.gitlab-ci.yml

image: $IMAGE

stages:
    - test
    - build
    - deploy

variables:
    DOCKERTAG: "medaka/medaka:latest"


# Install a particular Python and set PYTHON envvar for Makefile 
.install-pyenv: &install-pyenv |
    git clone https://github.com/pyenv/pyenv.git ~/.pyenv
    export PYENV_ROOT="$HOME/.pyenv"
    export PATH="$PYENV_ROOT/bin:$PATH"
    PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install ${PYENV_VERSION}
    export PYTHON=$(PYENV_VERSION=$PYENV_VERSION pyenv which python)

.preparetest: &preparetest
    stage: test
    before_script:
        - export DEBIAN_FRONTEND=noninteractive
        - apt-get update -qq
        - apt-get install -y -qq 
          gcc make cmake curl wget git
          zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libcurl4-gnutls-dev
          libssl-dev libffi-dev valgrind
          libreadline7 libreadline-dev sqlite3 libsqlite3-dev
        - *install-pyenv


.minimal-python: &minimal-python
    before_script:
        - export DEBIAN_FRONTEND=noninteractive
        - apt-get update -qq && apt-get install -y -qq
          python3-all-dev python3-venv


# medaka test suite on various Pythons
.pytest: &pytest
    <<: *preparetest
    script:
        - make test

test-3.7.9:
    variables:
        PYENV_VERSION: 3.7.9
    <<: *pytest

test-3.8.7:
    variables:
        PYENV_VERSION: 3.8.7
    <<: *pytest


test-3.9.9:
    variables:
        PYENV_VERSION: 3.9.9
    <<: *pytest


test-mem-check:
    variables:
        PYENV_VERSION: 3.8.7
    <<: *preparetest
    script:
        - make mem_check

test-docker:
    image: ${DOCKERDEV_IMAGE} 
    stage: test
    script:
        - apk --no-cache add make
        - DOCKERTAG=$DOCKERTAG make docker
        - docker run --rm -v $PWD:/data $DOCKERTAG medaka_consensus -x -i /data/medaka/test/data/test_reads.fasta.gz -d /data/medaka/test/data/draft_ref.fasta -o /data/dockertest

###
# Source distribution
#

build:sdist:
    stage: build
    <<: *minimal-python
    script:
        - make sdist
    artifacts:
        paths:
            - dist/*.tar.gz

###
# Many linux builds
#

.many-linux: &many-linux-def
  image: quay.io/pypa/manylinux2010_x86_64
  stage: build
  variables:
      DO_COUNT_TEST: 1
  artifacts:
      paths:
          - wheelhouse/*.whl
  only:
      - tags

.switch-to-cpu: &switch-to-cpu
    before_script:
        - export PACKAGE_NAME=medaka-cpu
        - export MEDAKA_CPU=1
        # this is still required, because otherwise test in build-wheel
        # will first install tensorflow, then try to install tensorflow-cpu
        # and complain
        - sed -i 's/tensorflow/tensorflow-cpu/' requirements.txt

### Tensorflow (gpu) builds

gpu:many-linux-7:
    <<: *many-linux-def
    script:
        - ./build-wheels.sh . 7

gpu:many-linux-8:
    <<: *many-linux-def
    script:
        - ./build-wheels.sh . 8

gpu:many-linux-9:
    <<: *many-linux-def
    script:
        - ./build-wheels.sh . 9

gpu:many-linux-8:branch:
    extends: gpu:many-linux-8
    only:
        - branches

### Tensorflow-cpu wheels

cpu:many-linux-7:
    <<: *many-linux-def
    <<: *switch-to-cpu
    script:
        - ./build-wheels.sh . 7

cpu:many-linux-8:
    <<: *many-linux-def
    <<: *switch-to-cpu
    script:
        - ./build-wheels.sh . 8

cpu:many-linux-9:
    <<: *many-linux-def
    <<: *switch-to-cpu
    script:
        - ./build-wheels.sh . 9

###
# ARM builds
#

.arm-many-linux: &arm-many-linux-def
    image: quay.io/pypa/manylinux2014_aarch64
    stage: build
    tags:
        - arm64
    variables:
        DO_COUNT_TEST: 0
    before_script:
        # ARM CI image doesn't have git lfs, so need to jump some hoops
        - yum install -y wget
        - mkdir git-lfs && cd git-lfs
          && wget https://github.com/git-lfs/git-lfs/releases/download/v2.12.0/git-lfs-linux-arm64-v2.12.0.tar.gz
          && tar -xzvf git-lfs-linux-arm64-v2.12.0.tar.gz
          && chmod +x install.sh && ./install.sh
          && cd ..
        - GIT_SSL_NO_VERIFY=1 git lfs pull
    artifacts:
        paths:
          - wheelhouse/*.whl
    only:
        - tags


arm-many-linux-7:
    <<: *arm-many-linux-def
    script:
        - ./build-wheels.sh . 7

arm-many-linux-8:
    <<: *arm-many-linux-def
    script:
        - ./build-wheels.sh . 8

arm-many-linux-9:
    <<: *arm-many-linux-def
    script:
        - ./build-wheels.sh . 9

arm-many-linux:branch:
    extends: arm-many-linux-8
    only:
        - branches

###
# Deploy stages
#

# Send all tags to PyPI
deploy:pypi:
    stage: deploy
    <<: *minimal-python
    script:
        - make pypi_build/bin/activate
        - source pypi_build/bin/activate
        - twine upload dist/*.tar.gz wheelhouse/*.whl
    only:
        - tags


.setup-gh-push:
    before_script:
        - apt-get update -qq && apt-get install -y -qq
          git python3-all-dev python3-venv git-lfs
        - mkdir ~/.ssh/
        - cp $RESEARCH_BOT_GH_KEY ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
        - echo -e "Host github.com\n\tStrictHostKeyChecking no\n\tHostname ssh.github.com\n\tPort 443\n\n" > ~/.ssh/config
        - git config --global user.email "research.git@nanoporetech.com"
        - git config --global user.name "ontresearch"
        - git remote add ont ${CI_REPOSITORY_URL} || true
        - git remote add github git@github.com:nanoporetech/${CI_PROJECT_NAME}.git || true
        - git fetch ont dev --tags

# Send all tags matching vX.Y.Z to github (code and release)
push-github:
    stage: deploy
    extends: .setup-gh-push
    script:
        # Push master and tag to github
        - git checkout ${CI_COMMIT_TAG}
        - git branch -D master || echo "No master branch to delete"
        - git checkout -b master
        - git push -f github master
        - git push github ${CI_COMMIT_TAG}
        # Make a github release page
        - python3 -m venv release_env --prompt "(release) "
        - source release_env/bin/activate
        - pip install pip --upgrade
        - pip install git+https://github.com/epi2me-labs/github_release.git
        - github_release ${CI_PROJECT_NAME} ${CI_COMMIT_TAG} CHANGELOG.md ${RESEARCH_BOT_GH_TOKEN} --artifacts dist/*.tar.gz
    rules:
        - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'

push-dockerhub:
    image: ${DOCKERDEV_IMAGE} 
    stage: deploy
    script:
        - apk --no-cache add make
        - echo ${DOCKERHUB_TOKEN} | docker login --username ${DOCKERHUB_USER} --password-stdin
        - DOCKERTAG=$DOCKERTAG make docker
        - LATEST="ontresearch/medaka:latest"
        - TAG="ontresearch/medaka:$CI_COMMIT_TAG"
        - docker tag $DOCKERTAG $LATEST 
        - docker tag $DOCKERTAG $TAG
        - docker push ${LATEST}
        - docker push ${TAG}
    rules:
        - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'