Merge pull request #165 from eseiler/misc/parser_meta

[MISC] Add and unify parser meta info

CMakeLists.txt

@@ -9,6 +9,16 @@ project (needle
          LANGUAGES CXX
          VERSION 1.0.3
          DESCRIPTION "A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences"
+         HOMEPAGE_URL "https://github.com/seqan/needle"
+)
+
+set (NEEDLE_ARGPARSE_VERSION
+     "${needle_VERSION}"
+     CACHE STRING "Needle version to display in the help message."
+)
+set (NEEDLE_ARGPARSE_DATE
+     "2024-11-07"
+     CACHE STRING "Needle's \"Last update:\" date to display in the help message."
 )
 
 # This allows including `*.cmake` files from the `cmake` directory without specifying the full path.

cmake/package.cmake

@@ -3,8 +3,9 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 ## PACKAGE
-# Change version in this file: project (needle VERSION x.x.x)
-# Change version in src/main.cpp: parser.info.version = "x.x.x";
+# Change in top-level CMakeLists.txt:
+#   Version -> project (needle VERSION x.x.x)
+#   Date -> set (NEEDLE_ARGPARSE_DATE "YYYY-MM-DD")
 # No dependencies should be locally installed.
 # To package, create a clean directory:
 #
@@ -19,6 +20,8 @@
 # cmake --build . --target package_source
 #
 # Will create needle-[VERSION]-Source.tar.xz{,.sha256}.
+#
+# Alternatively, the ci_install workflow will export the source package as artifact.
 
 cmake_minimum_required (VERSION 3.7...3.30)
 

src/CMakeLists.txt

@@ -14,6 +14,8 @@ target_include_directories ("${PROJECT_NAME}_lib" PUBLIC ../include)
 add_executable ("${PROJECT_NAME}" main.cpp)
 target_link_libraries ("${PROJECT_NAME}" PRIVATE "${PROJECT_NAME}_lib")
 set_target_properties ("${PROJECT_NAME}" PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
+target_compile_definitions ("${PROJECT_NAME}" PRIVATE NEEDLE_VERSION="${NEEDLE_ARGPARSE_VERSION}")
+target_compile_definitions ("${PROJECT_NAME}" PRIVATE NEEDLE_DATE="${NEEDLE_ARGPARSE_DATE}")
 
 include (GNUInstallDirs)
 install (TARGETS ${PROJECT_NAME} RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}")

src/main.cpp

@@ -15,6 +15,25 @@ uint32_t w_size;
 uint64_t shape{};
 uint64_t se;
 
+void add_parser_meta(seqan3::argument_parser & parser)
+{
+    parser.info.author = "Mitra Darvish";
+    parser.info.citation = "Needle: a fast and space-efficient prefilter for estimating the quantification of very "
+                           "large collections of expression experiments; Mitra Darvish, Enrico Seiler, Svenja "
+                           "Mehringer, René Rahn, and Knut Reinert; Bioinformatics, Volume 38, Issue 17, 1 September "
+                           "2022, Pages 4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492";
+    parser.info.date = NEEDLE_DATE;
+    // REUSE-IgnoreStart
+    parser.info.long_copyright = "This application uses SPDX identifiers.\n"
+                                 "SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin\n"
+                                 "SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik\n"
+                                 "SPDX-License-Identifier: BSD-3-Clause";
+    // REUSE-IgnoreEnd
+    parser.info.short_copyright = "BSD 3-Clause License";
+    parser.info.url = "https://github.com/seqan/needle";
+    parser.info.version = NEEDLE_VERSION;
+}
+
 void initialise_min_arguments(seqan3::argument_parser & parser, min_arguments & args)
 {
     parser.add_option(args.k, 'k', "kmer", "Define k-mer size for the minimisers. Default: 20.");
@@ -190,8 +209,6 @@ int run_needle_estimate(seqan3::argument_parser & parser)
     estimate_ibf_arguments args{};
     estimate_arguments estimate_args{};
     parser.info.short_description = "Estimate expression value of transcript based on the Needle index.";
-    parser.info.version = "1.0.3";
-    parser.info.author = "Mitra Darvish";
 
     args.path_out = "expressions.out";
 
@@ -579,11 +596,10 @@ int main(int argc, char const ** argv)
         argv,
         seqan3::update_notifications::on,
         {"count", "delete", "estimate", "genome", "ibf", "ibfmin", "insert", "insertmin", "minimiser"}};
+    add_parser_meta(needle_parser);
     needle_parser.info.description.push_back("Needle allows you to build an Interleaved Bloom Filter (IBF) with the "
                                              "command ibf or estimate the expression of transcripts with the command "
                                              "estimate.");
-    needle_parser.info.version = "1.0.3";
-    needle_parser.info.author = "Mitra Darvish";
 
     try
     {
@@ -595,6 +611,7 @@ int main(int argc, char const ** argv)
         return -1;
     }
     seqan3::argument_parser & sub_parser = needle_parser.get_sub_parser(); // hold a reference to the sub_parser
+    add_parser_meta(sub_parser);
     if (sub_parser.info.app_name == std::string_view{"needle-count"})
         run_needle_count(sub_parser);
     else if (sub_parser.info.app_name == std::string_view{"needle-delete"})