shippable.yml

language: python
notifications:
   email: false
archive: true

env:
  - secure: bMjk/u1ANHX7uJIPU5ZwKseWuftRdu6rmmUvmf0/dCnb1k3IiHSHP0Wv0ESf9JiNtzRxo1V+nzTpWwDL64hC4cuBHj7sOtBPnBqiDCDuE3mq5tVKDVQSo2og3O+j/0o2PsvFhAP0hzOzM2QXLCtgb6NQTemAEhsNCpMBCKepddpfD7ZN1xRcagZLUTmsBYO9+r95Z10/6pw8PI2wCTa22gSd49+bqMo96NpUEFgyaVZS9Lo+EOlcgS+8aCfbpyXDDL+ls/3TE0FaYTRRtuOCGuHNIItrrnrMmiUFpqCuJaVDVaKbJPK+Wk2EnioJUQPoc6BgI5enqIiJjpV2VEDp5Q==

build:
  pre_ci_boot:
      image_name: brettbj/continuous_analysis_base
      image_tag: latest
      pull: true
      options: "-e HOME=/root"

  ci:
    - cd /root/src/github.com/greenelab/continuous_analysis
    - nose2 --plugin nose2.plugins.junitxml --junit-xml test 
    - mv nose2-junit.xml shippable/testresults/tests.xml
    - coverage run --branch test.py
    - coverage xml -o shippable/codecoverage/coverage.xml test.py

    # run kallisto on a few simple tests
    - cd /kallisto/test
    - kallisto index -i transcripts.idx transcripts.fasta.gz
    - kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
    - cp -R /kallisto/test/output /root/src/github.com/greenelab/continuous_analysis/shippable/output

    # plot the results from a jupyter notebook
    - cd /root/src/github.com/greenelab/continuous_analysis
    - jupyter nbconvert --to html --execute ./Shippable_Plotting.ipynb

    # push the results back to github
    - git config user.email "brettbj@gmail.com"
    - git config user.name "Brett Beaulieu-Jones"
    - git config --global push.default simple
    - git remote set-url origin https://brettbj:$git_publish_key@github.com/greenelab/continuous_analysis.git

    - git checkout master
    - git pull
    - git add shippable/.
    - git commit -a -m "Shippable output [CI SKIP] [SKIP CI] ."
    - git stash
    - git push

  post_ci:
    - docker build -t brettbj/continuous_analysis .
    - docker push brettbj/continuous_analysis:latest

integrations:
  hub:
    - integrationName: brettbj/continuous_analysis
      type: docker