Merge pull request #249 from eseiler/infra/deps

[INFRA] Update dependencies and CI

.codecov.yml

@@ -16,3 +16,7 @@ coverage:
         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

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# 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
+
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci_codeql.yml

@@ -0,0 +1,41 @@
+name: CodeQL
+
+on:
+  schedule:
+    - cron: "0 6 * * SAT"
+  workflow_dispatch:
+
+concurrency:
+  group: codeql-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  SHARG_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  codeql:
+    name: CodeQL
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: cpp
+
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:cpp"

.github/workflows/ci_coverage.yml

@@ -19,89 +19,70 @@ env:
 
 defaults:
   run:
-    shell: bash -Eexuo pipefail {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build_type: Coverage
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ 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@v3
-        with:
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
+        uses: actions/checkout@v4
         with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 200M
+          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
-        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 .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+          mkdir build && cd build
+          cmake .. -DCMAKE_BUILD_TYPE=Coverage \
                    -DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size"
-          make -j2 gtest_main
+          make gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2 api_test cli_test display_layout measure_hyperloglog
-          ccache -sv
+          make -k api_test cli_test display_layout measure_hyperloglog
+          ccache -svvx
 
       - 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 }}/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/test/coverage \
-                ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/include \
-                --filter ${{ github.workspace }}/src \
-                --exclude ${{ github.workspace }}/src/util \
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/include \
+                --filter ${GITHUB_WORKSPACE}/src \
+                --exclude ${GITHUB_WORKSPACE}/src/util \
                 --exclude-lines-by-pattern '^\s*$' \
                 --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 build
-        uses: codecov/codecov-action@v3
+      - name: Submit coverage report
+        uses: codecov/codecov-action@v3.1.5
         with:
-          files: ${{ github.workspace }}/build/coverage_report.xml
+          files: build/coverage_report.xml
           fail_ci_if_error: false

.github/workflows/ci_documentation.yml

@@ -4,39 +4,39 @@ on:
   push:
     branches:
       - 'main'
-  pull_request:
+  pull_request_target:
     types:
       - unlabeled
+      - closed
   workflow_dispatch:
 
 concurrency:
   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 -Eexuo pipefail {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
     name: Documentation
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
-    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
+    runs-on: ubuntu-latest
+    if: ( github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' ) && github.event.action != 'closed'
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 1
+        if: github.event_name != 'pull_request_target'
+        uses: actions/checkout@v4
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      # pull_request_target does not checkout the merge commit by default
+      - name: Checkout
+        if: github.event_name == 'pull_request_target'
+        uses: actions/checkout@v4
         with:
-          cmake: 3.25.3
+          ref: "refs/pull/${{ github.event.number }}/merge"
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main
@@ -45,24 +45,45 @@ jobs:
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
+          mkdir build && cd build
           cmake ..
 
       - name: Run tests
+        working-directory: build
         run: |
-          cd build
-          make -k -j2 doc 2>doxygen_warnings.txt
+          make -k doc 2>doxygen_warnings.txt
           cat doxygen_warnings.txt
           test ! -s doxygen_warnings.txt
 
-      - name: Package documentation
-        continue-on-error: true
-        run: tar -zcf documentation.tar.gz build
+      - name: Deploy Preview
+        if: github.event_name == 'pull_request_target'
+        uses: seqan/actions/documentation_deploy_preview@main
+        with:
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          deploy_base_path: ${{ secrets.DEPLOY_PREVIEW_BASE_PATH }}
+          source_path_user_doc: build/doc/html
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
 
-      - name: Upload documentation
-        continue-on-error: true
-        uses: actions/upload-artifact@v3
+      - name: Deploy Documentation
+        if: github.event_name == 'push'
+        uses: seqan/actions/documentation_deploy_production@main
+        with:
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          source_path_user_doc: build/doc/html
+          deploy_path_user_doc: ${{ secrets.DEPLOY_PRODUCTION_BASE_PATH }}/main
+  delete:
+      name: Delete Preview
+      runs-on: ubuntu-latest
+      if: github.repository_owner == 'seqan' && github.event_name == 'pull_request_target' && github.event.action == 'closed'
+      steps:
+      - name: Delete Preview
+        uses: seqan/actions/documentation_delete_preview@main
         with:
-          name: documentation
-          path: documentation.tar.gz
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          deploy_base_path: ${{ secrets.DEPLOY_PREVIEW_BASE_PATH }}

.github/workflows/ci_header.yml

@@ -0,0 +1,70 @@
+name: Header
+
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+    types:
+      - unlabeled
+  workflow_dispatch:
+
+concurrency:
+  group: misc-${{ 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}
+
+jobs:
+  build:
+    name: ${{ matrix.compiler }}
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
+    strategy:
+      fail-fast: false
+      matrix:
+        compiler: ["clang-18", "gcc-14", "gcc-12", "intel"]
+        include:
+          - cxx_flags: "-Wno-interference-size"
+          - compiler: "clang-18"
+            cxx_flags: ""
+          - compiler: "intel"
+            cxx_flags: "-fp-model=strict -Wno-overriding-option"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Load ccache
+        uses: actions/cache@v4
+        with:
+          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 .. -DCMAKE_BUILD_TYPE=Release \
+                   -DCMAKE_CXX_FLAGS="-Werror ${{ matrix.cxx_flags }}" \
+                   -DCHOPPER_HEADER_TEST_ONLY=ON
+
+      - name: Build tests
+        working-directory: build
+        run: |
+          ccache -z
+          make -k test
+          ccache -svvx
+
+      - name: Run tests
+        working-directory: build
+        run: ctest . -j --output-on-failure