monkeypox-report

⚠️ This repository is now archived and the briefing report discontinued. Global.health has discontinued line-list reporting as of 2022-09-22. Our team completed a 100 days mission to provide early situational awareness through open-access, global line-list data for the 2022 monkeypox outbreak. Check-out our newsletter to see what's happening next with our data.

This repository contains code and templates to generate the briefing report at https://www.monkeypox.global.health

Setup

Setup is using poetry and renv. Python is used for the overall build process, while R is used to generate the figures. You can install poetry from your package manager or by

curl -sSL https://install.python-poetry.org | python3 -

followed by poetry install to install the dependencies.

For R setup, open R on the terminal and type

install.packages("renv")
renv::restore()

which will use the renv.lock file to install the dependencies.

Building the report

By default, the build process will fetch data from the globaldothealth/monkeypox repository, and Nextstrain data from a private S3 bucket.Nextstrain data is uploaded daily to the bucket by a GitHub Action.

You can run the build pipeline using poetry run python src/build.py, this will use the template, data files and Nextstrain data to update the variables for that day's report, which are written to build/index.json.

To check differences, use git diff.

Once you are okay with the changes, commit and push to the main branch. The deploy then deploys the latest report to S3.

In most cases, manual report generation is not required, as the build action builds a report each working day and opens a pull request for review.