Merge pull request #84 from eseiler/infra/ci

[INFRA] Update CI

.codecov.yml

@@ -19,3 +19,7 @@ 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/workflows/ci_coverage.yml

@@ -22,69 +22,48 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 125M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
-
-      - name: Install gcovr
-        run: |
-          sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==6.0
-
-      - name: Configure
+      - name: Configure tests
         run: |
-          mkdir build
-          cd build
+          mkdir build && cd build
           cmake .. -DCMAKE_BUILD_TYPE=Debug \
                    -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
                    -DCMAKE_C_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
                    -DCMAKE_EXE_LINKER_FLAGS="-Wl,-lgcov" \
                    -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-lgcov"
 
       - name: Build and run tests
-        run: |
-          cd build
-          make -j2 -k check
+        working-directory: build
+        run: make -k check
 
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }} \
-                ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/include \
-                --filter ${{ github.workspace }}/src \
+          gcovr --root ${GITHUB_WORKSPACE} \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/include \
+                --filter ${GITHUB_WORKSPACE}/src \
                 --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
+        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_cpm.yml

@@ -0,0 +1,33 @@
+# 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: Update CPM
+
+on:
+  schedule:
+    - cron: "0 12 * * SAT"
+  workflow_dispatch:
+
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: update-cpm-actions
+  cancel-in-progress: true
+
+jobs:
+  update_cpm:
+    name: Update CPM
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    if: github.repository_owner == 'seqan'
+    steps:
+      - name: Run update CPM
+        uses: seqan/actions/update_cpm_package_lock@main
+        with:
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
+          package_lock_file: cmake/package-lock.cmake
+

.github/workflows/ci_license.yml

@@ -19,7 +19,7 @@ env:
 jobs:
   check:
     name: REUSE Compliance
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
       - name: Checkout

.github/workflows/ci_linux.yml

@@ -22,53 +22,29 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     strategy:
       fail-fast: false
       matrix:
+        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
         include:
-          - name: "clang17"
-            compiler: "clang-17"
-            build_type: Release
-            cxx_flags: "-stdlib=libc++"
-
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build_type: Release
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build_type: Release
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build_type: Release
-
+          - compiler: "intel"
+            cxx_flags: "-fp-model=strict -Wno-overriding-option"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 75M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
-
-      - name: Configure
+      - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+          mkdir build && cd build
+          cmake .. -DCMAKE_BUILD_TYPE=Release \
                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Werror"
 
       - name: Build and run tests
-        run: |
-          cd build
-          make -j2 -k check
+        working-directory: build
+        run: make -k check

.github/workflows/ci_macos.yml

@@ -22,43 +22,32 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: macos-12
-    timeout-minutes: 120
+    name: ${{ matrix.compiler }}
+    runs-on: macos-14
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: "clang17"
-            compiler: "clang-17"
-            build_type: Release
-
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build_type: Release
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build_type: Release
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build_type: Release
-
+        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
+      - name: Setup compiler
+        uses: seqan/actions/setup-compiler@main
+        with:
+          compiler: ${{ matrix.compiler }}
+
+      - name: Patch M1 GCC
+        if: contains(matrix.compiler, 'gcc') && matrix.compiler != 'gcc-14'
+        uses: seqan/actions/patch-m1-gcc@main
         with:
           compiler: ${{ matrix.compiler }}
-          ccache_size: 75M
 
-      - name: Configure
+      - name: Configure tests
         run: |
           mkdir build && cd build
-          cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-Werror"
+          cmake .. -DCMAKE_BUILD_TYPE=Release \
+                   -DCMAKE_CXX_FLAGS="-Werror"
 
       - name: Build and run tests
         working-directory: build

CMakeLists.txt

@@ -11,6 +11,13 @@ project (app-template
          DESCRIPTION "My application description"
 )
 
+# LTO support.
+include (CheckIPOSupported)
+check_ipo_supported (RESULT result OUTPUT output)
+if (result)
+    set (CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+endif ()
+
 # This allows including `*.cmake` files from the `cmake` directory without specifying the full path.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 

cmake/CPM.cmake

@@ -2,8 +2,8 @@
 #
 # SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
 
-set (CPM_DOWNLOAD_VERSION 0.38.7)
-set (CPM_HASH_SUM "83e5eb71b2bbb8b1f2ad38f1950287a057624e385c238f6087f94cdfc44af9c5")
+set (CPM_DOWNLOAD_VERSION 0.40.2)
+set (CPM_HASH_SUM "c8cdc32c03816538ce22781ed72964dc864b2a34a310d3b7104812a5ca2d835d")
 
 if (CPM_SOURCE_CACHE)
     set (CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")

cmake/package-lock.cmake

@@ -6,65 +6,66 @@
 # This file should be committed to version control
 
 # hibf
-set (HIBF_VERSION 894f663c7b77f28cc2b1b8f4252e51c052c49bb2)
+set (HIBF_VERSION 1ce6960ce2400b53f3e64d2173b33d881d3358e0)
 CPMDeclarePackage (hibf
                    NAME hibf
-                   GIT_TAG ${HIBF_VERSION}
+                   GIT_TAG ${HIBF_VERSION} # main
                    GITHUB_REPOSITORY seqan/hibf
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_HIBF OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # sharg
-set (SHARG_VERSION 01f848eeb6dbac3d50a718a8ee26bcf695edf5a8)
+set (SHARG_VERSION c4367d1049322826e60c674b6bf24d3d0a8da999)
 CPMDeclarePackage (sharg
                    NAME sharg
-                   GIT_TAG ${SHARG_VERSION}
+                   GIT_TAG ${SHARG_VERSION} # main
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # seqan3
-set (SEQAN3_VERSION fee3fb8e5976b455e848dd68c57f64fd3f67c3c2)
+set (SEQAN3_VERSION a79244729de1fb45b030cb7a4d8078f47f81d5f1)
 CPMDeclarePackage (seqan3
                    NAME seqan3
-                   GIT_TAG ${SEQAN3_VERSION}
+                   GIT_TAG ${SEQAN3_VERSION} # main
                    GITHUB_REPOSITORY seqan/seqan3
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # fmindex
-set (FMINDEX_VERSION 822d4d1aa6fa725f7d34e1ea819e9c23a2b6ebc2)
+set (FMINDEX_VERSION cd34f30d57926b5f4d9d10f54b1d2a8036fc59f7)
 CPMDeclarePackage (fmindex
                    NAME fmindex
-                   GIT_TAG ${FMINDEX_VERSION}
+                   GIT_TAG ${FMINDEX_VERSION} # main
                    GITHUB_REPOSITORY SGSSGene/fmindex-collection
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # googletest
-set (GOOGLETEST_VERSION 1.14.0)
+set (GOOGLETEST_VERSION 1.15.2)
 CPMDeclarePackage (googletest
                    NAME GTest
                    VERSION ${GOOGLETEST_VERSION}
                    GITHUB_REPOSITORY google/googletest
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
-                   OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
+                   OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF" "CMAKE_CXX_STANDARD 20"
+                           "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # use_ccache
 set (USE_CCACHE_VERSION d2a54ef555b6fc2d496a4c9506dbeb7cf899ce37)
 CPMDeclarePackage (use_ccache
                    NAME use_ccache
-                   GIT_TAG ${USE_CCACHE_VERSION}
+                   GIT_TAG ${USE_CCACHE_VERSION} # main
                    GITHUB_REPOSITORY seqan/cmake-scripts
                    SOURCE_SUBDIR ccache
                    SYSTEM TRUE