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

# Conflicts:
#   pyproject.toml

Merge branch 'refactor-pipeline' of fhm-chicas-code.lancs.ac.uk:jewell/covid-pipeline into refactor-pipeline

CHANGES:

1. Add `PosteriorPredictiveFunctions` to return functions of
   the predictive distribution.
2. Factor out code common to `PosteriorPredictiveFunctions` and
   `PosteriorFunctions` and place in new superclass `PosteriorMetrics`.

CHANGES:

1. Introduce class `PosteriorFunctions` with methods to return
   functions of posterior samples (incidence, prevalence, etc)

2. Introduce class `Summarizer` which takes an instance of
   `PosteriorFunctions` and wraps the methods in a summary method.

CHANGES:

1. Script summarising posterior for crystalcast output modified to
   respond to DA-only analyses.
2. Pin to `covid19uk` v0.8.0-alpha1