add version bump script and have CMake use it

CMakeLists.txt

@@ -17,27 +17,49 @@ enable_testing()
 
 project (RapMap)
 
-set(CPACK_PACKAGE_VERSION "0.6.0")
-SET(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "6")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
+# auto-populate version:
+# from https://stackoverflow.com/questions/47066115/cmake-get-version-from-multi-line-text-file
+file(READ "current_version.txt" ver)
+
+string(REGEX MATCH "VERSION_MAJOR ([0-9]*)" _ ${ver})
+set(ver_major ${CMAKE_MATCH_1})
+
+string(REGEX MATCH "VERSION_MINOR ([0-9]*)" _ ${ver})
+set(ver_minor ${CMAKE_MATCH_1})
+
+string(REGEX MATCH "VERSION_PATCH ([0-9]*)" _ ${ver})
+set(ver_patch ${CMAKE_MATCH_1})
+
+set(CPACK_PACKAGE_VERSION_MAJOR ${ver_major})
+set(CPACK_PACKAGE_VERSION_MINOR ${ver_minor})
+set(CPACK_PACKAGE_VERSION_PATCH ${ver_patch})
+
+set(CPACK_PACKAGE_VERSION "${ver_major}.${ver_minor}.${ver_patch}")
+message("version: ${CPACK_PACKAGE_VERSION}")
+
 set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
 set(CPACK_PACKAGE_VENDOR "Stony Brook University")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RapMap - Wicked-fast quasi-mapping")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "rapmap - fast transcriptome mapping")
 set(CPACK_PACKAGE_NAME
   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME
   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}-Source")
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
-#include(FindSSE)
-#FindSSE ()
-#if(SSE4_2_FOUND)
-#    message("Enabling popcount")
-#    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.2 -DEMPHF_USE_POPCOUNT")
-#endif(SSE4_2_FOUND)
+
+# Set a default build type if none was specified
+set(default_build_type "Release")
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release")
+endif()
 
 include(CheckIPOSupported)
 

current_version.txt

@@ -0,0 +1,3 @@
+VERSION_MAJOR 0
+VERSION_MINOR 6
+VERSION_PATCH 0

scripts/bump_version.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+HERE="$( cd "$(dirname "$0")" ; pwd -P )"
+
+major_v=`${HERE}/../build/src/rapmap -v | cut -d ' ' -f 2 | cut -d '.' -f 1`
+minor_v=`${HERE}/../build/src/rapmap -v | cut -d ' ' -f 2 | cut -d '.' -f 2`
+patch_v=`${HERE}/../build/src/rapmap -v | cut -d ' ' -f 2 | cut -d '.' -f 3`
+
+echo "VERSION : ${major_v}.${minor_v}.${patch_v}"
+
+# update docker file
+#awk -v majv=${major_v} -v minv=${minor_v} -v patchv=${patch_v} '{ if ($0 ~ /ENV SALMON_VERSION/) { print "ENV SALMON_VERSION " majv"."minv"."patchv; } else { print $0; }}' \
+#    ${HERE}/../docker/Dockerfile > ${HERE}/../docker/Dockerfile.new && mv ${HERE}/../docker/Dockerfile.new ${HERE}/../docker/Dockerfile
+
+# update docker build script
+#awk -v majv=${major_v} -v minv=${minor_v} -v patchv=${patch_v} '{ if ($0 ~ /SALMON_VERSION=/) { print "SALMON_VERSION="majv"."minv"."patchv; } else { print $0; }}' \
+#    ${HERE}/../docker/build_test.sh > ${HERE}/../docker/build_test.sh.new && mv ${HERE}/../docker/build_test.sh.new ${HERE}/../docker/build_test.sh
+
+# update version file (which feeds cmake)
+echo -e "VERSION_MAJOR ${major_v}\nVERSION_MINOR ${minor_v}\nVERSION_PATCH ${patch_v}" > ${HERE}/../current_version.txt
+
+# update conf.py
+#awk -v majv=${major_v} -v minv=${minor_v} -v patchv=${patch_v} \
+#    '{ if ($0 ~ /version = /) { print "version = '\''" majv"."minv"'\''"; } else if ($0 ~ /release = /) { print "release = '\''" majv"."minv"."patchv"'\''"; } else { print $0; }}' \
+#    ${HERE}/../doc/source/conf.py > ${HERE}/../doc/source/conf.py.new && mv ${HERE}/../doc/source/conf.py.new ${HERE}/../doc/source/conf.py

src/RapMap.cpp

@@ -36,14 +36,14 @@ int rapMapSAMap(int argc, char* argv[]);
 
 void printUsage() {
     std::string versionString = rapmap::version;
-    std::cerr << "RapMap Transcriptome Aligner v"
+    std::cerr << "rapmap v"
               << versionString << '\n';
     std::cerr << "=====================================\n";
     auto usage =
         R"(
-There are currently 2 RapMap subcommands
-    quasiindex --- builds a suffix array-based (SA) index
-    quasimap   --- map reads using the SA-based index
+There are currently 2 rapmap subcommands
+    quasiindex --- builds a quasi-mapping index on the reference
+    quasimap   --- maps reads to a quasi-mapping index
 
 Run a corresponding command "rapmap <cmd> -h" for
 more information on each of the possible RapMap
@@ -77,14 +77,14 @@ int main(int argc, char* argv[]) {
         std::exit(0);
     }
 
-    if (std::string(argv[1]) == "pseudoindex") {
-        std::cerr << "This mode not enabled in this branch\n";
-        return 1;//rapMapIndex(argc - 1, args.data());
-    } else if (std::string(argv[1]) == "quasiindex") {
+    if (std::string(argv[1]) == "-v" or
+        std::string(argv[1]) == "--version") {
+      std::cout << "rapmap " << rapmap::version << "\n";
+      std::exit(0);
+    }
+
+    if (std::string(argv[1]) == "quasiindex") {
         return rapMapSAIndex(argc - 1, args.data());
-    } else if (std::string(argv[1]) == "pseudomap") {
-        std::cerr << "This mode not enabled in this branch\n";
-        return 1;//rapMapMap(argc - 1, args.data());
     } else if (std::string(argv[1]) == "quasimap") {
         return rapMapSAMap(argc - 1, args.data());
     } else {