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MachineLearningLifeScience/poli-docs

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Documentation for poli and poli-baselines πŸ§ͺ

This repository contains a jupyter-book with documentation for poli and poli-baselines

Building the documentation

The folder ./docs/poli-docs is a Jupyter Book. To build it, create a new environment (python>=3.10) and install the requirements:

conda create -n poli-docs python=3.10
conda activate poli-docs
pip install -r requirements.txt

Manual

These docs are a jupyter-book, which runs using Sphinx.

Adding a new black box

If you are adding a new black box to the docs, you can start by copying one of the .md files inside docs/poli-docs/using_poli/objective_repository and modifying it accordingly.

After you are happy with the contents of your markdown file, you have to:

  • add it to the _toc.yml file.
  • add it to the index.md as one more cell in the relevant section.
  • add it to the all_objectives.md as one more cell in the relevant section.

Adding a new optimizer

Similarly to black boxes, you can add solvers by going to docs/poli-docs/using_poli_baselines, duplicating one of the files and modifying it accordingly.

Once you're done, you have to:

  • add it to the _toc.yml file.
  • add it to the index.md as one more cell in the relevant section.

Adding relevant files to the _toc.yml

If you're building a new page, it's quite likely you'll have to add a new entry to the relevant section of _toc.yml.

(Maybe) Adding mock dependencies to the _config.yml

If you're implementing a new black box or solver, it is likely that some pages won't build in the API if the right dependencies are not installed for poli. Add mock dependencies in the _config.yml to prevent this.

Building

After this, you can build the documentation using

jupyter-book build --all docs/poli-docs

The whole _build folder is pushed to main.

Deployment

Since we are relying on building the website locally (because of foldx dependencies), you will need to

  1. pip install ghp-import
  2. run ghp-import -n -p -f ./docs/poli-docs/_build/html

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Documentation for poli and poli-baselines

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