<commit_before>box: brettbj/continuous_analysis_base
build:
  steps:
    - script:
        name: Run Tests + Coverage
        code: |
          pwd
          nose2 --plugin nose2.plugins.junitxml --junit-xml test 
          mkdir wercker
          mv nose2-junit.xml wercker/tests.xml
          coverage run --branch test.py
          coverage xml -o wercker/coverage.xml test.py<commit_msg>wercker start<commit_after>box: brettbj/continuous_analysis_base
build:
  steps:
    - script:
        name: Run Tests + Coverage
        code: |
          nose2 --plugin nose2.plugins.junitxml --junit-xml test 
          mkdir wercker
          mv nose2-junit.xml wercker/tests.xml
          coverage run --branch test.py
          coverage xml -o wercker/coverage.xml test.py
    
    - script:
        name: Run Kallisto
        code: |
          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

    - script:
        name: Plot Results
        code: |
          cd /pipeline/source
          jupyter nbconvert --to html --execute ./Wercker_Plotting.ipynb

    - script:
        name: Push Results back to github
        code: |
          git config user.email "<EMAIL>"
          git config user.name "<NAME>"
          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
{'fraction_non_alphanumeric': 0.08207705192629816, 'fraction_numerical': 0.006141820212171971, 'mean_word_length': 1.8087774294670846, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 1, 'lorem ipsum': 0, 'www.': 0, 'xml': 12}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '167717', 'n_tokens_mistral': 547, 'n_tokens_neox': 522, 'n_words': 146}