1. 11 Apr, 2021 2 commits
  2. 30 Mar, 2021 1 commit
  3. 24 Mar, 2021 2 commits
  4. 04 Mar, 2021 1 commit
    • 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
  5. 03 Feb, 2021 1 commit
    • Chris Jewell's avatar
      Productionised and web-automated pipeline · a6146241
      Chris Jewell authored
      CHANGES:
      
      1. Introduced default unit traffic flow;
      2. Removed old test data from data directory.  This now contains real static data only.
      3. Brought README.md up to date.
      4. Removed extraneous files from root project directory.
      a6146241
  6. 02 Feb, 2021 2 commits
  7. 11 Jan, 2021 1 commit
  8. 10 Jan, 2021 2 commits
    • Chris Jewell's avatar
      Moved pipeline into covid package directory. · 42f4435f
      Chris Jewell authored
      CHANGES:
      
      1. Committed missing `case_data.py` file
      2. Moved pipeline specification into `covid.ruffus_pipeline`
      3. Moved pipeline initialisation into `covid.pipeline`
      42f4435f
    • Chris Jewell's avatar
      Pipeline bugfixes · 9fe819d7
      Chris Jewell authored
      CHANGES:
      
      1. Replaced `read_phe_cases` with `CasesData`
      2. Column-name fix in `case_exceedance`
      3. Fix column heading in `summarize.infec_incidence`
      4. Add Rt_exceed to `summarize.rt`
      5. Add layer option to `summary_geopackage`
      6. Update `ruffus_pipeline.py` to reflect above changes
      7. Update `template_config.yaml` to reflect above changes
      9fe819d7
  9. 07 Jan, 2021 1 commit
  10. 05 Jan, 2021 1 commit
  11. 04 Jan, 2021 1 commit