[med-svn] [Git][med-team/salmon][master] 5 commits: routine-update: New upstream version
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Aug 16 12:18:21 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / salmon
Commits:
20b069d3 by Michael R. Crusoe at 2023-08-16T13:05:53+02:00
routine-update: New upstream version
- - - - -
032c1a8a by Michael R. Crusoe at 2023-08-16T13:05:54+02:00
New upstream version 1.10.2+ds1
- - - - -
19b46d2a by Michael R. Crusoe at 2023-08-16T13:05:58+02:00
Update upstream source from tag 'upstream/1.10.2+ds1'
Update to upstream version '1.10.2+ds1'
with Debian dir 61d4839aecbfecdee066e08a4ac8ce321fdbf84d
- - - - -
2f6e0601 by Michael R. Crusoe at 2023-08-16T13:05:58+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
2203ffb7 by Michael R. Crusoe at 2023-08-16T13:09:34+02:00
release to unstable
- - - - -
11 changed files:
- CMakeLists.txt
- current_version.txt
- debian/changelog
- debian/control
- doc/source/conf.py
- docker/Dockerfile
- docker/build_test.sh
- include/EffectiveLengthStats.hpp
- include/SalmonConfig.hpp
- include/SalmonExceptions.hpp
- scripts/fetchPufferfish.sh
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -642,7 +642,7 @@ endif()
message("Build system will fetch and build Intel Threading Building Blocks")
message("==================================================================")
# These are useful for the custom install step we'll do later
-set(TBB_SOURCE_DIR ${GAT_SOURCE_DIR}/external/oneTBB-2021.5.0)
+set(TBB_SOURCE_DIR ${GAT_SOURCE_DIR}/external/oneTBB-2021.9.0)
set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
if("${TBB_COMPILER}" STREQUAL "gcc")
@@ -655,9 +655,9 @@ set(TBB_CXXFLAGS "${TBB_CXXFLAGS} ${CXXSTDFLAG} ${SCHAR_FLAG}")
ExternalProject_Add(libtbb
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-DOWNLOAD_COMMAND curl -k -L https://github.com/oneapi-src/oneTBB/archive/refs/tags/v2021.5.0.tar.gz -o v2021.5.tar.gz &&
-${SHASUM} e5b57537c741400cf6134b428fc1689a649d7d38d9bb9c1b6d64f092ea28178a v2021.5.tar.gz &&
-tar -xzvf v2021.5.tar.gz
+DOWNLOAD_COMMAND curl -k -L https://github.com/oneapi-src/oneTBB/archive/refs/tags/v2021.9.0.tar.gz -o v2021.9.tar.gz &&
+${SHASUM} 1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e v2021.9.tar.gz &&
+tar -xzvf v2021.9.tar.gz
SOURCE_DIR ${TBB_SOURCE_DIR}
INSTALL_DIR ${TBB_INSTALL_DIR}
PATCH_COMMAND "${TBB_PATCH_STEP}"
=====================================
current_version.txt
=====================================
@@ -1,3 +1,3 @@
VERSION_MAJOR 1
VERSION_MINOR 10
-VERSION_PATCH 1
+VERSION_PATCH 2
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+salmon (1.10.2+ds1-1) unstable; urgency=medium
+
+ * New upstream version
+ Closes: #1043107
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 16 Aug 2023 13:09:23 +0200
+
salmon (1.10.1+ds1-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -36,7 +36,7 @@ Build-Depends: debhelper-compat (= 13),
liblzma-dev,
rapmap-dev,
libsimde-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/salmon
Vcs-Git: https://salsa.debian.org/med-team/salmon.git
Homepage: https://github.com/COMBINE-lab/salmon
=====================================
doc/source/conf.py
=====================================
@@ -57,7 +57,7 @@ copyright = u'2013-2021, Rob Patro, Geet Duggal, Mike Love, Rafael Irizarry and
# The short X.Y version.
version = '1.10'
# The full version, including alpha/beta/rc tags.
-release = '1.10.1'
+release = '1.10.2'
# 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 at 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 1.10.1
+ENV SALMON_VERSION 1.10.2
# salmon binary will be installed in /home/salmon/bin/salmon
=====================================
docker/build_test.sh
=====================================
@@ -1,3 +1,3 @@
#! /bin/bash
-SALMON_VERSION=1.10.1
-TMPDIR=/mnt/scratch2/DELETE_ME_TEMP docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .
+SALMON_VERSION=1.10.2
+TMPDIR=/mnt/scratch7/DELETE_ME_TEMP docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .
=====================================
include/EffectiveLengthStats.hpp
=====================================
@@ -1,6 +1,7 @@
#ifndef EFFECTIVE_LENGTH_STATS_HPP
#define EFFECTIVE_LENGTH_STATS_HPP
+#include <cstdint>
#include "Eigen/Dense"
/**
=====================================
include/SalmonConfig.hpp
=====================================
@@ -22,13 +22,14 @@
#ifndef SALMON_CONFIG_HPP
#define SALMON_CONFIG_HPP
+#include <cstdint>
#include <string>
namespace salmon {
constexpr char majorVersion[] = "1";
constexpr char minorVersion[] = "10";
-constexpr char patchVersion[] = "1";
-constexpr char version[] = "1.10.1";
+constexpr char patchVersion[] = "2";
+constexpr char version[] = "1.10.2";
constexpr uint32_t indexVersion = 5;
constexpr char requiredQuasiIndexVersion[] = "p7";
} // namespace salmon
=====================================
include/SalmonExceptions.hpp
=====================================
@@ -3,6 +3,7 @@
#include <sstream>
#include <stdexcept>
+#include <cstdint>
class InsufficientAssignedFragments : public std::runtime_error {
public:
=====================================
scripts/fetchPufferfish.sh
=====================================
@@ -23,11 +23,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
rm -fr ${INSTALL_DIR}/src/pufferfish
fi
-SVER=salmon-v1.10.1
+SVER=salmon-v1.10.2
#SVER=develop
#SVER=sketch-mode
-EXPECTED_SHA256=cf2a007f3817c1087abd4170db70e6b3c04aa24babecf92a2d9d2eb7784b6021
+EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
mkdir -p ${EXTERNAL_DIR}
curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/ecf5dfcb8a904b476b5f7e8169e63f80c22a73f6...2203ffb738057a99f4263a1c1baf7b8edf4a49b5
--
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/ecf5dfcb8a904b476b5f7e8169e63f80c22a73f6...2203ffb738057a99f4263a1c1baf7b8edf4a49b5
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