Merge pull request #536 from pepijndevos/new-branch

Change typeof(x) <: y to x isa y

src/ensemble/basic_ensemble_solve.jl

@@ -105,7 +105,7 @@ function batch_func(i, prob, alg; kwargs...)
     new_prob = prob.prob_func(_prob, i, iter)
     rerun = true
     x = prob.output_func(solve(new_prob, alg; kwargs...), i)
-    if !(typeof(x) <: Tuple)
+    if !(x isa Tuple)
         rerun_warn()
         _x = (x, false)
     else
@@ -117,7 +117,7 @@ function batch_func(i, prob, alg; kwargs...)
         _prob = prob.safetycopy ? deepcopy(prob.prob) : prob.prob
         new_prob = prob.prob_func(_prob, i, iter)
         x = prob.output_func(solve(new_prob, alg; kwargs...), i)
-        if !(typeof(x) <: Tuple)
+        if !(x isa Tuple)
             rerun_warn()
             _x = (x, false)
         else
@@ -170,7 +170,7 @@ function solve_batch(prob, alg, ensemblealg::EnsembleThreads, II, pmap_batch_siz
         return solve_batch(prob, alg, EnsembleSerial(), II, pmap_batch_size; kwargs...)
     end
 
-    if typeof(prob.prob) <: AbstractJumpProblem && length(II) != 1
+    if prob.prob isa AbstractJumpProblem && length(II) != 1
         probs = [deepcopy(prob.prob) for i in 1:nthreads]
     else
         probs = prob.prob

src/ensemble/ensemble_analysis.jl

@@ -7,15 +7,15 @@ get_timestep(sim, i) = (getindex(sol, i) for sol in sim)
 get_timepoint(sim, t) = (sol(t) for sol in sim)
 function componentwise_vectors_timestep(sim, i)
     arr = [get_timestep(sim, i)...]
-    if typeof(arr[1]) <: AbstractArray
+    if arr[1] isa AbstractArray
         return vecarr_to_vectors(VectorOfArray(arr))
     else
         return arr
     end
 end
 function componentwise_vectors_timepoint(sim, t)
     arr = [get_timepoint(sim, t)...]
-    if typeof(arr[1]) <: AbstractArray
+    if arr[1] isa AbstractArray
         return vecarr_to_vectors(VectorOfArray(arr))
     else
         return arr
@@ -123,7 +123,7 @@ end
 
 function SciMLBase.EnsembleSummary(sim::SciMLBase.AbstractEnsembleSolution{T, N},
     t = sim[1].t; quantiles = [0.05, 0.95]) where {T, N}
-    if typeof(sim[1]) <: SciMLSolution
+    if sim[1] isa SciMLSolution
         m, v = timeseries_point_meanvar(sim, t)
         med = timeseries_point_median(sim, t)
         qlow = timeseries_point_quantile(sim, quantiles[1], t)
@@ -190,13 +190,13 @@ function componentwise_mean(A)
     mean = zero(x0) ./ 1
     for x in A
         n += 1
-        if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+        if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
             mean .+= x
         else
             mean += x
         end
     end
-    if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+    if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
         mean ./= n
     else
         mean /= n
@@ -215,7 +215,7 @@ function componentwise_meanvar(A; bessel = true)
     delta2 = zero(x0) ./ 1
     for x in A
         n += 1
-        if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+        if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
             delta .= x .- mean
             mean .+= delta ./ n
             delta2 .= x .- mean
@@ -231,13 +231,13 @@ function componentwise_meanvar(A; bessel = true)
         return NaN
     else
         if bessel
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 M2 .= M2 ./ (n .- 1)
             else
                 M2 = M2 ./ (n .- 1)
             end
         else
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 M2 .= M2 ./ n
             else
                 M2 = M2 ./ n
@@ -257,7 +257,7 @@ function componentwise_meancov(A, B; bessel = true)
     dx = zero(x0) ./ 1
     for (x, y) in zip(A, B)
         n += 1
-        if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+        if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
             dx .= x .- meanx
             meanx .+= dx ./ n
             meany .+= (y .- meany) ./ n
@@ -273,13 +273,13 @@ function componentwise_meancov(A, B; bessel = true)
         return NaN
     else
         if bessel
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 C .= C ./ (n .- 1)
             else
                 C = C ./ (n .- 1)
             end
         else
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 C .= C ./ n
             else
                 C = C ./ n
@@ -293,7 +293,7 @@ function componentwise_meancor(A, B; bessel = true)
     mx, my, cov = componentwise_meancov(A, B; bessel = bessel)
     mx, vx = componentwise_meanvar(A; bessel = bessel)
     my, vy = componentwise_meanvar(B; bessel = bessel)
-    if typeof(vx) <: AbstractArray
+    if vx isa AbstractArray
         vx .= sqrt.(vx)
         vy .= sqrt.(vy)
     else
@@ -316,7 +316,7 @@ function componentwise_weighted_meancov(A, B, W; weight_type = :reliability)
     dx = zero(x0) ./ 1
     for (x, y, w) in zip(A, B, W)
         n += 1
-        if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+        if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
             wsum .+= w
             wsum2 .+= w .* w
             dx .= x .- meanx
@@ -336,19 +336,19 @@ function componentwise_weighted_meancov(A, B, W; weight_type = :reliability)
         return NaN
     else
         if weight_type == :population
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 C .= C ./ wsum
             else
                 C = C ./ wsum
             end
         elseif weight_type == :reliability
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 C .= C ./ (wsum .- wsum2 ./ wsum)
             else
                 C = C ./ (wsum .- wsum2 ./ wsum)
             end
         elseif weight_type == :frequency
-            if typeof(x0) <: AbstractArray && !(typeof(x0) <: StaticArraysCore.SArray)
+            if x0 isa AbstractArray && !(x0 isa StaticArraysCore.SArray)
                 C .= C ./ (wsum .- 1)
             else
                 C = C ./ (wsum .- 1)

src/ensemble/ensemble_solutions.jl

@@ -139,7 +139,7 @@ end
 ### Plot Recipes
 
 @recipe function f(sim::AbstractEnsembleSolution;
-    zcolors = typeof(sim.u) <: AbstractArray ? fill(nothing, length(sim.u)) :
+    zcolors = sim.u isa AbstractArray ? fill(nothing, length(sim.u)) :
               nothing,
     trajectories = eachindex(sim))
     for i in trajectories
@@ -156,16 +156,16 @@ end
 end
 
 @recipe function f(sim::EnsembleSummary;
-    trajectories = typeof(sim.u[1]) <: AbstractArray ? eachindex(sim.u[1]) :
+    trajectories = sim.u[1] isa AbstractArray ? eachindex(sim.u[1]) :
                    1,
     error_style = :ribbon, ci_type = :quantile)
     if ci_type == :SEM
-        if typeof(sim.u[1]) <: AbstractArray
+        if sim.u[1] isa AbstractArray
             u = vecarr_to_vectors(sim.u)
         else
             u = [sim.u.u]
         end
-        if typeof(sim.u[1]) <: AbstractArray
+        if sim.u[1] isa AbstractArray
             ci_low = vecarr_to_vectors(VectorOfArray([sqrt.(sim.v[i] / sim.num_monte) .*
                                                       1.96 for i in 1:length(sim.v)]))
             ci_high = ci_low
@@ -175,12 +175,12 @@ end
             ci_high = ci_low
         end
     elseif ci_type == :quantile
-        if typeof(sim.med[1]) <: AbstractArray
+        if sim.med[1] isa AbstractArray
             u = vecarr_to_vectors(sim.med)
         else
             u = [sim.med.u]
         end
-        if typeof(sim.u[1]) <: AbstractArray
+        if sim.u[1] isa AbstractArray
             ci_low = u - vecarr_to_vectors(sim.qlow)
             ci_high = vecarr_to_vectors(sim.qhigh) - u
         else

src/integrator_interface.jl

@@ -750,7 +750,7 @@ Base.length(iter::TimeChoiceIterator) = length(iter.ts)
 
 @recipe function f(integrator::DEIntegrator;
     denseplot = (integrator.opts.calck ||
-                 typeof(integrator) <: AbstractSDEIntegrator) &&
+                 integrator isa AbstractSDEIntegrator) &&
                 integrator.iter > 0,
     plotdensity = 10,
     plot_analytic = false, vars = nothing, idxs = nothing)
@@ -797,7 +797,7 @@ Base.length(iter::TimeChoiceIterator) = length(iter.ts)
             else # just get values
                 if x[j] == 0
                     push!(plot_vecs[j - 1], integrator.t)
-                elseif x[j] == 1 && !(typeof(integrator.u) <: AbstractArray)
+                elseif x[j] == 1 && !(integrator.u isa AbstractArray)
                     push!(plot_vecs[j - 1], integrator.u)
                 else
                     push!(plot_vecs[j - 1], integrator.u[x[j]])
@@ -816,7 +816,7 @@ Base.length(iter::TimeChoiceIterator) = length(iter.ts)
                 else # Just get values
                     if x[j] == 0
                         push!(plot_vecs[j], integrator.t)
-                    elseif x[j] == 1 && !(typeof(integrator.u) <: AbstractArray)
+                    elseif x[j] == 1 && !(integrator.u isa AbstractArray)
                         push!(plot_vecs[j],
                             integrator.sol.prob.f(Val{:analytic}, integrator.t,
                                 integrator.sol[1]))
@@ -840,7 +840,7 @@ Base.length(iter::TimeChoiceIterator) = length(iter.ts)
     end
 
     # Special case labels when idxs = (:x,:y,:z) or (:x) or [:x,:y] ...
-    if typeof(idxs) <: Tuple && (typeof(idxs[1]) == Symbol && typeof(idxs[2]) == Symbol)
+    if idxs isa Tuple && (typeof(idxs[1]) == Symbol && typeof(idxs[2]) == Symbol)
         xlabel --> idxs[1]
         ylabel --> idxs[2]
         if length(idxs) > 2

src/interpolation.jl

@@ -81,7 +81,7 @@ end
     continuity::Symbol = :left) where {I, D}
     t = id.t
     u = id.u
-    typeof(id) <: HermiteInterpolation && (du = id.du)
+    id isa HermiteInterpolation && (du = id.du)
     tdir = sign(t[end] - t[1])
     idx = sortperm(tvals, rev = tdir < 0)
     i = 2 # Start the search thinking it's between t[1] and t[2]
@@ -91,17 +91,17 @@ end
         error("Solution interpolation cannot extrapolate past the final timepoint. Either solve on a longer timespan or use the local extrapolation from the integrator interface.")
     tdir * tvals[idx[1]] < tdir * t[1] &&
         error("Solution interpolation cannot extrapolate before the first timepoint. Either start solving earlier or use the local extrapolation from the integrator interface.")
-    if typeof(idxs) <: Number
+    if idxs isa Number
         vals = Vector{eltype(first(u))}(undef, length(tvals))
-    elseif typeof(idxs) <: AbstractVector
+    elseif idxs isa AbstractVector
         vals = Vector{Vector{eltype(first(u))}}(undef, length(tvals))
     else
         vals = Vector{eltype(u)}(undef, length(tvals))
     end
     for j in idx
         tval = tvals[j]
         i = searchsortedfirst(@view(t[i:end]), tval, rev = tdir < 0) + i - 1 # It's in the interval t[i-1] to t[i]
-        avoid_constant_ends = deriv != Val{0} #|| typeof(tval) <: ForwardDiff.Dual
+        avoid_constant_ends = deriv != Val{0} #|| tval isa ForwardDiff.Dual
         avoid_constant_ends && i == 1 && (i += 1)
         if !avoid_constant_ends && t[i - 1] == tval # Can happen if it's the first value!
             if idxs === nothing
@@ -118,11 +118,11 @@ end
                 vals[j] = u[k][idxs]
             end
         else
-            typeof(id) <: SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
+            id isa SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
             dt = t[i] - t[i - 1]
             Θ = (tval - t[i - 1]) / dt
             idxs_internal = idxs
-            if typeof(id) <: HermiteInterpolation
+            if id isa HermiteInterpolation
                 vals[j] = interpolant(Θ, id, dt, u[i - 1], u[i], du[i - 1], du[i],
                     idxs_internal, deriv)
             else
@@ -143,7 +143,7 @@ times t (sorted), with values u and derivatives ks
     continuity::Symbol = :left) where {I, D}
     t = id.t
     u = id.u
-    typeof(id) <: HermiteInterpolation && (du = id.du)
+    id isa HermiteInterpolation && (du = id.du)
     tdir = sign(t[end] - t[1])
     idx = sortperm(tvals, rev = tdir < 0)
     i = 2 # Start the search thinking it's between t[1] and t[2]
@@ -156,7 +156,7 @@ times t (sorted), with values u and derivatives ks
     for j in idx
         tval = tvals[j]
         i = searchsortedfirst(@view(t[i:end]), tval, rev = tdir < 0) + i - 1 # It's in the interval t[i-1] to t[i]
-        avoid_constant_ends = deriv != Val{0} #|| typeof(tval) <: ForwardDiff.Dual
+        avoid_constant_ends = deriv != Val{0} #|| tval isa ForwardDiff.Dual
         avoid_constant_ends && i == 1 && (i += 1)
         if !avoid_constant_ends && t[i - 1] == tval # Can happen if it's the first value!
             if idxs === nothing
@@ -173,19 +173,19 @@ times t (sorted), with values u and derivatives ks
                 vals[j] = u[k][idxs]
             end
         else
-            typeof(id) <: SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
+            id isa SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
             dt = t[i] - t[i - 1]
             Θ = (tval - t[i - 1]) / dt
             idxs_internal = idxs
             if eltype(u) <: Union{AbstractArray, ArrayPartition}
-                if typeof(id) <: HermiteInterpolation
+                if id isa HermiteInterpolation
                     interpolant!(vals[j], Θ, id, dt, u[i - 1], u[i], du[i - 1], du[i],
                         idxs_internal, deriv)
                 else
                     interpolant!(vals[j], Θ, id, dt, u[i - 1], u[i], idxs_internal, deriv)
                 end
             else
-                if typeof(id) <: HermiteInterpolation
+                if id isa HermiteInterpolation
                     vals[j] = interpolant(Θ, id, dt, u[i - 1], u[i], du[i - 1], du[i],
                         idxs_internal, deriv)
                 else
@@ -206,7 +206,7 @@ times t (sorted), with values u and derivatives ks
     continuity::Symbol = :left) where {I, D}
     t = id.t
     u = id.u
-    typeof(id) <: HermiteInterpolation && (du = id.du)
+    id isa HermiteInterpolation && (du = id.du)
     tdir = sign(t[end] - t[1])
     t[end] == t[1] && tval != t[end] &&
         error("Solution interpolation cannot extrapolate from a single timepoint. Either solve on a longer timespan or use the local extrapolation from the integrator interface.")
@@ -215,7 +215,7 @@ times t (sorted), with values u and derivatives ks
     tdir * tval < tdir * t[1] &&
         error("Solution interpolation cannot extrapolate before the first timepoint. Either start solving earlier or use the local extrapolation from the integrator interface.")
     @inbounds i = searchsortedfirst(t, tval, rev = tdir < 0) # It's in the interval t[i-1] to t[i]
-    avoid_constant_ends = deriv != Val{0} #|| typeof(tval) <: ForwardDiff.Dual
+    avoid_constant_ends = deriv != Val{0} #|| tval isa ForwardDiff.Dual
     avoid_constant_ends && i == 1 && (i += 1)
     if !avoid_constant_ends && t[i] == tval
         lasti = lastindex(t)
@@ -232,11 +232,11 @@ times t (sorted), with values u and derivatives ks
             val = u[i - 1][idxs]
         end
     else
-        typeof(id) <: SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
+        id isa SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
         dt = t[i] - t[i - 1]
         Θ = (tval - t[i - 1]) / dt
         idxs_internal = idxs
-        if typeof(id) <: HermiteInterpolation
+        if id isa HermiteInterpolation
             val = interpolant(Θ, id, dt, u[i - 1], u[i], du[i - 1], du[i], idxs_internal,
                 deriv)
         else
@@ -256,7 +256,7 @@ times t (sorted), with values u and derivatives ks
     continuity::Symbol = :left) where {I, D}
     t = id.t
     u = id.u
-    typeof(id) <: HermiteInterpolation && (du = id.du)
+    id isa HermiteInterpolation && (du = id.du)
     tdir = sign(t[end] - t[1])
     t[end] == t[1] && tval != t[end] &&
         error("Solution interpolation cannot extrapolate from a single timepoint. Either solve on a longer timespan or use the local extrapolation from the integrator interface.")
@@ -265,7 +265,7 @@ times t (sorted), with values u and derivatives ks
     tdir * tval < tdir * t[1] &&
         error("Solution interpolation cannot extrapolate before the first timepoint. Either start solving earlier or use the local extrapolation from the integrator interface.")
     @inbounds i = searchsortedfirst(t, tval, rev = tdir < 0) # It's in the interval t[i-1] to t[i]
-    avoid_constant_ends = deriv != Val{0} #|| typeof(tval) <: ForwardDiff.Dual
+    avoid_constant_ends = deriv != Val{0} #|| tval isa ForwardDiff.Dual
     avoid_constant_ends && i == 1 && (i += 1)
     if !avoid_constant_ends && t[i] == tval
         lasti = lastindex(t)
@@ -282,11 +282,11 @@ times t (sorted), with values u and derivatives ks
             copy!(out, u[i - 1][idxs])
         end
     else
-        typeof(id) <: SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
+        id isa SensitivityInterpolation && error(SENSITIVITY_INTERP_MESSAGE)
         dt = t[i] - t[i - 1]
         Θ = (tval - t[i - 1]) / dt
         idxs_internal = idxs
-        if typeof(id) <: HermiteInterpolation
+        if id isa HermiteInterpolation
             interpolant!(out, Θ, id, dt, u[i - 1], u[i], du[i - 1], du[i], idxs_internal,
                 deriv)
         else