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Recent Releases of https://github.com/cdcgov/cfa-epinow2-pipeline

https://github.com/cdcgov/cfa-epinow2-pipeline - v0.2.0

This release was preceded by merging Micah's PR updating epinow2 version to 1.6.1 (see change log below). We created a release just before merging the PR as well in case we need to go back to that prior release (see the release titled 0.1.1)

What's Changed

  • updating epinow2 version to 1.6.1 by commit hash by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/324

Full Changelog: https://github.com/CDCgov/cfa-epinow2-pipeline/compare/0.1.1...v0.2.0

- R
Published by PatrickTCorbett about 1 year ago

https://github.com/cdcgov/cfa-epinow2-pipeline - 0.1.1

What's Changed

  • parametrizing container management tool by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/175
  • Automatically delete tags after branch is deleted by @gvegayon in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/168
  • Unique jobid and fixed batchjob_id by @amondal2 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/184
  • updating SOP by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/185
  • Bump cryptography from 44.0.0 to 44.0.1 in /azure by @dependabot in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/189
  • Update delete-container-tag.yaml by @gvegayon in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/188
  • Refactoring container build to use CDCgov/cfa-actions/twostep-container-build by @gvegayon in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/167
  • Small bug in delete-container-tag.yaml by @gvegayon in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/192
  • Write diagnostics to file by @zsusswein in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/193
  • Adds Container App Job Support (precommit friendly rework) by @dpechulis-bah in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/196
  • switching to stable 22.04 ubuntu vers by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/197
  • Dev update subnet mpw by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/201
  • adding test-batch to make file and documenting by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/203
  • Add the blob container name for exclusions to metadata by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/205
  • "Phase 1" discussed in PR-#194 by @aisha-cdc in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/206
  • Doc add task exclusions mpw by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/209
  • Container App Job python script added by @dpechulis-bah in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/207
  • "Phase-2" discussed in PR-#194 by @aisha-cdc in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/213
  • Added GitHub Actions workflow to start Azure Container App Job by @dpechulis-bah in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/212
  • Phase-2 remove az cli action on aca-runner by @aisha-cdc in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/215
  • Add output container to config by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/218
  • Hotfeature: rerun feature by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/222
  • Re-activate epinow2 logging by @kgostic in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/226
  • Updated SOP by @kgostic in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/225
  • Add data outliers rerun instructions by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/227
  • "Phase-3" discussed in PR-#194 by @aisha-cdc in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/214
  • Properly read "COVID-19/Omicron" into "COVID-19" by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/232
  • going to dockerfile unified build, updating makefile commands as such by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/231
  • Update outliers path documentation by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/235
  • Fix 'latest' tag for main branch by @giomrella in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/237
  • Nam exclusions didnt apply by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/236
  • 224 automate creating the outlier csv file by @PatrickTCorbett in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/228
  • adding sleep time as parameter to makefile by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/239
  • Dev config gen sensing by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/240
  • Swap job.py from running in Docker to being an inline metadata script by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/241
  • Fix typos in sop, DESCRIPTION by @dylanhmorris in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/243
  • Pin r version to 4.4.3 for CICD by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/245
  • Possible edits to SOP document by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/247
  • deleting tag from ghcr + OIDC login by @giomrella in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/260
  • A script for setting the pool by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/177
  • 254 state exclusion by @PatrickTCorbett in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/256
  • Add locked versions for future stability by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/262
  • Generate configs by calling config generator library directly by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/266
  • Add RSV where COVID and Influenza specified by @PatrickTCorbett in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/265
  • New production disease specification by @natemcintosh in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/267
  • Issue #271: Fix R code out of sync with docs by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/272
  • Gio rm selfhosted by @giomrella in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/277
  • fixing tag and pool deletion workflows by @giomrella in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/278
  • Issue #250: Change project owner by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/274
  • Add check that docs are up to date by @zsusswein in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/282
  • Issue #280: Change from contributors to authors by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/281
  • Issue #273: Document Makefile by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/275
  • Remove demo by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/289
  • Set up dependabot by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/297
  • Bump actions/checkout from 2 to 4 by @dependabot in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/299
  • Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.7.3 by @dependabot in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/300
  • Improve roxygen by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/295
  • Move batch autoscale text file by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/291
  • Dependabot update cfa actions by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/301
  • Simplify, standardise, reorganise README by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/284
  • Switch to air formatter by @zsusswein in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/288
  • Patch makefile test batch mpw by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/307
  • Convert "Drop Date(s) by @PatrickTCorbett in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/312
  • Dev update deps cmdstanr mpw by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/308
  • Adding Container App Jobs as a Batch Alternative by @giomrella in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/302
  • removes nulls that are produced in outliers.csv file by @kingsleyiyawe in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/320
  • Refactor unit tests to use global setup.R by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/309
  • plugging in r-ver to update base image by @micahwiesner67 in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/323
  • save point exclusions file only if data values are present by @kingsleyiyawe in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/326
  • Issue #296: Delete requirements by @athowes in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/305
  • removes quotes and row names azure picks up while processing exclusions by @kingsleyiyawe in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/333

New Contributors

  • @dependabot made their first contribution in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/189
  • @dpechulis-bah made their first contribution in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/196
  • @aisha-cdc made their first contribution in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/206
  • @dylanhmorris made their first contribution in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/243
  • @kingsleyiyawe made their first contribution in https://github.com/CDCgov/cfa-epinow2-pipeline/pull/320

Full Changelog: https://github.com/CDCgov/cfa-epinow2-pipeline/compare/v0.1.0...0.1.1

- R
Published by PatrickTCorbett about 1 year ago

https://github.com/cdcgov/cfa-epinow2-pipeline - v0.1.0

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.

Features

  • 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

- R
Published by zsusswein over 1 year ago