Remove auto propagation of diffeq keywords (#100)

* replace downloads

* fix deprec in estimate delay time

* fix deprc in traditional embedding

* bump version

* downloads depwarn

Project.toml

@@ -1,7 +1,7 @@
 name = "DelayEmbeddings"
 uuid = "5732040d-69e3-5649-938a-b6b4f237613f"
 repo = "https://github.com/JuliaDynamics/DelayEmbeddings.jl.git"
-version = "2.0.2"
+version = "2.0.3"
 
 [deps]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
@@ -16,17 +16,20 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 [compat]
 Distances = "0.7, 0.8, 0.9, 0.10"
 Distributions = "0.23, 0.24, 0.25"
+DynamicalSystemsBase = "2.3.4"
 Neighborhood = "0.2"
 StaticArrays = "0.8, 0.11, 0.12, 1.0"
 StatsBase = "0.24, 0.32, 0.33"
 julia = "1.5"
 
 [extras]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 Peaks = "18e31ff7-3703-566c-8e60-38913d67486b"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["DynamicalSystemsBase", "Test", "Random", "DelimitedFiles", "Peaks"]
+test = ["DynamicalSystemsBase", "Test", 
+"Random", "DelimitedFiles", "Peaks", "Downloads"]

test/runtests.jl

@@ -1,6 +1,7 @@
 using DelayEmbeddings
 using StaticArrays
 using Test
+import Downloads
 
 # Download some test timeseries
 
@@ -11,14 +12,14 @@ todownload = ["$n.csv" for n in 1:4]
 
 mkpath(tsfolder)
 for a in todownload
-    download(repo*"/"*a, joinpath(tsfolder, a))
+    Downloads.download(repo*"/"*a, joinpath(tsfolder, a))
 end
 
 #New:
 todownload = ["test_time_series_lorenz_standard_N_10000_multivariate.csv", "test_time_series_roessler_N_10000_multivariate.csv"]
 repo = "https://raw.githubusercontent.com/JuliaDynamics/JuliaDynamics/master/timeseries"
 for a in todownload
-    download(repo*"/"*a, joinpath(tsfolder, a))
+    Downloads.download(repo*"/"*a, joinpath(tsfolder, a))
 end
 
 ti = time()

test/traditional/delaytime_test.jl

@@ -1,7 +1,7 @@
 using DelayEmbeddings: localextrema, exponential_decay_fit
 using DynamicalSystemsBase, Test
 
-println("\nTesting delay estimation...")
+println("\nTesting delay time estimation...")
 
 testval = (val, vmin, vmax) -> @test vmin ≤ val ≤ vmax
 diffeq = (atol = 1e-9, rtol = 1e-9, maxiters = typemax(Int))
@@ -23,22 +23,22 @@ diffeq = (atol = 1e-9, rtol = 1e-9, maxiters = typemax(Int))
 
     ds = Systems.roessler(ones(3))
     Δt = 0.02
-    data = trajectory(ds,500.0;Δt,diffeq...)
+    data = trajectory(ds,500.0;Δt,diffeq)
     x = data[:,1]
     @test 1.3 ≤ estimate_delay(x,"ac_zero", 1:2:500)*Δt ≤ 1.7
     @test 2.6 ≤ estimate_delay(x,"ac_min", 1:2:500)*Δt  ≤ 3.4
     @test 1.0 ≤ estimate_delay(x,"mi_min", 1:2:500)*Δt ≤ 1.6
 
     Δt = 0.1
-    data = trajectory(ds,2000.0; Δt,diffeq...)
+    data = trajectory(ds,2000.0; Δt,diffeq)
     x = data[:,1]
     @test 1.3 ≤ estimate_delay(x,"ac_zero", 1:1:50)*Δt ≤ 1.7
     @test 2.6 ≤ estimate_delay(x,"ac_min", 1:1:50)*Δt  ≤ 3.4
     @test 1.15 ≤ estimate_delay(x,"mi_min", 1:1:50)*Δt ≤ 1.6
 
     ds = Systems.lorenz()
     Δt = 0.1
-    data = trajectory(ds,5000;Δt,diffeq...)
+    data = trajectory(ds,5000;Δt,diffeq)
     x = data[500:end,1]
     @test 0 < estimate_delay(x,"exp_extrema", 0:2:200)  < 200
 

test/traditional/embedding_dimension_test.jl

@@ -9,10 +9,10 @@ test_value = (val, vmin, vmax) -> @test vmin <= val <= vmax
 diffeq = (atol = 1e-9, rtol = 1e-9, maxiters = typemax(Int))
 s_sin = sin.(0:0.1:1000)
 ro = Systems.roessler(ones(3));
-data = trajectory(ro,1000;Δt=0.1,diffeq...)
+data = trajectory(ro,1000;Δt=0.1,diffeq)
 s_roessler = data[:,1]
 lo = Systems.lorenz96(4, [0.1, 0.2, 0.5, 0.1]; F = 16.0);
-data = trajectory(lo,5000.0;Δt=0.05, Ttr = 100.0, diffeq...)
+data = trajectory(lo,5000.0;Δt=0.05, Ttr = 100.0, diffeq)
 s_lorenz = data[:,1]
 
 @testset "Caos method" begin