Tidy up a few loose ends

alanderos91 · Nov 18, 2019 · 65d7b9f · 65d7b9f
1 parent fc31868
commit 65d7b9f
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Showing 5 changed files with 9 additions and 12 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BioSimulator"
 uuid = "b1b5f1a8-b9dc-11e8-34ec-e5bc9df8861c"
 authors = ["Alfonso Landeros <alanderos@ucla.edu>", "Timothy Stutz <stutztim@ucla.edu>"]
-version = "0.9.0-beta"
+version = "0.9.1-beta"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
@@ -22,3 +22,6 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 [extras]
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Statistics", "Test"]
diff --git a/src/NewBioSimulator.jl → src/BioSimulator.jl b/src/NewBioSimulator.jl → src/BioSimulator.jl
@@ -45,15 +45,9 @@ export PQBinaryHeap, peektop
 
 ## state
 include(joinpath("state", "site.jl"))
-# include(joinpath("state", "neighborhood.jl"))
 include(joinpath("state", "vonneumann.jl"))
-# include(joinpath("state", "sample_class.jl"))
-# include(joinpath("state", "neighborhood_class.jl"))
 include(joinpath("state", "hexagonal.jl"))
 include(joinpath("state", "Lattice.jl"))
-# include(joinpath("state", "abstract_lattice.jl"))
-# include(joinpath("state", "SLattice.jl"))
-# include(joinpath("state", "NLattice.jl"))
 
 export VonNeumann, Hexagonal
 export Lattice
@@ -67,7 +61,7 @@ include(joinpath("model", "ips.jl"))
 
 ## algorithms
 include(joinpath("algorithms", "ssa_utils.jl"))
-include(joinpath("algorithms", "abstract_algorithms.jl"))
+include(joinpath("algorithms", "abstract_algorithm.jl"))
 include(joinpath("algorithms", "direct.jl"))
 include(joinpath("algorithms", "enhanced_direct.jl"))
 include(joinpath("algorithms", "sorting_direct.jl"))
@@ -82,7 +76,7 @@ include(joinpath("algorithms", "stepanticipation.jl"))
 export HasRates, HasSums
 
 ## simulators
-include(joinpath("simulators", "abstract_simulators.jl"))
+include(joinpath("simulators", "abstract_simulator.jl"))
 include(joinpath("simulators", "exact.jl"))
 include(joinpath("simulators", "tauleap.jl"))
 include(joinpath("simulators", "tauleap_hybrid.jl"))

diff --git a/src/simulate.jl b/src/simulate.jl
@@ -15,7 +15,7 @@ function simulate(network::Network, algname::SimulationAlgorithm;
   initial_state, model = parse_model(network)
 
   # feedforward down the chain...
-  return simulate(initial_state, model, algname, tfinal, rates_cache)
+  return simulate(initial_state, model, algname, tfinal, rates_cache, save_points)
 end
 
 function simulate(initial_state, model, algname::SimulationAlgorithm;

diff --git a/src/simulators/abstract_simulators.jl → src/simulators/abstract_simulator.jl b/src/simulators/abstract_simulators.jl → src/simulators/abstract_simulator.jl
diff --git a/test/simulators/mean_convergence.jl b/test/simulators/mean_convergence.jl
@@ -26,10 +26,10 @@ import BioSimulator: parse_model
     msg = rates_cache == HasRates ? "linear search" : "binary search"
 
     @info "Precompiling $(alg) using $(msg)...\n"
-    @time simulate(state, model, alg, 4.0, rates_cache)
+    @time simulate(state, model, alg, tfinal = 4.0, rates_cache = rates_cache)
 
     @info "Running $(alg) using $(msg)...\n"
-    @time result = [simulate(state, model, alg, 4.0, rates_cache)[end][1] for i in 1:N]
+    @time result = [simulate(state, model, alg, tfinal = 4.0, rates_cache = rates_cache)[end][1] for i in 1:N]
 
     println("  absolute error = $(abs(mean(result) - expected))\n")
   end