seqan · eseiler · Dec 6, 2024 · Dec 6, 2024
diff --git a/.codecov.yml b/.codecov.yml
@@ -20,3 +20,7 @@ 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
diff --git a/.github/workflows/api.yml b/.github/workflows/api.yml
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
-name: Sharg API-Stability
+name: API-Stability
 
 on:
   # Will always run on the default branch
@@ -16,96 +16,82 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  CMAKE_VERSION: 3.16.9
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
   ISSUE: 146 # Issue number to use for reporting failures
 
 defaults:
   run:
-    shell: bash -exo pipefail {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
-    name: API-Stability gcc${{ matrix.compiler }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 300
+    name: API-Stability ${{ matrix.compiler }}
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        compiler: [11, 12, 13]
-
+        compiler: ["gcc-14", "gcc-13", "gcc-12"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      - name: Checkout Sharg
+      - name: Checkout
         uses: actions/checkout@v4
         with:
-          path: sharg
-          fetch-depth: 1
           submodules: true
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: gcc-${{ matrix.compiler }}
-          ccache_size: 75M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.16.9
-
       - name: Configure tests
         run: |
-          mkdir sharg-build
-          cd sharg-build
-          cmake ../sharg/test/api_stability -DCMAKE_BUILD_TYPE=Release
+          mkdir build && cd build
+          cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release
 
       - name: Build tests
-        run: |
-          cd sharg-build
-          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k 2>&1 | tee build.log
-
-      - name: Setup Python
-        if: ${{ failure() }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
-
-      - name: Process Log
-        if: ${{ failure() }}
-        run: |
-          FILE="seqan3/.github/ISSUE_TEMPLATE/cron_comment_template.md"
-          python3 seqan3/.github/workflows/scripts/process_compiler_error_log.py sharg-build/build.log >> $FILE
+        working-directory: build
+        run: make -k 2>&1 | tee build.log
 
       - name: Create comment body
-        if: ${{ failure() }}
+        if: always()
         id: comment-body
         run: |
-          FILE="sharg/.github/ISSUE_TEMPLATE/cron_comment_template.md"
-          URL="$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
-          sed -i "s@{{ build }}@${{ matrix.build }}@" $FILE
-          sed -i "s@{{ compiler }}@${{ matrix.compiler }}@" $FILE
-          sed -i "s@{{ url }}@$URL@" $FILE
-          echo "body<<EOF" >> $GITHUB_OUTPUT
-          cat $FILE >> $GITHUB_OUTPUT
-          echo "EOF" >> $GITHUB_OUTPUT
+          if [[ "${{ job.status }}" == "success" ]]; then
+            echo "body=Success ${{ matrix.build }} on ${{ matrix.compiler }}" >> $GITHUB_OUTPUT
+          else
+            FILE=".github/ISSUE_TEMPLATE/cron_comment_template.md"
+            python3 .github/workflows/scripts/process_compiler_error_log.py build/build.log >> ${FILE}
+            URL="$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+            sed -i "s@{{ build }}@${{ matrix.build }}@" ${FILE}
+            sed -i "s@{{ compiler }}@${{ matrix.compiler }}@" ${FILE}
+            sed -i "s@{{ url }}@$URL@" ${FILE}
+            echo "body<<EOF" >> $GITHUB_OUTPUT
+            cat ${FILE} >> $GITHUB_OUTPUT
+            echo "EOF" >> $GITHUB_OUTPUT
+          fi
 
       - name: Reopen issue
-        if: ${{ failure() }}
-        uses: octokit/[email protected]
-        with:
-          route: PATCH /repos/{owner}/{repo}/issues/{issue_number}
-          owner: ${{ github.repository_owner }}
-          repo: sharg-parser
-          issue_number: ${{ env.ISSUE }}
-          state: "open"
+        if: failure()
+        run: gh issue reopen ${{ env.ISSUE }}
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_TOKEN: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          GH_REPO: ${{ github.repository }}
 
-      - name: Create comment
-        if: ${{ failure() }}
+      - name: Find Comment
+        if: always()
+        uses: peter-evans/find-comment@v3
+        id: find_comment
+        with:
+          issue-number: ${{ env.ISSUE }}
+          body-includes: ${{ matrix.build }} on ${{ matrix.compiler }}
+
+      - name: Update comment
+        if: always()
         uses: peter-evans/create-or-update-comment@v4
         with:
+          comment-id: ${{ steps.find_comment.outputs.comment-id }}
           issue-number: ${{ env.ISSUE }}
           body: ${{ steps.comment-body.outputs.body }}
+          edit-mode: replace
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+
diff --git a/.github/workflows/ci_cmake.yml b/.github/workflows/ci_cmake.yml
@@ -28,59 +28,42 @@ defaults:
 jobs:
   build:
     name: "External project ${{ contains(matrix.SHARG_NO_TDL, 'OFF') && 'with TDL' || 'without TDL' }}"
-    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'
     strategy:
       fail-fast: false
       matrix:
         SHARG_NO_TDL: [ON, OFF]
-
+    container:
+      image: ghcr.io/seqan/gcc-14
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          path: sharg-parser
-          fetch-depth: 1
           submodules: true
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.16.9
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: gcc-13
-
       - name: Install dependencies
         if: matrix.SHARG_NO_TDL == 'OFF'
         run: |
           git clone --depth 1 --single-branch --branch 0.8.0 https://github.com/jbeder/yaml-cpp.git
-          cd yaml-cpp
-          mkdir build
-          cd build
+          cd yaml-cpp && mkdir build && cd build
           cmake ../ -DCMAKE_BUILD_TYPE=Debug \
                     -DYAML_CPP_BUILD_CONTRIB=OFF \
                     -DYAML_CPP_BUILD_TOOLS=OFF \
                     -DYAML_BUILD_SHARED_LIBS=OFF \
                     -DYAML_CPP_INSTALL=ON \
-                    -DYAML_CPP_BUILD_TESTS=OFF \
-                    -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
-          make -j2
-          sudo make install
+                    -DYAML_CPP_BUILD_TESTS=OFF
+          make install
 
       - name: Configure tests
         run: |
-          mkdir sharg-build
-          cd sharg-build
-          cmake ../sharg-parser/test/external_project -DCMAKE_BUILD_TYPE=Debug \
-                                                      -DSHARG_NO_TDL=${{ matrix.SHARG_NO_TDL }}
-          make -j2 sharg_test_prerequisite
+          mkdir build && cd build
+          cmake ../test/external_project -DCMAKE_BUILD_TYPE=Debug \
+                                         -DSHARG_NO_TDL=${{ matrix.SHARG_NO_TDL }}
+          make -k sharg_test_prerequisite
 
       - name: Build tests
-        run: |
-          cd sharg-build
-          make -k -j2
-
+        working-directory: build
+        run: make -k
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -7,21 +7,15 @@ name: Coverage
 on:
   push:
     branches:
-      # Push events to branches matching refs/heads/main
       - 'main'
-      # Push events to branches matching refs/heads/release*
-      - 'release*'
-  # Trigger after PR was unlabeled
   pull_request:
     types:
       - unlabeled
-  # Enables a manual trigger, may run on any branch
   workflow_dispatch:
 
-# Do not cancel on push events
 concurrency:
   group: coverage-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: false # PRs will be canceled by the clang-format CI
+  cancel-in-progress: false
 
 env:
   SHARG_NO_VERSION_CHECK: 1
@@ -33,70 +27,72 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: coverage
-            build_type: Coverage
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ 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@v4
         with:
-          path: sharg
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
+          fetch-depth: 0
           submodules: true
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 125M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.16.9
+          path: /home/runner/.ccache
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
+          restore-keys: |
+            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
+            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}
 
-      - name: Install gcovr
-        run: |
-          sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==6.0
+      - name: Increase ccache size
+        run: echo "CCACHE_MAXSIZE=300M" >> "${GITHUB_ENV}"
 
       - name: Configure tests
         run: |
-          mkdir sharg-build
-          cd sharg-build
-          cmake ../sharg/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                  -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                                  -DSHARG_VERBOSE_TESTS=OFF \
-                                                  -DSHARG_COVERAGE_PARALLEL_LEVEL=2
-          make -j2 gtest_build yaml-cpp
+          mkdir build && cd build
+          cmake ../test/coverage -DCMAKE_BUILD_TYPE=Coverage
+          make gtest_build yaml-cpp
 
       - name: Build tests
-        env:
-          CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
-          GCOV: ${{ github.workspace }}/sharg/.github/workflows/scripts/gcov.sh
+        working-directory: build
         run: |
           ccache -z
-          cd sharg-build
-          make -k -j2
-          ccache -sv
+          make -k
+          ccache -svvx
+
+      - name: Run tests
+        working-directory: build
+        run: ctest . -j --output-on-failure --no-tests=error
+
+      - name: Generate coverage report
+        run: |
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/include/sharg \
+                --filter ${GITHUB_WORKSPACE}/test/include/sharg/test \
+                --exclude ${GITHUB_WORKSPACE}/include/sharg/contrib \
+                --exclude ${GITHUB_WORKSPACE}/include/sharg/std \
+                --exclude-lines-by-pattern '^\s*$' \
+                --exclude-lines-by-pattern '^\s*};$' \
+                --exclude-unreachable-branches \
+                --exclude-throw-branches \
+                --exclude-noncode-lines \
+                -j \
+                --cobertura \
+                --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage build
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v3.1.5
         with:
-          files: ${{ github.workspace }}/sharg-build/sharg_coverage.xml
-          root_dir: ${{ github.workspace }}/sharg
+          files: build/coverage_report.xml
+          fail_ci_if_error: false
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
@@ -19,7 +19,7 @@ concurrency:
   cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SEQAN3_NO_VERSION_CHECK: 1
+  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults: