ matrix.hdf5 }}.txt
-
-###
-# Set environmental variables (for configuring)
-###
-
-    - run: echo "ENABLE_NC4=--disable-netcdf-4" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc3'
-    - run: echo "ENABLE_NC4=--enable-netcdf-4" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc4'
-
-    - run: echo "ENABLE_DAP=--disable-dap" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_off'
-    - run: echo "ENABLE_DAP=--enable-dap" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_on'
-
-###
-# Configure and Build and Run Tests
-###
-
-    - name: Autoreconf
-      shell: bash -l {0}
-      run: autoreconf -if
-    - name: Configure
-      shell: bash -l {0}
-      run: ./configure ${ENABLE_NC4_AC} ${ENABLE_DAP}
-    - name: Build
-      shell: bash -l {0}
-      run: make -j && make check TESTS="" -j
-    - name: Test
-      shell: bash -l {0}
-      run: make check -j
-
-#####
-# End Autotools Testing
-#####
-
-#####
-# CMake Testing
-#####
-
-  cmake:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        hdf5: [ 1.8.20, 1.10.7 ]
-        use_nc4: [ nc3, nc4 ]
-        use_dap: [ dap_off, dap_on ]
-    steps:
-    - name: Set up Included Actions
-      uses: actions/checkout@v2
-    - name: Install Conda ${{ matrix.hdf5 }}
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ${{ matrix.hdf5 }}
-        environment-file: .github/workflows/conda-env/${{ matrix.hdf5 }}.txt
-
-    #- name: Query User
-    #  run: whoami
-    #- name: Query System
-    #  run: uname -a
-    #- name: Directory Info
-    #  run: pwd && ls
-    #- name: Query Conda
-    #  shell: bash -l {0}
-    #  run: conda list
-    #- name: Query HDF5
-    #  shell: bash -l {0}
-    #  run: which h5dump
-    #- name: Run autoreconf
-    #  shell: bash -l {0}
-    #  run: autoreconf -if
-
-###
-# Set environmental variables (for configuring)
-###
-    - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
-
-    - run: echo "ENABLE_NC_NC4=OFF" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc3'
-    - run: echo "ENABLE_NC_NC4=ON" >> $GITHUB_ENV
-      if: matrix.use_nc4 == 'nc4'
-
-    - run: echo "ENABLE_NC_DAP=OFF" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_off'
-    - run: echo "ENABLE_NC_DAP=ON" >> $GITHUB_ENV
-      if: matrix.use_dap == 'dap_on'
-
-###
-# Configure and Build and Run Tests
-###
-
-    - name: Create build directory.
-      shell: bash -l {0}
-      run: mkdir build && cd build && pwd
-    #- name: Sanity Check
-    #  shell: bash -l {0}
-    #  run: pwd && ls && ls ..
-    - name: cmake
-      shell: bash -l {0}
-      run: cd build && cmake .. -DENABLE_NETCDF_4=${ENABLE_NC_NC4} -DENABLE_DAP=${ENABLE_NC_DAP}
-    - name: build
-      shell: bash -l {0}
-      run: cd build && make -j
-    - name: Test
-      shell: bash -l {0}
-      run: cd build && make test -j
--- a/.github/workflows/ignore.yml
+++ b/.github/workflows/ignore.yml
@ -1,30 +0,0 @@
-# This is a basic workflow that is manually triggered
-
-name: Ignore workflow
-
-# Controls when the action will run. Workflow runs when manually triggered using the UI
-# or API.
-on:
-  workflow_dispatch:
-    # Inputs the workflow accepts.
-    inputs:
-      name:
-        # Friendly description to be shown in the UI instead of 'name'
-        description: 'Person to greet'
-        # Default value if no value is explicitly provided
-        default: 'World'
-        # Input has to be provided for the workflow to run
-        required: true
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "greet"
-  greet:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-    # Runs a single command using the runners shell
-    - name: Send greeting
-      run: echo "Hello ${{ github.event.inputs.name }}"
--- a/.github/workflows/manual.yml
+++ b/.github/workflows/manual.yml
@ -1,30 +0,0 @@
-# This is a basic workflow that is manually triggered
-
-name: Manual workflow
-
-# Controls when the action will run. Workflow runs when manually triggered using the UI
-# or API.
-on:
-  workflow_dispatch:
-    # Inputs the workflow accepts.
-    inputs:
-      name:
-        # Friendly description to be shown in the UI instead of 'name'
-        description: 'Person to greet'
-        # Default value if no value is explicitly provided
-        default: 'World'
-        # Input has to be provided for the workflow to run
-        required: true
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "greet"
-  greet:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-    # Runs a single command using the runners shell
-    - name: Send greeting
-      run: echo "Hello ${{ github.event.inputs.name }}"
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@ -0,0 +1,233 @@
+###
+# Build hdf4, hdf5 dependencies and cache them in a combined directory.
+###
+
+name: Run netCDF Tests
+
+on: [push]
+
+jobs:
+
+  build-deps:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.8.21, 1.10.7 ]
+
+    steps:
+
+      - uses: actions/checkout@v2
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake
+
+        ###
+        # Installing libhdf4 and libhdf5
+        ###
+      - name: Cache libhdf5-${{ matrix.hdf5 }}
+        id: cache-hdf5
+        uses: actions/cache@v2
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+
+      - name: Build libhdf5-${{ matrix.hdf5 }}
+        if: steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          set -x
+          wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2
+          tar -jxf hdf-4.2.15.tar.bz2
+          pushd hdf-4.2.15
+          ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib
+          make -j
+          make install -j
+          popd
+          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
+          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
+          pushd hdf5-${{ matrix.hdf5 }}
+          ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} --enable-hl --with-szlib
+          make -j
+          make install -j
+          popd
+
+
+  nc-autotools:
+
+    needs: build-deps
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.8.21, 1.10.7 ]
+        use_nc4: [ nc3, nc4 ]
+        use_dap: [ dap_off, dap_on ]
+    steps:
+
+      - uses: actions/checkout@v2
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake
+
+###
+# Set Environmental Variables
+###
+
+      - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}/include" >> $GITHUB_ENV
+      - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
+      - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
+      - run: |
+          echo "ENABLE_HDF4=--disable-hdf4" >> $GITHUB_ENV
+          echo "ENABLE_NC4=--disable-netcdf-4" >> $GITHUB_ENV
+        if: matrix.use_nc4 == 'nc3'
+      - run: |
+          echo "ENABLE_HDF4=--enable-hdf4" >> $GITHUB_ENV
+          echo "ENABLE_NC4=--enable-netcdf-4" >> $GITHUB_ENV
+        if: matrix.use_nc4 == 'nc4'
+      - run: echo "ENABLE_DAP=--disable-dap" >> $GITHUB_ENV
+        if: matrix.use_dap == 'dap_off'
+      - run: echo "ENABLE_DAP=--enable-dap" >> $GITHUB_ENV
+        if: matrix.use_dap == 'dap_on'
+
+###
+# Fetch Cache
+###
+
+      - name: Fetch HDF Cache
+        id: cache-hdf
+        uses: actions/cache@v2
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+      - name: Check Cache
+        shell: bash -l {0}
+        run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib
+
+###
+# Configure and build
+###
+
+      - name: Run autoconf
+        shell: bash -l {0}
+        run: autoreconf -if
+
+      - name: Configure
+        shell: bash -l {0}
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure ${ENABLE_HDF4} ${ENABLE_NC4} ${ENABLE_DAP}
+
+      - name: Look at config.log if error
+        shell: bash -l {0}
+        run: cat config.log
+        if: ${{ failure() }}
+
+      - name: Print Summary
+        shell: bash -l {0}
+        run: cat libnetcdf.settings
+
+      - name: Build Library and Utilities
+        shell: bash -l {0}
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
+        if: ${{ success() }}
+
+      - name: Build Tests
+        shell: bash -l {0}
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
+        if: ${{ success() }}
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
+        if: ${{ success() }}
+
+      #- name: Make Distcheck
+      #  shell: bash -l {0}
+      #  run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make distcheck -j
+
+  nc-cmake:
+
+    needs: build-deps
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.8.21, 1.10.7 ]
+        use_nc4: [ nc3, nc4 ]
+        use_dap: [ dap_off, dap_on ]
+    steps:
+
+      - uses: actions/checkout@v2
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake
+
+###
+# Set Environmental Variables
+###
+
+      - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
+      - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
+      - run: |
+          echo "ENABLE_HDF4=OFF" >> $GITHUB_ENV
+          echo "ENABLE_NC4=OFF" >> $GITHUB_ENV
+        if: matrix.use_nc4 == 'nc3'
+      - run: |
+          echo "ENABLE_HDF4=ON" >> $GITHUB_ENV
+          echo "ENABLE_NC4=ON" >> $GITHUB_ENV
+        if: matrix.use_nc4 == 'nc4'
+      - run: echo "ENABLE_DAP=OFF" >> $GITHUB_ENV
+        if: matrix.use_dap == 'dap_off'
+      - run: echo "ENABLE_DAP=ON" >> $GITHUB_ENV
+        if: matrix.use_dap == 'dap_on'
+      - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
+
+###
+# Fetch Cache
+###
+
+      - name: Fetch HDF Cache
+        id: cache-hdf5
+        uses: actions/cache@v2
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+      - name: Check Cache
+        shell: bash -l {0}
+        run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib
+
+###
+# Configure and build
+###
+
+      - name: Perform out-of-directory build
+        shell: bash -l {0}
+        run: |
+          mkdir build
+          cd build
+          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DENABLE_HDF4=${ENABLE_HDF4} -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DENABLE_DAP=${ENABLE_DAP} -DENABLE_NETCDF_4=${ENABLE_NC4}
+
+      - name: Print Summary
+        shell: bash -l {0}
+        run: |
+          cd build
+          cat libnetcdf.settings
+
+      - name: Build All
+        shell: bash -l {0}
+        run: |
+          cd build
+          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12
+        if: ${{ success() }}
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: |
+          cd build
+          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 .
+        if: ${{ success() }}
--- a/.travis.yml
+++ b/.travis.yml
@ -1,7 +1,7 @@
 # blocklist
 branches:
  except:
-  - /.*[.]dmh/
+#  - /.*[.]dmh/
  - /.*[.]wif/

 sudo: required
--- a/appveyor.yml
+++ b/appveyor.yml
@ -13,7 +13,7 @@ platform:

 branches:
  except:
-    - /.*[.]dmh/
+#    - /.*[.]dmh/
    - /.*[.]wif/

 # Do not build feature branch with open Pull Requests
--- a/ncdap_test/CMakeLists.txt
+++ b/ncdap_test/CMakeLists.txt
@ -40,8 +40,9 @@ IF(ENABLE_TESTS)
      add_sh_test(ncdap tst_ber)
      add_sh_test(ncdap tst_remote3)
      add_sh_test(ncdap tst_zero_len_var)
-      add_sh_test(ncdap tst_encode)
-# not yet      add_sh_test(ncdap tst_hyrax)
+      MESSAGE(WARNING "ncdap_test/tst_encode temporarily disabled.")
+      #add_sh_test(ncdap tst_encode)
+      # not yet      add_sh_test(ncdap tst_hyrax)
      add_sh_test(ncdap tst_fillmismatch)
      IF(ENABLE_DAP_LONG_TESTS)
        add_sh_test(ncdap tst_longremote3)
--- a/ncdap_test/tst_encode.sh
+++ b/ncdap_test/tst_encode.sh
@ -8,7 +8,7 @@ set -e
 echo ""
 echo "*** Testing #encode=" mechanism

-${NCDUMP} -h 'http://opendap2.oceanbrowser.net/thredds/dodsC/data/emodnet1-domains/tmp%20test.nc?lon[0:8]#encode=none'
+#${NCDUMP} -h 'http://opendap2.oceanbrowser.net/thredds/dodsC/data/emodnet1-domains/tmp%20test.nc?lon[0:8]#encode=none'
 ${NCDUMP} -h 'http://iridl.ldeo.columbia.edu/SOURCES/.Indices/.soi/.c8110/.anomaly/T/%28Jan%201979%29/VALUE/dods?anomaly[0]'