Tools and software library developed by the ONT Applications group

Installation

Set up a virtual environment

virtualenv  --system-site-packages wub_env
source wub_env/bin/activate
pip install --upgrade pip
pip install requests[security]

Then install the package via pip:

pip install git+https://github.com/nanoporetech/wub.git

If you installed the package in a virtual environment then do not forget to load it before using the package:

source wub_env/bin/activate

Run the following to leave the virtual environment:

deactivate

You can also clone the repository and install using setup.py:

git clone https://github.com/nanoporetech/wub.git
cd wub
python setup.py install

Install the package in developer mode:

python setup.py develop

Run the tests:

make test

Build the documentation:

make docs

Issue make help to get a list of make targets.

Documentation

Online documentation is avalaible at wub.readthedocs.io.

Contributing

• Please fork the repository and create a merge request to contribute.
• Please respect the structure outlined in scripts/_template_script.py from command line tools so documentation can be generated automatically.
• All non-trivial functions should have at least one test (with the exception of plotting functions).
• Use your best judgement when deciding whether to put a piece of code in a script or make it more reusable by incorporating it into the module.
• Use bumpversion to manage package versioning.
• The code should be PEP8 compliant, which can be tested by make lint.

TODO