Publish Changes

Once you are satisfied with your new page, you need to commit your changes to the main and gh-pages branches of the repository.

  1. First, open a new terminal window (another terminal than where you started the mkdocs preview server)

  2. Then open the redmine-docs folder before doing the following steps

    • You can do this by using the shortcut crtl-shift-t on keyboard
    • Or by opening a new tab manually and navigating to the folder using cd /mnt/nas2/redmine/redmine-docs

  3. (OPTIONAL) run git status to see confirm what needs to be added to the commit

    • mkdocs.yml should be present under the 'Changes not staged for commit' section
    • your new file (e.g. docs/analysis/SISTR.md) should be present under the 'Untracked files' section

  4. Add your new file to the repository

    • e.g. git add mkdocs.yml docs/analysis/SISTR.md
    • tip: if you want to publish changes on multiple pages and want to repeat this line you can press the up arrowkey to copy your previous command

    changes_screenshot

  5. Commit your changes with a useful message

    • e.g. git commit -m "Added SISTR analysis"

  6. Push your commits

    • git push origin

  7. Use mkdocs to rebuild your site, and push the changes

    • mkdocs gh-deploy

If you have completed these steps successfully you should be given a message along the lines of "https://olc-bioinformatics.github.io/redmine-docs/ should reflect the changes within a few minutes".

Finding your Github Token

In order to push your changes, the terminal will request you enter your github credentials after the commands git push origin and mkdocs gh-deploy.

  • Your username will be your email you used to sign up for Github or your Github username
  • Your password will be your github token NOT your Github password

You can generate a personal access token in your Github settings under Developer Settings > Personal access tokens > Tokens (classic). Select an expiration date and your scopes (ie. what you want your token to give access to) then click Generate token.

Your token will be a string of characters that you will (probably) not remember, so be sure to record it in a secure document.

Note: the terminal will not show your password as you type it and using the ctrl-v shortcut won't work in the terminal so right-click and paste instead