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Reproducibility with CI

Circle CI

Instructions for Reproducing Analysis

  1. Fork repo
  2. Sign up for circle.ci, meaning that you should authenticate to allow Circle.ci to access your github, select your user or organization, and then select the newly forked repo and click "build."

Details

  1. Custom python setup commands go in config.py
  2. All anayses go in "analysis" folder and must start with "test"
  3. Output should go into "output folder"

Notes

  • The repo should have a python module that handles setting things up. This would include:
    • download functions and specified locations for the user to look for the data
    • functions to "initialize" a repo (put it into the correct format)
  • we can possibly set up an interactive browser to connect to (circle.ci uses selenium via xvfb)
  • pushing content back to gh-pages? Would require authentication, likely one step too much.
  • Circle.ci will "time out" if there is no output >10 minutes (something to keep in mind)
  • There should be a nice way to direct user to output interface, keep updated wrt timing, etc.

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