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