New network plotting methods inaccessible (plot_network, plot_complexes) #1282
Description
Describe the bug 🐞
The network graph visualization tools documented here do not work from the base tutorial, instead returning a MethodError.
Expected behavior
Plots should be made that match the tutorial at the provided link.
Minimal Reproducible Example 👇
brusselator = @reaction_network begin
A, ∅ --> X
1, 2X + Y --> 3X
B, X --> Y
1, X --> ∅
end
plot_network(brusselator)Error & Stacktrace
MethodError: no method matching plot_network(::ReactionSystem{Catalyst.NetworkProperties{Int64, SymbolicUtils.BasicSymbolic{Real}}})
The function `plot_network` exists, but no method is defined for this combination of argument types.
**Environment (please complete the following information):**
- Output of `using Pkg; Pkg.status()`
```julia
Status `C:\Users\isaac\OneDrive - Colorado School of Mines\Desktop\research\reaction_networks\Project.toml`
[336ed68f] CSV v0.10.15
[479239e8] Catalyst v15.0.8
[a93c6f00] DataFrames v1.7.0
[a2cc645c] GraphPlot v0.6.1
[ccbc3e58] JumpProcesses v9.16.0
[23fbe1c1] Latexify v0.16.8
[1dea7af3] OrdinaryDiffEq v6.98.0
[91a5bcdd] Plots v1.40.14
[b4db0fb7] ReactionNetworkImporters v0.16.1
[789caeaf] StochasticDiffEq v6.80.0
- Output of
using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
�[32m�[1mStatus�[22m�[39m `C:\Users\isaac\OneDrive - Colorado School of Mines\Desktop\research\reaction_networks\Manifest.toml`
�[90m[47edcb42] �[39mADTypes v1.14.0
�[90m[1520ce14] �[39mAbstractTrees v0.4.5
�[90m[7d9f7c33] �[39mAccessors v0.1.42
�[90m[79e6a3ab] �[39mAdapt v4.3.0
�[90m[66dad0bd] �[39mAliasTables v1.1.3
�[90m[ec485272] �[39mArnoldiMethod v0.4.0
�[90m[4fba245c] �[39mArrayInterface v7.19.0
�[90m[4c555306] �[39mArrayLayouts v1.11.1
�[90m[e2ed5e7c] �[39mBijections v0.2.2
�[90m[d1d4a3ce] �[39mBitFlags v0.1.9
�[90m[62783981] �[39mBitTwiddlingConvenienceFunctions v0.1.6
�[90m[8e7c35d0] �[39mBlockArrays v1.6.3
�[90m[70df07ce] �[39mBracketingNonlinearSolve v1.3.0
�[90m[2a0fbf3d] �[39mCPUSummary v0.2.6
�[90m[336ed68f] �[39mCSV v0.10.15
�[90m[479239e8] �[39mCatalyst v15.0.8
�[90m[d360d2e6] �[39mChainRulesCore v1.25.1
�[90m[fb6a15b2] �[39mCloseOpenIntervals v0.1.13
�[90m[944b1d66] �[39mCodecZlib v0.7.8
�[90m[35d6a980] �[39mColorSchemes v3.29.0
�[33m⌅�[39m �[90m[3da002f7] �[39mColorTypes v0.11.5
�[32m⌃�[39m �[90m[c3611d14] �[39mColorVectorSpace v0.10.0
�[33m⌅�[39m �[90m[5ae59095] �[39mColors v0.12.11
�[90m[861a8166] �[39mCombinatorics v1.0.3
�[90m[a80b9123] �[39mCommonMark v0.9.1
�[90m[38540f10] �[39mCommonSolve v0.2.4
�[90m[bbf7d656] �[39mCommonSubexpressions v0.3.1
�[90m[f70d9fcc] �[39mCommonWorldInvalidations v1.0.0
�[90m[34da2185] �[39mCompat v4.16.0
�[90m[a81c6b42] �[39mCompose v0.9.6
�[90m[b152e2b5] �[39mCompositeTypes v0.1.4
�[90m[a33af91c] �[39mCompositionsBase v0.1.2
�[90m[2569d6c7] �[39mConcreteStructs v0.2.3
�[90m[f0e56b4a] �[39mConcurrentUtilities v2.5.0
�[90m[187b0558] �[39mConstructionBase v1.6.0
�[90m[d38c429a] �[39mContour v0.6.3
�[90m[adafc99b] �[39mCpuId v0.3.1
�[90m[a8cc5b0e] �[39mCrayons v4.1.1
�[90m[9a962f9c] �[39mDataAPI v1.16.0
�[90m[a93c6f00] �[39mDataFrames v1.7.0
�[90m[864edb3b] �[39mDataStructures v0.18.22
�[90m[e2d170a0] �[39mDataValueInterfaces v1.0.0
�[90m[8bb1440f] �[39mDelimitedFiles v1.9.1
�[90m[2b5f629d] �[39mDiffEqBase v6.176.0
�[90m[459566f4] �[39mDiffEqCallbacks v4.6.0
�[90m[77a26b50] �[39mDiffEqNoiseProcess v5.24.1
�[90m[163ba53b] �[39mDiffResults v1.1.0
�[90m[b552c78f] �[39mDiffRules v1.15.1
�[33m⌅�[39m �[90m[a0c0ee7d] �[39mDifferentiationInterface v0.6.54
�[90m[8d63f2c5] �[39mDispatchDoctor v0.4.19
�[90m[b4f34e82] �[39mDistances v0.10.12
�[90m[31c24e10] �[39mDistributions v0.25.120
�[90m[ffbed154] �[39mDocStringExtensions v0.9.5
�[90m[5b8099bc] �[39mDomainSets v0.7.15
�[90m[7c1d4256] �[39mDynamicPolynomials v0.6.2
�[90m[06fc5a27] �[39mDynamicQuantities v1.8.0
�[90m[4e289a0a] �[39mEnumX v1.0.5
�[90m[f151be2c] �[39mEnzymeCore v0.8.12
�[90m[460bff9d] �[39mExceptionUnwrapping v0.1.11
�[90m[d4d017d3] �[39mExponentialUtilities v1.27.0
�[90m[e2ba6199] �[39mExprTools v0.1.10
�[90m[55351af7] �[39mExproniconLite v0.10.14
�[90m[c87230d0] �[39mFFMPEG v0.4.2
�[90m[7034ab61] �[39mFastBroadcast v0.3.5
�[90m[9aa1b823] �[39mFastClosures v0.3.2
�[90m[442a2c76] �[39mFastGaussQuadrature v1.0.2
�[90m[a4df4552] �[39mFastPower v1.1.2
�[90m[48062228] �[39mFilePathsBase v0.9.24
�[90m[1a297f60] �[39mFillArrays v1.13.0
�[90m[64ca27bc] �[39mFindFirstFunctions v1.4.1
�[90m[6a86dc24] �[39mFiniteDiff v2.27.0
�[90m[53c48c17] �[39mFixedPointNumbers v0.8.5
�[90m[1fa38f19] �[39mFormat v1.3.7
�[33m⌅�[39m �[90m[f6369f11] �[39mForwardDiff v0.10.38
�[90m[069b7b12] �[39mFunctionWrappers v1.1.3
�[90m[77dc65aa] �[39mFunctionWrappersWrappers v0.1.3
�[90m[d9f16b24] �[39mFunctors v0.5.2
�[90m[46192b85] �[39mGPUArraysCore v0.2.0
�[90m[28b8d3ca] �[39mGR v0.73.16
�[90m[c145ed77] �[39mGenericSchur v0.5.5
�[90m[c27321d9] �[39mGlob v1.3.1
�[90m[a2cc645c] �[39mGraphPlot v0.6.1
�[90m[86223c79] �[39mGraphs v1.13.0
�[90m[42e2da0e] �[39mGrisu v1.0.2
�[90m[cd3eb016] �[39mHTTP v1.10.16
�[90m[34004b35] �[39mHypergeometricFunctions v0.3.28
�[90m[615f187c] �[39mIfElse v0.1.1
�[90m[d25df0c9] �[39mInflate v0.1.5
�[90m[842dd82b] �[39mInlineStrings v1.4.4
�[90m[18e54dd8] �[39mIntegerMathUtils v0.1.2
�[90m[8197267c] �[39mIntervalSets v0.7.11
�[90m[3587e190] �[39mInverseFunctions v0.1.17
�[90m[41ab1584] �[39mInvertedIndices v1.3.1
�[90m[92d709cd] �[39mIrrationalConstants v0.2.4
�[90m[c8e1da08] �[39mIterTools v1.10.0
�[90m[82899510] �[39mIteratorInterfaceExtensions v1.0.0
�[90m[1019f520] �[39mJLFzf v0.1.11
�[90m[692b3bcd] �[39mJLLWrappers v1.7.0
�[90m[682c06a0] �[39mJSON v0.21.4
�[90m[ae98c720] �[39mJieko v0.2.1
�[90m[98e50ef6] �[39mJuliaFormatter v2.1.2
�[33m⌅�[39m �[90m[70703baa] �[39mJuliaSyntax v0.4.10
�[90m[ccbc3e58] �[39mJumpProcesses v9.16.0
�[90m[ba0b0d4f] �[39mKrylov v0.10.1
�[90m[b964fa9f] �[39mLaTeXStrings v1.4.0
�[90m[23fbe1c1] �[39mLatexify v0.16.8
�[90m[10f19ff3] �[39mLayoutPointers v0.1.17
�[90m[5078a376] �[39mLazyArrays v2.6.1
�[90m[2d8b4e74] �[39mLevyArea v1.0.0
�[90m[87fe0de2] �[39mLineSearch v0.1.4
�[90m[d3d80556] �[39mLineSearches v7.4.0
�[90m[7ed4a6bd] �[39mLinearSolve v3.17.0
�[90m[2ab3a3ac] �[39mLogExpFunctions v0.3.29
�[90m[e6f89c97] �[39mLoggingExtras v1.1.0
�[90m[d8e11817] �[39mMLStyle v0.4.17
�[90m[1914dd2f] �[39mMacroTools v0.5.16
�[90m[d125e4d3] �[39mManualMemory v0.1.8
�[90m[bb5d69b7] �[39mMaybeInplace v0.1.4
�[90m[739be429] �[39mMbedTLS v1.1.9
�[90m[442fdcdd] �[39mMeasures v0.3.2
�[90m[e1d29d7a] �[39mMissings v1.2.0
�[33m⌅�[39m �[90m[961ee093] �[39mModelingToolkit v9.80.5
�[90m[2e0e35c7] �[39mMoshi v0.3.5
�[90m[46d2c3a1] �[39mMuladdMacro v0.2.4
�[90m[102ac46a] �[39mMultivariatePolynomials v0.5.9
�[90m[d8a4904e] �[39mMutableArithmetics v1.6.4
�[90m[d41bc354] �[39mNLSolversBase v7.10.0
�[90m[2774e3e8] �[39mNLsolve v4.5.1
�[90m[77ba4419] �[39mNaNMath v1.1.3
�[90m[8913a72c] �[39mNonlinearSolve v4.9.0
�[90m[be0214bd] �[39mNonlinearSolveBase v1.12.0
�[90m[5959db7a] �[39mNonlinearSolveFirstOrder v1.5.0
�[90m[9a2c21bd] �[39mNonlinearSolveQuasiNewton v1.6.0
�[90m[26075421] �[39mNonlinearSolveSpectralMethods v1.2.0
�[90m[6fe1bfb0] �[39mOffsetArrays v1.17.0
�[90m[4d8831e6] �[39mOpenSSL v1.5.0
�[90m[429524aa] �[39mOptim v1.13.2
�[90m[bac558e1] �[39mOrderedCollections v1.8.1
�[90m[1dea7af3] �[39mOrdinaryDiffEq v6.98.0
�[90m[89bda076] �[39mOrdinaryDiffEqAdamsBashforthMoulton v1.2.0
�[90m[6ad6398a] �[39mOrdinaryDiffEqBDF v1.6.0
�[90m[bbf590c4] �[39mOrdinaryDiffEqCore v1.26.1
�[90m[50262376] �[39mOrdinaryDiffEqDefault v1.4.0
�[90m[4302a76b] �[39mOrdinaryDiffEqDifferentiation v1.10.0
�[90m[9286f039] �[39mOrdinaryDiffEqExplicitRK v1.1.0
�[90m[e0540318] �[39mOrdinaryDiffEqExponentialRK v1.4.0
�[90m[becaefa8] �[39mOrdinaryDiffEqExtrapolation v1.5.0
�[90m[5960d6e9] �[39mOrdinaryDiffEqFIRK v1.12.0
�[90m[101fe9f7] �[39mOrdinaryDiffEqFeagin v1.1.0
�[90m[d3585ca7] �[39mOrdinaryDiffEqFunctionMap v1.1.1
�[90m[d28bc4f8] �[39mOrdinaryDiffEqHighOrderRK v1.1.0
�[90m[9f002381] �[39mOrdinaryDiffEqIMEXMultistep v1.3.0
�[90m[521117fe] �[39mOrdinaryDiffEqLinear v1.3.0
�[90m[1344f307] �[39mOrdinaryDiffEqLowOrderRK v1.2.0
�[90m[b0944070] �[39mOrdinaryDiffEqLowStorageRK v1.3.0
�[90m[127b3ac7] �[39mOrdinaryDiffEqNonlinearSolve v1.10.0
�[90m[c9986a66] �[39mOrdinaryDiffEqNordsieck v1.1.0
�[90m[5dd0a6cf] �[39mOrdinaryDiffEqPDIRK v1.3.1
�[90m[5b33eab2] �[39mOrdinaryDiffEqPRK v1.1.0
�[90m[04162be5] �[39mOrdinaryDiffEqQPRK v1.1.0
�[90m[af6ede74] �[39mOrdinaryDiffEqRKN v1.1.0
�[90m[43230ef6] �[39mOrdinaryDiffEqRosenbrock v1.11.0
�[90m[2d112036] �[39mOrdinaryDiffEqSDIRK v1.3.0
�[90m[669c94d9] �[39mOrdinaryDiffEqSSPRK v1.3.0
�[90m[e3e12d00] �[39mOrdinaryDiffEqStabilizedIRK v1.3.0
�[90m[358294b1] �[39mOrdinaryDiffEqStabilizedRK v1.1.0
�[90m[fa646aed] �[39mOrdinaryDiffEqSymplecticRK v1.3.0
�[90m[b1df2697] �[39mOrdinaryDiffEqTsit5 v1.1.0
�[90m[79d7bb75] �[39mOrdinaryDiffEqVerner v1.2.0
�[90m[90014a1f] �[39mPDMats v0.11.35
�[90m[d96e819e] �[39mParameters v0.12.3
�[90m[69de0a69] �[39mParsers v2.8.3
�[90m[ccf2f8ad] �[39mPlotThemes v3.3.0
�[90m[995b91a9] �[39mPlotUtils v1.4.3
�[90m[91a5bcdd] �[39mPlots v1.40.14
�[90m[e409e4f3] �[39mPoissonRandom v0.4.4
�[90m[f517fe37] �[39mPolyester v0.7.18
�[90m[1d0040c9] �[39mPolyesterWeave v0.2.2
�[90m[2dfb63ee] �[39mPooledArrays v1.4.3
�[90m[85a6dd25] �[39mPositiveFactorizations v0.2.4
�[90m[d236fae5] �[39mPreallocationTools v0.4.27
�[33m⌅�[39m �[90m[aea7be01] �[39mPrecompileTools v1.2.1
�[90m[21216c6a] �[39mPreferences v1.4.3
�[90m[08abe8d2] �[39mPrettyTables v2.4.0
�[90m[27ebfcd6] �[39mPrimes v0.5.7
�[90m[43287f4e] �[39mPtrArrays v1.3.0
�[90m[1fd47b50] �[39mQuadGK v2.11.2
�[90m[74087812] �[39mRandom123 v1.7.1
�[90m[e6cf234a] �[39mRandomNumbers v1.6.0
�[90m[b4db0fb7] �[39mReactionNetworkImporters v0.16.1
�[90m[3cdcf5f2] �[39mRecipesBase v1.3.4
�[90m[01d81517] �[39mRecipesPipeline v0.6.12
�[90m[731186ca] �[39mRecursiveArrayTools v3.33.0
�[90m[189a3867] �[39mReexport v1.2.2
�[90m[05181044] �[39mRelocatableFolders v1.0.1
�[90m[ae029012] �[39mRequires v1.3.1
�[90m[ae5879a3] �[39mResettableStacks v1.1.1
�[90m[79098fc4] �[39mRmath v0.8.0
�[90m[7e49a35a] �[39mRuntimeGeneratedFunctions v0.5.15
�[90m[9dfe8606] �[39mSCCNonlinearSolve v1.2.0
�[90m[94e857df] �[39mSIMDTypes v0.1.0
�[90m[0bca4576] �[39mSciMLBase v2.101.0
�[90m[19f34311] �[39mSciMLJacobianOperators v0.1.6
�[90m[c0aeaf25] �[39mSciMLOperators v1.3.1
�[90m[53ae85a6] �[39mSciMLStructures v1.7.0
�[90m[6c6a2e73] �[39mScratch v1.2.1
�[90m[91c51154] �[39mSentinelArrays v1.4.8
�[90m[efcf1570] �[39mSetfield v1.1.2
�[90m[992d4aef] �[39mShowoff v1.0.3
�[90m[777ac1f9] �[39mSimpleBufferStream v1.2.0
�[90m[727e6d20] �[39mSimpleNonlinearSolve v2.5.0
�[90m[699a6c99] �[39mSimpleTraits v0.9.4
�[90m[ce78b400] �[39mSimpleUnPack v1.1.0
�[90m[a2af1166] �[39mSortingAlgorithms v1.2.1
�[90m[0a514795] �[39mSparseMatrixColorings v0.4.20
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�[90m[2913bbd2] �[39mStatsBase v0.34.5
�[90m[4c63d2b9] �[39mStatsFuns v1.5.0
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�[90m[19f23fe9] �[39mSymbolicLimits v0.2.2
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�[90m[41fe7b60] �[39mUnzip v0.2.0
�[90m[ea10d353] �[39mWeakRefStrings v1.4.2
�[90m[897b6980] �[39mWeakValueDicts v0.1.0
�[90m[76eceee3] �[39mWorkerUtilities v1.6.1
�[90m[6e34b625] �[39mBzip2_jll v1.0.9+0
�[90m[83423d85] �[39mCairo_jll v1.18.5+0
�[90m[ee1fde0b] �[39mDbus_jll v1.16.2+0
�[90m[2702e6a9] �[39mEpollShim_jll v0.0.20230411+1
�[90m[2e619515] �[39mExpat_jll v2.6.5+0
�[33m⌅�[39m �[90m[b22a6f82] �[39mFFMPEG_jll v4.4.4+1
�[90m[a3f928ae] �[39mFontconfig_jll v2.16.0+0
�[90m[d7e528f0] �[39mFreeType2_jll v2.13.4+0
�[90m[559328eb] �[39mFriBidi_jll v1.0.17+0
�[90m[0656b61e] �[39mGLFW_jll v3.4.0+2
�[90m[d2c73de3] �[39mGR_jll v0.73.16+0
�[90m[78b55507] �[39mGettext_jll v0.21.0+0
�[90m[7746bdde] �[39mGlib_jll v2.84.0+0
�[90m[3b182d85] �[39mGraphite2_jll v1.3.15+0
�[90m[2e76f6c2] �[39mHarfBuzz_jll v8.5.1+0
�[90m[1d5cc7b8] �[39mIntelOpenMP_jll v2025.0.4+0
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�[36m�[1mInfo�[22m�[39m Packages marked with �[32m⌃�[39m and �[33m⌅�[39m have new versions available. Those with �[32m⌃�[39m may be upgradable, but those with �[33m⌅�[39m are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
- Output of
versioninfo()
Julia Version 1.11.5
Commit 760b2e5b73 (2025-04-14 06:53 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: 16 × AMD Ryzen 7 7730U with Radeon Graphics
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 16 virtual cores)Additional context
The code
using Catalyst
Catalyst.plot_networkreturns
plot_network (generic function with 0 methods)These errors are the same for the plot_complexes function.
I think this is due to the following placeholder code:
Lines 156 to 159 in b2ef2f9