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| # CFAEpiNow2Pipeline (development version) | ||
| # CFAEpiNow2Pipeline v0.1.0 | ||
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| * Add functionality to pass `job_id` to config generation | ||
| * Refactor cleanup action to also delete jobs | ||
| * Fix Batch run trigger from Makefile and drop `test-` prefix | ||
| * Add fit observation data to summaries | ||
| * Use a consistent name scheme for geographies: `geo_value` | ||
| * Created workflow_dispatch docker system prune -a -f action; made container job ignore irrelevant changes | ||
| * Build Batch pool on merge to main | ||
| * Install suggests into base first-step image | ||
| * Fixed issue with running `make pull` while on main. | ||
| * Improved documentation of `format_stan_opts` | ||
| * Drop old pre-commit action in favor of CI service | ||
| * Improve documentation of `fetch_blob_container` | ||
| * Add warning and autofix for improperly specified GI PMF | ||
| * Read parameters on the same day correctly | ||
| * Re-add missing dependency in python venv | ||
| * Don't emit DEBUG level logs from EpiNow2 | ||
| * Clean up Azure Batch pools on PR close | ||
| * 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` | ||
| This initial release establishes minimal feature parity with the internal EpiNow2 Rt modeling pipeline. It adds wrappers to integrate with internal data schemas and ingest pre-estimated model parameters (i.e., generation intervals, right-truncation). It defines an output schema and adds comprehensive logging. The repository also has functionality to set up and deploy to Azure Batch. | ||
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| ## Features | ||
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| * GitHub Actions to build Docker images on PR and merge to main, deploy Azure Batch environments off the built images, and tear down the environment on PR close. | ||
| * Comprehensive documentation of pipeline code and validation of input data, parameters, and model run configs | ||
| * Set up comprehensive logging of model runs and handle pipeline failures to preserve logs where possible | ||
| * Automatically download and upload inputs and outputs from Azure Blob Storage |