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‎HISTORY.md‎

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## Catalyst unreleased (master branch)
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## Catalyst 14.0
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- The `reactionparams`, `numreactionparams`, and `reactionparamsmap` functions have been removed.
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- To be more consistent with ModelingToolkit's immutability requirement for systems, we have removed API functions that mutate `ReactionSystem`s such as `addparam!`, `addreaction!`, `addspecies`, `@add_reactions`, and `merge!`. Please use `ModelingToolkit.extend` and `ModelingToolkit.compose` to generate new merged and/or composed `ReactionSystem`s from multiple component systems.
8-
- Added CatalystStructuralIdentifiabilityExtension, which permits StructuralIdentifiability.jl function to be applied directly to Catalyst systems. E.g. use
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```julia
10-
using Catalyst, StructuralIdentifiability
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goodwind_oscillator = @reaction_network begin
12-
(mmr(P,pₘ,1), dₘ), 0 <--> M
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(pₑ*M,dₑ), 0 <--> E
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(pₚ*E,dₚ), 0 <--> P
15-
end
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assess_identifiability(goodwind_oscillator; measured_quantities=[:M])
17-
```
18-
to assess (global) structural identifiability for all parameters and variables of the `goodwind_oscillator` model (under the presumption that we can measure `M` only).
19-
- Automatically handles conservation laws for structural identifiability problems (eliminates these internally to speed up computations).
20-
- Adds a tutorial to illustrate the use of the extension.
21-
- Enable adding metadata to individual reactions, e.g:
22-
```julia
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rn = @reaction_network begin
24-
@parameters η
25-
k, 2X --> X2, [noise_scaling=η]
26-
end
27-
getnoisescaling(rn)
28-
```
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- `SDEProblem` no longer takes the `noise_scaling` argument (see above for new approach to handle noise scaling).
30-
- Changed fields of internal `Reaction` structure. `ReactionSystems`s saved using `serialize` on previous Catalyst versions cannot be loaded using this (or later) versions.
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- Simulation of spatial ODEs now supported. For full details, please see https://github.com/SciML/Catalyst.jl/pull/644 and upcoming documentation. Note that these methods are currently considered alpha, with the interface and approach changing even in non-breaking Catalyst releases.
32-
- LatticeReactionSystem structure represents a spatial reaction network:
6+
7+
#### Breaking changes
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Catalyst v14 was prompted by the (breaking) release of ModelingToolkit v9, which
9+
introduced several breaking changes to Catalyst. A summary of these (and how to
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handle them) can be found
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[here](https://docs.sciml.ai/Catalyst/stable/v14_migration_guide/). These are
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briefly summarised in the following bullet points:
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- `ReactionSystem`s must now be marked *complete* before they are exposed to
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most forms of simulation and analysis. With the exception of `ReactionSystem`s
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created through the `@reaction_network` macro, all `ReactionSystem`s are *not*
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marked complete upon construction. The `complete` function can be used to mark
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`ReactionSystem`s as complete. To construct a `ReactionSystem` that is not
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marked complete via the DSL the new `@network_component` macro can be used.
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- The `states` function has been replaced with `unknowns`. The `get_states`
20+
function has been replaced with `get_unknowns`.
21+
- Support for most units (with the exception of `s`, `m`, `kg`, `A`, `K`, `mol`,
22+
and `cd`) has currently been dropped by ModelingToolkit, and hence they are
23+
unavailable via Catalyst too. Its is expected that eventually support for
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relevant chemical units such as molar will return to ModelingToolkit (and
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should then immediately work in Catalyst too).
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- Problem parameter values are now accessed through `prob.ps[p]` (rather than
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`prob[p]`).
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- ModelingToolkit currently does not support the safe application of the
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`remake` function, or safe direct mutation, for problems for which
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`remove_conserved = true` was used when updating the values of initial
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conditions. Instead, the values of each conserved constant must be directly
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specified.
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- The `reactionparams`, `numreactionparams`, and `reactionparamsmap` functions
34+
have been deprecated and removed.
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- To be more consistent with ModelingToolkit's immutability requirement for
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systems, we have removed API functions that mutate `ReactionSystem`s such as
37+
`addparam!`, `addreaction!`, `addspecies`, `@add_reactions`, and `merge!`.
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Please use `ModelingToolkit.extend` and `ModelingToolkit.compose` to generate
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new merged and/or composed `ReactionSystem`s from multiple component systems.
40+
41+
#### General changes
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- The `default_t()` and `default_time_deriv()` functions are now the preferred
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approaches for creating the default time independent variable and its
44+
differential. i.e.
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```julia
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# do
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t = default_t()
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@species A(t)
49+
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# avoid
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@variables t
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@species A(t)
53+
- It is now possible to add metadata to individual reactions, e.g. using:
54+
```julia
55+
rn = @reaction_network begin
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@parameters η
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k, 2X --> X2, [description="Dimerisation"]
58+
end
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getdescription(rn)
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```
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a more detailed description can be found [here](https://docs.sciml.ai/Catalyst/dev/model_creation/dsl_advanced/#dsl_advanced_options_reaction_metadata).
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- `SDEProblem` no longer takes the `noise_scaling` argument. Noise scaling is
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now handled through the `noise_scaling` metadata (described in more detail
64+
[here](https://docs.sciml.ai/Catalyst/stable/model_simulation/simulation_introduction/#simulation_intro_SDEs_noise_saling))
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- Fields of the internal `Reaction` structure have been changed.
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`ReactionSystems`s saved using `serialize` on previous Catalyst versions
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cannot be loaded using this (or later) versions.
68+
- A new function, `save_reactionsystem`, which permits the writing of
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`ReactionSystem` models to files, has been created. A thorough description of
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this function can be found
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[here](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/#Saving-Catalyst-models-to,-and-loading-them-from,-Julia-files)
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- Updated how compounds are created. E.g. use
73+
```julia
74+
@variables t C(t) O(t)
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@compound CO2 ~ C + 2O
76+
```
77+
to create a compound species `CO2` that consists of `C` and two `O`.
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- Added documentation for chemistry-related functionality (compound creation and
79+
reaction balancing).
80+
- Added function `isautonomous` to check if a `ReactionSystem` is autonomous.
81+
- Added function `steady_state_stability` to compute stability for steady
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states. Example:
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```julia
84+
# Creates model.
3485
rn = @reaction_network begin
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(p,d), 0 <--> X
3687
end
37-
tr = @transport_reaction D X
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lattice = Graphs.grid([5, 5])
39-
lrs = LatticeReactionSystem(rn, [tr], lattice)
40-
```
41-
- Here, if a `u0` or `p` vector is given with scalar values:
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p = [:p => 1.0, :d => 0.5]
89+
90+
# Finds (the trivial) steady state, and computes stability.
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steady_state = [2.0]
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steady_state_stability(steady_state, rn, p)
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```
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Here, `steady_state_stability` takes an optional keyword argument `tol =
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10*sqrt(eps())`, which is used to check that the real part of all eigenvalues
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are at least `tol` away from zero. Eigenvalues within `tol` of zero indicate
97+
that stability may not be reliably calculated.
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- Added a DSL option, `@combinatoric_ratelaws`, which can be used to toggle
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whether to use combinatorial rate laws within the DSL (this feature was
100+
already supported for programmatic modelling). Example:
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```julia
102+
# Creates model.
103+
rn = @reaction_network begin
104+
@combinatoric_ratelaws false
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(kB,kD), 2X <--> X2
106+
end
107+
```
108+
- Added a DSL option, `@observables` for [creating
109+
observables](https://docs.sciml.ai/Catalyst/stable/model_creation/dsl_advanced/#dsl_advanced_options_observables)
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(this feature was already supported for programmatic modelling).
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- Added DSL options `@continuous_events` and `@discrete_events` to add events to
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a model as part of its creation (this feature was already supported for
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programmatic modelling). Example:
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```julia
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rn = @reaction_network begin
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@continuous_events begin
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[X ~ 1.0] => [X ~ X + 1.0]
118+
end
119+
d, X --> 0
120+
end
121+
```
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- Added DSL option `@equations` to add (algebraic or differential) equations to
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a model as part of its creation (this feature was already supported for
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programmatic modelling). Example:
42125
```julia
43-
u0 = [:X => 1.0]
44-
p = [:p => 1.0, :d => 0.5, :D => 0.1]
126+
rn = @reaction_network begin
127+
@equations begin
128+
D(V) ~ 1 - V
129+
end
130+
(p/V,d/V), 0 <--> X
131+
end
45132
```
46-
this value will be used across the entire system. If their values are instead vectors, different values are used across the spatial system. Here
133+
couples the ODE $dV/dt = 1 - V$ to the reaction system.
134+
- Coupled reaction networks and differential equation (or algebraic differential
135+
equation) systems can now be converted to `SDESystem`s and `NonlinearSystem`s.
136+
137+
#### Structural identifiability extension
138+
- Added CatalystStructuralIdentifiabilityExtension, which permits
139+
StructuralIdentifiability.jl to be applied directly to Catalyst systems. E.g.
140+
use
47141
```julia
48-
X0 = zeros(25)
49-
X0[1] = 1.0
50-
u0 = [:X => X0]
142+
using Catalyst, StructuralIdentifiability
143+
goodwind_oscillator = @reaction_network begin
144+
(mmr(P,pₘ,1), dₘ), 0 <--> M
145+
(pₑ*M,dₑ), 0 <--> E
146+
(pₚ*E,dₚ), 0 <--> P
147+
end
148+
assess_identifiability(goodwind_oscillator; measured_quantities=[:M])
51149
```
52-
X's value will be `1.0` in the first vertex, but `0.0` in the remaining one (the system have 25 vertexes in total). SInce th parameters `p` and `d` are part of the non-spatial reaction network, their values are tied to vertexes. However, if the `D` parameter (which governs diffusion between vertexes) is given several values, these will instead correspond to the specific edges (and transportation along those edges.)
150+
to assess (global) structural identifiability for all parameters and variables
151+
of the `goodwind_oscillator` model (under the presumption that we can measure
152+
`M` only).
153+
- Automatically handles conservation laws for structural identifiability
154+
problems (eliminates these internally to speed up computations).
155+
- A more detailed of how this extension works can be found
156+
[here](https://docs.sciml.ai/Catalyst/stable/inverse_problems/structural_identifiability/).
53157

54-
- Update how compounds are created. E.g. use
55-
```julia
56-
@variables t C(t) O(t)
57-
@compound CO2 ~ C + 2O
58-
```
59-
to create a compound species `CO2` that consists of `C` and 2 `O`.
60-
- Added documentation for chemistry related functionality (compound creation and reaction balancing).
61-
- Add a CatalystBifurcationKitExtension, permitting BifurcationKit's `BifurcationProblem`s to be created from Catalyst reaction networks. Example usage:
62-
```julia
63-
using Catalyst
64-
wilhelm_2009_model = @reaction_network begin
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k1, Y --> 2X
66-
k2, 2X --> X + Y
67-
k3, X + Y --> Y
68-
k4, X --> 0
69-
k5, 0 --> X
70-
end
158+
#### Bifurcation analysis extension
159+
- Add a CatalystBifurcationKitExtension, permitting BifurcationKit's
160+
`BifurcationProblem`s to be created from Catalyst reaction networks. Example
161+
usage:
162+
```julia
163+
using Catalyst
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wilhelm_2009_model = @reaction_network begin
165+
k1, Y --> 2X
166+
k2, 2X --> X + Y
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k3, X + Y --> Y
168+
k4, X --> 0
169+
k5, 0 --> X
170+
end
71171
72-
using BifurcationKit
73-
bif_par = :k1
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u_guess = [:X => 5.0, :Y => 2.0]
75-
p_start = [:k1 => 4.0, :k2 => 1.0, :k3 => 1.0, :k4 => 1.5, :k5 => 1.25]
76-
plot_var = :X
77-
bprob = BifurcationProblem(wilhelm_2009_model, u_guess, p_start, bif_par; plot_var=plot_var)
172+
using BifurcationKit
173+
bif_par = :k1
174+
u_guess = [:X => 5.0, :Y => 2.0]
175+
p_start = [:k1 => 4.0, :k2 => 1.0, :k3 => 1.0, :k4 => 1.5, :k5 => 1.25]
176+
plot_var = :X
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bprob = BifurcationProblem(wilhelm_2009_model, u_guess, p_start, bif_par; plot_var = plot_var)
78178
79-
p_span = (2.0, 20.0)
80-
opts_br = ContinuationPar(p_min = p_span[1], p_max = p_span[2], max_steps=1000)
179+
p_span = (2.0, 20.0)
180+
opts_br = ContinuationPar(p_min = p_span[1], p_max = p_span[2], max_steps = 1000)
81181
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bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside=true)
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bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside = true)
83183
84-
using Plots
85-
plot(bif_dia; xguide="k1", yguide="X")
86-
```
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- Automatically handles elimination of conservation laws for computing bifurcation diagrams.
184+
using Plots
185+
plot(bif_dia; xguide = "k1", guide = "X")
186+
```
187+
- Automatically handles elimination of conservation laws for computing
188+
bifurcation diagrams.
88189
- Updated Bifurcation documentation with respect to this new feature.
89-
- Added function `isautonomous` to check if a `ReactionSystem` is autonomous.
90-
- Added function `steady_state_stability` to compute stability for steady states. Example:
91-
```julia
92-
# Creates model.
93-
rn = @reaction_network begin
94-
(p,d), 0 <--> X
95-
end
96-
p = [:p => 1.0, :d => 0.5]
97-
98-
# Finds (the trivial) steady state, and computes stability.
99-
steady_state = [2.0]
100-
steady_state_stability(steady_state, rn, p)
101-
```
102-
Here, `steady_state_stability` take an optional argument `tol = 10*sqrt(eps())`, which is used to determine whether a eigenvalue real part is reliably less that 0.
103190

104191
## Catalyst 13.5
105192
- Added a CatalystHomotopyContinuationExtension extension, which exports the `hc_steady_state` function if HomotopyContinuation is exported. `hc_steady_state` finds the steady states of a reaction system using the homotopy continuation method. This feature is only available for julia versions 1.9+. Example:
@@ -658,7 +745,7 @@ hc_steady_states(wilhelm_2009_model, ps)
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field has been changed (only when created through the `@reaction_network`
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macro). Previously they were ordered according to the order with which they
660747
appeared in the macro. Now they are ordered according the to order with which
661-
they appeard after the `end` part. E.g. in
748+
they appeared after the `end` part. E.g. in
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```julia
663750
rn = @reaction_network begin
664751
(p,d), 0 <--> X
@@ -763,7 +850,7 @@ which gives
763850
![rn_complexes](https://user-images.githubusercontent.com/9385167/130252763-4418ba5a-164f-47f7-b512-a768e4f73834.png)
764851
765852
*2.* Support for units via ModelingToolkit and
766-
[Uniftul.jl](https://github.com/PainterQubits/Unitful.jl) in directly constructed
853+
[Unitful.jl](https://github.com/PainterQubits/Unitful.jl) in directly constructed
767854
`ReactionSystem`s:
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```julia
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# ]add Unitful

‎Project.toml‎

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@@ -1,6 +1,6 @@
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name = "Catalyst"
22
uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
3-
version = "13.5.1"
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version = "14.0.0"
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[deps]
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Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
@@ -76,6 +76,7 @@ SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
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SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
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SciMLNLSolve = "e9a6253c-8580-4d32-9898-8661bb511710"
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StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
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StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
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StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
@@ -84,4 +85,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
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[targets]
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test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]
88+
test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]

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