Merge pull request #415 from eseiler/infra/update_cpm

[INFRA] Update CPM

.clang-format

@@ -81,21 +81,21 @@ ForEachMacros:
 IfMacros:
 IncludeBlocks:   Regroup
 IncludeCategories:
-  - Regex:           '(<gtest/.*|<benchmark/.*)'
+  - Regex:           '<gtest/'
     Priority:        1
-  - Regex:           '<robin_hood'
-    Priority:        6
-  - Regex:           '(<[[:alnum:]._]+>|<seqan3/std/.*>)'
-    Priority:        3
-  - Regex:           '<lemon/'
+  - Regex:           '<benchmark/'
     Priority:        2
+  - Regex:           '<[[:alnum:]._]+>'
+    Priority:        3
   - Regex:           '<cereal/'
     Priority:        4
-  - Regex:           '<sdsl/'
+  - Regex:           '<yaml-cpp/'
     Priority:        5
   - Regex:           '<sharg/'
-    Priority:        7
+    Priority:        6
   - Regex:           '<seqan3/'
+    Priority:        7
+  - Regex:           '<hibf/'
     Priority:        8
   - Regex:           '<chopper/'
     Priority:        9

.cmake-format.yaml

@@ -13,9 +13,6 @@ parse:
     cpmgetpackage:
       pargs: 1
       spelling: CPMGetPackage
-    cpmgetsystempackage:
-      pargs: 1
-      spelling: CPMGetSystemPackage
     cpmaddpackage:
       pargs:
         nargs: '*'

.github/workflows/ci_codeql.yml

@@ -34,7 +34,7 @@ jobs:
     - name: Install CMake
       uses: seqan/actions/setup-cmake@main
       with:
-        cmake: 3.21.7
+        cmake: 3.25.3
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v3

.github/workflows/ci_coverage.yml

@@ -59,7 +59,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Install gcovr
         env:

.github/workflows/ci_documentation.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main

.github/workflows/ci_fortify.yml

@@ -51,7 +51,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_linux.yml

@@ -55,6 +55,12 @@ jobs:
             build_type: Release
             cxx_flags: "-std=c++23 -Wno-interference-size"
 
+          - name: "IntelLLVM"
+            compiler: "intel"
+            build: unit
+            build_type: Release
+            cxx_flags: "-fp-model=strict -Wno-overriding-t-option" # Ignore that googletest sets -fp-model=precise
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -72,7 +78,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_macos.yml

@@ -66,7 +66,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_misc.yml

@@ -72,7 +72,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_sanitizer.yml

@@ -71,7 +71,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_utility.yml

@@ -63,7 +63,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure tests
         run: |

.github/workflows/ci_workflows.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Install Nextflow
         if: matrix.name == 'Nextflow'

CMakeLists.txt

@@ -5,7 +5,7 @@
 # shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
 # --------------------------------------------------------------------------------------------------
 
-cmake_minimum_required (VERSION 3.21)
+cmake_minimum_required (VERSION 3.25)
 
 find_path (RAPTOR_MODULE_PATH "configuration.cmake" HINTS "${CMAKE_CURRENT_LIST_DIR}/cmake/")
 list (APPEND CMAKE_MODULE_PATH "${RAPTOR_MODULE_PATH}")

cmake/configuration.cmake

@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.21)
+cmake_minimum_required (VERSION 3.25)
 
 # ----------------------------------------------------------------------------
 # Short-circuit if Raptor is already configured
@@ -30,31 +30,23 @@ macro (raptor_config_error text)
     message (FATAL_ERROR "  ${text}")
 endmacro ()
 
-# ----------------------------------------------------------------------------
-# ccache
-# ----------------------------------------------------------------------------
-
-include (ccache)
-raptor_require_ccache ()
-
 # ----------------------------------------------------------------------------
 # CPM
 # ----------------------------------------------------------------------------
 
-set (CPM_INDENT "  CMake Package Manager CPM: ")
+set (CPM_INDENT "CMake Package Manager CPM: ")
 include (CPM)
 CPMUsePackageLock (${Raptor_SOURCE_DIR}/cmake/package-lock.cmake)
 
 # ----------------------------------------------------------------------------
 # Find or add dependencies
 # ----------------------------------------------------------------------------
 
-include (CPMGetSystemPackage)
-
-CPMGetSystemPackage (hibf)
-CPMGetSystemPackage (sharg)
-CPMGetSystemPackage (seqan3)
-CPMGetSystemPackage (chopper)
+CPMGetPackage (use_ccache)
+CPMGetPackage (hibf)
+CPMGetPackage (sharg)
+CPMGetPackage (seqan3)
+CPMGetPackage (chopper)
 
 # ----------------------------------------------------------------------------
 # Find Raptor include path

cmake/package-lock.cmake

@@ -6,50 +6,56 @@
 # This file should be committed to version control
 
 # hibf
-set (RAPTOR_HIBF_VERSION 2075a68d10f571399b5ff885f0b4cb2c94845601)
+set (RAPTOR_HIBF_VERSION 95c686c2a4147a364231aaeae88adbe93ce83181)
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${RAPTOR_HIBF_VERSION}
                    GITHUB_REPOSITORY seqan/hibf
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_HIBF OFF"
 )
 # sharg
-set (RAPTOR_SHARG_VERSION 3e96d37387125bd876ace3fdd11a20039ed0d21c)
+set (RAPTOR_SHARG_VERSION 39f65a4890f8c5108af2b5c7974893ff6ed87e50)
 CPMDeclarePackage (sharg
                    NAME sharg
                    GIT_TAG ${RAPTOR_SHARG_VERSION}
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
-                   OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF"
+                   EXCLUDE_FROM_ALL TRUE
+                   OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # seqan3
-set (RAPTOR_SEQAN3_VERSION 6268f1d11c58abf24c78c7f99a71817d13d5bddd)
+set (RAPTOR_SEQAN3_VERSION f489f67d9aaa6e72dc42c59a1e5ef8fc27fec9d6)
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    GIT_TAG ${RAPTOR_SEQAN3_VERSION}
                    GITHUB_REPOSITORY seqan/seqan3
                    SYSTEM TRUE
-                   OPTIONS "INSTALL_SEQAN3 OFF"
+                   EXCLUDE_FROM_ALL TRUE
+                   OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # chopper
-set (RAPTOR_CHOPPER_VERSION bdcecb6d0f022778ae690da419654f26c7989d2c)
+set (RAPTOR_CHOPPER_VERSION 4ff191e21def35cfd69e0242046f4b5188017a53)
 CPMDeclarePackage (chopper
                    NAME chopper
                    GIT_TAG ${RAPTOR_CHOPPER_VERSION}
                    GITHUB_REPOSITORY seqan/chopper
                    SYSTEM TRUE
                    OPTIONS "CHOPPER_INSTALL OFF" "CHOPPER_BUILD_DOC OFF" "CHOPPER_BUILD_TEST OFF"
+                           "CMAKE_MESSAGE_LOG_LEVEL WARNING"
                    EXCLUDE_FROM_ALL TRUE
 )
 # benchmark
-set (RAPTOR_BENCHMARK_VERSION 1.8.2)
+set (RAPTOR_BENCHMARK_VERSION 1.8.3)
 CPMDeclarePackage (benchmark
                    NAME benchmark
                    VERSION ${RAPTOR_BENCHMARK_VERSION}
                    GITHUB_REPOSITORY google/benchmark
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "BENCHMARK_ENABLE_TESTING OFF" "BENCHMARK_ENABLE_WERROR OFF"
+                           "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # googletest
 set (RAPTOR_GOOGLETEST_VERSION 1.14.0)
@@ -58,5 +64,15 @@ CPMDeclarePackage (googletest
                    VERSION ${RAPTOR_GOOGLETEST_VERSION}
                    GITHUB_REPOSITORY google/googletest
                    SYSTEM TRUE
-                   OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF"
+                   OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
+)
+# use_ccache
+set (USE_CCACHE_VERSION d2a54ef555b6fc2d496a4c9506dbeb7cf899ce37)
+CPMDeclarePackage (use_ccache
+                   NAME use_ccache
+                   GIT_TAG ${USE_CCACHE_VERSION}
+                   GITHUB_REPOSITORY seqan/cmake-scripts
+                   SOURCE_SUBDIR ccache
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
 )

cmake/raptor-package.cmake

@@ -7,7 +7,7 @@
 
 # This file describes how Sharg will be packaged.
 
-cmake_minimum_required (VERSION 3.21)
+cmake_minimum_required (VERSION 3.25)
 
 set (CPACK_GENERATOR "TXZ")