[INFRA] CI

seqan · Jun 7, 2024 · bde67b7 · bde67b7
1 parent 6982ec6
commit bde67b7
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Showing 25 changed files with 278 additions and 428 deletions.
diff --git a/.codecov.yml b/.codecov.yml
@@ -19,3 +19,8 @@ coverage:
       default:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
+        only_pulls: true      # only post codecov/patch status on PRs
+
+parsers:
+  cobertura:
+    partials_as_hits: true
diff --git a/.github/workflows/ci_codeql.yml b/.github/workflows/ci_codeql.yml
@@ -30,15 +30,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v4
-      with:
-        path: raptor
-        fetch-depth: 0
-        submodules: true
-
-    - name: Install CMake
-      uses: seqan/actions/setup-cmake@main
-      with:
-        cmake: 3.25.3
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v3

diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Coverage
@@ -23,96 +23,69 @@ env:
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: coverage
-            build_type: Coverage
-            cxx_flags: "-std=c++23"
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      # How many commits do we need to fetch to also fetch the branch point?
-      - name: Get fetch depth
-        id: fetch_depth
-        run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT
-
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          path: raptor
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-          submodules: true
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 525M
+          fetch-depth: 0
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.25.3
-
-      - name: Install gcovr
-        env:
-          CC: ${{ matrix.compiler }}
-        run: |
-          sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==6.0
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DHIBF_NATIVE_BUILD=OFF
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/coverage -DCMAKE_BUILD_TYPE=Coverage \
+                                                   -DCMAKE_CXX_FLAGS="-std=c++23 -Wno-interference-size"
+          make -j gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/raptor/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/raptor/test/coverage \
-                ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/raptor/include \
-                --filter ${{ github.workspace }}/raptor/src \
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/raptor/include \
+                --filter ${GITHUB_WORKSPACE}/raptor/src \
                 --exclude-lines-by-pattern '^\s*$' \
                 --exclude-lines-by-pattern '^\s*};$' \
-                --exclude-lines-by-pattern '^.*GCOVR_EXCL_LINE.*$' \
                 --exclude-unreachable-branches \
                 --exclude-throw-branches \
                 --exclude-noncode-lines \
-                -j 2 \
-                --xml \
-                --output ${{ github.workspace }}/build/coverage_report.xml
+                -j \
+                --cobertura \
+                --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v3.1.5
         with:
-          files: ${{ github.workspace }}/build/coverage_report.xml
-          root_dir: ${{ github.workspace }}/raptor
+          files: build/coverage_report.xml
           fail_ci_if_error: false
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Documentation
@@ -14,35 +14,24 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: doc-${{ github.event.pull_request.number || github.ref }}
+  group: documentation-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: Documentation
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main
@@ -51,12 +40,10 @@ jobs:
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/documentation
-          make -j2 download-cppreference-doxygen-web-tag
+          mkdir build && cd build
+          cmake ../test/documentation
+          make -j download-cppreference-doxygen-web-tag
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
diff --git a/.github/workflows/ci_fortify.yml b/.github/workflows/ci_fortify.yml
@@ -10,7 +10,7 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: fortify-${{ github.ref }}
+  group: fortify-actions
   cancel-in-progress: true
 
 env:
@@ -23,55 +23,38 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }} ${{ matrix.build_type }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 240
+    name: Fortify ${{ matrix.build_type }}
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
         include:
-          - name: "Fortify"
-            build_type: Release
+          - build_type: Release
             cxx_flags: "-fcf-protection=check"
 
-          - name: "Fortify"
-            build_type: Debug
+          - build_type: Debug
             cxx_flags: "-fcf-protection=full"
-
+    container:
+      image: ghcr.io/seqan/gcc-14
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 1
-          submodules: true
-
-      - name: Setup compiler
-        uses: seqan/actions/setup-compiler@main
-        with:
-          compiler: gcc-13
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                    -DCMAKE_CXX_FLAGS="-std=c++23 -fexceptions -g -grecord-gcc-switches -pipe -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mtune=native -fasynchronous-unwind-tables -fstack-clash-protection -Wno-interference-size ${{ matrix.cxx_flags }}"
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                             -DCMAKE_CXX_FLAGS="-std=c++23 -fexceptions -g -grecord-gcc-switches -pipe -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mtune=native -fasynchronous-unwind-tables -fstack-clash-protection -Wno-interference-size ${{ matrix.cxx_flags }}"
+          make -j gtest_main
 
       - name: Build tests
-        run: |
-          cd build
-          make -k -j2
+        working-directory: build
+        run: make -k -j
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
@@ -23,8 +23,7 @@ env:
 jobs:
   check:
     name: REUSE Compliance
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout