jbRothschild / fork.uoftbiophysics.github.io

Submitting and reviewing articles

Join the uoftbiophysics GitHub organization

1. Make a GitHub account and sign in.
2. Send your GitHub username to Matt or Jeremy to be added to our GitHub organization.

Fork the website repo

1. Go to the website repository.
2. In the top right, click "Fork". It should now exist at https://github.com/YOUR_USERNAME/uoftbiophysics.github.io.

Clone the forked copy, make your changes, commit and push them

1. Install Git locally. You can do everything from terminal or command line, or you can install a git GUI (e.g. SourceTree, GitKraken).
2. Clone the forked repo to your computer.

Update the code

2. Make changes to the site files.
3. Commit then push those changes.

Create a Pull Request

1. Go to the original website repo.
2. Click "Pull requests" (third tab at the top).
3. Click "New Pull Request".
4. Selection: pull your forked copy and its changes into the original copy.
5. Details: fill out the topic/description, add any reviewers or assignees, and submit.

Syncing a forked repository

If you've already forked the repo and cloned it a while ago, the upstream repository code may have changed. It should be synced before you add more code. There are two approaches to do this:

Web UI

• Navigate to your forked repo at https://github.com/YOUR_USERNAME/uoftbiophysics.github.io.
• Click "Fetch upstream" (below green Code button). Select "Fetch and merge".
• Locally, use git pull to update your copy of the fork.

Command line

• Configure upstream remote (if you haven't yet):
  git remote add upstream https://github.com/uoftbiophysics/uoftbiophysics.github.git
• Verify it was added: git remote -v
• To sync changes, do:
  • git fetch upstream
  • git checkout main
  • git merge upstream/main
• This syncs your local changes. To update your fork on Github you need to push any changes.

Locally viewing the website (and your changes to it)

Windows

• GitHub documentation
• Extra documentation

Prerequisites (details in the links above)

1. Install Ruby (under WITH DEVKIT, select option to add to PATH).
2. In command line: gem install bundler
3. In command line: gem install jekyll

Viewing the site

1. Open terminal or command line and change directory to the root of the cloned website repository.
2. bundle install
3. bundle exec jekyll serve
4. Navigate to http://localhost:4000/ and see if it worked.

Troubleshooting:

1. A gem file is needed, but should already be on git. In case it isn't, run > bundle init to make one.
2. On windows three lines should be added to the end of the file:

• gem 'wdm'
• gem 'jekyll'
• gem "webrick", "~> 1.7"

3. See if bundle exec jekyll serve works now.

Linux

Prerequisites (details in the links above)

You only need to do this once. Either

1. Install all dependencies by running the script linux-setup.sh; or
2. Follow this guide.

Viewing the site

Run the command

$ jekyll serve

and either navigate to http://localhost:4000/ or Ctrl+click the link in terminal for it to open automatically in browser.

Troubleshooting

1. If the following code appears

FATAL: Listen error: unable to monitor directories for changes.
        Visit https://github.com/guard/listen/blob/master/README.md#increasing-the-amount-of-inotify-watchers for info on how to fix this.

then it is likely your server didn't close properly in an earlier session. You can always increase the number of inotify-watchers by running

$ echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p