Get SPAdes version from single common place

ablab · May 13, 2024 · fb78220 · fb78220
1 parent 77aa33c
commit fb78220
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Showing 5 changed files with 55 additions and 33 deletions.
diff --git a/make-targz.sh b/make-targz.sh
@@ -5,7 +5,7 @@
 # See file LICENSE for details.
 ############################################################################
 
-VERSION="$(cat assembler/VERSION)"
+VERSION="$(cat VERSION)"
 : "${TARGET_DIR:=SPAdes-$VERSION}"
 rm -rf $TARGET_DIR
 SRC_DIR=$TARGET_DIR/src
@@ -15,11 +15,10 @@ cp -r src/common $SRC_DIR/
 cp -r src/projects $SRC_DIR/
 cp -r src/include $SRC_DIR/
 cp -r src/cmake $SRC_DIR/
-cp -r src/spades_pipeline $SRC_DIR/
 cp src/CMakeLists.txt $SRC_DIR/
 
-cp -r configs $TARGET_DIR/configs
 cp -r ext $TARGET_DIR/ext
+cp -r docs $TARGET_DIR/docs
 
 # cleaning .pyc and .pyo
 rm -f $SRC_DIR/*.pyc
@@ -35,23 +34,10 @@ rm -f $TARGET_DIR/ext/src/python_libs/*/*.pyc
 rm -f $TARGET_DIR/ext/src/python_libs/*/*.pyo
 rm -rf $TARGET_DIR/ext/src/python_libs/*/__pycache__/
 
-cp -r biosynthetic_spades_hmms $TARGET_DIR/
-cp -r coronaspades_hmms $TARGET_DIR/
-cp -r test_dataset $TARGET_DIR/test_dataset
-cp -r test_dataset_plasmid $TARGET_DIR/test_dataset_plasmid
 cp LICENSE $TARGET_DIR/
 cp README.md $TARGET_DIR/
 cp VERSION $TARGET_DIR/
-cp spades.py $TARGET_DIR/
-cp rnaviralspades.py $TARGET_DIR/
-cp rnaspades.py $TARGET_DIR/
-cp metaspades.py $TARGET_DIR/
-cp plasmidspades.py $TARGET_DIR/
-cp metaviralspades.py $TARGET_DIR/
-cp metaplasmidspades.py $TARGET_DIR/
-cp coronaspades.py $TARGET_DIR/
 cp spades_compile.sh $TARGET_DIR/
-cp spades_init.py $TARGET_DIR/
 cp changelog.html $TARGET_DIR/
 cp GPLv2.txt $TARGET_DIR/
 

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -77,6 +77,23 @@ if (NOT SPADES_GIT_SHA1)
   set(SPADES_GIT_SHA1 "N/A")
 endif()
 
+file(STRINGS "${CMAKE_SOURCE_DIR}/../VERSION" VERSION_STRING LIMIT_COUNT 1)
+string(REGEX MATCH "([a-zA-Z]*)-\?([0-9]+)\.([0-9]+)\.([0-9]+)(.*)" ver "${VERSION_STRING}")
+if (ver STREQUAL "")
+  message(FATAL_ERROR "Error to parse version string from ${VERSION_STRING}")
+endif()
+if (CMAKE_MATCH_1 STREQUAL "")
+  set(SPADES_FLAVOUR "SPAdes")
+else()
+  set(SPADES_FLAVOUR "${CMAKE_MATCH_1}")
+endif()
+set(SPADES_VERSION_MAJOR "${CMAKE_MATCH_2}")
+set(SPADES_VERSION_MINOR "${CMAKE_MATCH_3}")
+set(SPADES_VERSION_PATCH "${CMAKE_MATCH_4}")
+set(SPADES_VERSION_SUFFIX "${CMAKE_MATCH_5}")
+set(SPADES_PACKAGE_VERSION "${SPADES_VERSION_MAJOR}.${SPADES_VERSION_MINOR}.${SPADES_VERSION_PATCH}${SPADES_VERSION_SUFFIX}")
+message(STATUS "Building ${SPADES_FLAVOUR} version ${SPADES_PACKAGE_VERSION}")
+
 # Testing
 include(test)
 

diff --git a/src/cmake/pack.cmake b/src/cmake/pack.cmake
@@ -1,27 +1,21 @@
 # -*- cmake -*-
 
-# Binary stuff
 set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
-if (APPLE)
-  set(CPACK_GENERATOR "TGZ")
-else()
-  set(CPACK_GENERATOR "TGZ")
-endif()
 
-set(CPACK_PACKAGE_NAME "SPAdes")
-set(CPACK_PACKAGE_VENDOR "Saint Petersburg State University")
+# Binary stuff
+set(CPACK_GENERATOR "TGZ")
+set(CPACK_PACKAGE_NAME "${SPADES_FLAVOUR}")
+set(CPACK_PACKAGE_VENDOR "SPAdes Team")
 #set(CPACK_PACKAGE_DESCRIPTION_FILE "${SPADES_MAIN_SRC_DIR}/../README")
 set(CPACK_RESOURCE_FILE_LICENSE "${SPADES_MAIN_SRC_DIR}/../LICENSE")
-set(CPACK_PACKAGE_VERSION "3.16.0-dev")
-set(CPACK_PACKAGE_VERSION_MAJOR "3")
-set(CPACK_PACKAGE_VERSION_MINOR "16")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
-set(CPACK_STRIP_FILES bin/spades-bwa bin/spades-core bin/spades-corrector-core bin/spades-gbuilder bin/spades-gmapper bin/spades-hammer bin/spades-ionhammer bin/spades-kmercount)
-
+set(CPACK_PACKAGE_VERSION "${SPADES_PACKAGE_VERSION}")
+set(CPACK_PACKAGE_VERSION_MAJOR "${SPADES_VERSION_MAJOR}")
+set(CPACK_PACKAGE_VERSION_MINOR "${SPADES_VERSION_MINOR}")
+set(CPACK_PACKAGE_VERSION_PATCH "${SPADES_VERSION_PATCH}")
 
 # Source stuff
 set(CPACK_SOURCE_GENERATOR "TBZ2")
-set(CPACK_SOURCE_IGNORE_FILES tools test web_service online_vis cap)
+set(CPACK_SOURCE_IGNORE_FILES tools test online_vis)
 set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
 
 include(CPack)
diff --git a/src/common/utils/version.cpp b/src/common/utils/version.cpp
@@ -10,6 +10,26 @@
 
 namespace version {
 
+const char *major() {
+    return SPADES_VERSION_MAJOR;
+}
+
+const char *minor() {
+    return SPADES_VERSION_MINOR;
+}
+
+const char *patch() {
+    return SPADES_VERSION_PATCH;
+}
+
+const char *flavour() {
+    return SPADES_FLAVOUR;
+}
+
+const char *package() {
+    return SPADES_PACKAGE_VERSION;
+}
+
 const char *refspec() {
     return SPADES_GIT_REFSPEC;
 }

diff --git a/src/include/version-gen.hpp.in b/src/include/version-gen.hpp.in
@@ -1,7 +1,12 @@
 #ifndef __SPADES_VERSION_HPP__
 #define __SPADES_VERSION_HPP__
 
-#cmakedefine SPADES_GIT_REFSPEC "${SPADES_GIT_REFSPEC}"
-#cmakedefine SPADES_GIT_SHA1 "${SPADES_GIT_SHA1}"
+#define SPADES_FLAVOUR "${SPADES_FLAVOUR}"
+#define SPADES_PACKAGE_VERSION "${SPADES_PACKAGE_VERSION}"
+#define SPADES_VERSION_MAJOR "${SPADES_VERSION_MAJOR}"
+#define SPADES_VERSION_MINOR "${SPADES_VERSION_MINOR}"
+#define SPADES_VERSION_PATCH "${SPADES_VERSION_PATCH}"
+#define SPADES_GIT_REFSPEC "${SPADES_GIT_REFSPEC}"
+#define SPADES_GIT_SHA1 "${SPADES_GIT_SHA1}"
 
 #endif // __SPADES_VERSION_HPP__