diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..97d329adf49f9a4ca2bdb89ebb33025746a91f25 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,32 @@ +name: Continuous integration + +on: + pull_request: + paths: + - "**.wdl" # Workflow files and task + - "**.yml" # Ci configuration, tests and docker images + - "!docs/**" + +defaults: + run: + # This is needed for miniconda, see: + # https://github.com/marketplace/actions/setup-miniconda#important + shell: bash -l {0} + +jobs: + lint: + runs-on: ubuntu-latest + name: Womtool validate and submodule up to date. + steps: + - uses: actions/checkout@v2.3.4 + with: + submodules: recursive + - name: install miniconda + uses: conda-incubator/setup-miniconda@v2.0.1 + with: + channels: conda-forge,bioconda,defaults + # Conda-incubator uses 'test' environment by default. + - name: install requirements + run: conda install -n test cromwell miniwdl wdl-aid + - name: run linting + run: bash scripts/biowdl_lint.sh \ No newline at end of file diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 3cf0681f99cb49f3646f41e962b16517ff417741..0000000000000000000000000000000000000000 --- a/.travis.yml +++ /dev/null @@ -1,23 +0,0 @@ -# We use conda to install cromwell. - -language: python - -python: - - 3.6 - -before_install: - # Install conda - - export MINICONDA=${HOME}/miniconda - - export PATH=${MINICONDA}/bin:${PATH} - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh - - bash miniconda.sh -b -f -p ${MINICONDA} - - conda config --set always_yes yes - - conda config --add channels defaults - - conda config --add channels bioconda - - conda config --add channels conda-forge - -install: - - conda install --file requirements-test.txt - -script: - - bash scripts/biowdl_lint.sh diff --git a/requirements-test.txt b/requirements-test.txt deleted file mode 100644 index 0b01d193d495c1b118f95461d22fe08a0c595354..0000000000000000000000000000000000000000 --- a/requirements-test.txt +++ /dev/null @@ -1,11 +0,0 @@ -# These are the programs used for testing these biowdl tasks. -# These requirements can be installed with conda with the bioconda channel -# activated. -# For more information on how to set up conda with bioconda channel see: -# http://bioconda.github.io/#install-conda -# This file can be installed with "conda install --file requirements-test.txt". - -cromwell -womtool -miniwdl -wdl-aid