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Changelog

CFAEpiNow2Pipeline (development version)

  • Improved documentation of format_stan_opts
  • Drop old pre-commit action in favor of CI service
  • Improve documentation of fetch_blob_container
  • Read parameters on the same day correctly
  • Re-add missing dependency in python venv
  • Don’t emit DEBUG level logs from EpiNow2
  • Added function families to documentation
  • Renamed file containing diagnostic functions
  • Change formatting of metadata values to be atomic.
  • Add blob_storage_container as a field to the metadata.
  • Use empty string for paths when non-existant.
  • Add function families
  • Populated the default values of the metadata to be saved.
  • Working upload/download from ABS
  • Working Azure upload/download
  • Creating a Config class to make syncing configuration differences easier.
  • Add a JSON reader for the Config class.
  • Use the Config class throughout the pipeline.
  • Adding a script to setup the Azure Batch Pool to link the container.
  • Adding new action to post a comment on PRs with a link to the rendered pkgdown site.
  • Add inner pipeline responsible for running the model fitting process
  • Re-organizing GitHub workflows.
  • Checks if batch pool exists. Pools are named after branches. Also allows for deletion via commit message.
  • Merges workflows 1 and 2 into a single workflow.
  • Now uses CFA Azure ACR and images in the workflows and Dockerfiles, etc.
  • Added Docker image with all the requirements to build the package.
  • Bump pre-commit hooks
  • Fix bug in warning message for incomplete data read (h/t @damonbayer)
  • Fit EpiNow2 model using params and fixed seed
  • Removed .vscode folder from repo
  • Read and apply exclusions to case data
  • Data reader and processor
  • Parameters read from local parquet file or files
  • Additional CI bugs squashed
  • Bug fixed in the updated, faster pre-commit checks
  • Updated, faster pre-commit checks
  • Azure Blob file download utilities
  • CI running on Ubuntu only & working pkgdown deploy to Github Pages
  • Initial R package with checks running in CI
  • Updated DESCRIPTION and added guidelines for package authorship
  • Set up README with explanation of purpose and scope
  • Removed add.R placeholder
  • Fix bugs in date casting caused by DuckDB v1.1.1 release
  • Drop unused pre-commit hooks
  • Write outputs to file
  • Specify number of samples draws with iter_sampling
  • Fix NOTE from missing variable name used with NSE
  • Read from new parameters schema
  • Fix bugs in parameter reading from local test run
  • Fix bugs in parameter reading from local test run
  • Add “US” as an option in state_abb