partis 0.0.3

Top-level namespace package for partis packages

Readme for partis

Utilities for defining and validating schemas for YAML/JSON compatible data, and for configuring and running programs/workflows using the domain specific Nano Workflow Language (NWL).

Installation

Compatible with Python >= 3.6, pip >= 18.1.

For full install of core API, docs, runtime utilities, and GUI application:

python3 make_dists.py
pip3 install --find-links ./dist partis

To install only a particular set of sub-component(s), such as the nwl command-line runner:

pip3 install --find-links ./dist partis-pyproj
pip3 install --find-links ./dist partis-utils
pip3 install --find-links ./dist partis-schema
pip3 install --find-links ./dist partis-nwl

Note that unless distributions have already been generated and made available to pip, these must be done in the above order.

Building the Documentation

The doc folder is made as a runnable python module to conveniently build documentation. By default, html documentation will be generated in a build directory.

pip3 install --find-links ./dist '.[doc]'
python -m doc

Note

Any changes to source-code will not be reflected until the package is rebuilt.

Running the Tests

The test folder is made as a runnable python module to conveniently run automated test suite.

To test the GUI, Xvfb must also be installed on the system to create a virtual display in order to run the Qt application without displaying windows. If Xvfb is not found those tests will be skipped.

To test multiple versions of python, they must all be discoverable within the PATH environment variable. The tests configured for versions of python that cannot be found will be skipped. For example, if the python installations are being managed with the Environment Modules convention:

module load python/3.6.2
module load python/3.7.0
module load python/3.8.0
module load python/3.9.0

It is highly recommended to install package and dependencies within a virtual environment to isolate the effects of any changes it may cause.

pip install --find-links ./dist '.[test]'
python -m test

Development

pre-commit

Before committing any changes to this repo, please install pre-commit and hooks.

pip install pre-commit
pre-commit install
pre-commit run --all-files

A convenience script runme.py is placed in the root directory to perform this action, and needs to be run only once.

Note

The pre-commit program is installed as a Python package. If a virtual environment is used during development, ensure that pre-commit is installed in the environment active at the time of any commit.