Refactoring network analysis docs #1142
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Having network analysis be its own section is fine. LMK when you feel this is ready to review. |
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Can you remove the full repo format? We haven’t been using formatter due to the bugs it introduced in one release last year. While I’m fine with re-enabling it that should really be in a separate PR so we can check nothing is getting broken. (Feel free to run it on the files you are actually editing here though.) |
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@vyudu do you think you'll be able to clean this up with regards to the formatter changes soon so we can review? We are basically done now with the stuff that was holding back V15. |
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I will do this tonight
…On Tue, Apr 8, 2025 at 19:19 Sam Isaacson ***@***.***> wrote:
@vyudu <https://github.com/vyudu> do you think you'll be able to clean
this up with regards to the formatter changes soon so we can review? We are
basically done now with the stuff that was holding back V15.
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*isaacsas* left a comment (SciML/Catalyst.jl#1142)
<#1142 (comment)>
@vyudu <https://github.com/vyudu> do you think you'll be able to clean
this up with regards to the formatter changes soon so we can review? We are
basically done now with the stuff that was holding back V15.
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Great, thanks! |
This reverts commit 50ec948.
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@isaacsas Have gone through and made fixes |
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Haven't read the updated version (going to bed now), bit one thought. Noe that network analysis is its own section, wouldn't it make sense to put the network analysis section after the model simulation one? Simulation ls is arguably the primary aspect of Catalyst, so it would make sense to that it comes directly after the model creation section. |
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I think that'd make sense. Away from computer so can't change it at the
moment but can get to it later tonight.
…On Sun, Apr 13, 2025 at 6:14 PM Torkel Loman ***@***.***> wrote:
Haven't read the updated version (going to bed now), bit one thought. Noe
that network analysis is its own section, wouldn't it make sense to put the
network analysis section after the model simulation one? Simulation ls is
arguably the primary aspect of Catalyst, so it would make sense to that it
comes directly after the model creation section.
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*TorkelE* left a comment (SciML/Catalyst.jl#1142)
<#1142 (comment)>
Haven't read the updated version (going to bed now), bit one thought. Noe
that network analysis is its own section, wouldn't it make sense to put the
network analysis section after the model simulation one? Simulation ls is
arguably the primary aspect of Catalyst, so it would make sense to that it
comes directly after the model creation section.
—
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@vyudu, yes make that update when you chance, along with fixing the doc build error. I'd make that update myself but you seem to have your Catalyst fork setup so others don't have permission to push to it. |
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Hmm not sure why that is, it seems like I have allow edits by maintainers on. But I think I've fixed it, let me know when I should re-run this when the doc build is working again |
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Doc builds were working yesterday outside this PR. Are you sure that error isn’t from an update you made? |
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I think it because the Catalyst version on master have been updated to v15 however, in e.g. this PR the docs are marked as for Catlayst v14, which is incompatible with the Catalyst version. |
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I have updated the doc version here: #1233 Once merged this one should be able to run the docs again. |
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Tests and docs passes now |
| @@ -23,7 +23,7 @@ etc). | |||
| - The [Catalyst.jl API](@ref api) provides functionality for building networks programmatically and for composing multiple networks together. | |||
| - Leveraging ModelingToolkit, generated models can be converted to symbolic reaction rate equation ODE models, symbolic Chemical Langevin Equation models, and symbolic stochastic chemical kinetics (jump process) models. These can be simulated using any [DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/stable/) [ODE/SDE/jump solver](@ref simulation_intro), and can be used within `EnsembleProblem`s for carrying out [parallelized parameter sweeps and statistical sampling](@ref ensemble_simulations). Plot recipes are available for [visualization of all solutions](@ref simulation_plotting). | |||
| - Non-integer (e.g. `Float64`) stoichiometric coefficients [are supported](@ref dsl_description_stoichiometries_decimal) for generating ODE models, and symbolic expressions for stoichiometric coefficients [are supported](@ref parametric_stoichiometry) for all system types. | |||
| - A [network analysis suite](@ref network_analysis) permits the computation of linkage classes, deficiencies, reversibility, and other network properties. | |||
| - A [network analysis suite](@ref network_analysis_structural_aspects) permits the computation of linkage classes, deficiencies, reversibility, and other network properties. | |||
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A similar update will be needed on the GitHub main readme page. However, that links to the actual website, so if you want we can update after the docs have been pushed and are avaiable.
| @@ -0,0 +1,35 @@ | |||
| # [Caching of Network Properties in `ReactionSystems`](@id network_analysis_caching_properties) | |||
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I'd probably call this file "network_properties_caching" (since that is what it is about).
| (k1,k2),A <--> B | ||
| (k3,k4),A + C <--> D | ||
| (k5,k6),D <--> B+E | ||
| (k7,k8),B+E <--> A+C |
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Here and in some places there is no space between the rate and the reaction itself (but in other places there is). If this is not intentional you might want to update (but if it is, no worries!).
Probably worth discussing more but my thought here is to make Network Analysis its own section of the Catalyst docs, with subsections for the ODE decompositions, structural properties and chemical reaction network theory, and a third section for advanced stuff that links to CatalystNetworkAnalysis.
Added sections for the new API functions in #1134 and building symbolic functions from the ODEs to the ODE docs. Added a section on complex/detailed balance to the CRNT docs.
Need to: add a section on the deficiency one theorem, bring in the CatalystNetworkAnalysis docs, add code examples to the complex/detailed balance section (including stuff about the precision limitations of
isdetailedbalanced)