To ease the wiki development process we built a "wiki generator". You can find its source code at https://github.com/igemuoftATG/generator-igemwiki.

generator-igemwiki

Yeoman generator for iGEM wikis. Sets up a development environment with the ability to push entire codebase (including images) to live wiki pages.

Install

kek bro, whats the package name?

npm install -g generator-igemwiki

Node.js

This generator requires that you have Node.js installed on your system. If you are on OS X or Linux system, I recommend installing using one of these methods to avoid having to sudo. Furthermore see here to set up npm packages to install into a custom global directory without sudo. You can check if the install worked by running

node -v

in a terminal; it should return the version number. You don't need to worry about sudo on Windows, as Windows runs as admin by default. However, you may face some PATH issues on Windows (see below).

NPM

NPM is node package manager and is the "largest ecosystem of open source libraries in the world". All of this project's dependencies are held on npm, and this package is published on npm.

Node comes with npm, though it is usually not the latest version, and more importantly, it is not located where your global npm modules are installed. Before continuing, you should make sure your PATH variable catches the correct npm binary, or in simpler terms, running

npm -v
npm install -g npm
npm -v

should return a different value on the second npm -v. (You may need to open and close the terminal first). If it is not, compare the path returned by npm install -g npm (of the format path -> path) to which npm. If they are different, it is because the directory containing Node's npm is earlier in your PATH than the one containing the binaries of npm's global modules. For example, I have the following in my .bashrc:

# Node and NPM
export NPM_PACKAGES="$HOME/node/npm-packages"
export NODE_PATH="$NPM_PACKAGES/lib/node_modules:$NODE_PATH"
export PATH="$PATH:$NPM_PACKAGES/bin:$HOME/node/bin"
export MANPATH="$NPM_PACKAGES/share/man:$MANPATH"

You can see PATH is the original PATH, followed by npm-packages, followed by node. On OS X and Linux, you can add the above to your .bashrc or .profile, etc. to achieve the same effect. To see your environment's PATH, run echo $PATH. Note, I used the two methods mentioned above for not using sudo with Node and npm, with custom folder names (node, and npm-packages). On Windows, you can go to System -> Advanced Settings -> Environment Variables -> Path and edit it there.

Yeoman

Yeoman is "the Web's scaffoldig tool for modern webapps". To get it, install it globally with npm:

npm install -g yo

Once that is done, you can invoke the Yeoman with yo

Generator

Now we just need to install this generator:

npm install -g generator-igemwiki

Usage

Create a new project folder, cd into it (this generator dumps files into the current directory), and run

yo igemwiki

You will be asked for

• the year (will default to current year)
• team name is it appears exactly on the wiki (needed for push to live wiki)
• author (optional)
• GitHub repo in the format username/repo
  • Why? As you will see, this generator exposes features which it make it applicable for collobarative content editing when using the repo to modify markdown files.
  • Still confused? You can skip this by passing in the option --skip-repo. You can always push to a repo later.

Options

yo igemwiki --skip-install --skip-repo

--skip-install will prevent bower install and npm install from automatically running. Use this if you know you need sudo to npm install and it won't work anyways. --skip-repo will prevent the prompt asking you for your repository.

Tools

This generator is built using the following tools. You should have an idea what they are each doing in order to use them effectively.

Bower

Bower is "a package manager for the web". Use it to install frontend dependencies, such as bootstrap or fontawesome (todo: push font files to wiki*). Install packages like so:

bower install --save bootstrap

The --save is important as it adds bootstrap to the dependencies object in the bower.json file, and will be used by wiredep to inject the proper css and script tags into the outputted html. Browser all the Bower packages here.

Gulp

Gulp is a JavaScript task runner. It is the tool running everything behind the development environment, build scripts, and push to live wiki. You don't need to understand it's internals, and I will go over the tasks it provides. Everything is in the gulpfile. Feel free to add your own tasks and submit a pull request!

Handlebars

Handlebars is used to write templates. This templates, when combined with helper functions and a set of object values can be very powerful. This is how I am building links for development and live using the same source files. The custom helper functions are all here. This file is much smaller than the gulpfile, and I encourage you to quickly take a look. Using it, we can do things like:

{{capitals teamName}}

To get

TORONTO

Again, if you write your own helper functions which may be useful to other teams, send a pull request!

Markdown

Markdown is easy to learn. Markdown provides a way to write clunky HTML without having to write clunky HTML. Huh?

Consider this html for a level 1 heading:

<h1> Wheeeeee </h1>

Okay, that works, but in markdown it is sooo much cleaner:

# Wheeeeee

You can use # to ###### for <h1> to <h6>, respectably. Still not convinced?

<img src="http://45.55.193.224/logo_grey.png" />
<ul>
    <li> <a href="http://igemuoft.github.io">iGEM UofT Computational Biology</a> </li>
    <li> <b>wheeeee</b> </li>
    <li> <i>wahooooooo</i> </li>
</ul>

vs.

![logo](http://45.55.193.224/logo_grey.png)
* [iGEM UofT Computational Biology](http://igemuft.github.io)
* **wheeeeee**
* *wahooooo*

Oh and by the way, you just learned markdown. Still curious? See this Markdown Cheatsheet.

Tasks

Gulp tasks are run with gulp taskName. A lot of the tasks in the gulpfile are used internally within other tasks, though these are two you will most commonly run:

Default

gulp

Compiles sass, bundles CoffeeScript and JS, compiles handlebars templates, compiles markdown, and provides a local version of the wiki at http://localhost:3000 using Browsersync. (Which also sets up a UI at 3001 and an external IP to use from your phone, all connected!)

Push

gulp push

Runs build:live and then push. Same as above but uses live mode when compiling templates, and minifies Bower css into vendor.min.css, personal css into styles.min.css. Likewise for JS, except it uglifies as well, and personal JS goes into bundle.min.js. Then using the request package (in combination with Chrome's web inspector Network tab), I've emulated to "go to pageName?action=edit, copy/paste into textbox, click save". You will be asked for your username and password of course, and will automatically log out when all uploads are complete.

Pull

gulp pull

Run this to download all current live files into ./pulled.

Phantom

gulp phantom
gulp phantom:sync

Spawn up some Phantom process and store screenshots of your wiki across mobile, phablet, tablet, desktop, and desktophd resolutions in ./phantom/mobile, ./phantom/phablet, ...

Important Files

Template

The main template file is at ./src/template.json. This stores the team name, year, links, markdown files, and navigation bar settings. It's used in almost every helper function in ./helpers.coffee, and has a mode, either dev or live appended into it by the gulpfile before being used with handlebars. If you want to add new pages, change the ordering of the navigation, add new markdown files, edit this.

Styles

Page styles are stored in ./src/sass. There is a file there, styles.scss which gets compiled into ./build-dev/css/styles.css. All the other files here are prefixed with _ so that they don't compile for themselves (they are imported within styles.scss). Sass lets you use variables and functions in CSS, and is super awesome. It's very easy to learn, if you already know css, you know sass.

Scripts

You can write JS and CoffeeScript inside ./src/lib. You can use require syntax because Browserify is employed. Everything here will get bundled into ./build-dev/js/bundle.js

Pages

Pages are written as Handlebars templates in ./src/*.hbs.

Markdown

Markdown files are stored in ./src/markdown/*.md. You can also write inline markdown using the markdownHere helper.

Images

Images are stored in ./src/images. They will have teamName_YEAR_ appended to the filename when uploading. images.json will store a link to the full resolution of each image.

Helper Functions

For complete detail, read through helpers.coffee. Here is a summary of the helper functions which take parameters (other than mode, which is injected into a new template as either dev or live for the build:dev and build:live tasks, respectably).

images(image, format, mode)

image is the filename exactly as it appears in ./images, including the extension. format can be:

• "file" -> inline image using wiki code. forces breaking/reopening html
• "media" -> wiki code link to image without showing image, same as above with regards to html
• "directlink" -> The preferred method. Requires images.json to already store the image link.