Pipeline for submitting solubility simulations. Bonus output may include Unsaturated Mayer Bond Order amongst other things.

Currently installation involves first installing clancelot:

[user@local]~% cd ~; git clone git@github.com:clancylab/clancelot2.0.git

And then cloning this project:

[user@local]~% cd ~; git clone git@github.com:hherbol/frazier-pipeline.git

Note, you'll also have to append the frazier-pipeline/pys folder to your PYTHONPATH variable.

[user@local]~% echo '\nexport PYTHONPATH="/PATH/TO/FRAZIER/PIPELINE/pys:$PYTHONPATH"' >> ~/.zshrc

Documentation is necessary, and the following steps MUST be followed during contribution of new code:

Setup

1. Download Sphinx. This can be done simply if you have pip installed via pip install -U Sphinx
2. Wherever you have frazier-pipeline installed, you want another folder called frazier-pipeline-docs (NOT as a subfolder of frazier-pipeline).

[user@local]~% cd ~; mkdir frazier-pipeline-docs; cd frazier-pipeline-docs; git clone -b gh-pages git@github.com:hherbol/frazier-pipeline.git html

3. Forever more just ignore that directory (don't delete it though)

Adding Documentation

Documentation is done using ReStructuredText format docstrings, the Sphinx python package, and indices with autodoc extensions. To add more documentation, first add the file to be included in docs/source/conf.py under os.path.abspath('example/dir/to/script.py'). Secondly, ensure that you have proper docstrings in the python file, and finally run make full to re-generate the documentation and commit it to your local branch, as well as the git gh-pages branch.

For anymore information on documentation, here is a link to the followed sphinx_tutorial.