Prepare for release v2.3.6 (#465)

* Prepare for release v2.3.6

* Update gcc version for mac_gcc test to be consistent with current brew bottle

* brew install gcc@12

ChangeLog

@@ -1,3 +1,14 @@
+2023-05-02 Lauren Coombe <[email protected]>
+
+ * Release version 2.3.6
+
+ General:
+ * btllib is now a dependency
+ * Documentation updates
+
+ abyss-rresolver-short:
+ * btllib source code removed due to btllib now being a dependency
+
 2022-05-11 Vladimir Nikolic <[email protected]>
 
  * Release version 2.3.5

Misc/samtobreak.hs

@@ -279,7 +279,7 @@ parseArgs = do
  where
  help = putStr (usageInfo usage options) >> exitSuccess
  tryHelp = "Try 'abyss-samtobreak --help' for more information."
- version = "abyss-samtobreak (ABySS) 2.3.5\n"
+ version = "abyss-samtobreak (ABySS) 2.3.6\n"
  usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

azure-pipelines.yml

@@ -6,7 +6,7 @@ jobs:
  - script: |
  rm -f /usr/local/bin/2to3 # brew is having issues with installing Python
  brew update
- brew install automake boost openmpi google-sparsehash make pandoc ghc 
+ brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@12
  displayName: Install common
  - script: |
  wget https://github.com/bcgsc/btllib/releases/download/v1.5.1/btllib-1.5.1.tar.gz
@@ -15,7 +15,6 @@ jobs:
  tar xzf btllib-1.5.1.tar.gz
  cd btllib-1.5.1
  ./compile
- pwd
  displayName: Install btllib
  - script: |
  ./autogen.sh

bin/abyss-pe

@@ -414,7 +414,7 @@ help:
  @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or [email protected].'
 
 version:
- @echo "abyss-pe (ABySS) 2.3.5"
+ @echo "abyss-pe (ABySS) 2.3.6"
  @echo "Written by Shaun Jackman and Anthony Raymond."
  @echo
  @echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.3.5, [email protected], abyss,
+AC_INIT(ABySS, 2.3.6, [email protected], abyss,
  http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.6" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.6" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.6" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br