config.yml

# Use the latest 2.1 version of CircleCI pipeline process engine.

# See: https://circleci.com/docs/2.0/configuration-reference
version: 2.1
# Define a job to be invoked later in a workflow.
# See: https://circleci.com/docs/2.0/configuration-reference/#jobs

jobs:
  build_and_test:
    # Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
    # See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
    docker:
      - image: condaforge/mambaforge:latest
    # Add steps to the job
    # See: https://circleci.com/docs/2.0/configuration-reference/#steps
    steps:
      - add_ssh_keys:
          fingerprints:
            - "82:36:a6:28:7b:85:be:1e:52:91:f1:6f:3a:4b:b5:d6"
      - checkout
      - run:
          name: build_and_test_python
          command: |
            mamba install -c bioconda -c conda-forge -y curl gnupg pytest-cov pytest-lazy-fixture pandas snakemake
            pytest --cov=workflow/scripts --cov=lib workflow/scripts lib
            curl -Os https://uploader.codecov.io/latest/linux/codecov
            chmod +x codecov
            ./codecov -R . -c -F python
      - run:
          name: build_and_test_r
          command: |
            mamba install -c https://raw.githubusercontent.com/lightning-auriga/conda-builds/default/conda-builds -c conda-forge -c bioconda -y curl gnupg r-covr r-testthat r-ggplot2 r-stringr r-sveval r-jsonlite sed
            Rscript ./run_tests.R | sed 's|name":"|name":"workflow/scripts/|g' | tail -n 1 > r_coverage.json
            curl -Os https://uploader.codecov.io/latest/linux/codecov
            chmod +x codecov
            ./codecov -R . -c -f r_coverage.json -F r


# Invoke jobs via workflows
# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
workflows:
  ci:
    jobs:
      - build_and_test