Merge pull request #442 from eseiler/infra/cmake_update

[INFRA] Update CMake stuff
seqan · Oct 17, 2024 · da75ebe · da75ebe
2 parents 23770fa + 4d241ae
commit da75ebe
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Showing 55 changed files with 181 additions and 390 deletions.
diff --git a/.cmake-format.yaml b/.cmake-format.yaml
@@ -8,12 +8,11 @@ parse:
   _help_additional_commands:
   - Specify structure for custom cmake functions
   additional_commands:
-    declare_internal_datasource:
+    declare_datasource:
       kwargs:
-        FILE: '*'
-        URL: '*'
-        URL_HASH: '*'
-        CONFIGURE: '*'
+        FILE: 1
+        URL: +
+        URL_HASH: 1
     cpmgetpackage:
       pargs: 1
       spelling: CPMGetPackage

diff --git a/.reuse/dep5 b/.reuse/dep5
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 include (${CMAKE_CURRENT_LIST_DIR}/cmake/version.cmake)
 

diff --git a/cmake/configuration.cmake b/cmake/configuration.cmake
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 # ----------------------------------------------------------------------------
 # Short-circuit if Raptor is already configured

diff --git a/cmake/raptor-package.cmake b/cmake/raptor-package.cmake
@@ -4,7 +4,7 @@
 
 # This file describes how Sharg will be packaged.
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 set (CPACK_GENERATOR "TXZ")
 

diff --git a/include/raptor/argument_parsing/validators.hpp b/include/raptor/argument_parsing/validators.hpp
@@ -37,14 +37,19 @@ static inline std::vector<std::string> compression_extensions{[]()
 static inline std::vector<std::string> combined_extensions{
     []()
     {
-        if (compression_extensions.empty())
-            return sequence_extensions; // GCOVR_EXCL_LINE
         std::vector<std::string> result;
-        for (auto && sequence_extension : sequence_extensions)
+        if (compression_extensions.empty())
         {
-            result.push_back(sequence_extension);
-            for (auto && compression_extension : compression_extensions)
-                result.push_back(sequence_extension + std::string{'.'} + compression_extension);
+            result = sequence_extensions; // GCOVR_EXCL_LINE
+        }
+        else
+        {
+            for (auto && sequence_extension : sequence_extensions)
+            {
+                result.push_back(sequence_extension);
+                for (auto && compression_extension : compression_extensions)
+                    result.push_back(sequence_extension + std::string{'.'} + compression_extension);
+            }
         }
         return result;
     }()};

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor)
     return ()

diff --git a/src/argument_parsing/CMakeLists.txt b/src/argument_parsing/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::argument_parsing)
     return ()

diff --git a/src/build/CMakeLists.txt b/src/build/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::build)
     return ()

diff --git a/src/layout/CMakeLists.txt b/src/layout/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.15)
+cmake_minimum_required (VERSION 3.15...3.30)
 
 if (TARGET raptor::layout)
     return ()

diff --git a/src/prepare/CMakeLists.txt b/src/prepare/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::prepare)
     return ()

diff --git a/src/search/CMakeLists.txt b/src/search/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::search)
     return ()

diff --git a/src/threshold/CMakeLists.txt b/src/threshold/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::threshold)
     return ()

diff --git a/src/upgrade/CMakeLists.txt b/src/upgrade/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 if (TARGET raptor::upgrade)
     return ()

diff --git a/test/cmake/add_local_data.cmake b/test/cmake/add_local_data.cmake
@@ -0,0 +1,24 @@
+# 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
+
+set (DATASOURCES_DATA_DIR "${Raptor_SOURCE_DIR}/test/data")
+
+file (GLOB_RECURSE datasources
+      LIST_DIRECTORIES false
+      RELATIVE ${DATASOURCES_DATA_DIR}
+      CONFIGURE_DEPENDS ${DATASOURCES_DATA_DIR}/*
+)
+list (REMOVE_ITEM datasources datasources.cmake README.md REUSE.toml)
+
+foreach (datasource IN LISTS datasources)
+    get_filename_component (datasource_name "${datasource}" NAME)
+    set (data_dir "${CMAKE_CURRENT_BINARY_DIR}/data")
+    file (MAKE_DIRECTORY "${data_dir}")
+
+    if (datasource_name MATCHES ".*\.layout$")
+        configure_file ("${DATASOURCES_DATA_DIR}/${datasource}" "${data_dir}/${datasource_name}")
+    else ()
+        configure_file ("${DATASOURCES_DATA_DIR}/${datasource}" "${data_dir}/${datasource_name}" COPYONLY)
+    endif ()
+endforeach ()
diff --git a/test/cmake/app_internal_datasources.cmake b/test/cmake/app_internal_datasources.cmake
diff --git a/test/cmake/app_datasources.cmake → test/cmake/declare_datasource.cmake b/test/cmake/app_datasources.cmake → test/cmake/declare_datasource.cmake
@@ -1,8 +1,8 @@
 # SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-License-Identifier: CC0-1.0
 
-include (ExternalProject)
+include (FetchContent)
 
 # Example call:
 #
@@ -50,46 +50,15 @@ function (declare_datasource)
     # create data folder
     file (MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/data)
 
-    ExternalProject_Add ("${datasource_name}"
-                         URL "${ARG_URL}"
-                         URL_HASH "${ARG_URL_HASH}"
-                         DOWNLOAD_NAME "${ARG_FILE}"
-                         CONFIGURE_COMMAND ""
-                         BUILD_COMMAND ""
-                         INSTALL_COMMAND ${CMAKE_COMMAND} -E create_symlink <DOWNLOADED_FILE>
-                                         ${CMAKE_CURRENT_BINARY_DIR}/data/${ARG_FILE}
-                         TEST_COMMAND ""
-                         PREFIX "${CMAKE_CURRENT_BINARY_DIR}/_datasources"
-                         DOWNLOAD_NO_EXTRACT TRUE # don't extract archive files like .tar.gz.
-                         ${ARG_UNPARSED_ARGUMENTS}
+    FetchContent_Populate ("${datasource_name}"
+                           URL "${ARG_URL}"
+                           URL_HASH "${ARG_URL_HASH}"
+                           DOWNLOAD_NAME "${ARG_FILE}"
+                           DOWNLOAD_NO_EXTRACT TRUE # don't extract archive files like .tar.gz.
+                           SOURCE_DIR "${CMAKE_CURRENT_BINARY_DIR}/data/"
+                           BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}/data/"
+                           EXCLUDE_FROM_ALL TRUE ${ARG_UNPARSED_ARGUMENTS}
     )
-endfunction ()
-
-# Example call:
-#
-# ```cmake
-# # my_app uses and needs the files RF00001.fa.gz, pdb100d.ent.gz, and GRCh38_latest_clinvar.vcf.gz.
-# target_use_datasources (my_app FILES RF00001.fa.gz pdb100d.ent.gz GRCh38_latest_clinvar.vcf.gz)
-# ```
-#
-# Options:
-#
-# target_use_datasources (<target> FILES <file1> [<file2>...])
-#
-# It declares that a <target> uses and depends on the following files.
-#
-# This also sets the build requirement that the files must be downloaded before the <target> will be build.
-#
-# The named <target> must have been created by a command such as add_executable () or add_library ().
-function (target_use_datasources target)
-    set (options "")
-    set (one_value_args)
-    set (multi_value_args "FILES")
-
-    cmake_parse_arguments (ARG "${options}" "${one_value_args}" "${multi_value_args}" ${ARGN})
 
-    foreach (filename ${ARG_FILES})
-        string (TOLOWER "datasource--${filename}" datasource_name)
-        add_dependencies ("${target}" "${datasource_name}")
-    endforeach ()
+    add_dependencies (raptor_test "${datasource_name}")
 endfunction ()
diff --git a/test/cmake/raptor_path_longest_stem.cmake b/test/cmake/raptor_path_longest_stem.cmake
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 # A compatible function for cmake < 3.20 that basically returns `cmake_path (GET <filename> STEM LAST_ONLY <out_var>)`
 function (raptor_path_longest_stem out_var filename)

diff --git a/test/cmake/raptor_test_component.cmake b/test/cmake/raptor_test_component.cmake
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 include (raptor_path_longest_stem)
 

diff --git a/test/cmake/raptor_test_files.cmake b/test/cmake/raptor_test_files.cmake
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.17)
+cmake_minimum_required (VERSION 3.17...3.30)
 
 # Finds all files relative to the `test_base_path_` which satisfy the given file pattern.
 #

diff --git a/test/coverage/CMakeLists.txt b/test/coverage/CMakeLists.txt
@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-cmake_minimum_required (VERSION 3.25)
+cmake_minimum_required (VERSION 3.25...3.30)
 
 project (raptor_test_coverage LANGUAGES CXX C)
 

diff --git a/test/data/README.md b/test/data/README.md
diff --git a/test/data/REUSE.toml b/test/data/REUSE.toml
@@ -0,0 +1,14 @@
+# 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
+
+version = 1
+SPDX-PackageName = "Raptor"
+SPDX-PackageDownloadLocation = "https://github.com/seqan/raptor/"
+
+[[annotations]]
+path = "**"
+precedence = "aggregate"
+SPDX-FileCopyrightText = ["2006-2024, Knut Reinert & Freie Universität Berlin", "2016-2024, Knut Reinert & MPI für molekulare Genetik"]
+SPDX-License-Identifier = "CC0-1.0"
+