Try applied bioinformatics runipynbs

  - pip install -r requirements.txt

  - pip install coverage

  - pip install coveralls

  - ./runipynbs.py

script:

  - nosetests --with-coverage --cover-package=autocnet

    on_start: never     

  email:

      recipients:

          - kberry@usgs.gov

          - dmlytle@usgs.gov

          - jwbacker@usgs.gov

          - krodriguez@usgs.gov

#          - kberry@usgs.gov

#          - dmlytle@usgs.gov

#          - jwbacker@usgs.gov

#          - krodriguez@usgs.gov

      on_success: always

      on_failure: always

#!/usr/bin/env python

# -----------------------------------------------------------------------------

# This work is licensed under the Creative Commons

# Attribution-NonCommercial-ShareAlike 4.0 International License. To view a

# copy of this license, visit

# http://creativecommons.org/licenses/by-nc-sa/4.0/.

# -----------------------------------------------------------------------------

import logging

import os

import sys

from runipy.notebook_runner import NotebookRunner, NotebookError

from IPython.nbformat.current import read

# Taken and modified from

# https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/blob/master/runipynbs.py

# See licenses/ directory for runipy license.

def main():

    log_format = '%(asctime)s %(message)s'

    log_datefmt = '%m/%d/%Y %I:%M:%S %p'

    ignore_dirs = ['.git', '.ipynb_checkpoints']

    logging.basicConfig(level=logging.DEBUG, format=log_format,

                        datefmt=log_datefmt)

    if len(sys.argv) > 1:

        start_path = sys.argv[1]

    else:

        start_path = '.'

    if not os.path.exists(start_path):

        logging.error("Directory or file '%s' does not exist.", start_path)

        sys.exit(1)

    if os.path.isfile(start_path):

        run_notebook(start_path)

    else:

        for root, dirs, files in os.walk(start_path):

            dirs.sort()

            for ignore_dir in ignore_dirs:

                if ignore_dir in dirs:

                    dirs.remove(ignore_dir)

            for name in sorted(files):

                if name.endswith('.ipynb'):

                    nbpath = os.path.normpath(os.path.join(root, name))

                    run_notebook(nbpath)

def run_notebook(nbpath):

    logging.info("Reading notebook '%s'", nbpath)

    with open(nbpath) as nbfile:

        notebook = read(nbfile, 'json')

    runner = NotebookRunner(notebook, mpl_inline=True)

    try:

        runner.run_notebook()

    except NotebookError:

        logging.error("An error occurred while executing notebook '%s'. "

                      "Exiting with nonzero exit status", nbpath)

        sys.exit(1)

if __name__ == '__main__':

    main()

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