.travis.yml

language: bash
sudo: required

services:
  - docker

before_install:
  - docker pull brettbj/continuous_analysis_base
  - docker run --name con_test -t -d brettbj/continuous_analysis_base bin/bash
  - docker cp test.py con_test:test.py
  - docker cp simple_script.py con_test:simple_script.py
  - docker cp Travis_Plotting.ipynb con_test:Travis_Plotting.ipynb
  - docker exec con_test mkdir travis-ci

script:
  - ls
  - pwd
  - docker exec con_test pwd

  #Run tests
  - docker exec con_test nose2 --plugin nose2.plugins.junitxml --junit-xml test
  - docker exec con_test mv nose2-junit.xml travis-ci/tests.xml
  - docker exec con_test coverage run --branch test.py
  - docker exec con_test coverage xml -o travis-ci/coverage.xml test.py
  
  #Run kallisto
  - docker exec con_test kallisto index -i kallisto/test/transcripts.idx kallisto/test/transcripts.fasta.gz
  - docker exec con_test kallisto quant -i kallisto/test/transcripts.idx -o kallisto/test/output -b 100 kallisto/test/reads_1.fastq.gz kallisto/test/reads_2.fastq.gz
  
  #Gather output
  - docker exec con_test mv kallisto/test/output travis-ci/output
  
  #Plot results from a jupyter notebook
  - docker exec con_test jupyter nbconvert --to html --execute Travis_Plotting.ipynb

  #Copy output out of container
  - docker cp con_test:/travis-ci travis-ci
  
  #Push 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 travis-ci/.
  - git commit -a -m "Travis-CI output [CI SKIP] [SKIP CI] ."
  - git stash 
  - git push
  
after_success:
  - docker build -t brettbj/continuous_analysis .
  - docker push brettbj/continuous_analysis:latest