.travis.yml

sudo: required
language: python
jdk: openjdk8
python:
  - '2.7'
  - '3.5'
  - '3.6'
  - '3.7'
before_install:
  # PRs to master are only ok if coming from dev branch
  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
  # Check that the changelog has been updated if this is a PR
  - git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*" && git fetch
  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $(git diff --name-only HEAD origin/${TRAVIS_BRANCH} | grep CHANGELOG.md | wc -l) -ge 1 ]'
install:
  # Install Nextflow
  - mkdir /tmp/nextflow
  - cd /tmp/nextflow
  - wget -qO- get.nextflow.io | bash
  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
  # Set up nf-core and test/coverage modules
  - cd ${TRAVIS_BUILD_DIR}
  - pip install --upgrade pip # Get rid of dependency resolve issues from older pip versions
  - pip install .
  - pip install codecov 'pytest==3.6.4' pytest-datafiles pytest-cov mock jsonschema
  - pip install Sphinx sphinxcontrib-napoleon # For autodoc generation
  - sudo apt-get install npm && npm install -g markdownlint-cli # For documentation linting

script:
  # Test the main code in this repo
  - pytest --cov=nf_core .
  - markdownlint . -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
  # Test the pipeline template code
  - nf-core create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
  - nf-core lint nf-core-testpipeline
  - markdownlint nf-core-testpipeline -c nf-core-testpipeline/.github/markdownlint.yml

after_success:
  - codecov --rcfile=${TRAVIS_BUILD_DIR}/.github/coveragerc

jobs:
  include:
    - stage: docs generation
      if: (branch = "master" OR branch = "dev") AND type = push AND repo = nf-core/tools
      script: bash ./bin/push.sh

deploy:
  provider: pypi
  user: "ewels"
  password:
    secure: "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"
  on:
    tags: true
    distributions: sdist bdist_wheel
    repo: nf-core/tools
    python: '3.6'

# Sync pipelines with possible nf-core template changes
after_deploy:
  - ./bin/sync