Python Boilerplate contains all the boilerplate you need to create a Python NDEx Content Loader package.
- Free software: BSD license
- Documentation: https://ndexctdloader.readthedocs.io.
- ndexloadctd.py -- Loads CTD into NDEx
- Python 3.3+
git clone https://github.com/jingjingbic/ndexctdloader cd ndexctdloader make dist pip install dist/ndexloadctd*whl
Run make command with no arguments to see other build/deploy options including creation of Docker image
make
Output:
clean remove all build, test, coverage and Python artifacts clean-build remove build artifacts clean-pyc remove Python file artifacts clean-test remove test and coverage artifacts lint check style with flake8 test run tests quickly with the default Python test-all run tests on every Python version with tox coverage check code coverage quickly with the default Python docs generate Sphinx HTML documentation, including API docs servedocs compile the docs watching for changes testrelease package and upload a TEST release release package and upload a release dist builds source and wheel package install install the package to the active Python's site-packages dockerbuild build docker image and store in local repository dockerpush push image to dockerhub
The ndexloadctd.py requires a configuration file in the following format be created.
The default path for this configuration is ~/.ndexutils.conf but can be overridden with
--conf flag.
Format of configuration file
[<value in --profile (default ndexctdloader)>] user = <NDEx username> password = <NDEx password> server = <NDEx server(omit http) ie public.ndexbio.org> style = <NDEx UUID of network to use for styling networks created>
The NDEx UUID needed for style can be obtained by uploading the style.cx file found under
the data/ directory of this repository. NOTE: The network needs to be uploaded to the same
server as defined in style public.ndexbio.org is NDEx production. Also the network needs
to be visible to the user
Example configuration file
[ndexctdloader_dev] user = joe123 password = somepassword123 server = dev.ndexbio.org style = 86f63bf8-1b48-11e9-a05d-525400c25d22
TODO: Add description of needed files
For information invoke ndexloadctd.py -h
Example usage
TODO: Add information about example usage
ndexloadctd.py # TODO Add other needed arguments here
Example usage
TODO: Add information about example usage
docker run -v `pwd`:`pwd` -w `pwd` jingjingbic/ndexctdloader:0.1.0 ndexloadctd.py --conf conf # TODO Add other needed arguments here
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.