bump version to accomodate new libstaden version

CMakeLists.txt

@@ -785,7 +785,7 @@ find_package(CURL)
 if (FETCH_STADEN)
   set(LIBSTADEN_FOUND FALSE)
 else ()
-  find_package(libstadenio 1.14.15)
+  find_package(libstadenio 1.15.0)
 endif()
 
 if (NOT LIBSTADENIO_FOUND)
@@ -808,8 +808,6 @@ if (NOT LIBSTADENIO_FOUND)
     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
     CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
     BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG}
-
-
     BUILD_IN_SOURCE 1
     INSTALL_COMMAND make install
   )

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
 VERSION_MINOR 10
-VERSION_PATCH 2
+VERSION_PATCH 3

doc/source/conf.py

@@ -57,7 +57,7 @@
 # The short X.Y version.
 version = '1.10'
 # The full version, including alpha/beta/rc tags.
-release = '1.10.2'
+release = '1.10.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER [email protected]
 
 ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget
-ENV SALMON_VERSION 1.10.2
+ENV SALMON_VERSION 1.10.3
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,3 +1,3 @@
 #! /bin/bash
-SALMON_VERSION=1.10.2
+SALMON_VERSION=1.10.3
 TMPDIR=/mnt/scratch7/DELETE_ME_TEMP docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

include/SalmonConfig.hpp

@@ -1,10 +1,10 @@
 /**
 >HEADER
-    Copyright (c) 2014-2022 Rob Patro [email protected]
+    Copyright (c) 2014-2024 Rob Patro [email protected]
 
     This file is part of Salmon.
 
-    Sailfish is free software: you can redistribute it and/or modify
+    Salmon is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
     the Free Software Foundation, either version 3 of the License, or
     (at your option) any later version.
@@ -28,8 +28,8 @@
 namespace salmon {
 constexpr char majorVersion[] = "1";
 constexpr char minorVersion[] = "10";
-constexpr char patchVersion[] = "2";
-constexpr char version[] = "1.10.2";
+constexpr char patchVersion[] = "3";
+constexpr char version[] = "1.10.3";
 constexpr uint32_t indexVersion = 5;
 constexpr char requiredQuasiIndexVersion[] = "p7";
 } // namespace salmon

scripts/fetchPufferfish.sh

@@ -23,11 +23,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
     rm -fr ${INSTALL_DIR}/src/pufferfish
 fi
 
-SVER=salmon-v1.10.2
+SVER=salmon-v1.10.3
 #SVER=develop
 #SVER=sketch-mode
 
-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
+EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860 
 
 mkdir -p ${EXTERNAL_DIR}
 curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip