Release 1.12

.appveyor.yml

@@ -5,11 +5,6 @@ version: 'vers.{build}'
 
 # branches to build
 branches:
-    # Whitelist
-    only:
-      - develop
-
-    # Blacklist
     except:
       - gh-pages
 
@@ -22,6 +17,9 @@ skip_tags: true
 #    - docs/*
 #    - '**/*.html'
 
+# Appveyor Windows images are based on Visual studio version
+image: Visual Studio 2019
+
 # We use Mingw/Msys, so use pacman for installs
 install:
   - set HOME=.
@@ -37,15 +35,15 @@ install:
 clone_script:
   - "sh -lc \"if test x$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME != x ; then git clone --branch=$APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH https://github.com/$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME $APPVEYOR_BUILD_FOLDER ; else false ; fi || git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\""
   - "sh -lc \"git show-branch --sha1-name HEAD"
-  - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \""
+  - "sh -lc \"git clone --recurse-submodules --shallow-submodules --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone --recurse-submodules --shallow-submodules https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \""
   - "sh -lc \"cd $APPVEYOR_BUILD_FOLDER/htslib && git show-branch --sha1-name HEAD\""
 
 build_script:
   - set HOME=.
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
-  - "sh -lc \"(cd htslib; aclocal && autoheader && autoconf)\""
-  - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\""
+  - "sh -lc \"(cd htslib; autoreconf -i)\""
+  - "sh -lc \"autoreconf -i && ./configure --enable-werror && make -j2\""
 
 test_script:
   - set HOME=.

.ci_helpers/clone

@@ -0,0 +1,17 @@
+#!/bin/sh
+# Usage: .ci_helpers/clone REPOSITORY [DIR] [BRANCH]
+#
+# Creates a shallow clone, checking out the specified branch.  If BRANCH is
+# omitted or if there is no branch with that name, checks out origin/HEAD
+# from the samtools/htslib repository.
+
+repository=$1
+localdir=$2
+branch=$3
+
+ref=''
+[ -n "$branch" ] && ref=$(git ls-remote --heads "$repository" "$branch" 2>/dev/null)
+[ -z "$ref" ] && repository='git://github.com/samtools/htslib.git'
+
+set -x
+git clone --recurse-submodules --shallow-submodules --depth=1 ${ref:+--branch="$branch"} "$repository" "$localdir"

.cirrus.yml

@@ -0,0 +1,161 @@
+# Note we have a maximum of 16 CPUs available, so adjust our
+# builds so we can start all concurrently without needing to schedule.
+
+# Sadly though there is still a finite limit to macOS of one instance.
+# Can we cull our Mac test to just one instance?
+
+timeout_in: 10m
+
+#--------------------------------------------------
+# Template: htslib clone & build
+#
+# We try to clone htslib using the same branch name and owner as this
+# bcftools branch.  If it exists, it's likely the user is making a
+# joint bcftools+htslib PR and wants both checked in unison.
+# Failing that we use samtools/htslib:develop.
+# Note this only works on the users own forks.  Once in the samtools
+# organisation the branch name becomes pull/<num>.
+
+# Logic for choosing which to use is in the .ci_helpers/clone script.
+# Note we could also use "clone_script" if we want to replace the bcftools
+# clone with our own commands too.
+clone_template: &HTSLIB_CLONE
+  htslib_clone_script: |
+    .ci_helpers/clone "git://github.com/${CIRRUS_REPO_OWNER}/htslib" "${HTSDIR}" "${CIRRUS_BRANCH}"
+
+
+#--------------------------------------------------
+# Template: bcftools compile and test
+
+compile_template: &COMPILE
+  << : *HTSLIB_CLONE
+
+  compile_script: |
+    if test "$USE_CONFIG" = "yes"; then
+      (cd $HTSDIR && autoreconf -i)
+      autoreconf -i
+      ./configure --enable-werror || (cat config.log; /bin/false)
+      make -j3
+    else
+      make -j3 plugindir=$CIRRUS_WORKING_DIR/plugins -e
+    fi
+
+test_template: &TEST
+  test_script: |
+    make -e test
+
+
+#--------------------------------------------------
+# Task: linux builds.
+
+# Debian + latest GCC
+gcc_task:
+  name: debian-gcc
+  container:
+    image: gcc:latest
+    cpu: 1
+    memory: 1G
+
+  environment:
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    HTSDIR: ./htslib
+
+  matrix:
+    - environment:
+       USE_CONFIG: no
+    - environment:
+       USE_CONFIG: yes
+       CFLAGS: -std=gnu99 -O0
+
+  << : *COMPILE
+  << : *TEST
+
+
+# Ubuntu + Clang
+ubuntu_task:
+  name: ubuntu-clang
+  container:
+    image: ubuntu:devel
+    cpu: 2
+    memory: 1G
+
+  environment:
+    CC: clang
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    HTSDIR: ./htslib
+
+  matrix:
+    - environment:
+       USE_CONFIG: no
+    - container:
+       memory: 2G
+      environment:
+       USE_CONFIG: yes
+       CFLAGS: -g -Wall -O3 -fsanitize=address
+       LDFLAGS: -fsanitize=address -Wl,-rpath,`pwd`/inst/lib
+
+  # NB: we could consider building a docker image with these
+  # preinstalled and specifying that instead, to speed up testing.
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends \
+        ca-certificates clang git autoconf automake  \
+        make zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev   \
+        libssl-dev libdeflate-dev libncurses5-dev
+
+  << : *COMPILE
+  << : *TEST
+
+
+# CentOS
+centos_task:
+  name: centos-gcc
+  container:
+    image: centos:latest
+    cpu: 2
+    memory: 1G
+
+  environment:
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    HTSDIR: ./htslib
+    USE_CONFIG: yes
+
+  # NB: we could consider building a docker image with these
+  # preinstalled and specifying that instead, to speed up testing.
+  install_script: |
+    yum install -y autoconf automake make gcc perl-Data-Dumper zlib-devel \
+        bzip2 bzip2-devel xz-devel curl-devel openssl-devel ncurses-devel \
+        git diffutils
+
+  << : *COMPILE
+  << : *TEST
+
+
+#--------------------------------------------------
+# Task: macOS builds
+
+macosx_task:
+  name: macosx + clang
+  osx_instance:
+    image: catalina-base
+
+  environment:
+    CC: clang
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    HTSDIR: ./htslib
+
+  matrix:
+    - environment:
+       USE_CONFIG: no
+    - environment:
+       USE_CONFIG: yes
+
+  package_install_script:
+    - HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz
+
+  << : *COMPILE
+  << : *TEST

.gitattributes

@@ -5,6 +5,8 @@
 *.bam           -text diff=bam
 
 # Omit these files from release tarballs.
+/.appveyor.yml  export-ignore
+/.cirrus.yml    export-ignore
 .git*           export-ignore
-.travis*        export-ignore
+.ci_helpers     export-ignore
 README.md       export-ignore

.gitignore

@@ -24,6 +24,7 @@ configure
 
 /TAGS
 
+test/*.fa.fai
 test/vkrs.unsorted.hex
 test/rsvk.unsorted.hex
 test/nrvk.unsorted.tsv

INSTALL

@@ -3,7 +3,7 @@ For the impatient
 
 The latest source code can be downloaded from github and compiled using:
 
-    git clone git://github.com/samtools/htslib.git
+    git clone --recurse-submodules git://github.com/samtools/htslib.git
     git clone git://github.com/samtools/bcftools.git
     cd bcftools
      # The following is optional: