OLS

Sharing. Connecting. Empowering

Find all the information about our community and projects at https://open-life-science.github.io.

Welcome!

First and foremost, Welcome! 🎉 Willkommen! 🎊 Bienvenue! 🙏 सुस्वागत (Suswagat)🎈🎈🎈

This document (the README file) is a hub to give you some information about the project. Jump straight to one of the sections below, or just scroll down to find out more.

What are we doing?

We are working to create a mentoring program for individuals interested in becoming ambassadors for Open Science practice, training and education in their communities.

Our outcome is to support early stage researchers and young leaders by sharing Open Science skills, connecting them to others in the community, and empowering them to become ambassadors for Open Science practice, training and education in their communities.

Who are we?

We are currently a team of people who share a passion for Open Research and inclusiveness in Open Science. Please read more on our website.

What do we need?

You! In whatever way you can help.

We need expertise in open-science, training, mentoring, communication. We'd love your feedback along the way, of course.

Get involved

If you think you can help in any of the areas listed above (and we bet you can) or in any of the many areas that we haven't yet thought of (and here we're sure you can), then please check out our contributors' guidelines and our roadmap.

Please note that it's very important to us that we maintain a positive and supportive environment for everyone who wants to participate. When you join us, we ask that you follow our code of conduct in all interactions, both on and offline.

How can I generate the website and contribute using GitPod?

GitPod is an open-source developer platform for remote development. You can use it to generate the website without installing anything on your computer.

Setting up GitPod
1. Create a fork of the OLS GitHub repository (to do only 1 time)
  1. Go on the GitHub repository: github.com/open-life-science/open-life-science.github.io
  2. Click on the Fork button (top-right corner of the page)
2. Open your browser and navigate to gitpod.io
3. Log in with GitHub
4. Copy the link to your fork of the GTN, e.g. https://github.com/bebatut/open-life-science.github.io
  
  Gitpod will now configure your environment. This may take some time.
  
  Once the setup is finished, you should see a page with:
  - On the Left: All the files in the OLS repository.
  - Top: The main window where you can view and edit files.
  - Bottom: Terminal window, where you can type commands (e.g. to build the website preview) and read output and error messages.
Build and preview the OLS website
1. Type the following command make serve-gitpod in the terminal window (bottom)
2. Click on the link in the terminal to see the OLS in full-screen: Server address: http://127.0.0.1:4000
Make and view changes
1. Open and/or create files via the file browser on the left
2. Make and save the changes in the files
3. Reload the preview page to view the changes
Saving changes back to GitHub
1. Option 1: via the terminal
  1. Create a new branch with git checkout
  2. Commit your changes with git add and git commit
  3. Push changes with git push origin
2. Option 2: via the web interface
  1. Create a new branch
    1. Click on the bottom-left on the branch logo button on the bottom of the page with the current branch (probably "main")
    2. Give your new branch a name (at top of window)
    3. Choose "+ Create new branch..." from the dropdown
  2. Commit changes
    1. Click on the "Source Control" tab button (branch) on the left menu to show changed files.
    2. Click on the "+" icon next to the edited files to stage changes (stage changes button).
    3. Hit the checkmark icon at the top to commit the changes.
    4. Enter a commit message (top of window) - Publish changes.
    5. Click the cloud button at bottom left to publish your changes (publish changes button).
      
      Changes are now saved to your fork, and you can make a PR via the GitHub interface

How can I generate the website locally?

You need a ruby environment (version >= 2.4). Either you have it installed and you know how to install Bundler and Jekyll and then run Jekyll, or you use (mini-)conda, a package management system that can install all these tools for you. You can install it by following the instructions on this page: https://conda.io/docs/user-guide/install/index.html

In the sequel, we assume you use miniconda.

Open a terminal

Clone this GitHub repository:

$ git clone https://github.com/open-life-science/open-life-science.github.io.git

Navigate to the open-life-science.github.io/ folder with the cd command
Set up the conda environment:
```
$ make create-env
```
Install the project's dependencies:
```
$ make install
```
Start the website:
```
$ make serve
```
Open the website in your favorite browser at: http://127.0.0.1:4000/

Run the link checks

To avoid dead or wrong links, run the link checkers:

$ make check-html

Add people or organization, update schedule, add post or event etc

Our knowledge about our different programs, our community, etc is managed via this repository, CiviCRM, and documents stored in Google Drive. It is then added to the website as explained in our Knowledge Management System documentation

Deploy Preview for Pull Requests

This repository uses GitHub Actions to generate a preview deployment of pull requests. This allows contributors to see changes live before merging them into the main branch.

How It Works

When a pull request is created against main, the GitHub Actions workflow (.github/workflows/deploy-preview.yml) runs automatically.
The workflow:
- Checks out the repository code.
- Sets up Ruby and installs dependencies.
- Builds the Jekyll site.
- Deploys the built site to a separate repository (ols-site-preview) on the gh-pages branch.
- Comments on the pull request with a preview link in the format:
```
🎉 A preview of this PR is available at: https://we-are-ols.org/ols-site-preview
```
Contributors can visit this link to view the changes live.

Why This Setup?

Allows easy previewing of pull request changes without merging.
Uses GitHub Pages for hosting, avoiding the need for third-party services.
Automates the process via GitHub Actions to ensure consistency.
The preview deploys to ols-site-preview, keeping the main repo clean.

Usage Notes

The preview is only available while the PR is open. Once merged or closed, the preview will be removed.
Ensure that the PR_PREVIEW_TOKEN secret is correctly set up in the repository settings for authentication.

🚨 Access Restrictions

This workflow uses a Personal Access Token (PAT) (PR_PREVIEW_TOKEN) to deploy previews. Due to GitHub security restrictions, contributors who are not part of the Open Life Science organisation may not have their PR previews generated automatically.

Organisation members’ PRs will automatically receive a preview link.
External contributors' PRs may require a manual workflow run by a maintainer to generate a preview.

License

The content of this website are licensed under the Creative Commons Attribution 4.0 International License.

The code behind the infrastructure is licensed under the MIT License

License

NPDebs/open-life-science.github.io

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