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The repository has been replaced by the new HuBMAP Documentation Repository please use this repository instead.

HuBMAP Software Documentation

This repository contains the documentation hosted via GitHub Pages at https://software.docs.hubmapconsortium.org.

Contents

• /src/- Any source code used to generate the hosted documents (not directly published)
• /docs/ - Contains the markdown files that are hosted as html by GitHub Pages.
• /docker/ - The files to create a docker image which can be run locally to test the site. This image is built and available from DockerHub as hubmap/github-pages-server

Working with submodule

This repository relies on the data_submission_guide as a submodule to function. The file .gitmodules contains the configuration for the URL and specific branch of the submodule that is to be used. Once you already have cloned this repository and switched to the target branch, to load the latest data_submission_guide submodule:

git submodule update --init --remote

Mimicking GitHub Pages Locally

The docker image built out of the /docker directory provides a local server to mimic the GitHub Pages server. This image has been built and pushed to DockerHub. To run it you must mount a local copy of the /documentation/ repo as a volume in the container as the volume /software-docs/ and expose port 4000 locally. The run.sh script is provided to help with this. You must have docker installed and running.

To test this repository locally using the docker image execute the run.sh script included in this directory like:

sh ./run.sh /full/absolute/path/to/the/downloaded/repository When the container is running correctly you'll be able to navigate to https://localhost:4000/ in a local browser.

Layouts

There are 3 layouts available within docs/_layouts/

1. home.html
2. page.html
3. default.html (This layout auto generates Table of Contents, Breadcrumbs and offers additional functionality as described below.)

Usage

• Save your documentation files in the docs/ directory.
• Properly name the documents and directories as path names are used to automatically generate the Breadcrumbs when the layout: default is used
• Properly use H headings, in their correct rankings as these are pulled from the documents to automatically generate the Table of Contents
• For convenience, within docs/lang/en.json, you are free to change the text:
  • And links of the menu property without having to rebuild the html files. The menu property is an array of objects in format of {name: "Link name", href: "/link-url"}
  • Of the breadcrumbRoot property without having to rebuild the html files. The change here will appear on the Breadcrumbs component. If you remove this property, no root will be included.
  • Of the sidebars property without having to rebuild the html files. These sidebars determine are for setting custom Table of Contents per document instead of the automatically generated one. Configure the sidebars property with a key that is the value of location.pathname or the base path of the .md within docs. Each pathname is an object with keys items (array of objects) and isCascading (boolean). Setting isCascading to true means that any subsequent docs within the pathname subdirectories will also have the same Table of Contents.

Development

Only need to set this up if there is a need to add new functionality, features, styles to the templates such as _layouts/default.html. To view /docs as they'd appear on GitHub pages, see mimicking GitHub pages.

Install

cd documentation
npm i .

Run Dev Server

npm start

Open http://localhost:3005 with your browser to see the result.
Note: This is only for viewing the styles, layouts and JS functionality generated through /src changes, ideally should set up the docker server for mimicking of GitHub pages to test fully.
See Below: Mimicking GitHub Pages Locally

CSS

npm run css # builds CSS files to `/docs/css/main.css` and copies to `./docs/_site` GitHub build folder

JS

npm run js # builds Js files to `/docs/js/main.js` and copies to `./docs/_site` GitHub build folder

html

npm run html # builds the PUG layout and pages to `/docs[/_layouts]`

Build All

npm run build # builds all of the above

Serve docs folder locally.
Should have serve module installed after running npm i .
Note: This is only for viewing the styles, layouts and JS functionality generated through /src changes, ideally should set up the docker server for mimicking of GitHub pages to test fully.
See Below: Mimicking GitHub Pages Locally

serve ./docs 

Coding Conventions

• Do use dash casing to separate words for directories in docs:
  • correct: foo-who/ , incorrect: foo_who/
• Please set up prettier in your IDE to keep code formatting consistent or just follow the prettier rules as described in ./package.json
• Do follow any additional code formatting and styles as seen in the project