Merge pull request #91 from eseiler/misc/update

[INFRA,DOC] Update CMake and Copyright year
seqan · Feb 4, 2025 · 3228cca · 3228cca
2 parents 0d456fc + 7d1139b
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diff --git a/.clang-format b/.clang-format
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # Format all files in include folder, including std module, excluding contrib module

diff --git a/.cmake-format.yaml b/.cmake-format.yaml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 _template_cmake_format_documentation_only:

diff --git a/.codecov.yml b/.codecov.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # See https://docs.codecov.io/docs/codecovyml-reference

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates

diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Coverage

diff --git a/.github/workflows/ci_cpm.yml b/.github/workflows/ci_cpm.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Update CPM

diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: License

diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Linux

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: macOS

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Lint

diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # Prerequisites

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 cmake_minimum_required (VERSION 3.25)
@@ -13,7 +13,7 @@ project (app-template
 
 # LTO support.
 include (CheckIPOSupported)
-check_ipo_supported (RESULT result OUTPUT output)
+check_ipo_supported (RESULT result OUTPUT output LANGUAGES CXX)
 if (result)
     set (CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
 endif ()

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <!--
-SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC0-1.0
 -->
 
@@ -129,7 +129,7 @@ If you want to add a new cpp file (e.g., tutorial1.cpp) that is compiled and lin
 
 1. Create a new file `tutorial1.cpp` in the `src/` directory.
    <details><summary>The file content could look like this:</summary><br>
-       
+
    ```cpp
    #include <seqan3/core/debug_stream.hpp>
 

diff --git a/cmake/output_directories.cmake b/cmake/output_directories.cmake
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")

diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # CPM Package Lock

diff --git a/cmake/test/add_local_data.cmake b/cmake/test/add_local_data.cmake
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 set (DATASOURCES_DATA_DIR "${${PROJECT_NAME}_SOURCE_DIR}/test/data")

diff --git a/cmake/test/config.cmake b/cmake/test/config.cmake
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 CPMGetPackage (googletest)
@@ -24,6 +24,11 @@ if (NOT TARGET ${PROJECT_NAME}_test)
         if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
             target_compile_options (${PROJECT_NAME}_test INTERFACE "-Wno-interference-size")
         endif ()
+
+        # Warn about failed return value optimization.
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 14)
+            target_compile_options (${PROJECT_NAME}_lib PUBLIC "-Wnrvo")
+        endif ()
     endif ()
 
     # GCC12 has some bogus warnings. They will not be fixed in googletest.

diff --git a/cmake/test/declare_datasource.cmake b/cmake/test/declare_datasource.cmake
@@ -1,8 +1,12 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
-include (ExternalProject)
+if (CMAKE_VERSION VERSION_LESS 3.30)
+    include (ExternalProject)
+else ()
+    include (FetchContent)
+endif ()
 
 # Example call:
 #
@@ -38,6 +42,7 @@ include (ExternalProject)
 # This uses under the hood ExternalProject's and you can pass any viable option of ExternalProject to this function and
 # overwrite the default behaviour. See https://cmake.org/cmake/help/latest/module/ExternalProject.html for more
 # information.
+
 function (declare_datasource)
     set (options "")
     set (one_value_args FILE URL_HASH)
@@ -50,20 +55,32 @@ 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.
-                         EXCLUDE_FROM_ALL TRUE
-                         ${ARG_UNPARSED_ARGUMENTS}
-    )
+    if (CMAKE_VERSION VERSION_LESS 3.30)
+        ExternalProject_Add ("${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.
+                             EXCLUDE_FROM_ALL TRUE
+                             ${ARG_UNPARSED_ARGUMENTS}
+        )
+    else ()
+        FetchContent_Populate ("${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}
+        )
+    endif ()
 
     add_dependencies (${PROJECT_NAME}_test "${datasource_name}")
 endfunction ()
diff --git a/include/configuration.hpp b/include/configuration.hpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #pragma once

diff --git a/include/fastq_conversion.hpp b/include/fastq_conversion.hpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #pragma once

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 cmake_minimum_required (VERSION 3.25)

diff --git a/src/fastq_conversion.cpp b/src/fastq_conversion.cpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #include "fastq_conversion.hpp"

diff --git a/src/main.cpp b/src/main.cpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #include <sharg/all.hpp>

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 cmake_minimum_required (VERSION 3.25)

diff --git a/test/api_fastq_coversion_test.cpp b/test/api_fastq_coversion_test.cpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #include <gtest/gtest.h>

diff --git a/test/app_test.hpp b/test/app_test.hpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #pragma once

diff --git a/test/cli_fastq_coversion_test.cpp b/test/cli_fastq_coversion_test.cpp
@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: CC0-1.0
 
 #include "app_test.hpp"

diff --git a/test/data/README.md b/test/data/README.md
@@ -1,6 +1,6 @@
 <!--
-SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC0-1.0
 -->
 

diff --git a/test/data/datasources.cmake b/test/data/datasources.cmake
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 # This includes `cmake/test/declare_datasource.cmake`, which provides the `declare_datasource` function.

diff --git a/test/data/in.fastq.license b/test/data/in.fastq.license
@@ -1,3 +1,3 @@
-SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC0-1.0
diff --git a/test/data/out.fasta.license b/test/data/out.fasta.license
@@ -1,3 +1,3 @@
-SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC0-1.0