.disabled-travis.yml

version: ~> 1.0
language: generic
group: travis_latest

# Only build for develop and master (and PRs)
branches:
  only:
    - master
    - develop

os:
  linux

env:
  global:
    - secure: "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"
    - GH_DOC_BRANCH=develop
    - GH_REPOSITORY=github.com/MDAnalysis/mdanalysis.git
    - GIT_CI_USER=TravisCI
    - GIT_CI_EMAIL=TravisCI@mdanalysis.org
    - MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html
    - MAINTAIN_DIR=${TRAVIS_BUILD_DIR}/maintainer
    # Set default python version to avoid repetition later
    - PYTHON_VERSION=3.6
    - BUILD_DOCS=false
    - CODECOV=false
    - PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
    - PYTEST_LIST="testsuite/MDAnalysisTests"
    - MAIN_CMD="pytest ${PYTEST_LIST}"
    - SETUP_CMD="${PYTEST_FLAGS}"
    - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
    - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py openmm"
    - CONDA_CHANNELS='biobuilds conda-forge'
    - CONDA_CHANNEL_PRIORITY=True
    - PIP_DEPENDENCIES="duecredit parmed"
    - NUMPY_VERSION=stable
    - INSTALL_HOLE="true"
    - CYTHON_TRACE_NOGIL=1
    - MPLBACKEND=agg
    - MAMBA=true

  matrix:
    # Run a coverage test for most versions
    - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
    - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" 
    - PYTHON_VERSION=3.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
    - NUMPY_VERSION=1.16.0
    - NUMPY_VERSION=dev  EVENT_TYPE="cron"

matrix:
  fast_finish: true
  include:
    - env: NAME="Doc"
           MAIN_CMD="cd package && python setup.py"
           SETUP_CMD="build_sphinx"
           PYTHON_VERSION=3.7
           BUILD_DOCS=true
           BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
           INSTALL_HOLE="false"
           PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0"

    - env: NAME="Lint"
           PYLINTRC="${TRAVIS_BUILD_DIR}/package/.pylintrc"
           MAIN_CMD="pylint --py3k package/MDAnalysis && pylint --py3k testsuite/MDAnalysisTests"
           SETUP_CMD=""
           BUILD_CMD=""
           CONDA_DEPENDENCIES=""
           INSTALL_HOLE="false"

    - env: NAME="asv check"
           PYTHON_VERSION=3.6
           CODECOV="false"
           MAIN_CMD=""
           SETUP_CMD=""
           PIP_DEPENDENCIES="${PIP_DEPENDENCIES} setuptools<45.0.0"
           ASV_CHECK="true"

    - env: NAME="pypi check"
           PYTHON_VERSION=3.7
           CODECOV="false"
           MAIN_CMD="cd package && python setup.py"
           SETUP_CMD="sdist"
           BUILD_CMD=""
           INSTALL_HOLE="false"
           CONDA_DEPENDENCIES="setuptools cython twine"
           PYPI_CHECK="true"

    - os: osx
      env: PYTHON_VERSION=3.6
           NUMPY_VERSION=1.17.3

    - env: NAME='minimal'
           PIP_DEPENDENCIES=""
           CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}
           INSTALL_HOLE="false"
           CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"

    - os: linux
      language: python
      arch: arm64-graviton2
      python:
        - "3.7"
      dist: focal
      virt: vm
      group: edge
      before_install:
        - python -m pip install cython numpy scipy
        - python -m pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm
      install:
        - cd package
        - python setup.py install
        - cd ../testsuite
        - python setup.py install
        - cd ..
      script:
        - cd testsuite
        - python -m pytest ./MDAnalysisTests --disable-pytest-warnings -n 8 -rsx --cov=MDAnalysis
      after_success:
        - echo "Override this stage for ARM64"

  allow_failures:
    - env: NUMPY_VERSION=dev EVENT_TYPE="cron"

before_install:
  # Workaround for Travis CI macOS bug (https://github.com/travis-ci/travis-ci/issues/6307)
  # See https://github.com/searchivarius/nmslib/pull/259
  - |
     if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
        command curl -sSL https://rvm.io/mpapis.asc | gpg --import -;
        rvm get head || true
     fi

install:
  # download hole first to use system curl
  # additional external tools (Issue #898) -- HOLE
  - |
    if [[ $INSTALL_HOLE == 'true' ]]; then \
        bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}"; \
        HOLE_BINDIR="${HOME}/hole2/exe"; \
        export PATH=${PATH}:${HOLE_BINDIR}; \
    fi
  - git clone git://github.com/astropy/ci-helpers.git
  - source ci-helpers/travis/setup_conda.sh
  - eval $BUILD_CMD

script:
  - cd ${TRAVIS_BUILD_DIR}
  - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then ulimit -S -n 2048; fi
  - echo $MAIN_CMD $SETUP_CMD
  - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then pip install pytest; fi
  - eval $MAIN_CMD $SETUP_CMD
  # check benchmark suite for basic issues
  - |
    if [ "${ASV_CHECK}" == "true" ]; then
      python -m pip install asv
      cd testsuite
      python setup.py install
      cd ../benchmarks
      time python -m asv check -E existing
    fi
  # check pypi package build
  - |
    if [[ "${PYPI_CHECK}" == "true" ]]; then
       DISTRIBUTION=$(ls -t1 ${TRAVIS_BUILD_DIR}/package/dist/MDAnalysis-*.tar.gz | head -n 1)
       test -n "${DISTRIBUTION}" || { echo "no distribution package/dist/MDAnalysis-*.tar.gz found"; exit 1; }
       echo "twine check $DISTRIBUTION"
       twine check $DISTRIBUTION
    fi

after_success:
  - |
    if [[ $CODECOV == 'true' ]]; then \
      codecov; \
    fi

  # can't use test here since this leads to travis fails even though the build passes
  # turn off blocking as it causes large writes to stdout to fail
  # (see https://github.com/travis-ci/travis-ci/issues/4704)
  - |
    if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] ; then
      python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
      cd ${TRAVIS_BUILD_DIR}/package/MDAnalysis
      export GH_DOC_BRANCH=${TRAVIS_BRANCH}
      export VERSION=$(python -c "import version; print(version.__version__)")
      cd -
      bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs_via_travis.sh;
    fi