.gitlab-ci.yml

image: "python:3.8"

#cache:
#  key:
#    files:
#      - poetry.lock
#    prefix: "${CI_JOB_NAME}"
#  paths:
#    - .venv

stages:
  - tests
  - deploy

.install-deps-template: &install-deps
  before_script:
    - pip install --upgrade pip virtualenv
    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | python - --version 1.1.8
    - export PATH="/root/.local/bin:$PATH"
    - poetry --version
    # Force a recent pip version inside the virtualenv
    - virtualenv .venv
    - .venv/bin/pip install --upgrade pip
    - poetry config virtualenvs.in-project true
    - poetry install -E all -E webserver
    # Install mmseqs2 SSE2 (the slowest version, for compatibility)
    - wget https://mmseqs.com/latest/mmseqs-linux-sse2.tar.gz; tar xvfz mmseqs-linux-sse2.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH

.test-template: &test
  <<: *install-deps
  variables:
    SKIP_NEGLECTED_EMBEDDER_TESTS: 1
    SKIP_AVX2_TESTS: 1
  stage: tests
  coverage: '/TOTAL.*\s(\d+\.\d+\%)/'
  script: poetry run pytest -v

python3.8:
  <<: *test
  image: python:3.8

python3.9:
  <<: *test
  image: python:3.9

# Those two are ran weekly to also run test the more expensive tests
python3.8-scheduled:
  <<: *install-deps
  stage: tests
  variables:
    SKIP_AVX2_TESTS: 1
  rules:
    - if: $CI_PIPELINE_SOURCE == "schedule"
  image: python:3.8
  script: poetry run pytest -v

python3.9-scheduled:
  <<: *install-deps
  stage: tests
  variables:
    SKIP_AVX2_TESTS: 1
  rules:
    - if: $CI_PIPELINE_SOURCE == "schedule"
  image: python:3.9
  script: poetry run pytest -v

docs:
  <<: *install-deps
  stage: deploy
  rules:
    - if: '$CI_COMMIT_BRANCH == "develop"'
      when: always
    - if: '$CI_COMMIT_TAG'
      when: always
  script:
    - . .venv/bin/activate
    - cd docs
    - make html
    # https://about.gitlab.com/blog/2017/11/02/automating-boring-git-operations-gitlab-ci/
    - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
    - eval $(ssh-agent -s)
    - ssh-add <(echo "$GIT_SSH_PRIV_KEY")
    - git config --global user.name "bio_embeddings"
    - git config --global user.email "support@bioembeddings.com"
    # https://stackoverflow.com/a/29380765/3549270
    - mkdir ~/.ssh
    - ssh-keyscan -t rsa github.com >> ~/.ssh/known_hosts
    - git clone git@github.com:sacdallago/bio_embeddings.git docs-branch
    - cd docs-branch
    - git checkout gh-pages
    # We want to have separate documentation for every release while updating develop with every commit
    # https://unix.stackexchange.com/a/412262/77322
    - cp -r ../_build/html/. ${CI_COMMIT_TAG:-develop}
    # Update the index page redirect to the latest tag
    - if [ -n "$CI_COMMIT_TAG" ]; then echo "<meta http-equiv=refresh content=0;url='$CI_COMMIT_TAG/'>" > index.html; fi
    # Update the "latest" redirect to the latest tag
    - if [ -n "$CI_COMMIT_TAG" ]; then rm latest && ln -s $CI_COMMIT_TAG latest; fi
    - git add .
    - git commit --allow-empty -m 'Upload docs'
    - git push

.setup-kaniko-template: &setup-kaniko
  rules:
    - if: '$CI_COMMIT_BRANCH == "develop"'
      when: always
    - if: '$CI_COMMIT_TAG'
      when: always
  image:
    name: gcr.io/kaniko-project/executor:debug
    entrypoint: [ "" ]
  before_script:
    - mkdir -p /kaniko/.docker
    - echo "{\"auths\":{\"ghcr.io\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json

docker-webserver-develop:
  <<: *setup-kaniko
  stage: deploy
  script:
    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/webserver/Dockerfile.webserver --destination ghcr.io/bioembeddings/webserver:${CI_COMMIT_TAG:-latest}

docker-worker-develop:
  <<: *setup-kaniko
  stage: deploy
  script:
    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/webserver/Dockerfile.worker --destination ghcr.io/bioembeddings/worker:${CI_COMMIT_TAG:-latest}

docker-bio_embeddings-develop:
  <<: *setup-kaniko
  stage: deploy
  script:
    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --destination ghcr.io/bioembeddings/bio_embeddings:${CI_COMMIT_TAG:-latest}

release-to-pypi:
  stage: deploy
  rules:
    - if: '$CI_COMMIT_TAG'
      when: always
  image: python:3.8
  script:
    - pip install --upgrade pip virtualenv
    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
    - source $HOME/.local/env
    - poetry --version
    - poetry publish --build -u __token__ -p $PYPI_TOKEN