BPA Workshops

Workshops run by BPA.
To see information on the initial Mkdocs setup see: https://bpa-csiro-workshops.github.io/btp-module-template-md/modules/setup_editing/mkdocs_setup/

Deployment

The tutorials have been deployed here: https://bpa-csiro-workshops.github.io/cancer-manuals
The template has been depolyed here: https://bpa-csiro-workshops.github.io/btp-module-template-md/

Github Repository

The tutorials Github repo is here: https://github.com/BPA-CSIRO-Workshops/cancer-manuals
The template GitHub repo is here: https://github.com/BPA-CSIRO-Workshops/btp-module-template-md

How to work on them locally

We are using the Python package MkDocs and the Material for MkDocs theme. On OS X, if you haven't got commandline tools installed you can follow this guide.

You can install MkDocs and extensions into a virtualenv:

virtualenv mkdocs_dev
source mkdocs_dev/bin/activate
pip install package_name

Alternatively, if you have not installed in a virtualenv and do not have sudo permissions, you can install as a user only, using --user

pip install --user package_name

Install the mkdocs tools needed

pip install mkdocs markdown-include mkdocs-alabaster mkdocs-bootstrap python-markdown-math mkdocs-material pymdown-extensions pygments

To update a package

pip install -U package_name

Fork and cloning the repo

We will be using a fork and pull collaborative model: https://github.com/BPA-CSIRO-Workshops/btp-workshop-template#fork-and-pull-collaborative-model

First fork https://github.com/BPA-CSIRO-Workshops/cancer-manuals to your own GitHub account.

You can then clone the repo from your GitHub account

git clone https://github.com/*Your_GitHub*/cancer-manuals
cd cancer-manuals

GitHub Desktop is an alternative for command line git.

Syncing a fork

1. First configure a remote for a fork (i.e let git know what the original upstream BPA repo is): https://help.github.com/articles/configuring-a-remote-for-a-fork/ a) git remote -v b) git remote add upstream https://github.com/BPA-CSIRO-Workshops/cancer-manuals.git c) git remote -v

2. Sync a fork of a repository to keep it up-to-date with the upstream repository (i.e. changes that have been made to the BPA repository since you forked and cloned it). https://help.github.com/articles/syncing-a-fork/

Tip: Syncing your fork only updates your local copy of the repository. To update your fork on GitHub, you must push your changes.

The master document is a YAML file

This file contains the instructions of what to display. It has already been configured for BPA so shouldn't require any editing unless a new module is being added or new styling is required.

less mkdocs.yml

The actual Markdown pages are in the docs folder:

If making a new module from scratch

cd docs;
mkdir module_name;
mkdir module_name/images

To add a new page, say a page on the 'Canu' assembler, find the right location and create a page. In this case it would be docs/modules/module_name/canu.md. Write the tutorial in that file, and then add the file to the master document mkdocs.yml in the correct section under pages:

If editing an existing module

Existing modules are located in https://github.com/BPA-CSIRO-Workshops/cancer-manuals/tree/master/docs/modules. Navigate to the appropriate module and directly edit the .md file. Images relating to the .md file should be located in module_name/images

You do not have to add the module to mkdocs.yml as it would have previously been added.

Editing markdown files

You can edit the .md file with any text editor. Atom works really well as an editor and it highlights files that have been updated.

BTP template

You should apply the BTP template in your .md file.

The built version can be seen here: https://bpa-csiro-workshops.github.io/btp-module-template-md/modules/example/example/
The corresponding raw Markdown and underlying syntax for this can be viewed here: https://raw.githubusercontent.com/BPA-CSIRO-Workshops/btp-module-template-md/master/docs/modules/example/example.md

Please feel free free to add to, or edit, the template here: https://github.com/BPA-CSIRO-Workshops/btp-module-template-md

Browse the site locally without deploying to public internet.

In same directory as mkdocs.yml file

mkdocs serve

or

python -m mkdocs serve

Open your web browser to http://127.0.0.1:8000/ and leave it open. This will update automatically as you make changes to the documentation and allow you to view changes you have made.

When you are happy, add it the repo

git add docs/modules/module_name/canu.md
git commit -m "Added canu" docs/modules/module_name/canu.md
git push origin master

Your private local web version http://127.0.0.1:8000/ will also update.

Pushing changes and pull requests

Once you have added it to the repo, you can push changes to the repo in your own GitHub account and can then put in a pull request and BTP admin will review your changes.

(BTP Admin Step): To deploy the whole lot to the public website

Important: Building the public website will be done by BTP Admin.
Your changes will not be publicly seen until Admin has deployed the changes.

mkdocs gh-deploy --clean --message "Added canu"

This first builds a web HTML version of our Markdown hierarchy into the site/ folder, then pushes it to a special branch of the github repo called gh-pages which GitHub makes available at the public URL https://bpa-csiro-workshops.github.io/cancer-manuals