Merge branch 'main' into 64-build-vtk-for-pychaste

Chaste · May 7, 2024 · dd29a54 · dd29a54
2 parents 7392e6a + 0375a66
commit dd29a54
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diff --git a/.github/actions/set-env/action.yml b/.github/actions/set-env/action.yml
@@ -0,0 +1,19 @@
+name: set-env
+description: set ubuntu os version and modules base directory
+outputs:
+  modules_dir:
+    description: "the modules base directory"
+    value: ${{ steps.set-vars.outputs.modules_dir }}
+  os_ver:
+    description: "the ubuntu os version"
+    value: ${{ steps.set-vars.outputs.os_ver }}
+runs:
+  using: composite
+  steps:
+    - id: set-vars
+      run: |
+        source /etc/os-release
+        os_ver="$(echo ${ID}${VERSION_ID} | sed 's/\.//')"
+        echo "os_ver=${os_ver}" >> $GITHUB_OUTPUT
+        echo "modules_dir=$HOME/modules" >> $GITHUB_OUTPUT
+      shell: bash
diff --git a/.github/actions/setup-boost/action.yml b/.github/actions/setup-boost/action.yml
@@ -7,24 +7,32 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-boost
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/boost/${{ inputs.boost_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/boost/${{ inputs.boost_ver }}
-        key: ${{ env.OS_VERSION }}-boost-${{ inputs.boost_ver }}-${{ hashFiles('scripts/install_boost.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/boost/${{ inputs.boost_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/boost/${{ inputs.boost_ver }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-boost-${{ inputs.boost_ver }}-${{ hashFiles('scripts/install_boost.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-boost-${{ inputs.boost_ver }}-
-    
+          ${{ steps.set-env.outputs.os_ver }}-boost-${{ inputs.boost_ver }}-
+
     - name: install boost module
       if: steps.cache-boost.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_boost.sh --version=${{ inputs.boost_ver }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_boost.sh \
+          --version=${{ inputs.boost_ver }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
-        
+
     - name: test boost module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load boost/${{ inputs.boost_ver }}
         module test boost/${{ inputs.boost_ver }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0} # login to source /etc/profile.d/modules.sh
diff --git a/.github/actions/setup-defaults/action.yml b/.github/actions/setup-defaults/action.yml
@@ -3,26 +3,15 @@ description: setup environment and dependencies
 runs:
   using: composite
   steps:
-    - name: set environment variables
-      run: |
-        . /etc/os-release
-        os_version="$(echo ${ID}${VERSION_ID} | sed 's/\.//')"
-        echo "OS_VERSION=${os_version}" >> ${GITHUB_ENV}
-        echo "MODULES_DIR=${{ github.workspace }}/modules" >> ${GITHUB_ENV}
-        echo "CHASTE_TEST_OUTPUT=${{ github.workspace }}/testoutput" >> ${GITHUB_ENV}
-      shell: bash
+    - id: set-env
+      uses: ./.github/actions/set-env
 
-    - name: install dependencies
-      working-directory: ${{ github.workspace }}
-      run: sudo ./scripts/setup_${{ env.OS_VERSION }}.sh
-      shell: bash
-
-    - name: configure environment modules
-      run: |
-        mkdir -p ${{ env.MODULES_DIR }}/modulefiles
-        echo "module use ${{ env.MODULES_DIR }}/modulefiles" | sudo tee -a /etc/profile.d/modules.sh
+    - name: install os dependencies
+      run: ./scripts/setup_${{ steps.set-env.outputs.os_ver }}.sh
       shell: bash
 
     - name: test module command
-      run: module avail
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      run: |
+        source /etc/profile.d/modules.sh
+        module avail
+      shell: bash
diff --git a/.github/actions/setup-petsc_hdf5/action.yml b/.github/actions/setup-petsc_hdf5/action.yml
@@ -13,24 +13,34 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-petsc_hdf5
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}/${{ inputs.petsc_arch }}
-        key: ${{ env.OS_VERSION }}-petsc_hdf5-${{ inputs.petsc_ver }}-${{ inputs.hdf5_ver }}-${{ inputs.petsc_arch }}-${{ hashFiles('scripts/install_petsc_hdf5.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}/${{ inputs.petsc_arch }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-petsc_hdf5-${{ inputs.petsc_ver }}-${{ inputs.hdf5_ver }}-${{ inputs.petsc_arch }}-${{ hashFiles('scripts/install_petsc_hdf5.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-petsc_hdf5-${{ inputs.petsc_ver }}-${{ inputs.hdf5_ver }}-${{ inputs.petsc_arch }}-
-    
+          ${{ steps.set-env.outputs.os_ver }}-petsc_hdf5-${{ inputs.petsc_ver }}-${{ inputs.hdf5_ver }}-${{ inputs.petsc_arch }}-
+
     - name: build and install petsc_hdf5 module
       if: steps.cache-petsc_hdf5.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_petsc_hdf5.sh --petsc-version=${{ inputs.petsc_ver }} --hdf5-version=${{ inputs.hdf5_ver }} --petsc-arch=${{ inputs.petsc_arch }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_petsc_hdf5.sh \
+          --petsc-version=${{ inputs.petsc_ver }} \
+          --hdf5-version=${{ inputs.hdf5_ver }} \
+          --petsc-arch=${{ inputs.petsc_arch }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
 
     - name: test petsc_hdf5 module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}/${{ inputs.petsc_arch }}
         module test petsc_hdf5/${{ inputs.petsc_ver }}_${{ inputs.hdf5_ver }}/${{ inputs.petsc_arch }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0} # login to source /etc/profile.d/modules.sh
diff --git a/.github/actions/setup-sundials/action.yml b/.github/actions/setup-sundials/action.yml
@@ -7,24 +7,32 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-sundials
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/sundials/${{ inputs.sundials_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/sundials/${{ inputs.sundials_ver }}
-        key: ${{ env.OS_VERSION }}-sundials-${{ inputs.sundials_ver }}-${{ hashFiles('scripts/install_sundials.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/sundials/${{ inputs.sundials_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/sundials/${{ inputs.sundials_ver }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-sundials-${{ inputs.sundials_ver }}-${{ hashFiles('scripts/install_sundials.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-sundials-${{ inputs.sundials_ver }}-
-    
+          ${{ steps.set-env.outputs.os_ver }}-sundials-${{ inputs.sundials_ver }}-
+
     - name: build and install sundials module
       if: steps.cache-sundials.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_sundials.sh --version=${{ inputs.sundials_ver }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_sundials.sh \
+          --version=${{ inputs.sundials_ver }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
-        
+
     - name: test sundials module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load sundials/${{ inputs.sundials_ver }}
         module test sundials/${{ inputs.sundials_ver }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0} # login to source /etc/profile.d/modules.sh
diff --git a/.github/actions/setup-vtk/action.yml b/.github/actions/setup-vtk/action.yml
@@ -7,24 +7,32 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-vtk
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/vtk/${{ inputs.vtk_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/vtk/${{ inputs.vtk_ver }}
-        key: ${{ env.OS_VERSION }}-vtk-${{ inputs.vtk_ver }}-${{ hashFiles('scripts/install_vtk.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/vtk/${{ inputs.vtk_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/vtk/${{ inputs.vtk_ver }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-vtk-${{ inputs.vtk_ver }}-${{ hashFiles('scripts/install_vtk.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-vtk-${{ inputs.vtk_ver }}-
-    
-    - name: Build and install vtk module
+          ${{ steps.set-env.outputs.os_ver }}-vtk-${{ inputs.vtk_ver }}-
+
+    - name: build and install vtk module
       if: steps.cache-vtk.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_vtk.sh --version=${{ inputs.vtk_ver }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_vtk.sh \
+          --version=${{ inputs.vtk_ver }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
-        
+
     - name: test vtk module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load vtk/${{ inputs.vtk_ver }}
         module test vtk/${{ inputs.vtk_ver }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0} # login to source /etc/profile.d/modules.sh
diff --git a/.github/actions/setup-xercesc/action.yml b/.github/actions/setup-xercesc/action.yml
@@ -7,24 +7,32 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-xercesc
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/xercesc/${{ inputs.xercesc_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/xercesc/${{ inputs.xercesc_ver }}
-        key: ${{ env.OS_VERSION }}-xercesc-${{ inputs.xercesc_ver }}-${{ hashFiles('scripts/install_xercesc.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/xercesc/${{ inputs.xercesc_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/xercesc/${{ inputs.xercesc_ver }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-xercesc-${{ inputs.xercesc_ver }}-${{ hashFiles('scripts/install_xercesc.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-xercesc-${{ inputs.xercesc_ver }}-
+          ${{ steps.set-env.outputs.os_ver }}-xercesc-${{ inputs.xercesc_ver }}-
     
     - name: build and install xercesc module
       if: steps.cache-xercesc.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_xercesc.sh --version=${{ inputs.xercesc_ver }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_xercesc.sh \
+          --version=${{ inputs.xercesc_ver }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
 
     - name: test xercesc module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load xercesc/${{ inputs.xercesc_ver }}
         module test xercesc/${{ inputs.xercesc_ver }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0}  # login to source /etc/profile.d/modules.sh
diff --git a/.github/actions/setup-xsd/action.yml b/.github/actions/setup-xsd/action.yml
@@ -7,24 +7,32 @@ inputs:
 runs:
   using: composite
   steps:
+    - id: set-env
+      uses: ./.github/actions/set-env
+
     - id: cache-xsd
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
-          ${{ env.MODULES_DIR }}/opt/xsd/${{ inputs.xsd_ver }}
-          ${{ env.MODULES_DIR }}/modulefiles/xsd/${{ inputs.xsd_ver }}
-        key: ${{ env.OS_VERSION }}-xsd-${{ inputs.xsd_ver }}-${{ hashFiles('scripts/install_xsd.sh') }}
+          ${{ steps.set-env.outputs.modules_dir }}/opt/xsd/${{ inputs.xsd_ver }}
+          ${{ steps.set-env.outputs.modules_dir }}/modulefiles/xsd/${{ inputs.xsd_ver }}
+        key: |
+          ${{ steps.set-env.outputs.os_ver }}-xsd-${{ inputs.xsd_ver }}-${{ hashFiles('scripts/install_xsd.sh') }}
         restore-keys: |
-          ${{ env.OS_VERSION }}-xsd-${{ inputs.xsd_ver }}-
-    
+          ${{ steps.set-env.outputs.os_ver }}-xsd-${{ inputs.xsd_ver }}-
+
     - name: install xsd module
       if: steps.cache-xsd.outputs.cache-hit != 'true'
-      working-directory: ${{ github.workspace }}
-      run: ./scripts/install_xsd.sh --version=${{ inputs.xsd_ver }} --modules-dir=${{ env.MODULES_DIR }}
+      run: |
+        ./install_xsd.sh \
+          --version=${{ inputs.xsd_ver }} \
+          --modules-dir=${{ steps.set-env.outputs.modules_dir }}
+      working-directory: ${{ github.workspace }}/scripts
       shell: bash
-        
+
     - name: test xsd module
       run: |
+        module use ${{ steps.set-env.outputs.modules_dir }}/modulefiles
         module load xsd/${{ inputs.xsd_ver }}
         module test xsd/${{ inputs.xsd_ver }}
-      shell: bash --login -e -o pipefail {0}  # login to load /etc/profile.d/modules.sh
+      shell: bash --login -e -o pipefail {0} # login to source /etc/profile.d/modules.sh
diff --git a/.github/workflows/boost.yml b/.github/workflows/boost.yml
@@ -4,29 +4,31 @@ on:
   workflow_dispatch:
     inputs:
       boost_ver:
-        description: 'Boost version'
+        description: "Boost version"
         required: true
         type: string
-        default: '1.74.0'
+        default: "1.83.0"
 
       os:
-        description: 'OS'
+        description: "OS"
         required: true
         type: choice
         options:
-          - 'ubuntu-20.04'
-          - 'ubuntu-22.04'
-        default: 'ubuntu-22.04'
+          - "ubuntu:22.04"
+          - "ubuntu:24.04"
+        default: "ubuntu:24.04"
 
 jobs:
   setup:
     name: build and cache boost
-
-    runs-on: ${{ github.event.inputs.os }}
+
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ github.event.inputs.os }}
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: setup os
         uses: ./.github/actions/setup-defaults