template to publish a pdf (and all associated generation files) to Github Pages using whedon docker
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README.md

README.md

Open Bases Paper Builder

img/preview.png

Hi friend! 👋

CircleCI

This is an openbases paper builder to use the pre-build openbases-pdf to generate a paper for you! You can:

  1. Fork the repository to your Github account
  2. Add your paper (and associated paper files) in the paper folder
  3. Connect to CircleCI to generate a PDF on commits.

The simple setup will give you PDFs for preview as Artifacts, and depending on your needs to you set up environment variables to build and package your paper to send it back to Github pages and preview like this.

1. Preparation

First fork the repostitory to your account, and clone the fork.

git clone https://www.github.com/<username>/builder-pdf
git clone git@github.com:<username>/builder-pdf.git

Next, add your paper! You should have a submission (in a folder paper) called paper.md and a matching paper.bib.

paper
   paper.md
   paper.bib

Custom Logo

If you want a custom logo, add it as logo.png. If not, a beautiful icon will be selected from openbases-icons

paper
   paper.md
   paper.bib
   logo.png

Custom Latex Template

The same goes for the latex template! To customize it, just add a "latex.template" to the same directory

paper
    paper.md
    paper.bib
    latex.template

If not found, by default, we use the template served by whedon An example is provided here, in paper.

Step 2. Configuration

Next, we will talk about setting up the services! If you are interested specifically in developing the openbases-pdf doing the heavy lifting to generate the PDF, take a look as his code.

The hidden folder .circleci/config.yml has instructions for CircleCI to automatically discover and build your paper. If you choose to deploy back to Github pages, there is also a template.html file that is used as a template. The first does most of the steps required for build and deploy, including:

  1. clone of the repository with your paper folder
  2. build your pdf using the openbsaes-pdf container
  3. (optional) generate a container to serve your paper
  4. (optional) push back to Github pages

Thus, if you have forked the repository and cloned your fork, you should be able to use the files that are pulled. And if you are an advanced user, you could even customize if you want.

Step 3. Generation

This happens all in the CI, and is ready to go for you! If you go under the "build" step in your workflow, you can click on the "artifacts" tab to see your paper outputs.

Step 4. (optional) Github Machine User

If you want to deploy the manifests and paper back to Github pages, the easiest option (and one that doesn't put your entire Github account under risk) is to create a machine user. This comes down to creating a second Github user account (with a different email) and then giving the account permission to the repository, and generate an ssh key for it. You won't need to worry about how the deploy is done - this is handled in the circleCI recipe included with the template. Here are instructions for setting up credentials, derived from this great resource.

Why do I need to do this?

Pushing content back to Github pages requires a deploy key. Although Circle will generate a deploy key for you, it only has read access. We need to generate a machine user with write access. Read more about machine user keys keys

Instructions

  1. Open a second browser so you can stay logged into your main Github account in one browser, and create a new Github account there. You will basically need another email address, and a creative username.
  2. In your main Github account (the primary browser) add this user as a collaborator to your repository. They will need push access.
  3. Accept the invitation in the second browser, or the emali sent to you.
  4. In the second browser, again log in to Circle CI with your new Github account. Make sure you log in via your Github machine user account, and that you have accepted the invitation.
  5. Click on "Add Projects", and select your regular Github username under "Choose Organization". This is the owner of the project. Then click "Follow Project" next to the repository name on the left of the menu.
  6. This is important! Once followed, go to the Project Settings -> "Checkout SSH keys", and click on the button to "Authorize with GitHub." You will be taken back to Github, signed in as the machine user, and you should click "Authorize Application." Finally, click the Create and add machine user github name key button on the same page.

Generate Key Follow the instructions here to generate a new ssh key. The steps to add it to your project are a little weird, but I'll try to be specific:

  • your machine user must first be added as a collaborator to the project
  • you must then log in to CircleCI with your machine user and click on Jobs to see the project
  • when you see it, click on any of the steps and click on "Follow Project" in the upper right
  • Under the project settings (gear icon in the upper right) under "Permissions" click on "Checkout SSH keys" and then click the button to "Add user key." If you don't do this, it will give you an error that the key is read only.

Step 5. Connect to CircleCI

If you do not already have a Circle CI account, head here and create one, and add your project to your Circle CI account. Here are instructions if you've never done this before.

Once you have an account, if you navigate to the main app page you should be able to click "Add Projects" and then select your repository. If you don't see it on the list, then select a different organization in the top left. Once you find the repository, you can click the button to "Start Building" adn accept the defaults.

Before you push or trigger a build, let's set up the following environment variables. Also in the project interface on CirleCi, click the gears icon next to the project name to get to your project settings. Under settings, click on the "Environment Variables" tab. In this section, you want to define the following:

  • GITHUB_USER and GITHUB_EMAIL should be your machine user Github account
  • OPENBASES_PAPER_ARGS should define any additional argument pairs (--arg1 value1 --bool) to pass to the openbases/openbases-pdf container entrypoint. This will be passed as followed:
/bin/bash entrypoint.sh paper.md "${OPENBASES_PAPER_ARGS}"

Step 6. Push and Deploy!

Once the environment variables are set up, you can push or issue a pull request to see circle build the workflow. Remember that you only need the .circleci/config.yml, .circleci/template.html and not any other files in the repository. If your notebook is hosted in the same repo, you might want to add these, along with your requirements.txt, etc.

FAQ

How do I customize the build?

The circle configuration file is the entire workflow that does build, test, and deploy. This literally means you can edit this text file and change any or all behavior. This could be as simple as changing some of the text output, to adding an additional set of testing or deployment options, or more complex like adding entire new steps in the workflow.

How do I customize the template? The template.html is the same! You can tweak it, completely change it, or throw it out and push something entirely different back to Github pages. It's populated with environment variables, and so if you want to add variable content this is how to do it. You can add variables to:

  • an environment section defined in the defaults section of the config.yml
  • directly in the step of the manifest section where you see the template.html being generated
  • in CircleCI settings (appropriate for secrets)

How do I run builds for pull requests?

By default, new builds on CircleCI will not build for pull requests and you can change this default in the settings. You can easily add filters (or other criteria and actions) to be performed during or after the build by editing the .circleci/config.yml file in your repository.

Development

Build the container

docker build -t openbases/builder-pdf .

Credits

  • The beautiful viewer is the slightly modified ng-pdf-viewer from @samrose3.