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Update summary_dha.py - colour intervals updated

See merge request !8

Merge change to configDHA into add-dha-history

Update summary_dha.py: adjust colour scales as number of cases has increased...

See merge request !7

Update summary_dha.py: adjust colour scales as number of cases has increased so much - 'colgrades_Ints' is edited for incidence (abs and 100k), prevalence/100k and cumulative incidence.

CHANGES:

1. Lancaster CC risk report integrated into pipeline;
2. DSTL Scotland estimates adaptor code incorporated;
3. Update to covid19uk v0.8.0-alpha.5

New features
=============

1. Update to `covid19uk` version 0.8.0-alpha.4
2. Add Dynamic Health Atlas output to pipeline.

Update summary_dha.py to include new url argument which needs to be included when calling summary_dha(input_files, output_folder, num_weeks, ci_list, config, url=""). To map to minio baysstm use  url="https://fhm-chicas-storage.lancs.ac.uk/bayesstm/latest/"

Updates: a) added package pathlib; b) parameter "output_folders" replaced by new parameter "output_folder"; c) makes folders "data" and "js" in "output_folder" if they don't exist.

CHANGES:

1. Added missing argument to `insample_write_json`
2. Reformatted code a la PEP

This reverts commit 9e6bb98f

Add pipeline `Summarizer` class

See merge request !2

Refactor pipeline

See merge request !4