Skip to content

Commit b576c0d

Browse files
thevolatilebitthevolatilebit
committed
agentize state, observables
Signed-off-by: Bíma, Jan <jan.bima@merck.com>
1 parent d0e195b commit b576c0d

File tree

11 files changed

+109
-406
lines changed

11 files changed

+109
-406
lines changed

‎LICENSE‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
The MIT License
22

3-
Copyright © 2022 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
3+
Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
44

55
Jan Bima (MSD), Otto Ritter (MSD), Sean L. Wu (Merck)
66

‎LICENSES_THIRD_PARTY‎

Lines changed: 3 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,40 +1,10 @@
1-
ReactiveDynamics.jl depends on third-party Julia packages which may be distributed under different licenses. We have listed all of these third party packages and their licenses below. For the most up-to-date information, see `Project.toml`.
1+
ReactiveDynamics.jl depends on third-party Julia packages, which may be distributed under various licenses. For the most recent list of these packages, refer to `Project.toml` and consult the license terms of the individual packages.
22

3-
You must agree to the terms of these licenses, in addition to the ReactiveDynamics source code license, in order to use this software.
3+
You must agree to the terms of these licenses, in addition to the ReactiveDynamics.jl source code license, in order to use this software.
44

55
--------------------------------------------------
66
Third party software listed by License type
77
--------------------------------------------------
88

99
MIT License (or adaptations) (https://www.opensource.org/licenses/MIT)
10-
* The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md
11-
* BenchmarkTools.jl - https://github.com/JuliaCI/BenchmarkTools.jl
12-
* CSV - https://github.com/JuliaData/CSV.jl
13-
* Catlab - https://github.com/AlgebraicJulia/Catlab.jl
14-
* ComponentArrays.jl - https://github.com/jonniedie/ComponentArrays.jl
15-
* Crayons - https://github.com/KristofferC/Crayons.jl
16-
* DataFrames.jl - https://github.com/JuliaData/DataFrames.jl
17-
* DiffEqBase.jl - https://github.com/SciML/DiffEqBase.jl
18-
* DifferentialEquations.jl - https://github.com/SciML/DifferentialEquations.jl
19-
* Distributions.jl - https://github.com/JuliaStats/Distributions.jl
20-
* Documenter - https://github.com/JuliaDocs/Documenter.jl
21-
* DocumenterMarkdown - https://github.com/JuliaDocs/DocumenterMarkdown.jl
22-
* GeneratedExpressions.jl - https://github.com/Merck/GeneratedExpressions.jl
23-
* IJulia - https://github.com/JuliaLang/IJulia.jl
24-
* JLD2 - https://github.com/JuliaIO/JLD2.jl
25-
* JSON.jl - https://github.com/JuliaIO/JSON.jl
26-
* MacroTools.jl - https://github.com/FluxML/MacroTools.jl
27-
* NLopt - https://github.com/JuliaOpt/NLopt.jl
28-
* OrdinaryDiffEq - https://github.com/SciML/OrdinaryDiffEq.jl
29-
* Plots - https://github.com/JuliaPlots/Plots.jl
30-
* Pluto.jl - https://github.com/fonsp/Pluto.jl
31-
* Reexport - https://github.com/simonster/Reexport.jl
32-
* SafeTestsets - https://github.com/YingboMa/SafeTestsets.jl
33-
* Statistics.jl - https://github.com/JuliaStats/Statistics.jl
34-
* StatsFuns.jl - https://github.com/JuliaStats/StatsFuns.jl
35-
* Symbolics.jl - https://github.com/JuliaSymbolics/Symbolics.jl
36-
* TOML.jl - https://github.com/JuliaLang/TOML.jl
37-
* Tables.jl - https://github.com/JuliaData/Tables.jl
38-
39-
The Unlicense (https://opensource.org/licenses/unlicense)
40-
* PlutoUI.jl - https://github.com/JuliaPluto/PlutoUI.jl
10+
* The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md

‎Project.toml‎

Lines changed: 19 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@ uuid = "c7456e7d-545a-4b79-91ea-6e93d96dd4d4"
33
version = "0.2.7"
44

55
[deps]
6+
AlgebraicAgents = "f6eb0ae3-10fa-40e6-88dd-9006ba45093a"
67
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
78
Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
89
ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
@@ -23,6 +24,7 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
2324
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
2425
Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
2526
PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
27+
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
2628
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
2729
SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
2830
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -33,31 +35,31 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
3335
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
3436

3537
[compat]
36-
julia = "1.9"
37-
DifferentialEquations = "7.9"
38-
StatsFuns = "1.3"
38+
CSV = "0.10"
3939
Catlab = "0.14"
40+
ComponentArrays = "0.14"
41+
Crayons = "4.1"
4042
DataFrames = "1.6"
41-
PlutoUI = "0.7"
42-
Statistics = "1.9"
43+
DiffEqBase = "6.128"
44+
DifferentialEquations = "7.9"
45+
Distributions = "0.25"
46+
Documenter = "0.27"
4347
DocumenterMarkdown = "0.2"
44-
ComponentArrays = "0.14"
45-
JLD2 = "0.4"
4648
GeneratedExpressions = "0.1"
47-
DiffEqBase = "6.128"
49+
IJulia = "1.24"
50+
JLD2 = "0.4"
4851
JSON = "0.21"
52+
MacroTools = "0.5"
4953
NLopt = "1.0"
5054
OrdinaryDiffEq = "6.55"
51-
Symbolics = "5.5"
52-
IJulia = "1.24"
53-
SafeTestsets = "0.1"
54-
CSV = "0.10"
5555
Plots = "1.39"
56+
Pluto = "0.19"
57+
PlutoUI = "0.7"
5658
Reexport = "1.2"
59+
SafeTestsets = "0.1"
60+
Statistics = "1.9"
61+
StatsFuns = "1.3"
62+
Symbolics = "5.5"
5763
TOML = "1.0"
58-
MacroTools = "0.5"
59-
Crayons = "4.1"
60-
Documenter = "0.27"
6164
Tables = "1.10"
62-
Distributions = "0.25"
63-
Pluto = "0.19"
65+
julia = "1.9"

‎src/ReactiveDynamics.jl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -220,7 +220,7 @@ include.(readdir(joinpath(@__DIR__, "interface"); join = true))
220220
include.(readdir(joinpath(@__DIR__, "utils"); join = true))
221221
include.(readdir(joinpath(@__DIR__, "operators"); join = true))
222222
include("solvers.jl")
223-
include("optim.jl")
223+
#include("optim.jl")
224224
include("loadsave.jl")
225225

226226
end

‎src/compilers.jl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -112,7 +112,7 @@ function wrap_expr(fex, species_names, prm_names, varmap)
112112
)
113113
push!(letex.args[2].args, fex)
114114

115-
# the function shall be a function of the dynamic ReactiveDynamicsState structure: letex -> :(state -> $letex)
115+
# the function shall be a function of the dynamic ReactiveNetwork structure: letex -> :(state -> $letex)
116116
# eval the expression to a Julia function, save that function into the "compiled" acset
117117
return eval(:(state -> $letex))
118118
end

‎src/interface/reaction_parser.jl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ function recursively_choose(r_line, state)
2929
end
3030
end
3131

32-
function extract_reactants(r_line, state::ReactiveDynamicsState)
32+
function extract_reactants(r_line, state::ReactiveNetwork)
3333
r_line = recursively_choose(r_line, state)
3434

3535
return recursive_find_reactants!(

0 commit comments

Comments
 (0)