seqan · eseiler · Dec 23, 2023 · Dec 23, 2023
diff --git a/.cmake-format.yaml b/.cmake-format.yaml
@@ -10,6 +10,76 @@ parse:
         URL: '*'
         URL_HASH: '*'
         CONFIGURE: '*'
+    cpmgetpackage:
+      pargs: 1
+      spelling: CPMGetPackage
+    cpmaddpackage:
+      pargs:
+        nargs: '*'
+        flags: []
+      spelling: CPMAddPackage
+      kwargs: &cpmaddpackagekwargs
+        NAME: 1
+        FORCE: 1
+        VERSION: 1
+        GIT_TAG: 1
+        DOWNLOAD_ONLY: 1
+        GITHUB_REPOSITORY: 1
+        GITLAB_REPOSITORY: 1
+        GIT_REPOSITORY: 1
+        SVN_REPOSITORY: 1
+        SVN_REVISION: 1
+        SOURCE_DIR: 1
+        DOWNLOAD_COMMAND: 1
+        FIND_PACKAGE_ARGUMENTS: 1
+        NO_CACHE: 1
+        GIT_SHALLOW: 1
+        URL: 1
+        URL_HASH: 1
+        URL_MD5: 1
+        DOWNLOAD_NAME: 1
+        DOWNLOAD_NO_EXTRACT: 1
+        HTTP_USERNAME: 1
+        HTTP_PASSWORD: 1
+        EXCLUDE_FROM_ALL: 1
+        SYSTEM: 1
+        SOURCE_SUBDIR: 1
+        OPTIONS: +
+    cpmfindpackage:
+      pargs:
+        nargs: '*'
+        flags: []
+      spelling: CPMFindPackage
+      kwargs: *cpmaddpackagekwargs
+    cpmdeclarepackage:
+      pargs:
+        nargs: '*'
+        flags: []
+      spelling: CPMDeclarePackage
+      kwargs: *cpmaddpackagekwargs
+    packageproject:
+      pargs:
+        nargs: '*'
+        flags: []
+      spelling: packageProject
+      kwargs:
+        NAME: 1
+        VERSION: 1
+        INCLUDE_DIR: 1
+        INCLUDE_DESTINATION: 1
+        BINARY_DIR: 1
+        COMPATIBILITY: 1
+        VERSION_HEADER: 1
+        DEPENDENCIES: +
+    cpmusepackagelock:
+      pargs: 1
+      spelling: CPMUsePackageLock
+    cpmregisterpackage:
+      pargs: 1
+      spelling: CPMRegisterPackage
+    cpmgetpackageversion:
+      pargs: 2
+      spelling: CPMGetPackageVersion
   _help_override_spec:
   - Override configurations per-command where available
   override_spec: {}

diff --git a/.github/workflows/ci_codeql.yml b/.github/workflows/ci_codeql.yml
@@ -34,17 +34,17 @@ jobs:
     - name: Install CMake
       uses: seqan/actions/setup-cmake@main
       with:
-        cmake: 3.18.4
+        cmake: 3.21.7
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v2
       with:
         languages: cpp
 
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+      uses: github/codeql-action/autobuild@v2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v2
       with:
         category: "/language:cpp"
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -59,7 +59,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Install gcovr
         env:
@@ -74,8 +74,8 @@ jobs:
           cd build
           cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                                                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DRAPTOR_NATIVE_BUILD=OFF
-          make -j2 gtest_build
+                                                   -DHIBF_NATIVE_BUILD=OFF
+          make -j2 gtest_main
 
       - name: Build tests
         run: |
@@ -91,7 +91,7 @@ jobs:
 
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/raptor/lib/seqan3/.github/workflows/scripts/gcov.sh \
+          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 \

diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
@@ -38,7 +38,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main

diff --git a/.github/workflows/ci_fortify.yml b/.github/workflows/ci_fortify.yml
@@ -51,15 +51,15 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - 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_build
+          make -j2 gtest_main
 
       - name: Build tests
         run: |

diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -69,23 +69,19 @@ jobs:
           compiler: ${{ matrix.compiler }}
           ccache_size: 150M
 
-      - name: Install OpenMP
-        if: contains(matrix.name, 'clang')
-        run: install libomp-17-dev
-
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - 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 }}" \
-                                                   -DRAPTOR_NATIVE_BUILD=OFF
-          make -j2 gtest_build
+                                                   -DHIBF_NATIVE_BUILD=OFF
+          make -j2 gtest_main
 
       - name: Build tests
         run: |

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
@@ -66,16 +66,16 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - 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" \
-                                                   -DRAPTOR_NATIVE_BUILD=OFF
-          make -j2 gtest_build
+                                                   -DHIBF_NATIVE_BUILD=OFF
+          make -j2 gtest_main
 
       - name: Build tests
         run: |

diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
@@ -72,19 +72,19 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Configure tests
         run: |
           mkdir build
           cd build
           cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                                                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DRAPTOR_NATIVE_BUILD=OFF
+                                                   -DHIBF_NATIVE_BUILD=OFF
           case "${{ matrix.build }}" in
-            snippet) make -j${{ matrix.build_threads }} gtest_build;;
-            performance) make -j${{ matrix.build_threads }} gbenchmark_build;;
-            header) make -j${{ matrix.build_threads }} gtest_build gbenchmark_build;;
+            snippet) make -j${{ matrix.build_threads }} gtest_main;;
+            performance) make -j${{ matrix.build_threads }} benchmark_main;;
+            header) make -j${{ matrix.build_threads }} gtest_main benchmark_main;;
           esac
 
       - name: Build tests

diff --git a/.github/workflows/ci_sanitizer.yml b/.github/workflows/ci_sanitizer.yml
@@ -71,15 +71,15 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Configure tests
         run: |
           mkdir build
           cd build
           cmake ../raptor/test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                                     -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j2 gtest_build
+          make -j2 gtest_main
 
       - name: Build tests
         run: |

diff --git a/.github/workflows/ci_utility.yml b/.github/workflows/ci_utility.yml
@@ -63,7 +63,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Configure tests
         run: |

diff --git a/.github/workflows/ci_workflows.yml b/.github/workflows/ci_workflows.yml
@@ -57,7 +57,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.18.4
+          cmake: 3.21.7
 
       - name: Install Nextflow
         if: matrix.name == 'Nextflow'
@@ -77,7 +77,7 @@ jobs:
           cd build
           cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                           -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                          -DRAPTOR_NATIVE_BUILD=OFF
+                          -DHIBF_NATIVE_BUILD=OFF
 
       - name: Build Raptor
         run: |
@@ -98,6 +98,6 @@ jobs:
         run: |
           raptor build --export-help cwl > raptor.cwl
           cwltool --validate raptor.cwl
-          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-0_bins_window_19.yml | grep 87bb8bcd1c9ffc2f7ed6e6d1ecc3ca799a8620ff
-          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-16_bins_window_19.yml | grep bae996beebec30b48d3bc6f42ef8af7e143effad
+          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-0_bins_window_19.yml
+          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-16_bins_window_19.yml
 
diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# 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
+
+set -Eeuo pipefail
+
+args=${@/--branch-counts/""}
+args=${args/--branch-probabilities/""}
+
+exec gcov $args
diff --git a/.gitmodules b/.gitmodules
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -7,7 +7,7 @@
 
 cmake_minimum_required (VERSION 3.18)
 
-find_path (RAPTOR_MODULE_PATH "raptor-config.cmake" HINTS "${CMAKE_CURRENT_LIST_DIR}/build_system/")
+find_path (RAPTOR_MODULE_PATH "raptor-config.cmake" HINTS "${CMAKE_CURRENT_LIST_DIR}/cmake/")
 list (APPEND CMAKE_MODULE_PATH "${RAPTOR_MODULE_PATH}")
 
 include (raptor-config-version)