tfbpmodeling

Documentation

See here for more complete documentation

Installation

This repo has not yet been added to PyPI. See the developer installation below.

Development

1. If you plan on making pull requests, fork the repo to your own github account

2. git clone the repo (possibly your fork)

   • If you cloned your fork, add the BrentLab repo as your upstream remote

     git remote add upstream https://github.com/BrentLab/tfbpmodeling.git

3. cd into your local repo

4. poetry install to install the dependencies. If you don't have poetry, see the poetry instructions below.

5. Install pre-commit hooks. If you do not have pre-commit, install it first. Then run:

   pre-commit install

When adding/refactoring code, please make sure that you do so in a feature branch that is branched from dev. Please keep your dev up to date by rebasing it onto main after pulling from upstream/main. Similarly, keep your feature branch up to date with dev by rebasing your dev branch onto upstream/dev, and then rebasing your feature branch onto dev. This will help avoid merge conflicts when you make a pull request.

When you are ready to make a pull request, please make sure that the pre-commit hooks all pass locally. You can run pre-commit manually (before committing) with:

pre-commit run --all-files

if you properly installed the pre-commit hooks, pre-commit will automatically run when you attempt to make a commit, also.

tmp/

There is a [tmp/] directory set up for exploratory data analysis and interactive development. See the tmp/README.md for more information. ipykernel is installed in the dev environment, so jupyter notebooks can be run from tmp/ in the virtual environment.

poetry

To install poetry, follow the instructions here.

I prefer setting the following configuration option so that virtual environments are installed in the project directory:

poetry config virtualenvs.in-project true

So that the virtual environments are installed in the project directory as .venv

After cloning and cding into the repo, you can install the dependencies with:

poetry install

mkdocs

The documentation is build with mkdocs:

Commands

• mkdocs new [dir-name] - Create a new project.
• mkdocs serve - Start the live-reloading docs server.
• mkdocs build - Build the documentation site.
• mkdocs -h - Print help message and exit.

Project layout

• mkdocs.yml # The configuration file.
• docs/
  • index.md # The documentation homepage.
  • ... # Other markdown pages, images and other files.

To update the gh-pages documentation, use poetry run mkdocs gh-deply