Changes:

1. Brought UncalibratedLogRandomWalk up to speed with latest tfp changes (stateless seed)
2. Added thin to example_config.yaml
3. Added parameter 'xi' to model to allow time-varying infec rate
4. Added parameter 'xi' to overall MCMC scheme.

Changes:

1. Replaced 149 UTLAs with 315 LTLAs mixing matrix;
2. Wrote geometric initialisation for censored event times;
3. Modified data ingester to take PHE Anonymised Line Listing data.

Bug in discrete_markov.propagate found, introduced after changes for vectorised
likelihood.

Changes:

1. Added occult Metropolis Hastings update.
2. Factored out Categorical2 distribution for use by both event time move and occults.
3. Refactored mcmc.py script for HDF5 output purposes
4. Apply compression to HDF5 output file.

Changes:

1. Fixed bug in inner tf.while_loop in sample()
2. Made number of event time updates per sweep a config file
parameter.

Also add a script to tune MH for event times

1. Formatting -- black style!
2. After profiling, implemented a better workaround for the
tfd.Categorical bug.  Replaced with an inherited Categorical2 class,
with overloaded log_prob function.
3. Fixed a  bug in EventTimeProposal where tfd.FiniteDiscrete was
being used on a non-strictly-increasing outcomes vector.
4. Increased number of meta-populations to 149 to mirror UK UTLA regions.

Added a "medium" simulation, which assumes 10 meta-populations of 1000 individuals each.

Implemented custom nametuple for tracing innerd of UncalibratedEventTimesUpdate

Got stochastic model fitting with new bounded convergence respecting adaptive proposal.  However, XLA appears now very slow.

1. chainbinom* file and methods renamed to discrete_markov* files and methods.

2. Implemented batched hazard rate calculation, adding functions to automatically broadcast rates to the Markov transition rate matrix.

3. Implemented test simulation and MCMC algorithm.

Updated ODE model with overall number of starting individuals parameter, and daily confirmed cases up to 27th March (PHE, whole of England).