[med-svn] [Git][med-team/abyss][master] 6 commits: New upstream version 2.3.10

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sat Nov 2 13:03:59 GMT 2024 


Étienne Mollier pushed to branch master at Debian Med / abyss


Commits:
9a865ba8 by Étienne Mollier at 2024-11-02T13:43:30+01:00
New upstream version 2.3.10
- - - - -
020cc95f by Étienne Mollier at 2024-11-02T13:43:32+01:00
Update upstream source from tag 'upstream/2.3.10'

Update to upstream version '2.3.10'
with Debian dir df819f3915d86accfbce88267c56ff77cdf4be86
- - - - -
4fadf4b2 by Étienne Mollier at 2024-11-02T13:46:10+01:00
fix-privacy-breach.patch: refresh.

- - - - -
e580efa9 by Étienne Mollier at 2024-11-02T13:53:38+01:00
d/manpages: install abyss-pe.1.

- - - - -
9ac41d1a by Étienne Mollier at 2024-11-02T13:56:09+01:00
abyss-pe.patch: declare forwarding not needed.

- - - - -
1c30ee65 by Étienne Mollier at 2024-11-02T14:03:27+01:00
d/changelog: ready for sid upload.

- - - - -


13 changed files:

- ChangeLog
- Misc/samtobreak.hs
- README.md
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- debian/changelog
- debian/manpages
- debian/patches/abyss-pe.patch
- debian/patches/fix-privacy-breach.patch
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+2024-10-18 Lauren Coombe <lcoombe at bcgsc.ca>
+
+  * Release version 2.3.10
+
+      General:
+	    * Fix usage of `N` and `S` parameters for scaffolding stage
+
 2024-09-11 Johnathan Wong <jowong at bcgsc.ca>
 
   * Release version 2.3.9


=====================================
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) 2.3.9\n"
+  version = "abyss-samtobreak (ABySS) 2.3.10\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 


=====================================
README.md
=====================================
@@ -1,5 +1,5 @@
 [![Release](https://img.shields.io/github/release/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/releases)
-[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.9/abyss-2.3.9.tar.gz)
+[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz)
 [![Conda](https://img.shields.io/conda/dn/bioconda/abyss?label=Conda)](https://anaconda.org/bioconda/abyss)
 [![Issues](https://img.shields.io/github/issues/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/issues)
 


=====================================
azure-pipelines.yml
=====================================
@@ -33,13 +33,20 @@ jobs:
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
       mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
     displayName: Install dependencies
   - script: |
@@ -50,68 +57,116 @@ jobs:
     displayName: Compiling ABySS
 
 - job:
-  displayName: mac_clang14
+  displayName: mac_clang16
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.7.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 16
 
 - job:
-  displayName: mac_clang13
+  displayName: mac_clang15
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.6.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS with clang 13
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 15
 
 - job:
-  displayName: mac_clang12
+  displayName: mac_clang14
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
       make -j12 distcheck
-    displayName: Compiling ABySS with clang 12
+    displayName: Compiling ABySS with clang 14
 
+- job:
+  displayName: mac_clang13
+  pool:
+    vmImage: 'macOS-latest'
+  steps:
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
+  - script: conda create --yes --quiet --name abyss_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate abyss_CI
+      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+    displayName: Install dependencies
+  - script: |
+      source activate abyss_CI
+      ./autogen.sh
+      ./configure
+      make -j12 distcheck
+    displayName: Compiling ABySS with clang 13
 
 - job: linux_gcc12
   pool:


=====================================
bin/abyss-pe
=====================================
@@ -349,12 +349,12 @@ L?=$l
 S?=100-5000
 N?=15-20
 SCAFFOLD_DE_S?=$(shell echo $S | sed 's/-.*//')
-SCAFFOLD_DE_N?=$N
+SCAFFOLD_DE_N?=$(shell echo $N | sed 's/-.*//')
 SCAFFOLD_DE_OPTIONS?=$(DISTANCEEST_OPTIONS)
-$(foreach i,$(mp),$(eval $i_l?=$L))
-$(foreach i,$(mp),$(eval $i_s?=$(SCAFFOLD_DE_S)))
-$(foreach i,$(mp),$(eval $i_n?=$(SCAFFOLD_DE_N)))
-override scaffold_deopt=$v $(dbopt) --dot --median -j$j -k$k $(SCAFFOLD_DE_OPTIONS) -l$($*_l) -s$($*_s) -n$($*_n) $($*_de)
+$(foreach i,$(mp),$(eval $i_scaf_l?=$L))
+$(foreach i,$(mp),$(eval $i_scaf_s?=$(SCAFFOLD_DE_S)))
+$(foreach i,$(mp),$(eval $i_scaf_n?=$(SCAFFOLD_DE_N)))
+override scaffold_deopt=$v $(dbopt) --dot --median -j$j -k$k $(SCAFFOLD_DE_OPTIONS) -l$($*_scaf_l) -s$($*_scaf_s) -n$($*_scaf_n) $($*_de)
 scopt += $v $(dbopt) $(SS) -k$k
 ifdef G
 scopt += -G$G
@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.9"
+	@echo "abyss-pe (ABySS) 2.3.10"
 	@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, 2.3.9, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.10, abyss-users at bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+abyss (2.3.10-1) unstable; urgency=medium
+
+  * New upstream version 2.3.10
+  * fix-privacy-breach.patch: refresh.
+  * d/manpages: install abyss-pe.1.
+  * abyss-pe.patch: declare forwarding not needed.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 02 Nov 2024 14:00:42 +0100
+
 abyss (2.3.9-1) unstable; urgency=medium
 
   * New upstream version 2.3.9  (Closes: #1080071)


=====================================
debian/manpages
=====================================
@@ -1 +1,2 @@
 debian/tmp/usr/share/man/man1/*.1
+doc/abyss-pe.1


=====================================
debian/patches/abyss-pe.patch
=====================================
@@ -1,5 +1,9 @@
 Author: Shaun Jackman <sjackman at debian.org>
 Description: Add internal PATH to find abyss tools
+ This change is to accomodate file layout in the Debian package, thus
+ unnecessary upstream.
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
 
 --- a/bin/abyss-pe
 +++ b/bin/abyss-pe


=====================================
debian/patches/fix-privacy-breach.patch
=====================================
@@ -9,7 +9,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 +++ abyss/README.md
 @@ -1,8 +1,3 @@
 -[![Release](https://img.shields.io/github/release/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/releases)
--[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.9/abyss-2.3.9.tar.gz)
+-[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz)
 -[![Conda](https://img.shields.io/conda/dn/bioconda/abyss?label=Conda)](https://anaconda.org/bioconda/abyss)
 -[![Issues](https://img.shields.io/github/issues/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/issues)
 -


=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.9" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.10" "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) 2.3.9" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.10" "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 2.3.9" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.10" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br



View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/4a4dda3e7de1de6b926fe3f1e64001d98786938a...1c30ee656293e4298e424f77c59bb88018a7d67f

-- 
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/4a4dda3e7de1de6b926fe3f1e64001d98786938a...1c30ee656293e4298e424f77c59bb88018a7d67f
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