.cirrus.yml

# 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: |
    # Tricky, but when run as a PR Cirrus-CI obscures the branch name and
    # replaces it by pull/<num>.  This means we can't automatically get PRs
    # to test whether the user has a similarly named branch to compiler and
    # test against.
    #
    # Instead if we add htslib#NUM into the first line of the commit then
    # we will use that PR from htslib instead.  This is only needed when
    # making a PR, so for development prior to the PR being made the
    # CIRRUS_BRANCH will be used in preference.
    .ci_helpers/clone ${CIRRUS_REPO_OWNER} htslib "${HTSDIR}" "${CIRRUS_BRANCH}" `printenv CIRRUS_CHANGE_TITLE | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`

#--------------------------------------------------
# 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 $CONFIG_OPTS \
           ${CC:+CC="$CC"} \
           ${CFLAGS:+CFLAGS="$CFLAGS"} \
           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
           ${LDFLAGS:+LDFLAGS="$LDFLAGS"} \
         || (cat config.log; /bin/false)
      make -j3
    else
      make -j3 plugindir="$CIRRUS_WORKING_DIR/plugins" \
           ${HTSDIR:+HTSDIR="$HTSDIR"} \
           ${CC:+CC="$CC"} \
           ${CFLAGS:+CFLAGS="$CFLAGS"} \
           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
    fi

test_template: &TEST
  test_script: |
    if test "$USE_CONFIG" = "yes"; then
        make test
    else
        make test  \
           ${HTSDIR:+HTSDIR="$HTSDIR"} \
           ${CC:+CC="$CC"} \
           ${CFLAGS:+CFLAGS="$CFLAGS"} \
           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
    fi

#--------------------------------------------------
# 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
       CFLAGS:  -g -Og -Wall -Werror -fsanitize=address
       LDFLAGS: -fsanitize=address
    - environment:
       USE_CONFIG: yes
       CONFIG_OPTS: --enable-libgsl --enable-perl-filters 
       CFLAGS: -std=gnu99 -g -Og -Wall -fsanitize=address
       LDFLAGS: -fsanitize=address

  install_script: |
    apt-get update
    apt-get install -y --no-install-suggests --no-install-recommends \
        libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl


  << : *COMPILE
  << : *TEST


# Ubuntu + Clang
ubuntu_task:
  name: ubuntu-clang
  container:
    image: ubuntu:latest
    cpu: 2
    memory: 1G

  environment:
    CC: clang
    LC_ALL: C
    CIRRUS_CLONE_DEPTH: 1
    HTSDIR: ./htslib

  matrix:
    - environment:
       USE_CONFIG: no
       CFLAGS: -g -O2 -Werror -Wall -Wformat -Wformat=2
    - container:
       memory: 2G
      environment:
       USE_CONFIG: yes
       CONFIG_OPTS: --enable-libgsl --enable-perl-filters
       CFLAGS: -g -Wall -O3
       LDFLAGS: -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 libperl-dev libgsl0-dev libio-pty-perl

  << : *COMPILE
  << : *TEST


# Rocky Linux
rockylinux_task:
  name: rockylinux-gcc
  container:
    image: rockylinux:9
    cpu: 2
    memory: 1G

  environment:
    LC_ALL: C
    CIRRUS_CLONE_DEPTH: 1
    HTSDIR: ./htslib
    USE_CONFIG: yes
    CONFIG_OPTS: --enable-libgsl --enable-perl-filters

  # 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 perl-FindBin \
        zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel \
        git diffutils gsl-devel perl-ExtUtils-Embed

  << : *COMPILE
  << : *TEST


#--------------------------------------------------
# Task: macOS builds

macosx_task:
  name: macosx + clang
  macos_instance:
    image: ghcr.io/cirruslabs/macos-runner:sonoma

  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