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.

Added cumulative incidence to `summary_longformat.xlsx`

See merge request !29

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.

Added daily absolute incidence and incidence per 100k to summary_longformat.py

See merge request !28

Added insample7 summary to summary_longformat.xlsx

See merge request !27

Weekly 100k

See merge request !26

Switched to NetCDF4 storage of predictive output

See merge request !25

Chris Jewell authored Feb 24, 2021 and Chris Jewell committed Feb 24, 2021

Changes:

1. Where xarrays were pickled to disc, we now use xarray.to_netcdf
2. Where xarrays were read from Python pickles, we now use xarray.load_dataset


(cherry picked from commit 63519eb3)

Fixed incorrect events dimension

See merge request !22

Created lower bound for posterior events chunk size

See merge request !21

Add missing 21 day incidence and prevalence summary.

See merge request !20

Added mean summary longformat

See merge request !19

Make data summaries weekly

See merge request !18

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.