Merge pull request #14 from himoto/develop

Bump version to 0.2.0

Author: Hiroaki Imoto

Project.toml

@@ -1,7 +1,7 @@
 name = "BioMASS"
 uuid = "324734c7-f323-4536-9335-775d9be9d101"
 authors = ["Hiroaki Imoto <himoto@protein.osaka-u.ac.jp>"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"

fos_model/fitness.jl

@@ -60,15 +60,13 @@ function objective(indiv_gene::Vector{Float64})::Float64
                             Sim.simulations[
                                 i,
                                 Sim.normalization[obs_name]["timepoint"],
-                                [conditions_index(c) for c in
-                                    Sim.normalization[obs_name]["condition"]]
+                                [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                             ]
                         ) : maximum(
                             Sim.simulations[
                                 i,
                                 :,
-                                [conditions_index(c) for c in
-                                    Sim.normalization[obs_name]["condition"]]
+                                [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                             ]
                         )
                     )

src/visualize.jl

@@ -62,16 +62,14 @@ function get_norm_max(
                     i,
                     j,
                     Sim.normalization[obs_name]["timepoint"],
-                    [conditions_index(c) for c in
-                        Sim.normalization[obs_name]["condition"]]
+                    [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                 ]
             ) : maximum(
                 simulations_all[
                     i,
                     j,
                     :,
-                    [conditions_index(c) for c in
-                        Sim.normalization[obs_name]["condition"]]
+                    [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                 ]
             )
         )
@@ -126,7 +124,7 @@ function plot_timecourse(
                         plot(
                             Sim.t,
                             simulations_all[i,j,:,l] ./ ifelse(
-                                length(Sim.normalization) == 0,
+                                length(Sim.normalization) == 0 || maximum(simulations_all[i,j,:,l]) == 0.0,
                                 1.0,
                                 norm_max
                             ),
@@ -148,7 +146,7 @@ function plot_timecourse(
                     @simd for l in eachindex(Sim.conditions)
                         normalized[i,j,:,l] = (
                             simulations_all[i,j,:,l] ./ ifelse(
-                                length(Sim.normalization) == 0,
+                                length(Sim.normalization) == 0 || maximum(simulations_all[i,j,:,l]) == 0.0,
                                 1.0,
                                 norm_max
                             )
@@ -172,7 +170,9 @@ function plot_timecourse(
                     for j in eachindex(n_file)
                         for k in eachindex(Sim.t)
                             for l in eachindex(Sim.conditions)
-                                @inbounds normalized[i,j,k,l] /= mean_norm_max
+                                if !isnan(mean_norm_max) && mean_norm_max != 0.0
+                                    @inbounds normalized[i,j,k,l] /= mean_norm_max
+                                end
                             end
                         end
                     end
@@ -220,23 +220,21 @@ function plot_timecourse(
                         Sim.simulations[
                             i,
                             Sim.normalization[obs_name]["timepoint"],
-                            [conditions_index(c) for c in
-                                Sim.normalization[obs_name]["condition"]]
+                            [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                         ]
                     ) : maximum(
                         Sim.simulations[
                             i,
                             :,
-                            [conditions_index(c) for c in
-                                Sim.normalization[obs_name]["condition"]]
+                            [conditions_index(c) for c in Sim.normalization[obs_name]["condition"]]
                         ]
                     )
                 )
                 for (l,condition) in enumerate(Sim.conditions)
                     plot(
                         Sim.t,
                         Sim.simulations[i,:,l] ./ ifelse(
-                            length(Sim.normalization) == 0,
+                            length(Sim.normalization) == 0 || maximum(Sim.simulations[i,:,l]) == 0.0,
                             1.0,
                             norm_max
                         ),

test/parameter_estimation.jl

@@ -24,7 +24,14 @@ output = []
     if isinstalled("matplotlib")
         @testset "visualization" begin
             visualize(model, viz_type="best")
-            @test isdir("../fos_model/figure/simulation/best")
+            files = readdir("../fos_model/figure/simulation/best")
+            n_pdf = 0
+            for file in files
+                if occursin(".pdf", file)
+                    n_pdf += 1
+                end
+            end
+            @test n_pdf == 8  # length(observables)
             push!(output, "figure")
         end
     end