yeastdnnexplorer¶

Introduction¶

yeastdnnexplorer is intended to serve as a development environment for exploring different DNN models to infer the relationship between transcription factors and target genes using binding and perturbation expression data.

Installation¶

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

Development¶

git clone the repo
cd into the local version of the repo
choose one (or more) of the following (only poetry currently supported)

poetry¶

You can also install the dependencies using poetry. I prefer setting the following:

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¶

After building the environment with poetry, you can use poetry run or a poetry shell to execute the following:

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