[WIP] Update

seqan · Dec 22, 2023 · 56cafce · 56cafce
1 parent 591433c
commit 56cafce
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Showing 51 changed files with 228 additions and 490 deletions.
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_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -74,7 +74,7 @@ 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
+                                                   -DHIBF_NATIVE_BUILD=OFF
           make -j2 gtest_build
 
       - name: Build tests

diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -69,22 +69,13 @@ 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
-
       - 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
+                                                   -DHIBF_NATIVE_BUILD=OFF
           make -j2 gtest_build
 
       - name: Build tests

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
@@ -74,7 +74,7 @@ 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
+                                                   -DHIBF_NATIVE_BUILD=OFF
           make -j2 gtest_build
 
       - name: Build tests

diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
@@ -80,7 +80,7 @@ jobs:
           cd build
           cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                                                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DRAPTOR_NATIVE_BUILD=OFF
+                                                   -DHIBF_NATIVE_BUILD=OFF
           case "${{ matrix.build }}" in
             snippet) make -j${{ matrix.build_threads }} gtest_build;;
             performance) make -j${{ matrix.build_threads }} gbenchmark_build;;

diff --git a/.github/workflows/ci_workflows.yml b/.github/workflows/ci_workflows.yml
@@ -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: |

diff --git a/.gitmodules b/.gitmodules
@@ -1,30 +1,3 @@
-[submodule "lib/seqan3"]
-	path = lib/seqan3
-	url = https://github.com/seqan/seqan3
-[submodule "lib/robin-hood-hashing"]
-	path = lib/robin-hood-hashing
-	url = https://github.com/martinus/robin-hood-hashing.git
-[submodule "lib/submodules/cereal"]
-	path = lib/submodules/cereal
-	url = https://github.com/USCiLab/cereal
-[submodule "lib/submodules/sdsl-lite"]
-	path = lib/submodules/sdsl-lite
-	url = https://github.com/xxsds/sdsl-lite
-[submodule "lib/chopper"]
-	path = lib/chopper
-	url = https://github.com/seqan/chopper.git
-[submodule "lib/simde"]
-	path = lib/simde
-	url = https://github.com/simd-everywhere/simde
-[submodule "lib/sharg-parser"]
-	path = lib/sharg-parser
-	url = https://github.com/seqan/sharg-parser
-[submodule "lib/tool_description_lib"]
-	path = lib/tool_description_lib
-	url = https://github.com/deNBI-cibi/tool_description_lib.git
 [submodule "include/raptor/contrib/std"]
 	path = include/raptor/contrib/std
 	url = https://github.com/seqan/seqan-std.git
-[submodule "lib/hibf"]
-	path = lib/hibf
-	url = https://github.com/seqan/hibf.git
diff --git a/build_system/CPM.cmake b/build_system/CPM.cmake
@@ -0,0 +1,23 @@
+# SPDX-License-Identifier: MIT
+#
+# SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
+
+set (CPM_DOWNLOAD_VERSION 0.38.7)
+set (CPM_HASH_SUM "83e5eb71b2bbb8b1f2ad38f1950287a057624e385c238f6087f94cdfc44af9c5")
+
+if (CPM_SOURCE_CACHE)
+    set (CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+elseif (DEFINED ENV{CPM_SOURCE_CACHE})
+    set (CPM_DOWNLOAD_LOCATION "$ENV{CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+else ()
+    set (CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+endif ()
+
+# Expand relative path. This is important if the provided path contains a tilde (~)
+get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE)
+
+file (DOWNLOAD https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
+      ${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM}
+)
+
+include (${CPM_DOWNLOAD_LOCATION})
diff --git a/build_system/package-lock.cmake b/build_system/package-lock.cmake
@@ -0,0 +1,62 @@
+# 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
+
+# CPM Package Lock
+# This file should be committed to version control
+
+# hibf
+set (RAPTOR_HIBF_VERSION 2075a68d10f571399b5ff885f0b4cb2c94845601)
+CPMDeclarePackage (hibf
+                   NAME hibf
+                   GIT_TAG ${RAPTOR_HIBF_VERSION}
+                   GITHUB_REPOSITORY seqan/hibf
+                   SYSTEM TRUE
+                   OPTIONS "INSTALL_HIBF OFF"
+)
+# sharg
+set (RAPTOR_SHARG_VERSION 3e96d37387125bd876ace3fdd11a20039ed0d21c)
+CPMDeclarePackage (sharg
+                   NAME sharg
+                   GIT_TAG ${RAPTOR_SHARG_VERSION}
+                   GITHUB_REPOSITORY seqan/sharg-parser
+                   SYSTEM TRUE
+                   OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF"
+)
+# seqan3
+set (RAPTOR_SEQAN3_VERSION 6268f1d11c58abf24c78c7f99a71817d13d5bddd)
+CPMDeclarePackage (seqan3
+                   NAME seqan3
+                   GIT_TAG ${RAPTOR_SEQAN3_VERSION}
+                   GITHUB_REPOSITORY seqan/seqan3
+                   SYSTEM TRUE
+                   OPTIONS "INSTALL_SEQAN3 OFF"
+)
+# chopper
+set (RAPTOR_CHOPPER_VERSION bdcecb6d0f022778ae690da419654f26c7989d2c)
+CPMDeclarePackage (chopper
+                   NAME chopper
+                   GIT_TAG ${RAPTOR_CHOPPER_VERSION}
+                   GITHUB_REPOSITORY seqan/chopper
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
+                   OPTIONS "CHOPPER_INSTALL OFF" "CHOPPER_BUILD_DOC OFF" "CHOPPER_BUILD_TEST OFF"
+)
+# benchmark
+set (RAPTOR_BENCHMARK_VERSION 1.8.2)
+CPMDeclarePackage (benchmark
+                   NAME benchmark
+                   VERSION ${RAPTOR_BENCHMARK_VERSION}
+                   GITHUB_REPOSITORY google/benchmark
+                   SYSTEM TRUE
+                   OPTIONS "BENCHMARK_ENABLE_TESTING OFF" "BENCHMARK_ENABLE_WERROR OFF"
+)
+# googletest
+set (RAPTOR_GOOGLETEST_VERSION 1.14.0)
+CPMDeclarePackage (googletest
+                   NAME GTest
+                   VERSION ${RAPTOR_GOOGLETEST_VERSION}
+                   GITHUB_REPOSITORY google/googletest
+                   SYSTEM TRUE
+                   OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF"
+)