Run a single model for a single timestep

[tomalrussell]

This will close #402 - work in progress.

The main thing here is the introduction of new smif CLI subcommands.

Run smif run <modelrun> --dry-run to see how to use these subcommands to step through running a model run.

Essentially there are three steps:

• smif decide sets up decisions and reports on the timesteps and decisions that the DecisionManager says should run
• smif before_step initialises a model - this should only need to be run once per modelrun, and not all models do work in this step
• smif step runs a single model for a single timestep and single decision, setting up the data handle and calling Model.simulate

TODO:

• [ ] checking/thinking for robustness - may write up properly handling decisions as a separate issue
• [x] integration testing
• [x] fix unit tests

  tests\cli\test_cli.py ....F.................
  tests\controller\test_modelrun.py ..FF........
  tests\controller\test_scheduler.py ......F..FF
  tests\data_layer\test_data_handle.py .........................F.........
  tests\model\test_sector_model.py F.........

[codecov[bot]]

Codecov Report

Merging #404 into master will decrease coverage by 0.05%. The diff coverage is 87.5%.

@@            Coverage Diff             @@
##           master     #404      +/-   ##
==========================================
- Coverage   70.91%   70.85%   -0.06%     
==========================================
  Files          64       65       +1     
  Lines        5717     5758      +41     
  Branches      730      736       +6     
==========================================
+ Hits         4054     4080      +26     
- Misses       1559     1572      +13     
- Partials      104      106       +2

Flag	Coverage Δ
#javascript	70.85% <87.5%> (-0.06%)	:arrow_down:
#python	77.87% <87.5%> (-0.13%)	:arrow_down:

Impacted Files	Coverage Δ
src/smif/decision/decision.py	93.22% <ø> (ø)	:arrow_up:
src/smif/cli/log.py	95.83% <100%> (ø)	:arrow_up:
src/smif/data_layer/data_array.py	87.24% <100%> (+0.35%)	:arrow_up:
src/smif/model/model.py	100% <100%> (ø)	:arrow_up:
src/smif/data_layer/file/file_data_store.py	90.66% <100%> (+1%)	:arrow_up:
src/smif/model/sector_model.py	100% <100%> (ø)	:arrow_up:
src/smif/controller/build.py	77.27% <50%> (-0.67%)	:arrow_down:
src/smif/controller/modelrun.py	88.95% <66.66%> (-3.05%)	:arrow_down:
src/smif/controller/job/serial_job_scheduler.py	86.88% <80%> (-0.81%)	:arrow_down:
src/smif/controller/execute_run.py	89.65% <91.66%> (ø)
... and 6 more

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