update prepare for release

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
-VERSION_MINOR 5
-VERSION_PATCH 2
+VERSION_MINOR 6
+VERSION_PATCH 0

doc/source/conf.py

@@ -48,16 +48,16 @@
 
 # General information about the project.
 project = u'Salmon'
-copyright = u'2013-2017, Rob Patro, Geet Duggal, Mike Love, Rafael Irizarry and Carl Kingsford'
+copyright = u'2013-2021, Rob Patro, Geet Duggal, Mike Love, Rafael Irizarry and Carl Kingsford'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.5'
+version = '1.6'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.2'
+release = '1.6.0'
 
 # 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 1.5.2
+ENV SALMON_VERSION 1.6.0
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,3 +1,3 @@
 #! /bin/bash
-SALMON_VERSION=1.5.2
+SALMON_VERSION=1.6.0
 docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

include/SalmonConfig.hpp

@@ -26,9 +26,9 @@
 
 namespace salmon {
 constexpr char majorVersion[] = "1";
-constexpr char minorVersion[] = "5";
-constexpr char patchVersion[] = "2";
-constexpr char version[] = "1.5.2";
+constexpr char minorVersion[] = "6";
+constexpr char patchVersion[] = "0";
+constexpr char version[] = "1.6.0";
 constexpr uint32_t indexVersion = 5;
 constexpr char requiredQuasiIndexVersion[] = "p7";
 } // namespace salmon

include/cuckoohash_map.hh

@@ -113,7 +113,7 @@ public:
         maximum_hashpower_(NO_MAXIMUM_HASHPOWER),
         max_num_worker_threads_(0) {
     all_locks_.emplace_back(std::min(bucket_count(), size_type(kMaxNumLocks)),
-                            spinlock(), get_allocator());
+                            get_allocator());
   }
 
   /**
@@ -695,7 +695,7 @@ private:
 
   void add_locks_from_other(const cuckoohash_map &other) {
     locks_t &other_locks = other.get_current_locks();
-    all_locks_.emplace_back(other_locks.size(), spinlock(), get_allocator());
+    all_locks_.emplace_back(other_locks.size(), get_allocator());
     std::copy(other_locks.begin(), other_locks.end(),
               get_current_locks().begin());
   }
@@ -794,7 +794,7 @@ private:
   // under this lock. One can compute the size of the table by summing the
   // elem_counter over all locks.
   //
-  // - is_migrated: When resizing with cuckoo_fast_doulbe, we do not
+  // - is_migrated: When resizing with cuckoo_fast_double, we do not
   // immediately rehash elements from the old buckets array to the new one.
   // Instead, we'll mark all of the locks as not migrated. So anybody trying to
   // acquire the lock must also migrate the corresponding buckets if
@@ -1823,7 +1823,7 @@ private:
     }
 
     locks_t new_locks(std::min(size_type(kMaxNumLocks), new_bucket_count),
-                      spinlock(), get_allocator());
+                      get_allocator());
     assert(new_locks.size() > current_locks.size());
     std::copy(current_locks.begin(), current_locks.end(), new_locks.begin());
     for (spinlock &lock : new_locks) {