bump version prepare for 1.5.2

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
 VERSION_MINOR 5
-VERSION_PATCH 1
+VERSION_PATCH 2

doc/source/conf.py

@@ -57,7 +57,7 @@
 # The short X.Y version.
 version = '1.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.1'
+release = '1.5.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER salmon.maintainer@gmail.com
 
 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 1.5.1
+ENV SALMON_VERSION 1.5.2
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,3 +1,3 @@
 #! /bin/bash
-SALMON_VERSION=1.5.1
+SALMON_VERSION=1.5.2
 docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

include/SalmonConfig.hpp

@@ -9,13 +9,13 @@
     the Free Software Foundation, either version 3 of the License, or
     (at your option) any later version.
 
-    Sailfish is distributed in the hope that it will be useful,
+    Salmon is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with Sailfish.  If not, see <http://www.gnu.org/licenses/>.
+    along with Salmon.  If not, see <http://www.gnu.org/licenses/>.
 <HEADER
 **/
 
@@ -27,8 +27,8 @@
 namespace salmon {
 constexpr char majorVersion[] = "1";
 constexpr char minorVersion[] = "5";
-constexpr char patchVersion[] = "1";
-constexpr char version[] = "1.5.1";
+constexpr char patchVersion[] = "2";
+constexpr char version[] = "1.5.2";
 constexpr uint32_t indexVersion = 5;
 constexpr char requiredQuasiIndexVersion[] = "p7";
 } // namespace salmon

include/cuckoohash_map.hh

@@ -705,7 +705,9 @@ private:
   // true if the key is small and simple, which means using partial keys for
   // lookup would probably slow us down
   static constexpr bool is_simple() {
-    return std::is_pod<key_type>::value && sizeof(key_type) <= 8;
+    return std::is_standard_layout<key_type>::value &&
+           std::is_trivial<key_type>::value &&
+           sizeof(key_type) <= 8;
   }
 
   // Whether or not the data is nothrow-move-constructible.

scripts/fetchPufferfish.sh

@@ -22,11 +22,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
     rm -fr ${INSTALL_DIR}/src/pufferfish
 fi
 
-#SVER=salmon-v1.5.1
-SVER=develop
+SVER=salmon-v1.5.2
+#SVER=develop
 #SVER=sketch-mode
 
-EXPECTED_SHA256=468e0c23a32d81524f7acadc8326efb155628970c15fd6cb843d26a61478bfde
+EXPECTED_SHA256=86c7ff465d40b8184dca7f6afee693ad1db63be5bf63242161ea39d3507d6d25
 
 mkdir -p ${EXTERNAL_DIR}
 curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip