ENH: CompositionSet-based solver API

[richardotis]

• Created new SystemState and SystemSpecification objects. SystemSpecification captures the desired result of a particular calculation and associated convergence criteria, while SystemState represents the state of a calculation. The pre-existing Solver object now uses a SystemSpecification to evolve a SystemState object until it achieves the convergence criteria in the specification (this is the specification's run_loop method). SystemSpecification provides a convenience method, get_new_state, which allows users to pass in a list of CompositionSet objects and get back a SystemState.
• Removed update_composition_sets and solve_and_update in eqsolver

Solver.solve can still be used as normal, but because the solver internals have been modularized, users have more control over the minimization process now. For example, solves can now be performed with a list CompositionSet objects as both input and output (mutated in place).

# composition_sets is a list of CompositionSet representing a starting point
# conditions is a dict mapping state variable strings to floats
solver = Solver(remove_metastable=False) # will not delete CompositionSets found to be metastable
spec = solver.get_system_spec(composition_sets, conditions)
state = spec.get_new_state(composition_sets)
converged = spec.run_loop(state, 1000)
# composition_sets has been mutated with the result (solution meets convergence criteria if converged is True)

This is also useful for toggling the fixed state of a list of CompositionSet objects in place, which makes it convenient to do sequences of minimization operations with varying conditions.

[codecov]

Codecov Report

Merging #415 (4d3910d) into develop (f8e3951) will decrease coverage by 0.44%.
The diff coverage is 88.00%.

@@             Coverage Diff             @@
##           develop     #415      +/-   ##
===========================================
- Coverage    90.67%   90.22%   -0.45%     
===========================================
  Files           45       50       +5     
  Lines         6335     7696    +1361     
===========================================
+ Hits          5744     6944    +1200     
- Misses         591      752     +161     

Impacted Files	Coverage Δ
pycalphad/core/minimizer.pyx	83.47% <84.04%> (ø)
pycalphad/core/eqsolver.pyx	85.00% <100.00%> (ø)
pycalphad/core/solver.py	100.00% <100.00%> (ø)
pycalphad/codegen/sympydiff_utils.py	98.21% <0.00%> (-1.79%)	⬇️
pycalphad/tests/test_utils.py	100.00% <0.00%> (ø)
pycalphad/models/model_mqmqa.py	88.42% <0.00%> (ø)
pycalphad/tests/test_database.py	100.00% <0.00%> (ø)
pycalphad/tests/test_calculate.py	100.00% <0.00%> (ø)
pycalphad/core/hyperplane.pyx	93.67% <0.00%> (ø)
... and 9 more

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[bocklund]

Thanks for getting coverage working. Looks like Cython code isn't far from the rest of the repo in coverage. For the minimizer, it looks like a fixed compset + free state variable would cover many of the missed lines (not a blocker for this PR, IMO).

[bocklund]

@richardotis is this ready for re-review now?

[richardotis]

@bocklund It's ready as of 4d3910d. I made a small refactor to solve_state which doesn't do much here, but it makes it easier to implement dot derivatives for some uncommitted local changes which are allowing me to compute the key differential quantity in Equation 78 of Sundman et al, 2015. I thought it made sense to get it in now as part of this review.