Merge pull request seqan#277 from eseiler/infra/ci

[INFRA] Update CI

Author: eseiler

.codecov.yml

@@ -4,7 +4,6 @@
 
 # See https://docs.codecov.io/docs/codecovyml-reference
 codecov:
-  token: b5e588e8-7b85-46f1-bad6-e0a5c19d7d67
   require_ci_to_pass: no  # codecov reports its results independent of whether CI passed
   notify:
     wait_for_ci: no       # codecov has not to wait until the CI is finished to post its results

.github/workflows/ci_cmake.yml

@@ -35,9 +35,7 @@ jobs:
       matrix:
         SHARG_NO_TDL: [ON, OFF]
     container:
-      image: ghcr.io/seqan/gcc-14
-      volumes:
-        - /home/runner:/home/runner
+      image: ghcr.io/seqan/gcc-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -47,7 +45,7 @@ jobs:
       - 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
+          git clone --depth 1 --single-branch --branch master https://github.com/jbeder/yaml-cpp.git
           cd yaml-cpp && mkdir build && cd build
           cmake ../ -DCMAKE_BUILD_TYPE=Debug \
                     -DYAML_CPP_BUILD_CONTRIB=OFF \

.github/workflows/ci_coverage.yml

@@ -33,11 +33,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["gcc-14"]
+        compiler: ["gcc-latest"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -75,17 +73,20 @@ jobs:
                 --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-lines-by-pattern '^\s*}|^\s*};' \
                 --exclude-noncode-lines \
+                --exclude-throw-branches \
+                --exclude-unreachable-branches \
+                --merge-mode-functions separate \
                 -j \
                 --cobertura \
                 --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage build
-        uses: codecov/codecov-action@v3.1.5
+        uses: codecov/codecov-action@v5.4.3
         with:
-          files: build/coverage_report.xml
+          disable_search: true
           fail_ci_if_error: false
+          files: build/coverage_report.xml
+          plugins: noop
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/lint.yml .github/workflows/ci_lint.yml.github/workflows/lint.yml renamed to .github/workflows/ci_lint.yml

@@ -33,14 +33,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
-        include:
-          - compiler: "intel"
-            cxx_flags: "-fp-model=strict -Wno-overriding-option"
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/ci_linux.yml

@@ -28,12 +28,12 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.compiler }}
-    runs-on: macos-14
+    runs-on: macos-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/ci_macos.yml

@@ -33,15 +33,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "gcc-14", "gcc-12", "intel"]
+        compiler: ["clang-latest", "gcc-latest", "gcc-third-latest", "intel"]
         build: ["snippet", "header"]
-        include:
-          - 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

.github/workflows/ci_misc.yml

@@ -32,11 +32,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["gcc-14", "gcc-13", "gcc-12"]
+        compiler: ["gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/api.yml .github/workflows/cron_api.yml.github/workflows/api.yml renamed to .github/workflows/cron_api.yml

@@ -15,6 +15,7 @@ concurrency:
 
 env:
   SHARG_NO_VERSION_CHECK: 1
+  CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES: false
   TZ: Europe/Berlin
 
 defaults:
@@ -29,9 +30,7 @@ jobs:
     permissions:
       security-events: write
     container:
-      image: ghcr.io/seqan/gcc-14
-      volumes:
-        - /home/runner:/home/runner
+      image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4