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Pharmaverse Website

Overview

The pharmaverse.org website is maintained and governed by our website community. For more details on community involvement, please visit our contribution page. The community lead serves as the product owner for the website and has the final say on any website-related decisions.

For questions or enhancement suggestions, please create issues in this repository.

Hosted Sites

The website is available at two locations:

Development / Git Flow

Workflow

This section outlines the development workflow that is followed to streamline the process of ensuring efficient collaboration, continuous integration, and smooth deployment.

  • Push to develop or create a pull request onto develop.
  • The GitHub Action is then triggered, rendering and deploying the site to the deployment server. For main branch, the deployment server is GitHub Pages and for develop branch, it is Netlify.
  • The develop branch is considered the UAT branch for pre-production checks.

Important notes:

  • The git workflow is designed with the assumption that typically only one person will be actively working on the site at any given time.
  • Direct work on the main branch is not allowed.
  • All changes must come through develop via a pull request.

Pull Request Requirements

  • PRs require approval from one other Technology and Templates WG member.
  • PRs will be denied if they haven't come through the develop branch.

Data Flows

Scraped Data

The passive data is collected via OpenPharma, which is a sister organization that:

  • Has a completely un-opinionated approach and a wider remit spanning discovery to access.
  • Contains no curated data beyond package names.
  • Focuses on collecting and sharing:
    • Open source health data
    • Related metadata (e.g., CRAN status, riskmetric scores)

For detailed information on the collected data, visit: https://openpharma.github.io/#data

Package Info

Curated package info is stored in the data/ folder.

  • data/packages/ contains pharmaverse packages details
  • data/nonpharma/ contains non-pharma packages details

Each of the packages has a unique .yaml file

Example structure:

name: admiral
repo: pharmaverse/admiral
repo_source: github.com
docs: https://pharmaverse.github.io/admiral/cran-release/
hex: https://github.com/insightsengineering/hex-stickers/raw/main/PNG/admiral.png
task: ADaM
details: (ADaM In R Asset Library) - Modular framework to generate ADaM via R functions relying on community contributions
splash: include # this controls what is shown on the main page. The plan is to deprecate and put all the hexes up.

Deployment

The main branch is deployed to GitHub Pages, while the develop branch is deployed to Netlify. Hugo creates the static site in the public directory in the root of the project. This includes the HTML files, and assets such as images, CSS files, and JavaScript files.

  • For the main branch, the secret token is securely stored in the GitHub environemnt.
  • For the develop branch, the Netlify authorization token and site id are also securely stored in the GitHub environemnt.

People

  • Info on people is in data/people/
  • Filename should be the GitHub handle

Example structure:

name: James Black
pharmaverse_roles: tech
company: Roche
company_logo: roche.png
# Following is more of a nice to have for profile pages [and optional]
linkedin: https://www.linkedin.com/in/epijim/
site: https://epijim.uk
title: People and Product Family Leader for Insights Engineering, Scientific Computing Environment Product Owner
bio: James is currently leading our pan-study codebase for insights

Site Content

The site content is in the content/ directory. It contains standard markdown files. See markdown-guide.md for more information.

Calling Package Info in the Site

To reference packages in the site content, use the following shortcodes:

  • For pharmaverse packages (located in data/packages/):
{{< pharmaverse pkg="rtables" >}}
  • For non-pharmaverse packages (located in data/nonpharma/):
{{< otherpackages pkg="gt" >}}

These shortcodes will automatically pull and display the relevant package information from the corresponding YAML files.

Council Minutes of Meeting

  • From 2023 onwards, monthly council meeting minutes are published in static/council meeting minutes/
  • Other static files (e.g., images) are stored in the static/ directory

Contributing

We welcome contributions from the community! To ensure a smooth process, please review our CONTRIBUTING.md guide for detailed instructions on how to get involved.