Development guidelines:

Contributing to the documentation

For the docs, we use MkDocs because of its flexibility:
- mkdocs-material: look and feel
- mkdocs-bibtex: literature reference
- MkPDFs: PDF version

Modify any of the doc files

vi docs/setup.md 

Test the changes locally

mkdocs serve

If everything looks fine you can submit a patch or pull-request.

Deploy changes

This requires permissions from the GitHub organization.

mkdocs gh-deploy

Setting up mkdocs

# osx specific settings
conda install pango cairo

pip install mkdocs
pip install mkdocs-material
pip install mkdocs-bibtex
pip install -e git+https://github.com/jwaschkau/mkpdfs-mkdocs-plugin.git#egg=mkpdfs-mkdocs-plugin

# osx specific settings
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8

Updating docker containers

The dockerfiles for containers reside at the docker/ directory. Some of the environments use conda recipes, which reside in the envs/ directory. After updating a recipe, to build and upload its container, one should use:

cd Baltica/
docker build -f <dockerfile> --tag <name>:<tag> .
docker push <tag>

For example, - dockerfile: docker/baltica/1.0/Dockerfile - name: tbrittoborges/baltica - tag: 1.0

Once the container is updated, its tag version (tag) should be updated as well as it the container directive in the snakemake workflows.

docker hub hosts the container and can change this location at the container directive at the snakefiles.

Testing Baltica

Baltica's continuous integration testing suite is under development.