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Add more systems (#5)
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* Add more systems

There were still some systems missing that were defined in the style of
```python
class BlinkingVortex(BlinkingRotlet):
    pass
```
This PR adds them

* Test that the documentation works - mostly for codecov

* Fix a typo

* Add new systems to `visualize_all_systems.jl`

* JuliaFormatter.jl

* Add the new systems to the tests
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@nathanaelbosch
nathanaelbosch authored Dec 23, 2023
1 parent 95be70d commit 85b84b8
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Showing 3 changed files with 136 additions and 14 deletions.
133 changes: 119 additions & 14 deletions src/chaotic_attractors.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -755,8 +755,23 @@ function LidDrivenCavityFlow()
return prob
end

# class BlinkingVortex(BlinkingRotlet):
# pass
function BlinkingVortex end
function originalcode(::typeof(BlinkingVortex))
"""
class BlinkingVortex(BlinkingRotlet):
pass
"""
end
@doc make_docstring(BlinkingVortex) BlinkingVortex
function BlinkingVortex()
prob = BlinkingRotlet()
u0 = Float64.(ATTRACTOR_DATA["BlinkingVortex"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["BlinkingVortex"]["parameters"])
T = ATTRACTOR_DATA["BlinkingVortex"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

# class InteriorSquirmer(DynSys):

Expand Down Expand Up @@ -2050,8 +2065,23 @@ function Arneodo()
return prob
end

# class Coullet(Arneodo):
# pass
function Coullet end
function originalcode(::typeof(Coullet))
"""
class Coullet(Arneodo):
pass
"""
end
@doc make_docstring(Coullet) Coullet
function Coullet()
prob = Arneodo()
u0 = Float64.(ATTRACTOR_DATA["Coullet"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["Coullet"]["parameters"])
T = ATTRACTOR_DATA["Coullet"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

function Rucklidge end
originalcode(::typeof(Rucklidge)) = """
Expand Down Expand Up @@ -2109,8 +2139,23 @@ function Sakarya()
return prob
end

# class LiuChen(Sakarya):
# pass
function LiuChen end
function originalcode(::typeof(LiuChen))
"""
class LiuChen(Sakarya):
pass
"""
end
@doc make_docstring(LiuChen) LiuChen
function LiuChen()
prob = Sakarya()
u0 = Float64.(ATTRACTOR_DATA["LiuChen"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["LiuChen"]["parameters"])
T = ATTRACTOR_DATA["LiuChen"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

function RayleighBenard end
originalcode(::typeof(RayleighBenard)) = """
Expand Down Expand Up @@ -2196,8 +2241,23 @@ function Bouali2()
return prob
end

# class Bouali(Bouali2):
# pass
function Bouali end
function originalcode(::typeof(Bouali))
"""
class Bouali(Bouali2):
pass
"""
end
@doc make_docstring(Bouali) Bouali
function Bouali()
prob = Bouali2()
u0 = Float64.(ATTRACTOR_DATA["Bouali"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["Bouali"]["parameters"])
T = ATTRACTOR_DATA["Bouali"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

function LuChenCheng end
originalcode(::typeof(LuChenCheng)) = """
Expand Down Expand Up @@ -2535,11 +2595,41 @@ function DequanLi()
return prob
end

# class PanXuZhou(DequanLi):
# pass
function PanXuZhou end
function originalcode(::typeof(PanXuZhou))
"""
class PanXuZhou(DequanLi):
pass
"""
end
@doc make_docstring(PanXuZhou) PanXuZhou
function PanXuZhou()
prob = DequanLi()
u0 = Float64.(ATTRACTOR_DATA["PanXuZhou"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["PanXuZhou"]["parameters"])
T = ATTRACTOR_DATA["PanXuZhou"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

# class Tsucs2(DequanLi):
# pass
function Tsucs2 end
function originalcode(::typeof(Tsucs2))
"""
class Tsucs2(DequanLi):
pass
"""
end
@doc make_docstring(Tsucs2) Tsucs2
function Tsucs2()
prob = DequanLi()
u0 = Float64.(ATTRACTOR_DATA["Tsucs2"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["Tsucs2"]["parameters"])
T = ATTRACTOR_DATA["Tsucs2"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

function ArnoldWeb end
originalcode(::typeof(ArnoldWeb)) = """
Expand Down Expand Up @@ -3874,8 +3964,23 @@ function Torus()
return prob
end

# class CaTwoPlusQuasiperiodic(CaTwoPlus):
# pass
function CaTwoPlusQuasiperiodic end
function originalcode(::typeof(CaTwoPlusQuasiperiodic))
"""
class CaTwoPlusQuasiperiodic(CaTwoPlus):
pass
"""
end
@doc make_docstring(CaTwoPlusQuasiperiodic) CaTwoPlusQuasiperiodic
function CaTwoPlusQuasiperiodic()
prob = CaTwoPlus()
u0 = Float64.(ATTRACTOR_DATA["CaTwoPlusQuasiperiodic"]["initial_conditions"])
p = format_parameters(ATTRACTOR_DATA["CaTwoPlusQuasiperiodic"]["parameters"])
T = ATTRACTOR_DATA["CaTwoPlusQuasiperiodic"]["period"] * N
tspan = (0.0, T)
prob = remake(prob, u0 = u0, p = p, tspan = tspan)
return prob
end

function Hopfield end
originalcode(::typeof(Hopfield)) = """
Expand Down
10 changes: 10 additions & 0 deletions test/test_chaotic_attractors.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,12 @@ using SafeTestsets
ChaoticDynamicalSystemLibrary.BickleyJet,
ChaoticDynamicalSystemLibrary.Blasius,
ChaoticDynamicalSystemLibrary.BlinkingRotlet,
ChaoticDynamicalSystemLibrary.BlinkingVortex,
ChaoticDynamicalSystemLibrary.Bouali,
ChaoticDynamicalSystemLibrary.Bouali2,
ChaoticDynamicalSystemLibrary.BurkeShaw,
ChaoticDynamicalSystemLibrary.CaTwoPlus,
ChaoticDynamicalSystemLibrary.CaTwoPlusQuasiperiodic,
ChaoticDynamicalSystemLibrary.CellCycle,
ChaoticDynamicalSystemLibrary.CellularNeuralNetwork,
ChaoticDynamicalSystemLibrary.Chen,
Expand All @@ -27,6 +30,7 @@ using SafeTestsets
ChaoticDynamicalSystemLibrary.CircadianRhythm,
ChaoticDynamicalSystemLibrary.CoevolvingPredatorPrey,
ChaoticDynamicalSystemLibrary.Colpitts,
ChaoticDynamicalSystemLibrary.Coullet,
ChaoticDynamicalSystemLibrary.Dadras,
ChaoticDynamicalSystemLibrary.DequanLi,
ChaoticDynamicalSystemLibrary.DoubleGyre,
Expand Down Expand Up @@ -70,6 +74,7 @@ using SafeTestsets
ChaoticDynamicalSystemLibrary.LorenzBounded,
ChaoticDynamicalSystemLibrary.LorenzCoupled,
ChaoticDynamicalSystemLibrary.LorenzStenflo,
ChaoticDynamicalSystemLibrary.LiuChen,
ChaoticDynamicalSystemLibrary.LuChen,
ChaoticDynamicalSystemLibrary.LuChenCheng,
ChaoticDynamicalSystemLibrary.MacArthur,
Expand All @@ -79,6 +84,7 @@ using SafeTestsets
ChaoticDynamicalSystemLibrary.NoseHoover,
ChaoticDynamicalSystemLibrary.NuclearQuadrupole,
ChaoticDynamicalSystemLibrary.OscillatingFlow,
ChaoticDynamicalSystemLibrary.PanXuZhou,
ChaoticDynamicalSystemLibrary.PehlivanWei,
ChaoticDynamicalSystemLibrary.Qi,
ChaoticDynamicalSystemLibrary.QiChen,
Expand Down Expand Up @@ -117,13 +123,17 @@ using SafeTestsets
ChaoticDynamicalSystemLibrary.SwingingAtwood,
ChaoticDynamicalSystemLibrary.Thomas,
ChaoticDynamicalSystemLibrary.Torus,
ChaoticDynamicalSystemLibrary.Tsucs2,
ChaoticDynamicalSystemLibrary.TurchinHanski,
ChaoticDynamicalSystemLibrary.VallisElNino,
ChaoticDynamicalSystemLibrary.WangSun,
ChaoticDynamicalSystemLibrary.WindmiReduced,
ChaoticDynamicalSystemLibrary.YuWang,
ChaoticDynamicalSystemLibrary.YuWang2,
ChaoticDynamicalSystemLibrary.ZhouChen)
@test ChaoticDynamicalSystemLibrary.originalcode(System) isa String
@test_nowarn ChaoticDynamicalSystemLibrary.make_docstring(System)

prob = @test_nowarn System()
@test prob isa ODEProblem
@test_nowarn solve(prob, Tsit5(), abstol = 1e-6, reltol = 1e-4)
Expand Down
7 changes: 7 additions & 0 deletions visualize_all_systems.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,12 @@ ALL_SYSTEMS = (ChaoticDynamicalSystemLibrary.Aizawa,
ChaoticDynamicalSystemLibrary.BickleyJet,
ChaoticDynamicalSystemLibrary.Blasius,
ChaoticDynamicalSystemLibrary.BlinkingRotlet,
ChaoticDynamicalSystemLibrary.BlinkingVortex,
ChaoticDynamicalSystemLibrary.Bouali,
ChaoticDynamicalSystemLibrary.Bouali2,
ChaoticDynamicalSystemLibrary.BurkeShaw,
ChaoticDynamicalSystemLibrary.CaTwoPlus,
ChaoticDynamicalSystemLibrary.CaTwoPlusQuasiperiodic,
ChaoticDynamicalSystemLibrary.CellCycle,
ChaoticDynamicalSystemLibrary.CellularNeuralNetwork,
ChaoticDynamicalSystemLibrary.Chen,
Expand All @@ -22,6 +25,7 @@ ALL_SYSTEMS = (ChaoticDynamicalSystemLibrary.Aizawa,
ChaoticDynamicalSystemLibrary.CircadianRhythm,
ChaoticDynamicalSystemLibrary.CoevolvingPredatorPrey,
ChaoticDynamicalSystemLibrary.Colpitts,
ChaoticDynamicalSystemLibrary.Coullet,
ChaoticDynamicalSystemLibrary.Dadras,
ChaoticDynamicalSystemLibrary.DequanLi,
ChaoticDynamicalSystemLibrary.DoubleGyre,
Expand Down Expand Up @@ -65,6 +69,7 @@ ALL_SYSTEMS = (ChaoticDynamicalSystemLibrary.Aizawa,
ChaoticDynamicalSystemLibrary.LorenzBounded,
ChaoticDynamicalSystemLibrary.LorenzCoupled,
ChaoticDynamicalSystemLibrary.LorenzStenflo,
ChaoticDynamicalSystemLibrary.LiuChen,
ChaoticDynamicalSystemLibrary.LuChen,
ChaoticDynamicalSystemLibrary.LuChenCheng,
ChaoticDynamicalSystemLibrary.MacArthur,
Expand All @@ -74,6 +79,7 @@ ALL_SYSTEMS = (ChaoticDynamicalSystemLibrary.Aizawa,
ChaoticDynamicalSystemLibrary.NoseHoover,
ChaoticDynamicalSystemLibrary.NuclearQuadrupole,
ChaoticDynamicalSystemLibrary.OscillatingFlow,
ChaoticDynamicalSystemLibrary.PanXuZhou,
ChaoticDynamicalSystemLibrary.PehlivanWei,
ChaoticDynamicalSystemLibrary.Qi,
ChaoticDynamicalSystemLibrary.QiChen,
Expand Down Expand Up @@ -112,6 +118,7 @@ ALL_SYSTEMS = (ChaoticDynamicalSystemLibrary.Aizawa,
ChaoticDynamicalSystemLibrary.SwingingAtwood,
ChaoticDynamicalSystemLibrary.Thomas,
ChaoticDynamicalSystemLibrary.Torus,
ChaoticDynamicalSystemLibrary.Tsucs2,
ChaoticDynamicalSystemLibrary.TurchinHanski,
ChaoticDynamicalSystemLibrary.VallisElNino,
ChaoticDynamicalSystemLibrary.WangSun,
Expand Down

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Registration pull request created: JuliaRegistries/General/97672

Tip: Release Notes

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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

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git tag -a v0.1.0 -m "<description of version>" 85b84b8a1b00d02e7b9e7c6967d9b7523a8a4fee
git push origin v0.1.0

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