1. 24 Mar, 2021 1 commit
  2. 18 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Add push to AWS S3 option · 16bad2b7
      Chris Jewell authored
      CHANGES:
      
      1. Add option to upload results to AWS S3 bucket
      2. Remove generation of insample plots from pipeline
      16bad2b7
  3. 16 Mar, 2021 1 commit
    • Chris Jewell's avatar
      Bugfix to naming in thin_samples.pkl · 264cea5c
      Chris Jewell authored
      CHANGES:
      
      1. `thin_samples['init_state']` --> `thin_samples['initial_state']`
      2. `thin_samples['events']` --> `thin_samples['seir']`
      3. add time dimension to next generation matrix
      4. update downstream scripts to changes.
      264cea5c
  4. 04 Mar, 2021 2 commits
    • Chris Jewell's avatar
      Use xarray/netCDF4 throughout the pipeline · 023cbc5f
      Chris Jewell authored
      CHANGES
      
      1. Most tasks touched to use netCDF4 inferencedata file.
      2. Added netCDF4 metadata copy to covid.util
      3. Updated model_spec.py to use xarray
      4. Updated covid.ruffus_pipeline to use netCDF4 files, adding pipeline metadata
      5. Updated pyproject.toml
      6. Removed chunk specification in inference.py.  Defer to automatic chunking for now.
      023cbc5f
    • Chris Jewell's avatar
      Added cumulative incidence to `summary_longformat.xlsx` · bc43cd97
      Chris Jewell authored
      CHANGES:
      
      1.  Added code in `summary_longformat.py` to calculate cumulative incidence;
      2.  Switched from `openpyxl` to `xlsxwriter` for lower memory usage when writing
          to summary_longformat.xlsx.
      bc43cd97
  5. 07 Feb, 2021 1 commit
  6. 03 Feb, 2021 2 commits
  7. 10 Jan, 2021 2 commits
  8. 07 Jan, 2021 1 commit
  9. 04 Jan, 2021 1 commit
  10. 09 Nov, 2020 1 commit
  11. 03 Nov, 2020 1 commit
  12. 02 Nov, 2020 1 commit
  13. 22 Oct, 2020 3 commits