.gitlab-ci.yml

# This file is a template, and might need editing before it works on your project.
# To contribute improvements to CI/CD templates, please follow the Development guide at:
# https://docs.gitlab.com/ee/development/cicd/templates.html
# This specific template is located at:
# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/C++.gitlab-ci.yml

# use the official gcc image, based on debian
# can use verions as well, like gcc:5.2
# see https://hub.docker.com/_/gcc/

image: lightning-auriga/snakemake-gcc

stages:
  - build_and_test

workflow:
  rules:
    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH

build:
  stage: build_and_test
  # instead of calling g++ directly you can also use some build toolkit like make
  # install the necessary build tools when needed
  script:
    - ./generate.bash
    - ./configure --with-boost=$CONDA_PREFIX --with-boost-libdir=$CONDA_PREFIX/lib
    - make -j2 CXXFLAGS=" --coverage -fprofile-arcs -ftest-coverage -fPIC "
    - ./imputed-data-dynamic-threshold.out -h
    - ./test-suite.out
    - $CONDA_PREFIX/bin/x86_64-conda-linux-gnu-gcov -r $(find imputed-data-dynamic-threshold \( -name "*gcda" -and -not -iname "*test*" \) -print | sed 's/gcda/cc/g') | tail -n 1
  coverage: '/Lines executed:\d+\.?\d*% of .*/'