Merge pull request #2502 from eseiler/infra/ci

[INFRA] Update CI
seqan · Oct 25, 2023 · d37bdec · d37bdec
2 parents e91c71d + 059bfc8
commit d37bdec
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diff --git a/.github/workflows/ci_icc.yml b/.github/workflows/ci_icc.yml
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -1,24 +1,22 @@
-name: CI on Linux
+name: Linux
 
 on:
   push:
     branches:
       - 'main'
   pull_request:
-  # Enables a manual trigger, may run on any branch
   workflow_dispatch:
 
 concurrency:
   group: linux-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  CMAKE_VERSION: 3.12.4
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
@@ -30,78 +28,66 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: "gcc12 (c++23)"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "clang17"
+            compiler: "clang-17"
             build_type: Release
             cxx_flags: "-std=c++23"
 
-          - name: "gcc11 (c++23)"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "clang16"
+            compiler: "clang-16"
             build_type: Release
-            cxx_flags: "-std=c++23"
+            cxx_flags: "-std=c++20"
 
-          - name: "gcc10 (c++20)"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "clang15"
+            compiler: "clang-15"
             build_type: Release
             cxx_flags: "-std=c++20"
 
-          - name: "clang14 (c++23)"
-            cxx: "clang++-14"
-            cc: "clang-14"
+          - name: "gcc13"
+            compiler: "gcc-13"
             build_type: Release
-            cxx_flags: "-std=c++2b"
+            cxx_flags: "-std=c++23"
 
-          - name: "clang13 (c++23)"
-            cxx: "clang++-13"
-            cc: "clang-13"
+          - name: "gcc12"
+            compiler: "gcc-12"
             build_type: Release
-            cxx_flags: "-std=c++2b"
+            cxx_flags: "-std=c++20"
 
-          - name: "clang12 (c++20)"
-            cxx: "clang++-12"
-            cc: "clang-12"
+          - name: "gcc11"
+            compiler: "gcc-11"
             build_type: Release
             cxx_flags: "-std=c++20"
 
-    steps:
-      - name: Checkout SeqAn2
-        uses: actions/checkout@v4
-        with:
-          path: seqan
-          fetch-depth: 2
+          - name: "IntelLLVM"
+            compiler: "intel"
+            build_type: Release
+            cxx_flags: "-std=c++20 -fp-model=strict"
 
-      - name: Checkout SeqAn3
+    steps:
+      - name: Checkout
         uses: actions/checkout@v4
         with:
-          repository: seqan/seqan3
-          ref: 39e696830bbdcde0e520c87811db3eb5e083d7c0
-          path: seqan3
           fetch-depth: 1
-          submodules: false
-
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
 
-      - name: Install CMake
-        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install ccache
-        run: sudo apt-get install --yes ccache
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
+        with:
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 125M
 
-      - name: Install compiler ${{ matrix.cxx }}
-        run: sudo apt-get install --yes ${{ matrix.cxx }}
+      - name: Install dependencies
+        run: install libboost-dev libxml2-utils
 
-      - name: Tool versions
-        run: |
-          env cmake --version
-          env ${{ matrix.cxx }} --version
+      - name: Install OpenMP
+        if: contains(matrix.name, 'clang')
+        env:
+          SEQAN_CLANG: ${{ matrix.compiler }}
+        run: install libomp-${SEQAN_CLANG:6}-dev
 
-      - name: Install dependencies
-        run: sudo apt-get install --yes libboost-dev libbz2-dev libxml2-utils zlib1g-dev
+      - name: Install CMake
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.27.7
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -111,47 +97,37 @@ jobs:
       - name: Install Python dependencies
         run: |
           pip install setuptools wheel
-          pip install -r seqan/manual/requirements.txt
-
-      - name: Load ccache
-        uses: actions/cache@v3
-        with:
-          path: .ccache
-          key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
-          # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-
+          pip install -r manual/requirements.txt
 
       - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
         run: |
-          mkdir seqan-build
-          cd seqan-build
-          cmake ../seqan -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                         -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wextra -Werror" \
-                         -DSEQAN_DISABLE_VERSION_CHECK=ON \
-                         -DSEQAN_GH_ACTIONS_BUILD:BOOL=ON \
-                         -DPython3_ROOT_DIR=${pythonLocation} \
-                         -DPython3_EXECUTABLE=${pythonLocation}/bin/python3 \
-                         -DCMAKE_C_COMPILER_LAUNCHER=ccache \
-                         -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+          mkdir build
+          cd build
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wextra -Wall -pedantic -Werror" \
+                   -DSEQAN_DISABLE_VERSION_CHECK=ON \
+                   -DSEQAN_GH_ACTIONS_BUILD:BOOL=ON \
+                   -DPython3_ROOT_DIR=${pythonLocation} \
+                   -DPython3_EXECUTABLE=${pythonLocation}/bin/python3 \
+                   -DCMAKE_C_COMPILER_LAUNCHER=ccache \
+                   -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 
       - name: Build tests
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 6
-          CCACHE_MAXSIZE: 200M
         run: |
-          cd seqan-build
+          ccache -z
+          cd build
           make -k -j2
+          ccache -sv
 
       - name: Run tests
+        continue-on-error: true
+        id: test
+        run: |
+          cd build
+          ctest . -j2 --output-on-failure --timeout 240
+
+      - name: Rerun failed tests
+        if: steps.test.outcome == 'failure'
         run: |
-          cd seqan-build
-          ctest . -j2 --output-on-failure --timeout 240 || ctest . -j2 --output-on-failure --timeout 240 --rerun-failed
+          cd build
+          ctest . -j2 --output-on-failure --timeout 240 --rerun-failed