Mass rename of step to time in implementation

[richfitz]

No new features, but a fairly painful rename here.

For mode models we need to work in terms of "time", but for dust models we used "step". Seemed like a good idea at the time. However, this causes all sorts of pain in getting a uniform interface for both model types, and there is more of a concept of time in a discrete time model than there is a concept of step in an ode model so dust should be the one to change.

I've added a little explanatory section in dust_generator.R (via the template)

##' For discrete time models, dust has an internal "time", which was
##' called `step` in version `0.11.x` and below.  This must always
##' be non-negative (i.e., zero or more) and always increases in
##' unit increments.  Typically a model will remap this internal
##' time onto a more meaningful time in model space, e.g. by applying
##' the transform `model_time = offset + time * dt`; with this approach
##' you can start at any real valued time and scale the unit increments
##' to control the model dynamics.

Before this can be merged I need to prepare PRs to adapt dependent packages:

• mcstate: Update to use "time" not "step" in dust 0.12.x mcstate#222
• odin.dust: Update to use "time" not "step" in dust 0.12.x odin.dust#116
• sircovid: Update requirements and regenerate sircovid#430
• spimalot: Update for dust 0.12.0 spimalot#243 (Ed has checked this)

No changes required to:

• mode: Update requirements mode#37 - but the PR needs to exist so that pak doesn't get confused installing deps

There's another change to make at some point where we replace "step" with "time" within odin discrete time models to complete this, but that's an even more disruptive change that might be hard to make

This is ready for review, but probably best to consider all at once - particularly the odin.dust and mcstate ones

[codecov]

Codecov Report

Base: 99.83% // Head: 99.83% // No change to project coverage 👍

Coverage data is based on head (f6ee988) compared to base (2c1ff23).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #375   +/-   ##
=======================================
  Coverage   99.83%   99.83%           
=======================================
  Files          67       67           
  Lines        3542     3542           
=======================================
  Hits         3536     3536           
  Misses          6        6           

Impacted Files	Coverage Δ
R/examples.R	100.00% <ø> (ø)
R/interface.R	100.00% <ø> (ø)
R/compile.R	100.00% <100.00%> (ø)
R/data.R	100.00% <100.00%> (ø)
inst/include/dust/dust_cpu.hpp	100.00% <100.00%> (ø)
inst/include/dust/filter.hpp	100.00% <100.00%> (ø)
inst/include/dust/filter_state.hpp	100.00% <100.00%> (ø)
inst/include/dust/gpu/dust_gpu.hpp	99.62% <100.00%> (ø)
inst/include/dust/gpu/filter.hpp	100.00% <100.00%> (ø)
inst/include/dust/gpu/filter_state.hpp	100.00% <100.00%> (ø)
... and 4 more

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