Web site creation

CRISPR-Cas screening documentation

Creation of Github repository to store website code

Created empty repository named crispr-docs.

Cloned this repository on local computer:

$ git clone git@github.com:niekwit/crispr_docs.git

Building documentation using Sphinx (Python Documentation Generator)

https://www.sphinx-doc.org/en/master/index.html

Created new Conda environment

$ mamba create -n crispr-docs  python=3.9 sphinx=7.2.5 sphinx_rtd_theme=1.3.0
$ mamba activate crispr-docs

Inititated Sphinx documentation

$ cd /home/niek/Dropbox/scripts/crispr-docs
$ sphinx-quickstart

Test documentation

To test documentation, run the below command and open index.html in the test_docs directory:

$ sphinx-build -b html . test_docs/

Creating website using Readthedocs

https://readthedocs.org/

Created account and linked Github account.

Created .readthedocs.yaml and requirement.txt, and added relevant information (https://docs.readthedocs.io/en/stable/config-file/v2.html)

.readthedocs.yaml:

# Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the OS, Python version and other tools you might need
build:
os: ubuntu-22.04
tools:
   python: "3.9"

# Build documentation in the "docs/" directory with Sphinx
sphinx:
configuration: conf.py
# You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
# builder: "dirhtml"
# Fail on all warnings to avoid broken references
# fail_on_warning: true

# Optionally build your docs in additional formats such as PDF and ePub
# formats:
#    - pdf
#    - epub

# Optional but recommended, declare the Python requirements required
# to build your documentation
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
python:
install:
   - requirements: requirements.txt

requirements.txt:

sphinx==7.2.5
sphinx_rtd_theme==1.3.0