diff --git a/Manifest.toml b/Manifest.toml
new file mode 100644
index 0000000000000000000000000000000000000000..0c3c0d1a30a62081b30f10e137878741851e6b40
--- /dev/null
+++ b/Manifest.toml
@@ -0,0 +1,522 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[ArgTools]]
+git-tree-sha1 = "bdf73eec6a88885256f282d48eafcad25d7de494"
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
+
+[[Artifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.3.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Calculus]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
+uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
+version = "0.5.1"
+
+[[ChainRulesCore]]
+deps = ["Compat", "LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "32ad4ece064a61855a35bdc34e3da0b495e01169"
+uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+version = "1.12.2"
+
+[[ChangesOfVariables]]
+deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
+git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53"
+uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
+version = "0.1.3"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "b153278a25dd42c65abbf4e62344f9d22e59191b"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "3.43.0"
+
+[[CompilerSupportLibraries_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70"
+uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
+version = "0.3.4+0"
+
+[[Conda]]
+deps = ["Downloads", "JSON", "VersionParsing"]
+git-tree-sha1 = "6e47d11ea2776bc5627421d59cdcc1296c058071"
+uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+version = "1.7.0"
+
+[[Crayons]]
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+uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
+version = "4.0.4"
+
+[[DataAPI]]
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+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.10.0"
+
+[[DataFrames]]
+deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "daa21eb85147f72e41f6352a57fccea377e310a9"
+uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+version = "1.3.4"
+
+[[DataStructures]]
+deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "cc1a8e22627f33c789ab60b36a9132ac050bbf75"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.18.12"
+
+[[DataValueInterfaces]]
+git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
+uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
+version = "1.0.0"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[DensityInterface]]
+deps = ["InverseFunctions", "Test"]
+git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b"
+uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
+version = "0.4.0"
+
+[[Distances]]
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+git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04"
+uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+version = "0.10.7"
+
+[[Distributed]]
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+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[DistributedArrays]]
+deps = ["Distributed", "LinearAlgebra", "Primes", "Random", "Serialization", "SparseArrays", "Statistics"]
+git-tree-sha1 = "8b73f8289d73306e3fc04e8622a2db562e01cd07"
+uuid = "aaf54ef3-cdf8-58ed-94cc-d582ad619b94"
+version = "0.6.6"
+
+[[Distributions]]
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+git-tree-sha1 = "8a6b49396a4058771c5c072239b2e0a76e2e898c"
+uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
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+[[DocStringExtensions]]
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+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
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+
+[[Downloads]]
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+git-tree-sha1 = "39e99578597b4b1660b63cdabd5224ba53e3e71a"
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+version = "1.6.0"
+
+[[DualNumbers]]
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+git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566"
+uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74"
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+
+[[FileWatching]]
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+
+[[FillArrays]]
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+git-tree-sha1 = "deed294cde3de20ae0b2e0355a6c4e1c6a5ceffc"
+uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
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+
+[[Formatting]]
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+uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
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+
+[[FunctionWrappers]]
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+
+[[Future]]
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+uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
+
+[[HypergeometricFunctions]]
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+git-tree-sha1 = "65e4589030ef3c44d3b90bdc5aac462b4bb05567"
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+
+[[IntegerMathUtils]]
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+uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235"
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+
+[[InteractiveUtils]]
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+
+[[InverseFunctions]]
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+[[InvertedIndices]]
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+[[IrrationalConstants]]
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+
+[[IterTools]]
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+
+[[IteratorInterfaceExtensions]]
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+
+[[JLLWrappers]]
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+[[JSON]]
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+[[LibCURL]]
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+[[Random]]
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+[[Reexport]]
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+[[ScikitLearn]]
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+[[ScikitLearnBase]]
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+[[SortingAlgorithms]]
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+[[SparseArrays]]
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+[[SpecialFunctions]]
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+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[StatsAPI]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "c82aaa13b44ea00134f8c9c89819477bd3986ecd"
+uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
+version = "1.3.0"
+
+[[StatsBase]]
+deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
+git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291"
+uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+version = "0.33.16"
+
+[[StatsFuns]]
+deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "ca9f8a0c9f2e41431dc5b7697058a3f8f8b89498"
+uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
+version = "1.0.0"
+
+[[SuiteSparse]]
+deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
+uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
+
+[[TOML]]
+deps = ["Dates"]
+git-tree-sha1 = "44aaac2d2aec4a850302f9aa69127c74f0c3787e"
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.3"
+
+[[TableTraits]]
+deps = ["IteratorInterfaceExtensions"]
+git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "1.0.1"
+
+[[Tables]]
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
+git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "1.7.0"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[UnPack]]
+git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b"
+uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
+version = "1.0.2"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[VersionParsing]]
+git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
+uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
+version = "1.3.0"
+
+[[Zlib_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.11+18"
+
+[[nghttp2_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "8e2c44ab4d49ad9518f359ed8b62f83ba8beede4"
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.40.0+2"
diff --git a/Project.toml b/Project.toml
new file mode 100644
index 0000000000000000000000000000000000000000..b67a1d6c253e4cdc57d242928af6f0b7c3855bff
--- /dev/null
+++ b/Project.toml
@@ -0,0 +1,21 @@
+name = "MarkovProcesses"
+uuid = "c0b3d30c-0dcf-40cf-8981-542ba9d93cb6"
+authors = ["Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>"]
+version = "0.1.0"
+
+[deps]
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+DistributedArrays = "aaf54ef3-cdf8-58ed-94cc-d582ad619b94"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+ScikitLearn = "3646fa90-6ef7-5e7e-9f22-8aca16db6324"
+SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
diff --git a/README.md b/README.md
index fd602230bc6bff67692e14cdc4c342e913120363..0888528068efb028d1d09257674299cd7670320a 100644
--- a/README.md
+++ b/README.md
@@ -17,11 +17,11 @@ It implements:
This package is not yet accessible via the Julia package manager. For the install of the package:
1. Clone this git repository on your computer.
-2. Add the "core" directory of this repository to your `LOAD_PATH`. This can be done by two different ways:
+2. Add the "src" directory of this repository to your `LOAD_PATH`. This can be done by two different ways:
* Add the Julia line code
```julia
import Distributed: @everywhere
- @everywhere push!(LOAD_PATH, "/path/to/markovprocesses.jl/core")
+ @everywhere push!(LOAD_PATH, /path/to/markovprocesses.jl/src")
```
on your Julia startup file which is often located in `~/.julia/config/startup.jl` in Unix systems.
"/path/to/markovprocesses.jl/core" is the path to the core directory of this git repository.
@@ -36,9 +36,9 @@ A few notebooks are available in examples/notebooks for a quick presentation of
Execution tests and statistical tests are available. It can be run by:
-`julia tests/run_all.jl`
+`julia test/run_all.jl`
-> :warning: The statistical tests run by `tests/run_cosmos.jl` needs [Cosmos](http://cosmos.lacl.fr/) in your PATH environment variable.
+> :warning: The statistical tests run by `test/run_cosmos.jl` needs [Cosmos](http://cosmos.lacl.fr/) in your PATH environment variable.
## Benchmarks
diff --git a/bench/array_memory_order/access_trajectory.jl b/bench/array_memory_order/access_trajectory.jl
index 4936299beee22d95d7b222f6991bf7503c084c08..2138bbd28b55c279015aee859c4156970c92fc6f 100644
--- a/bench/array_memory_order/access_trajectory.jl
+++ b/bench/array_memory_order/access_trajectory.jl
@@ -2,7 +2,7 @@
using BenchmarkTools
import BenchmarkTools: mean
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
BenchmarkTools.DEFAULT_PARAMETERS.samples = 20000
if ARGS[1] == "SIR"
diff --git a/bench/array_memory_order/multiple_dist_lp_view.jl b/bench/array_memory_order/multiple_dist_lp_view.jl
index 49972a4dbe6b573273fcb3927fd237ccaea9da60..167a78f82c56ef3d87e41b03baff8945aa8f87c1 100644
--- a/bench/array_memory_order/multiple_dist_lp_view.jl
+++ b/bench/array_memory_order/multiple_dist_lp_view.jl
@@ -2,7 +2,7 @@
using BenchmarkTools
import BenchmarkTools: mean
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
str_model = ARGS[1]
load_model(str_model)
diff --git a/bench/array_memory_order/multiple_sim.jl b/bench/array_memory_order/multiple_sim.jl
index 32c75e782f6cb2cd5438131bddcaa958a0590d9b..fd4ec42173b229bca06a91670de7668266915341 100644
--- a/bench/array_memory_order/multiple_sim.jl
+++ b/bench/array_memory_order/multiple_sim.jl
@@ -3,7 +3,7 @@ using BenchmarkTools
import BenchmarkTools: mean
BenchmarkTools.DEFAULT_PARAMETERS.samples = 20000
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
if ARGS[1] == "SIR"
l_var = [:S, :I, :R]
diff --git a/bench/array_memory_order/multiple_sim_view.jl b/bench/array_memory_order/multiple_sim_view.jl
index 6b1af301d5861162dc5969a0690df774c8e7510b..0c853d5ec6ef51f89acc736853452b5e7dc299da 100644
--- a/bench/array_memory_order/multiple_sim_view.jl
+++ b/bench/array_memory_order/multiple_sim_view.jl
@@ -2,7 +2,7 @@
using BenchmarkTools
import BenchmarkTools: mean
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
str_model = ARGS[1]
load_model(str_model)
diff --git a/bench/array_memory_order/read_random_state_trajectory.jl b/bench/array_memory_order/read_random_state_trajectory.jl
index 5fe0da5faa03cba0e94d53b6a05664aa66b9109d..f7141324105ff20abea992f406bccc728295061b 100644
--- a/bench/array_memory_order/read_random_state_trajectory.jl
+++ b/bench/array_memory_order/read_random_state_trajectory.jl
@@ -2,7 +2,7 @@
using BenchmarkTools
import BenchmarkTools: mean
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
BenchmarkTools.DEFAULT_PARAMETERS.samples = 20000
if ARGS[1] == "SIR"
diff --git a/bench/array_memory_order/read_trajectory.jl b/bench/array_memory_order/read_trajectory.jl
index c1af4e574f712762f905d6462046414c2fd08cfe..3d8d28801bd4363c2cfbe6d50dcae74d5aac62b9 100644
--- a/bench/array_memory_order/read_trajectory.jl
+++ b/bench/array_memory_order/read_trajectory.jl
@@ -2,7 +2,7 @@
using BenchmarkTools
import BenchmarkTools: mean
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
BenchmarkTools.DEFAULT_PARAMETERS.samples = 20000
if ARGS[1] == "SIR"
diff --git a/bench/array_memory_order/sim.jl b/bench/array_memory_order/sim.jl
index 7df223eb4da8ca1023e2766fe1ee7d3afae949cc..4e114755f72d572f00206b33cb5022e60d1ae857 100644
--- a/bench/array_memory_order/sim.jl
+++ b/bench/array_memory_order/sim.jl
@@ -3,7 +3,7 @@ using BenchmarkTools
import BenchmarkTools: mean
BenchmarkTools.DEFAULT_PARAMETERS.samples = 20000
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
if ARGS[1] == "SIR"
l_var = [:S, :I, :R]
diff --git a/bench/pkg/bench1_cosmos.jl b/bench/pkg/bench1_cosmos.jl
index 16f2b1e8e097b9cfaa7bfa7675df9185ff027f98..d973e01656767403a40aabce7d740d6e9b9b64d1 100644
--- a/bench/pkg/bench1_cosmos.jl
+++ b/bench/pkg/bench1_cosmos.jl
@@ -4,7 +4,7 @@ using Statistics
using DelimitedFiles
import Distributed: nworkers
-absolute_path = get_module_path() * "/tests/cosmos/"
+absolute_path = get_module_path() * "/test/cosmos/"
path_latex = "./"
dict_automata_lha = Dict("A_G" => (absolute_path * "distance_G/dist_G_ER.lha"))
diff --git a/bench/pkg/bench2_cosmos.jl b/bench/pkg/bench2_cosmos.jl
index d735dd1376c00ad2b7cf30895533062672e75f47..d74a049b332af7564667f0087c98932e59d9d431 100644
--- a/bench/pkg/bench2_cosmos.jl
+++ b/bench/pkg/bench2_cosmos.jl
@@ -4,7 +4,7 @@ using Statistics
using DelimitedFiles
import Distributed: nworkers
-absolute_path = get_module_path() * "/tests/cosmos/"
+absolute_path = get_module_path() * "/test/cosmos/"
path_latex = haskey(ENV, "BENTRIOU_THESIS") ? ENV["BENTRIOU_THESIS"] * "/appendices/bench_cosmos/" : "./"
dict_automata_lha = Dict("A_G" => (absolute_path * "distance_G/dist_G_ER.lha"))
diff --git a/models/SIR_tauleap.jl b/models/SIR_tauleap.jl
index e6743b5d27f0935eef71f63af27e3d28f9424b0b..ec676abca8b29c8eec8e6db57705dc0fd117580b 100644
--- a/models/SIR_tauleap.jl
+++ b/models/SIR_tauleap.jl
@@ -1,13 +1,13 @@
@everywhere import Distributions: Poisson, rand
-d=3
+d=4
k=3
-dict_var_SIR_tauleap = Dict(:S => 1, :I => 2, :R => 3)
+dict_var_SIR_tauleap = Dict(:S => 1, :I => 2, :R => 3, :step => 4)
dict_p_SIR_tauleap = Dict(:ki => 1, :kr => 2, :tau => 3)
l_tr_SIR_tauleap = [:U]
p_SIR_tauleap = [0.0012, 0.05, 5.0]
-x0_SIR_tauleap = [95, 5, 0]
+x0_SIR_tauleap = [95, 5, 0, 0]
t0_SIR_tauleap = 0.0
@everywhere function SIRTauleap_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition},
xn::Vector{Int}, tn::Float64, p::Vector{Float64})
@@ -28,6 +28,7 @@ t0_SIR_tauleap = 0.0
for i = 1:3
@inbounds xnplus1[i] = xn[i]+ nbr_R1*nu_1[i] + nbr_R2*nu_2[i]
end
+ xnplus1[4] += 1
l_t[1] = tn + tau
l_tr[1] = :U
end
diff --git a/core/MarkovProcesses.jl b/src/MarkovProcesses.jl
similarity index 100%
rename from core/MarkovProcesses.jl
rename to src/MarkovProcesses.jl
diff --git a/core/_tests_simulate.jl b/src/_tests_simulate.jl
similarity index 100%
rename from core/_tests_simulate.jl
rename to src/_tests_simulate.jl
diff --git a/core/common.jl b/src/common.jl
similarity index 100%
rename from core/common.jl
rename to src/common.jl
diff --git a/core/lha.jl b/src/lha.jl
similarity index 100%
rename from core/lha.jl
rename to src/lha.jl
diff --git a/core/model.jl b/src/model.jl
similarity index 100%
rename from core/model.jl
rename to src/model.jl
diff --git a/core/network_model.jl b/src/network_model.jl
similarity index 100%
rename from core/network_model.jl
rename to src/network_model.jl
diff --git a/core/plots.jl b/src/plots.jl
similarity index 100%
rename from core/plots.jl
rename to src/plots.jl
diff --git a/core/trajectory.jl b/src/trajectory.jl
similarity index 100%
rename from core/trajectory.jl
rename to src/trajectory.jl
diff --git a/core/utils.jl b/src/utils.jl
similarity index 92%
rename from core/utils.jl
rename to src/utils.jl
index 4abde85c61418e2fd1287c7b64a61d7e7c684669..d333f365eb735d7a7af27237406e420a05a77ee6 100644
--- a/core/utils.jl
+++ b/src/utils.jl
@@ -25,7 +25,7 @@ end
load_model(name_model::String) = Base.MainInclude.include("$(get_module_path())/models/$(name_model).jl")
load_automaton(automaton::String) = Base.MainInclude.include("$(get_module_path())/automata/$(automaton).jl")
-load_plots() = Base.MainInclude.include(get_module_path() * "/core/plots.jl")
+load_plots() = Base.MainInclude.include(get_module_path() * "/src/plots.jl")
newid() = Dates.format(Dates.now(), "YmHMs")
diff --git a/tests/README b/test/README
similarity index 100%
rename from tests/README
rename to test/README
diff --git a/tests/abc_model_choice/toy_example.jl b/test/abc_model_choice/toy_example.jl
similarity index 100%
rename from tests/abc_model_choice/toy_example.jl
rename to test/abc_model_choice/toy_example.jl
diff --git a/tests/abc_model_choice/toy_example_ma.jl b/test/abc_model_choice/toy_example_ma.jl
similarity index 100%
rename from tests/abc_model_choice/toy_example_ma.jl
rename to test/abc_model_choice/toy_example_ma.jl
diff --git a/tests/abc_model_choice/toy_model.ipynb b/test/abc_model_choice/toy_model.ipynb
similarity index 100%
rename from tests/abc_model_choice/toy_model.ipynb
rename to test/abc_model_choice/toy_model.ipynb
diff --git a/tests/automata/absorbing_x0_p.jl b/test/automata/absorbing_x0_p.jl
similarity index 100%
rename from tests/automata/absorbing_x0_p.jl
rename to test/automata/absorbing_x0_p.jl
diff --git a/tests/automata/accept_R5.jl b/test/automata/accept_R5.jl
similarity index 100%
rename from tests/automata/accept_R5.jl
rename to test/automata/accept_R5.jl
diff --git a/tests/automata/euclidean_distance.jl b/test/automata/euclidean_distance.jl
similarity index 100%
rename from tests/automata/euclidean_distance.jl
rename to test/automata/euclidean_distance.jl
diff --git a/tests/automata/euclidean_distance_on_bound.jl b/test/automata/euclidean_distance_on_bound.jl
similarity index 100%
rename from tests/automata/euclidean_distance_on_bound.jl
rename to test/automata/euclidean_distance_on_bound.jl
diff --git a/tests/automata/period_automaton_doping_single.jl b/test/automata/period_automaton_doping_single.jl
similarity index 100%
rename from tests/automata/period_automaton_doping_single.jl
rename to test/automata/period_automaton_doping_single.jl
diff --git a/tests/automata/read_trajectory_last_state_F.jl b/test/automata/read_trajectory_last_state_F.jl
similarity index 100%
rename from tests/automata/read_trajectory_last_state_F.jl
rename to test/automata/read_trajectory_last_state_F.jl
diff --git a/tests/automata/read_trajectory_last_state_G.jl b/test/automata/read_trajectory_last_state_G.jl
similarity index 100%
rename from tests/automata/read_trajectory_last_state_G.jl
rename to test/automata/read_trajectory_last_state_G.jl
diff --git a/tests/automata/sync_simulate_last_state_F.jl b/test/automata/sync_simulate_last_state_F.jl
similarity index 100%
rename from tests/automata/sync_simulate_last_state_F.jl
rename to test/automata/sync_simulate_last_state_F.jl
diff --git a/tests/automata/sync_simulate_last_state_G.jl b/test/automata/sync_simulate_last_state_G.jl
similarity index 100%
rename from tests/automata/sync_simulate_last_state_G.jl
rename to test/automata/sync_simulate_last_state_G.jl
diff --git a/tests/automata/two_automata.jl b/test/automata/two_automata.jl
similarity index 100%
rename from tests/automata/two_automata.jl
rename to test/automata/two_automata.jl
diff --git a/tests/automaton_abc/R1.jl b/test/automaton_abc/R1.jl
similarity index 100%
rename from tests/automaton_abc/R1.jl
rename to test/automaton_abc/R1.jl
diff --git a/tests/automaton_abc/R2.jl b/test/automaton_abc/R2.jl
similarity index 100%
rename from tests/automaton_abc/R2.jl
rename to test/automaton_abc/R2.jl
diff --git a/tests/automaton_abc/R3.jl b/test/automaton_abc/R3.jl
similarity index 100%
rename from tests/automaton_abc/R3.jl
rename to test/automaton_abc/R3.jl
diff --git a/tests/automaton_abc/R6.jl b/test/automaton_abc/R6.jl
similarity index 100%
rename from tests/automaton_abc/R6.jl
rename to test/automaton_abc/R6.jl
diff --git a/tests/automaton_abc/abc_euclidean_distance_automaton.jl b/test/automaton_abc/abc_euclidean_distance_automaton.jl
similarity index 100%
rename from tests/automaton_abc/abc_euclidean_distance_automaton.jl
rename to test/automaton_abc/abc_euclidean_distance_automaton.jl
diff --git a/tests/automaton_abc/distributed_R1.jl b/test/automaton_abc/distributed_R1.jl
similarity index 94%
rename from tests/automaton_abc/distributed_R1.jl
rename to test/automaton_abc/distributed_R1.jl
index 18e0ad0c08db2cf686f20b03f8fb7d69f9fadd46..e88621aea1f011285e302b67380699bc17f9163f 100644
--- a/tests/automaton_abc/distributed_R1.jl
+++ b/test/automaton_abc/distributed_R1.jl
@@ -4,7 +4,7 @@ using Distributed
addprocs(2)
module_path = get_module_path()
@everywhere module_path = $module_path
-@everywhere push!(LOAD_PATH, "$(module_path)/core")
+@everywhere push!(LOAD_PATH, "$(module_path)/src")
@everywhere using MarkovProcesses
#=
@everywhere begin
diff --git a/tests/automaton_abc/distributed_abc_euclidean_distance_automaton.jl b/test/automaton_abc/distributed_abc_euclidean_distance_automaton.jl
similarity index 95%
rename from tests/automaton_abc/distributed_abc_euclidean_distance_automaton.jl
rename to test/automaton_abc/distributed_abc_euclidean_distance_automaton.jl
index fc653e73350ccd8f788d2bf6960de72613afcaff..d3263cbbede8a250785c08e30c0f49663dacdaf7 100644
--- a/tests/automaton_abc/distributed_abc_euclidean_distance_automaton.jl
+++ b/test/automaton_abc/distributed_abc_euclidean_distance_automaton.jl
@@ -4,7 +4,7 @@ using Distributed
addprocs(2)
module_path = get_module_path()
@everywhere module_path = $module_path
-@everywhere push!(LOAD_PATH, "$(module_path)/core")
+@everywhere push!(LOAD_PATH, "$(module_path)/src")
@everywhere using MarkovProcesses
import LinearAlgebra: dot
diff --git a/tests/cosmos/distance_F/ER_1D.jl b/test/cosmos/distance_F/ER_1D.jl
similarity index 97%
rename from tests/cosmos/distance_F/ER_1D.jl
rename to test/cosmos/distance_F/ER_1D.jl
index 7eaac2dfb429deffe05974cf0a50072a923bb864..1c3b586a79b609e6428fc50b85996ebf985402bd 100644
--- a/tests/cosmos/distance_F/ER_1D.jl
+++ b/test/cosmos/distance_F/ER_1D.jl
@@ -2,7 +2,7 @@
@everywhere begin
using MarkovProcesses
import Distributed: nworkers
- absolute_path = get_module_path() * "/tests/cosmos/"
+ absolute_path = get_module_path() * "/test/cosmos/"
# Values x1, x2 t1, t2
dict_exp = Dict(
:R1 => [50, 75, 0.025, 0.05],
diff --git a/tests/cosmos/distance_F/dist_F_ER.lha b/test/cosmos/distance_F/dist_F_ER.lha
similarity index 100%
rename from tests/cosmos/distance_F/dist_F_ER.lha
rename to test/cosmos/distance_F/dist_F_ER.lha
diff --git a/tests/cosmos/distance_G/ER_R5.jl b/test/cosmos/distance_G/ER_R5.jl
similarity index 97%
rename from tests/cosmos/distance_G/ER_R5.jl
rename to test/cosmos/distance_G/ER_R5.jl
index ce300bf12947640e8c419f65951989bb5c8713c4..db83ea09a1ca51d969df6f3b34b069d2597bb577 100644
--- a/tests/cosmos/distance_G/ER_R5.jl
+++ b/test/cosmos/distance_G/ER_R5.jl
@@ -2,7 +2,7 @@
@everywhere begin
using MarkovProcesses
import Distributed: nworkers
- absolute_path = get_module_path() * "/tests/cosmos/"
+ absolute_path = get_module_path() * "/test/cosmos/"
# Values x1, x2 t1, t2
str_model = "ER"
load_model(str_model)
diff --git a/tests/cosmos/distance_G/dist_G_ER.lha b/test/cosmos/distance_G/dist_G_ER.lha
similarity index 100%
rename from tests/cosmos/distance_G/dist_G_ER.lha
rename to test/cosmos/distance_G/dist_G_ER.lha
diff --git a/tests/cosmos/distance_G_F/ER_R6.jl b/test/cosmos/distance_G_F/ER_R6.jl
similarity index 98%
rename from tests/cosmos/distance_G_F/ER_R6.jl
rename to test/cosmos/distance_G_F/ER_R6.jl
index 3d411b983bf9eafe23fa41a193ae2c9c04eda6d9..fb851eccbe3039edbe382a3080239f1ec653417e 100644
--- a/tests/cosmos/distance_G_F/ER_R6.jl
+++ b/test/cosmos/distance_G_F/ER_R6.jl
@@ -2,7 +2,7 @@
@everywhere begin
using MarkovProcesses
import Distributed: nworkers
- absolute_path = get_module_path() * "/tests/cosmos/"
+ absolute_path = get_module_path() * "/test/cosmos/"
# Values x1, x2 t1, t2
str_model = "ER"
load_model(str_model)
diff --git a/tests/cosmos/distance_G_F/dist_G_F_ER.lha b/test/cosmos/distance_G_F/dist_G_F_ER.lha
similarity index 100%
rename from tests/cosmos/distance_G_F/dist_G_F_ER.lha
rename to test/cosmos/distance_G_F/dist_G_F_ER.lha
diff --git a/tests/cosmos/models/ER.gspn b/test/cosmos/models/ER.gspn
similarity index 100%
rename from tests/cosmos/models/ER.gspn
rename to test/cosmos/models/ER.gspn
diff --git a/tests/cosmos/models/SIR.gspn b/test/cosmos/models/SIR.gspn
similarity index 100%
rename from tests/cosmos/models/SIR.gspn
rename to test/cosmos/models/SIR.gspn
diff --git a/tests/dist_lp/dist_case_2.jl b/test/dist_lp/dist_case_2.jl
similarity index 100%
rename from tests/dist_lp/dist_case_2.jl
rename to test/dist_lp/dist_case_2.jl
diff --git a/tests/dist_lp/dist_case_3.jl b/test/dist_lp/dist_case_3.jl
similarity index 100%
rename from tests/dist_lp/dist_case_3.jl
rename to test/dist_lp/dist_case_3.jl
diff --git a/tests/dist_lp/dist_l1_case_1.jl b/test/dist_lp/dist_l1_case_1.jl
similarity index 100%
rename from tests/dist_lp/dist_l1_case_1.jl
rename to test/dist_lp/dist_l1_case_1.jl
diff --git a/tests/dist_lp/dist_sim_sir.jl b/test/dist_lp/dist_sim_sir.jl
similarity index 100%
rename from tests/dist_lp/dist_sim_sir.jl
rename to test/dist_lp/dist_sim_sir.jl
diff --git a/tests/run_abc_smc.jl b/test/run_abc_smc.jl
similarity index 100%
rename from tests/run_abc_smc.jl
rename to test/run_abc_smc.jl
diff --git a/tests/run_all.jl b/test/run_all.jl
similarity index 100%
rename from tests/run_all.jl
rename to test/run_all.jl
diff --git a/tests/run_automata.jl b/test/run_automata.jl
similarity index 100%
rename from tests/run_automata.jl
rename to test/run_automata.jl
diff --git a/tests/run_bench.jl b/test/run_bench.jl
similarity index 100%
rename from tests/run_bench.jl
rename to test/run_bench.jl
diff --git a/tests/run_cosmos.jl b/test/run_cosmos.jl
similarity index 100%
rename from tests/run_cosmos.jl
rename to test/run_cosmos.jl
diff --git a/tests/run_dist_lp.jl b/test/run_dist_lp.jl
similarity index 100%
rename from tests/run_dist_lp.jl
rename to test/run_dist_lp.jl
diff --git a/tests/run_simulation.jl b/test/run_simulation.jl
similarity index 93%
rename from tests/run_simulation.jl
rename to test/run_simulation.jl
index b79d69e178929268486d921aac87a7d945e2062a..6ce755fb3b6383021c9fee59ad0befdfd97fec95 100644
--- a/tests/run_simulation.jl
+++ b/test/run_simulation.jl
@@ -2,7 +2,7 @@
using Test
import MarkovProcesses: get_module_path
-str_dir_pics = get_module_path() * "/tests/simulation/res_pics"
+str_dir_pics = get_module_path() * "/test/simulation/res_pics"
if !isdir(str_dir_pics) mkdir(str_dir_pics) end
@testset "Simulation tests" begin
diff --git a/tests/run_unit.jl b/test/run_unit.jl
similarity index 100%
rename from tests/run_unit.jl
rename to test/run_unit.jl
diff --git a/test/runtests.jl b/test/runtests.jl
new file mode 100644
index 0000000000000000000000000000000000000000..708e8086b82b92ac526601382cb0236578b4b5fc
--- /dev/null
+++ b/test/runtests.jl
@@ -0,0 +1,8 @@
+
+include("run_unit.jl")
+include("run_simulation.jl")
+include("run_dist_lp.jl")
+include("run_automata.jl")
+include("run_abc_smc.jl")
+include("run_abc_model_choice.jl")
+
diff --git a/tests/simulation/plot_pkg.jl b/test/simulation/plot_pkg.jl
similarity index 100%
rename from tests/simulation/plot_pkg.jl
rename to test/simulation/plot_pkg.jl
diff --git a/tests/simulation/plot_sync_doping_3way_oscillator.jl b/test/simulation/plot_sync_doping_3way_oscillator.jl
similarity index 91%
rename from tests/simulation/plot_sync_doping_3way_oscillator.jl
rename to test/simulation/plot_sync_doping_3way_oscillator.jl
index 389b07998a6ae5b03df9ae19afe2f7a52be925fa..abe43d1b741cf9b8b20a0065e5dc5ef148ec8da0 100644
--- a/tests/simulation/plot_sync_doping_3way_oscillator.jl
+++ b/test/simulation/plot_sync_doping_3way_oscillator.jl
@@ -1,7 +1,7 @@
using MarkovProcesses
load_plots()
-path_pics = get_module_path() * "/tests/simulation/res_pics/"
+path_pics = get_module_path() * "/test/simulation/res_pics/"
load_model("doping_3way_oscillator")
observe_all!(doping_3way_oscillator)
diff --git a/tests/simulation/plot_sync_repressilator.jl b/test/simulation/plot_sync_repressilator.jl
similarity index 89%
rename from tests/simulation/plot_sync_repressilator.jl
rename to test/simulation/plot_sync_repressilator.jl
index de4e56a03e5bec5c4bb5acf9dea447724ad68a12..b1c05d2533e6b338bf4f47ae8fb77ef6b1f282af 100644
--- a/tests/simulation/plot_sync_repressilator.jl
+++ b/test/simulation/plot_sync_repressilator.jl
@@ -1,7 +1,7 @@
using MarkovProcesses
load_plots()
-path_pics = get_module_path() * "/tests/simulation/res_pics/"
+path_pics = get_module_path() * "/test/simulation/res_pics/"
load_model("repressilator")
observe_all!(repressilator)
diff --git a/tests/simulation/sim_er.jl b/test/simulation/sim_er.jl
similarity index 69%
rename from tests/simulation/sim_er.jl
rename to test/simulation/sim_er.jl
index 96857f4db14fa2e2a5a0305e95e1010aa9a18912..09f7698309578450ccdbd4fd9b5565a2a364c0e0 100644
--- a/tests/simulation/sim_er.jl
+++ b/test/simulation/sim_er.jl
@@ -7,7 +7,7 @@ load_model("ER")
σ = simulate(ER)
plt.figure()
plt.step(times(σ), σ[:P], "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_er.png", dpi=480)
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_er.png", dpi=480)
plt.close()
return true
diff --git a/tests/simulation/sim_er_row_buffer_bounded.jl b/test/simulation/sim_er_row_buffer_bounded.jl
similarity index 66%
rename from tests/simulation/sim_er_row_buffer_bounded.jl
rename to test/simulation/sim_er_row_buffer_bounded.jl
index c92dd9e82f2958db59cde9452419e5f67ef32263..b4c3e022a7e60ba7ba3070127343c790fb52d65a 100644
--- a/tests/simulation/sim_er_row_buffer_bounded.jl
+++ b/test/simulation/sim_er_row_buffer_bounded.jl
@@ -1,6 +1,6 @@
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
using PyPlot
load_model("_bench_perf_test/ER_row_buffer")
@@ -9,7 +9,7 @@ ER_row_buffer.time_bound = 10.0
σ = _simulate_row_buffer(ER_row_buffer)
plt.figure()
plt.step(times(σ), _get_values_row(σ,:P), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_er_row_buffer_bounded.svg")
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_er_row_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_pm_er.jl b/test/simulation/sim_pm_er.jl
similarity index 69%
rename from tests/simulation/sim_pm_er.jl
rename to test/simulation/sim_pm_er.jl
index 42efe9410471ad05e7f245eec272de9ec60a1204..e739d607ddbb7e03fdf451012adb4decd567cea9 100644
--- a/tests/simulation/sim_pm_er.jl
+++ b/test/simulation/sim_pm_er.jl
@@ -9,7 +9,7 @@ pm_ER = ParametricModel(ER, (:k1, Uniform(0.0,100.0)), (:k2, Uniform(0.0,100.0))
prior_p = [0.2, 40.0]
σ = simulate(pm_ER, prior_p)
-plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_er_long.svg")
+plot(σ; filename = get_module_path() * "/test/simulation/res_pics/sim_pm_er_long.svg")
return true
diff --git a/tests/simulation/sim_pm_sync_er.jl b/test/simulation/sim_pm_sync_er.jl
similarity index 76%
rename from tests/simulation/sim_pm_sync_er.jl
rename to test/simulation/sim_pm_sync_er.jl
index 19b612224bea9470eecd81273a5d8b3d3de2da98..39c1d83791d5681638399b73a3b87d3a8b74eed2 100644
--- a/tests/simulation/sim_pm_sync_er.jl
+++ b/test/simulation/sim_pm_sync_er.jl
@@ -11,7 +11,7 @@ pm_sync_ER = ParametricModel(ER*A_F, (:k1, Uniform(0.0,100.0)), (:k2, Uniform(0.
prior_p = [0.2, 40.0]
σ = simulate(pm_sync_ER, prior_p)
-plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_sync_er_long.svg")
+plot(σ; filename = get_module_path() * "/test/simulation/res_pics/sim_pm_sync_er_long.svg")
return true
diff --git a/test/simulation/sim_poisson.jl b/test/simulation/sim_poisson.jl
new file mode 100644
index 0000000000000000000000000000000000000000..75f0818f56b6898c47bb391cbf093357ea894c29
--- /dev/null
+++ b/test/simulation/sim_poisson.jl
@@ -0,0 +1,11 @@
+
+using MarkovProcesses
+load_plots()
+
+load_model("poisson")
+σ = simulate(poisson)
+#plot(σ; filename = get_module_path() * "/test/simulation/res_pics/sim_poisson.svg")
+plot(σ; filename = get_module_path() * "/test/simulation/res_pics/sim_poisson.svg")
+
+return true
+
diff --git a/tests/simulation/sim_repressilator.jl b/test/simulation/sim_repressilator.jl
similarity index 100%
rename from tests/simulation/sim_repressilator.jl
rename to test/simulation/sim_repressilator.jl
diff --git a/tests/simulation/sim_sir.jl b/test/simulation/sim_sir.jl
similarity index 72%
rename from tests/simulation/sim_sir.jl
rename to test/simulation/sim_sir.jl
index fe2740a63c5a057d7f832dc8c2aac027cbd2a6fe..c0e8da5ff98a7a76a4b6f61fc144cec758f1a9da 100644
--- a/tests/simulation/sim_sir.jl
+++ b/test/simulation/sim_sir.jl
@@ -7,7 +7,7 @@ load_model("SIR")
σ = simulate(SIR)
plt.figure()
plt.step(times(σ), σ[:I], "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir.svg")
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_sir.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_bounded.jl b/test/simulation/sim_sir_bounded.jl
similarity index 72%
rename from tests/simulation/sim_sir_bounded.jl
rename to test/simulation/sim_sir_bounded.jl
index fe3dcc76264b74fcce2b83bc51b11ed7610508fc..1e9ab1ff5d569734bdcdb4a21c35e84d070542a3 100644
--- a/tests/simulation/sim_sir_bounded.jl
+++ b/test/simulation/sim_sir_bounded.jl
@@ -8,7 +8,7 @@ SIR.time_bound = 100.0
σ = simulate(SIR)
plt.figure()
plt.step(times(σ), σ[:I], "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_bounded.svg")
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_sir_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_col_buffer_bounded.jl b/test/simulation/sim_sir_col_buffer_bounded.jl
similarity index 66%
rename from tests/simulation/sim_sir_col_buffer_bounded.jl
rename to test/simulation/sim_sir_col_buffer_bounded.jl
index d68f9901db947487057269c01e643af529e6fb6b..d3f6887a52618b8e07bece852aa2d8d3e3cc8a01 100644
--- a/tests/simulation/sim_sir_col_buffer_bounded.jl
+++ b/test/simulation/sim_sir_col_buffer_bounded.jl
@@ -1,6 +1,6 @@
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
using PyPlot
load_model("_bench_perf_test/SIR_col_buffer")
@@ -9,7 +9,7 @@ SIR_col_buffer.time_bound = 100.0
σ = _simulate_col_buffer(SIR_col_buffer)
plt.figure()
plt.step(times(σ), _get_values_col(σ,:I), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_col_buffer_bounded.svg")
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_sir_col_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_row_buffer_bounded.jl b/test/simulation/sim_sir_row_buffer_bounded.jl
similarity index 66%
rename from tests/simulation/sim_sir_row_buffer_bounded.jl
rename to test/simulation/sim_sir_row_buffer_bounded.jl
index d10633dc4f8131fd1224e99e5e27ed6768a4c451..329aea537f5557d955a73f9ca202b76db6c1b132 100644
--- a/tests/simulation/sim_sir_row_buffer_bounded.jl
+++ b/test/simulation/sim_sir_row_buffer_bounded.jl
@@ -1,6 +1,6 @@
using MarkovProcesses
-include(get_module_path() * "/core/_tests_simulate.jl")
+include(get_module_path() * "/src/_tests_simulate.jl")
using PyPlot
load_model("_bench_perf_test/SIR_row_buffer")
@@ -9,7 +9,7 @@ SIR_row_buffer.time_bound = 100.0
σ = _simulate_row_buffer(SIR_row_buffer)
plt.figure()
plt.step(times(σ), _get_values_row(σ,:I), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_row_buffer_bounded.svg")
+plt.savefig(get_module_path() * "/test/simulation/res_pics/sim_sir_row_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_tauleap.jl b/test/simulation/sim_sir_tauleap.jl
similarity index 53%
rename from tests/simulation/sim_sir_tauleap.jl
rename to test/simulation/sim_sir_tauleap.jl
index 841953a96d160a5248ce8b78c577b87a73b7f1d6..805b2a567048d20a457e5f88613c5ca441eb80b4 100644
--- a/tests/simulation/sim_sir_tauleap.jl
+++ b/test/simulation/sim_sir_tauleap.jl
@@ -4,7 +4,7 @@ load_plots()
load_model("SIR_tauleap")
σ = simulate(SIR_tauleap)
-plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_sir_tauleap.svg")
+plot(σ; filename = get_module_path() * "/test/simulation/res_pics/sim_sir_tauleap.svg")
return true
diff --git a/tests/unit/absorbing_x0.jl b/test/unit/absorbing_x0.jl
similarity index 100%
rename from tests/unit/absorbing_x0.jl
rename to test/unit/absorbing_x0.jl
diff --git a/tests/unit/change_obs_var_sir.jl b/test/unit/change_obs_var_sir.jl
similarity index 100%
rename from tests/unit/change_obs_var_sir.jl
rename to test/unit/change_obs_var_sir.jl
diff --git a/tests/unit/change_obs_var_sir_2.jl b/test/unit/change_obs_var_sir_2.jl
similarity index 100%
rename from tests/unit/change_obs_var_sir_2.jl
rename to test/unit/change_obs_var_sir_2.jl
diff --git a/tests/unit/check_model_consistency.jl b/test/unit/check_model_consistency.jl
similarity index 100%
rename from tests/unit/check_model_consistency.jl
rename to test/unit/check_model_consistency.jl
diff --git a/tests/unit/check_trajectory_consistency.jl b/test/unit/check_trajectory_consistency.jl
similarity index 100%
rename from tests/unit/check_trajectory_consistency.jl
rename to test/unit/check_trajectory_consistency.jl
diff --git a/tests/unit/create_automata.jl b/test/unit/create_automata.jl
similarity index 100%
rename from tests/unit/create_automata.jl
rename to test/unit/create_automata.jl
diff --git a/tests/unit/create_models.jl b/test/unit/create_models.jl
similarity index 100%
rename from tests/unit/create_models.jl
rename to test/unit/create_models.jl
diff --git a/tests/unit/density_pm.jl b/test/unit/density_pm.jl
similarity index 100%
rename from tests/unit/density_pm.jl
rename to test/unit/density_pm.jl
diff --git a/tests/unit/dist_lp.jl b/test/unit/dist_lp.jl
similarity index 100%
rename from tests/unit/dist_lp.jl
rename to test/unit/dist_lp.jl
diff --git a/tests/unit/dist_lp_var.jl b/test/unit/dist_lp_var.jl
similarity index 100%
rename from tests/unit/dist_lp_var.jl
rename to test/unit/dist_lp_var.jl
diff --git a/tests/unit/distributed_simulation.jl b/test/unit/distributed_simulation.jl
similarity index 98%
rename from tests/unit/distributed_simulation.jl
rename to test/unit/distributed_simulation.jl
index 06db472f208a4afb71685b0471bb2bf5b8ba5d8b..e3504ac6d4fe2c03bb67d0c6ff3546b6d59e366f 100644
--- a/tests/unit/distributed_simulation.jl
+++ b/test/unit/distributed_simulation.jl
@@ -6,7 +6,7 @@ using MarkovProcesses
addprocs(2)
module_path = get_module_path()
@everywhere module_path = $module_path
-@everywhere push!(LOAD_PATH, "$(module_path)/core")
+@everywhere push!(LOAD_PATH, "$(module_path)/src")
@everywhere using MarkovProcesses
test_all = true
diff --git a/tests/unit/draw_pm.jl b/test/unit/draw_pm.jl
similarity index 100%
rename from tests/unit/draw_pm.jl
rename to test/unit/draw_pm.jl
diff --git a/tests/unit/getindex_access_trajectory.jl b/test/unit/getindex_access_trajectory.jl
similarity index 100%
rename from tests/unit/getindex_access_trajectory.jl
rename to test/unit/getindex_access_trajectory.jl
diff --git a/tests/unit/is_always_bounded_sir.jl b/test/unit/is_always_bounded_sir.jl
similarity index 100%
rename from tests/unit/is_always_bounded_sir.jl
rename to test/unit/is_always_bounded_sir.jl
diff --git a/tests/unit/l_dist_lp.jl b/test/unit/l_dist_lp.jl
similarity index 100%
rename from tests/unit/l_dist_lp.jl
rename to test/unit/l_dist_lp.jl
diff --git a/tests/unit/length_obs_var.jl b/test/unit/length_obs_var.jl
similarity index 100%
rename from tests/unit/length_obs_var.jl
rename to test/unit/length_obs_var.jl
diff --git a/tests/unit/load_model.jl b/test/unit/load_model.jl
similarity index 100%
rename from tests/unit/load_model.jl
rename to test/unit/load_model.jl
diff --git a/tests/unit/load_model_bench.jl b/test/unit/load_model_bench.jl
similarity index 100%
rename from tests/unit/load_model_bench.jl
rename to test/unit/load_model_bench.jl
diff --git a/tests/unit/load_module.jl b/test/unit/load_module.jl
similarity index 100%
rename from tests/unit/load_module.jl
rename to test/unit/load_module.jl
diff --git a/tests/unit/long_sim_er.jl b/test/unit/long_sim_er.jl
similarity index 100%
rename from tests/unit/long_sim_er.jl
rename to test/unit/long_sim_er.jl
diff --git a/tests/unit/macro_network_model.jl b/test/unit/macro_network_model.jl
similarity index 100%
rename from tests/unit/macro_network_model.jl
rename to test/unit/macro_network_model.jl
diff --git a/tests/unit/model_prior.jl b/test/unit/model_prior.jl
similarity index 100%
rename from tests/unit/model_prior.jl
rename to test/unit/model_prior.jl
diff --git a/tests/unit/models_exps_er_1d.jl b/test/unit/models_exps_er_1d.jl
similarity index 100%
rename from tests/unit/models_exps_er_1d.jl
rename to test/unit/models_exps_er_1d.jl
diff --git a/tests/unit/models_exps_er_2d.jl b/test/unit/models_exps_er_2d.jl
similarity index 100%
rename from tests/unit/models_exps_er_2d.jl
rename to test/unit/models_exps_er_2d.jl
diff --git a/tests/unit/observe_all.jl b/test/unit/observe_all.jl
similarity index 100%
rename from tests/unit/observe_all.jl
rename to test/unit/observe_all.jl
diff --git a/tests/unit/prints.jl b/test/unit/prints.jl
similarity index 100%
rename from tests/unit/prints.jl
rename to test/unit/prints.jl
diff --git a/tests/unit/set_param.jl b/test/unit/set_param.jl
similarity index 100%
rename from tests/unit/set_param.jl
rename to test/unit/set_param.jl
diff --git a/tests/unit/set_x0.jl b/test/unit/set_x0.jl
similarity index 100%
rename from tests/unit/set_x0.jl
rename to test/unit/set_x0.jl
diff --git a/tests/unit/side_effects_1.jl b/test/unit/side_effects_1.jl
similarity index 100%
rename from tests/unit/side_effects_1.jl
rename to test/unit/side_effects_1.jl
diff --git a/tests/unit/simulate_available_models.jl b/test/unit/simulate_available_models.jl
similarity index 100%
rename from tests/unit/simulate_available_models.jl
rename to test/unit/simulate_available_models.jl
diff --git a/tests/unit/simulate_er.jl b/test/unit/simulate_er.jl
similarity index 100%
rename from tests/unit/simulate_er.jl
rename to test/unit/simulate_er.jl
diff --git a/tests/unit/simulate_sir.jl b/test/unit/simulate_sir.jl
similarity index 100%
rename from tests/unit/simulate_sir.jl
rename to test/unit/simulate_sir.jl
diff --git a/tests/unit/simulate_sir_bounded.jl b/test/unit/simulate_sir_bounded.jl
similarity index 100%
rename from tests/unit/simulate_sir_bounded.jl
rename to test/unit/simulate_sir_bounded.jl
diff --git a/tests/unit/simulation_stop_criteria.jl b/test/unit/simulation_stop_criteria.jl
similarity index 100%
rename from tests/unit/simulation_stop_criteria.jl
rename to test/unit/simulation_stop_criteria.jl
diff --git a/tests/unit/square_wave_oscillator.jl b/test/unit/square_wave_oscillator.jl
similarity index 100%
rename from tests/unit/square_wave_oscillator.jl
rename to test/unit/square_wave_oscillator.jl
diff --git a/tests/unit/vectorize.jl b/test/unit/vectorize.jl
similarity index 100%
rename from tests/unit/vectorize.jl
rename to test/unit/vectorize.jl
diff --git a/tests/simulation/sim_poisson.jl b/tests/simulation/sim_poisson.jl
deleted file mode 100644
index 93a55c9f004842b44ec242039badf9257bc7cee9..0000000000000000000000000000000000000000
--- a/tests/simulation/sim_poisson.jl
+++ /dev/null
@@ -1,11 +0,0 @@
-
-using MarkovProcesses
-load_plots()
-
-load_model("poisson")
-σ = simulate(poisson)
-#plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_poisson.svg")
-plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_poisson.svg")
-
-return true
-