DARPA ASKEM 6 Month Evaluations

Reproducing the Results

This system is a fully reproducer builder that generates the results from scratch. It downloads Julia, downloads the packages, builds the results, and then hosts them at the website https://chrisrackauckas.github.io/ASKEMEvaluationStaging/dev/.

Running the Builder

The simplest way to reproduce the results is to run the builder by opening a PR. The Documentation job is the job generating the results, and if successful (green) then its artifacts are pushed to the repository on merge.

Running Locally via the `make.jl` Script

To run locally, start by downloading the Github repository and set the current directory to ASKEM_Evaluation_Staging/docs. Then open Julia and run:

cd("to the ASKEM_Evaluation_Staging/docs directory")

# Setup packages
using Pkg
Pkg.activate(".")
Pkg.instantiate()

# Run the build script
include("make.jl")

The outputs will be generated into the ASKEM_Evaluation_Staging/docs/build directory and can be opened in a web browser.

Running Individual Files

The individual files can be built as well by running the code in the Markdown files. We recommend grabbing the packages using the Project.toml via:

cd("to the ASKEM_Evaluation_Staging/docs directory")

# Setup packages
using Pkg
Pkg.activate(".")
Pkg.instantiate()

Then open up the .md and run the code! If using the Julia VS Code plugin then inline evaluation will directly work.

Contributing

Please refer to the SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages for guidance on PRs, issues, and other matters relating to contributing to SciML.
See the SciML Style Guide for common coding practices and other style decisions.
There are a few community forums:
- The #diffeq-bridged and #sciml-bridged channels in the Julia Slack
- The #diffeq-bridged and #sciml-bridged channels in the Julia Zulip
- On the Julia Discourse forums
- See also SciML Community page

Reproducibility

The documentation of this SciML package was built using these direct dependencies,

Status `~/work/ASKEM_Evaluation_Staging/ASKEM_Evaluation_Staging/docs/Project.toml`
  [d1df7db2] ASKEM_Evaluation_Staging v1.1.0 `~/work/ASKEM_Evaluation_Staging/ASKEM_Evaluation_Staging`
  [4f99eebe] AlgebraicPetri v0.8.4
  [336ed68f] CSV v0.10.9
  [134e5e36] Catlab v0.14.14
  [a93c6f00] DataFrames v1.4.4
  [0c46a032] DifferentialEquations v7.6.0
  [e30172f5] Documenter v0.27.24
  [ef4b24a4] EasyModelAnalysis v0.1.8
  [b6b21f68] Ipopt v1.1.0
  [961ee093] ModelingToolkit v8.46.0
  [76087f3c] NLopt v0.6.5
  [7f7a1694] Optimization v3.11.2
  [fd9f6733] OptimizationMOI v0.1.7
  [91a5bcdd] Plots v1.38.4
  [e5567a89] SBML v1.4.0
  [86080e66] SBMLToolkit v0.1.20
  [3a884ed6] UnPack v1.0.2
  [fdbf4ff8] XLSX v0.8.4
  [3c863552] Graphviz_jll v2.50.0+1
  [f43a241f] Downloads v1.6.0
  [37e2e46d] LinearAlgebra
  [44cfe95a] Pkg v1.8.0
  [9a3f8284] Random

and using this machine and Julia version.

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 2 × Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

A more complete overview of all dependencies and their versions is also provided.

Status `~/work/ASKEM_Evaluation_Staging/ASKEM_Evaluation_Staging/docs/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [d1df7db2] ASKEM_Evaluation_Staging v1.1.0 `~/work/ASKEM_Evaluation_Staging/ASKEM_Evaluation_Staging`
  [c3fe647b] AbstractAlgebra v0.27.8
  [621f4979] AbstractFFTs v1.2.1
  [80f14c24] AbstractMCMC v4.4.0
⌅ [7a57a42e] AbstractPPL v0.5.3
  [1520ce14] AbstractTrees v0.4.4
  [79e6a3ab] Adapt v3.5.0
  [0bf59076] AdvancedHMC v0.4.2
  [5b7e9947] AdvancedMH v0.7.2
  [576499cb] AdvancedPS v0.4.3
  [b5ca4192] AdvancedVI v0.1.6
  [4f99eebe] AlgebraicPetri v0.8.4
  [dce04be8] ArgCheck v2.3.0
  [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v6.0.25
  [30b0a656] ArrayInterfaceCore v0.1.29
  [6ba088a2] ArrayInterfaceGPUArrays v0.2.2
  [015c0d05] ArrayInterfaceOffsetArrays v0.1.7
  [b0d46f97] ArrayInterfaceStaticArrays v0.1.5
  [dd5226c6] ArrayInterfaceStaticArraysCore v0.1.3
  [4c555306] ArrayLayouts v0.8.18
  [15f4f7f2] AutoHashEquals v0.2.0
  [13072b0f] AxisAlgorithms v1.0.1
  [39de3d68] AxisArrays v0.4.6
  [aae01518] BandedMatrices v0.17.10
  [198e06fe] BangBang v0.3.37
  [9718e550] Baselet v0.1.1
  [6e4b80f9] BenchmarkTools v1.3.2
  [e2ed5e7c] Bijections v0.1.4
⌅ [76274a88] Bijectors v0.10.6
  [d1d4a3ce] BitFlags v0.1.7
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [a134a8b2] BlackBoxOptim v0.6.2
  [764a87c0] BoundaryValueDiffEq v2.11.0
  [fa961155] CEnum v0.4.2
  [2a0fbf3d] CPUSummary v0.2.2
  [a9c8d775] CPUTime v1.0.0
  [00ebfdb7] CSTParser v3.3.6
  [336ed68f] CSV v0.10.9
  [49dc2e85] Calculus v0.5.1
  [479239e8] Catalyst v12.3.2
  [134e5e36] Catlab v0.14.14
  [082447d4] ChainRules v1.46.1
  [d360d2e6] ChainRulesCore v1.15.7
  [9e997f8a] ChangesOfVariables v0.1.5
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  [5ae59095] Colors v0.12.10
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  [a80b9123] CommonMark v0.8.10
  [38540f10] CommonSolve v0.2.3
  [bbf7d656] CommonSubexpressions v0.3.0
  [0fb5dd42] CompTime v0.1.2
  [34da2185] Compat v4.6.0
  [a81c6b42] Compose v0.9.4
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  [88cd18e8] ConsoleProgressMonitor v0.1.2
  [187b0558] ConstructionBase v1.4.1
  [d38c429a] Contour v0.6.2
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.14.0
  [a93c6f00] DataFrames v1.4.4
  [864edb3b] DataStructures v0.18.13
  [e2d170a0] DataValueInterfaces v1.0.0
  [244e2a9f] DefineSingletons v0.1.2
  [bcd4f6db] DelayDiffEq v5.40.6
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  [2b5f629d] DiffEqBase v6.114.2
  [459566f4] DiffEqCallbacks v2.24.3
  [77a26b50] DiffEqNoiseProcess v5.15.2
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.12.2
  [0c46a032] DifferentialEquations v7.6.0
  [b4f34e82] Distances v0.10.7
  [31c24e10] Distributions v0.25.80
  [ced4e74d] DistributionsAD v0.6.43
  [ffbed154] DocStringExtensions v0.9.3
  [e30172f5] Documenter v0.27.24
⌅ [5b8099bc] DomainSets v0.5.15
  [fa6b7ba4] DualNumbers v0.6.8
  [366bfd00] DynamicPPL v0.21.6
  [7c1d4256] DynamicPolynomials v0.4.6
  [ef4b24a4] EasyModelAnalysis v0.1.8
  [cad2338a] EllipticalSliceSampling v1.0.0
  [4e289a0a] EnumX v1.0.4
  [d4d017d3] ExponentialUtilities v1.22.0
  [e2ba6199] ExprTools v0.1.8
  [8f5d6c58] EzXML v1.1.0
  [c87230d0] FFMPEG v0.4.1
  [7a1cc6ca] FFTW v1.5.0
  [7034ab61] FastBroadcast v0.2.4
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v1.2.8
  [48062228] FilePathsBase v0.9.20
  [1a297f60] FillArrays v0.13.7
  [6a86dc24] FiniteDiff v2.17.0
  [53c48c17] FixedPointNumbers v0.8.4
  [59287772] Formatting v0.4.2
  [f6369f11] ForwardDiff v0.10.34
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.1
⌅ [d9f16b24] Functors v0.3.0
  [0c68f7d7] GPUArrays v8.6.2
  [46192b85] GPUArraysCore v0.1.3
  [28b8d3ca] GR v0.71.5
  [6b9d7cbe] GeneralizedGenerated v0.3.3
  [c145ed77] GenericSchur v0.5.3
  [c27321d9] Glob v1.3.0
  [af5da776] GlobalSensitivity v2.1.3
  [86223c79] Graphs v1.7.4
  [42e2da0e] Grisu v1.0.2
  [0b43b601] Groebner v0.2.11
  [d5909c97] GroupsCore v0.4.0
  [19dc6840] HCubature v1.5.1
  [cd3eb016] HTTP v1.7.4
  [3e5b6fbb] HostCPUFeatures v0.1.14
  [34004b35] HypergeometricFunctions v0.3.11
  [b5f81e59] IOCapture v0.2.2
  [7869d1d1] IRTools v0.4.7
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.3
  [83e8ac13] IniFile v0.5.1
  [22cec73e] InitialValues v0.3.1
  [842dd82b] InlineStrings v1.4.0
  [505f98c9] InplaceOps v0.3.0
  [18e54dd8] IntegerMathUtils v0.1.0
  [de52edbc] Integrals v3.4.0
  [a98d9a8b] Interpolations v0.14.7
⌅ [8197267c] IntervalSets v0.7.3
  [3587e190] InverseFunctions v0.1.8
  [41ab1584] InvertedIndices v1.2.0
  [b6b21f68] Ipopt v1.1.0
  [92d709cd] IrrationalConstants v0.1.1
  [c8e1da08] IterTools v1.4.0
  [42fd0dbc] IterativeSolvers v0.9.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [1019f520] JLFzf v0.1.5
  [692b3bcd] JLLWrappers v1.4.1
  [682c06a0] JSON v0.21.3
  [98e50ef6] JuliaFormatter v1.0.20
  [b14d175d] JuliaVariables v0.2.4
  [ccbc3e58] JumpProcesses v9.3.1
  [ef3ab10e] KLU v0.4.0
  [5ab0869b] KernelDensity v0.6.5
  [ba0b0d4f] Krylov v0.9.0
  [0b1a1467] KrylovKit v0.6.0
  [929cbde3] LLVM v4.15.0
  [8ac3fa9e] LRUCache v1.4.0
  [b964fa9f] LaTeXStrings v1.3.0
  [2ee39098] LabelledArrays v1.13.0
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.15.18
  [a5e1c1ea] LatinHypercubeSampling v1.8.0
  [73f95e8e] LatticeRules v0.0.1
  [10f19ff3] LayoutPointers v0.1.13
  [1d6d02ad] LeftChildRightSiblingTrees v0.2.0
  [2d8b4e74] LevyArea v1.0.0
  [6f1fad26] Libtask v0.8.5
  [9c8b4983] LightXML v0.9.0
  [d3d80556] LineSearches v7.2.0
  [7ed4a6bd] LinearSolve v1.34.1
  [6fdf6af0] LogDensityProblems v2.1.0
  [996a588d] LogDensityProblemsAD v1.2.0
  [2ab3a3ac] LogExpFunctions v0.3.20
  [e6f89c97] LoggingExtras v1.0.0
  [bdcacae8] LoopVectorization v0.12.149
  [c7f686f2] MCMCChains v5.7.1
  [be115224] MCMCDiagnosticTools v0.2.6
  [e80e1ace] MLJModelInterface v1.8.0
  [d8e11817] MLStyle v0.4.16
  [1914dd2f] MacroTools v0.5.10
  [d125e4d3] ManualMemory v0.1.8
  [dbb5928d] MappedArrays v0.4.1
  [abcecc63] MathML v0.1.13
  [b8f27783] MathOptInterface v1.11.5
  [fdba3010] MathProgBase v0.7.8
  [739be429] MbedTLS v1.1.7
  [442fdcdd] Measures v0.3.2
⌅ [e9d8d322] Metatheory v1.3.5
  [128add7d] MicroCollections v0.1.3
  [e1d29d7a] Missings v1.1.0
  [961ee093] ModelingToolkit v8.46.0
⌅ [4886b29c] MonteCarloIntegration v0.0.3
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.4.6
  [d8a4904e] MutableArithmetics v1.1.0
  [d41bc354] NLSolversBase v7.8.3
  [76087f3c] NLopt v0.6.5
  [2774e3e8] NLsolve v4.5.1
  [872c559c] NNlib v0.8.16
  [77ba4419] NaNMath v1.0.1
  [71a1bf82] NameResolution v0.1.5
  [86f7a689] NamedArrays v0.9.6
  [c020b1a1] NaturalSort v1.0.0
  [8913a72c] NonlinearSolve v1.3.0
  [6fe1bfb0] OffsetArrays v1.12.9
  [4d8831e6] OpenSSL v1.3.3
  [429524aa] Optim v1.7.4
  [3bd65402] Optimisers v0.2.14
  [7f7a1694] Optimization v3.11.2
  [3e6eede4] OptimizationBBO v0.1.4
  [fd9f6733] OptimizationMOI v0.1.7
  [4e6fcdb7] OptimizationNLopt v0.1.2
  [bac558e1] OrderedCollections v1.4.1
  [1dea7af3] OrdinaryDiffEq v6.41.0
  [90014a1f] PDMats v0.11.16
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.5.4
  [b98c9c47] Pipe v1.3.0
  [ccf2f8ad] PlotThemes v3.1.0
  [995b91a9] PlotUtils v1.3.4
  [91a5bcdd] Plots v1.38.4
  [e409e4f3] PoissonRandom v0.4.3
  [f517fe37] Polyester v0.7.2
  [1d0040c9] PolyesterWeave v0.2.1
  [2dfb63ee] PooledArrays v1.4.2
  [85a6dd25] PositiveFactorizations v0.2.4
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  [8162dcfd] PrettyPrint v0.2.0
  [08abe8d2] PrettyTables v2.2.2
  [27ebfcd6] Primes v0.5.3
  [33c8b6b6] ProgressLogging v0.1.4
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  [8a4e6c94] QuasiMonteCarlo v0.2.19
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  [fb686558] RandomExtensions v0.4.3
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  [f2c3362d] RecursiveFactorization v0.2.17
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  [ae029012] Requires v1.3.0
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  [476501e8] SLEEFPirates v0.6.38
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  [afe9f18d] SciMLExpectations v2.0.1
  [e9a6253c] SciMLNLSolve v0.1.3
  [30f210dd] ScientificTypesBase v3.0.0
  [6c6a2e73] Scratch v1.1.1
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  [66db9d55] SnoopPrecompile v1.0.3
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  [e56a9233] Sparspak v0.3.7
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  [4c63d2b9] StatsFuns v1.1.1
  [9672c7b4] SteadyStateDiffEq v1.11.0
  [789caeaf] StochasticDiffEq v6.57.4
  [7792a7ef] StrideArraysCore v0.4.6
  [892a3eda] StringManipulation v0.3.0
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  [6ec83bb0] StructEquality v2.1.0
  [c3572dad] Sundials v4.13.0
  [2efcf032] SymbolicIndexingInterface v0.2.1
⌅ [d1185830] SymbolicUtils v0.19.11
⌅ [0c5d862f] Symbolics v4.14.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.10.0
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⌅ [8ea1fca8] TermInterface v0.2.3
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  [2e76f6c2] HarfBuzz_jll v2.8.1+1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2
⌅ [9cc047cb] Ipopt_jll v300.1400.400+0
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⌅ [e9f186c6] Libffi_jll v3.2.2+1
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  [94ce4f54] Libiconv_jll v1.16.1+2
  [4b2f31a3] Libmount_jll v2.35.0+0
  [89763e89] Libtiff_jll v4.4.0+0
  [38a345b3] Libuuid_jll v2.36.0+0
  [d00139f3] METIS_jll v5.1.2+0
  [856f044c] MKL_jll v2022.2.0+0
⌅ [d7ed1dd3] MUMPS_seq_jll v5.4.1+0
  [079eb43e] NLopt_jll v2.7.1+0
  [e7412a2a] Ogg_jll v1.3.5+1
⌅ [656ef2d0] OpenBLAS32_jll v0.3.17+0
  [458c3c95] OpenSSL_jll v1.1.19+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.2+0
  [36c8627f] Pango_jll v1.50.9+0
  [30392449] Pixman_jll v0.40.1+0
  [ea2cea3b] Qt5Base_jll v5.15.3+2
  [f50d1b31] Rmath_jll v0.4.0+0
  [bb12108a] SBML_jll v5.19.7+0
  [fb77eaff] Sundials_jll v5.2.1+0
  [a2964d1f] Wayland_jll v1.21.0+0
  [2381bf8a] Wayland_protocols_jll v1.25.0+0
  [02c8fc9c] XML2_jll v2.10.3+0
  [aed1982a] XSLT_jll v1.1.34+0
  [4f6342f7] Xorg_libX11_jll v1.6.9+4
  [0c0b7dd1] Xorg_libXau_jll v1.0.9+4
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.3+4
  [1082639a] Xorg_libXext_jll v1.3.4+4
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.10+4
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
  [c7cfdc94] Xorg_libxcb_jll v1.13.0+3
  [cc61e674] Xorg_libxkbfile_jll v1.1.0+4
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.2+4
  [33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
  [c5fb5394] Xorg_xtrans_jll v1.4.0+3
  [3161d3a3] Zstd_jll v1.5.2+0
⌅ [214eeab7] fzf_jll v0.29.0+0
  [a4ae2306] libaom_jll v3.4.0+0
  [0ac62f75] libass_jll v0.15.1+0
  [f638f0a6] libfdk_aac_jll v2.0.2+0
  [b53b4c65] libpng_jll v1.6.38+0
  [f27f6e37] libvorbis_jll v1.3.7+1
  [1270edf5] x264_jll v2021.5.5+0
  [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.3
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.8.0
  [de0858da] Printf
  [9abbd945] Profile
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.0
  [a4e569a6] Tar v1.10.1
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.0.1+0
  [deac9b47] LibCURL_jll v7.84.0+0
  [29816b5a] LibSSH2_jll v1.10.2+0
  [c8ffd9c3] MbedTLS_jll v2.28.0+0
  [14a3606d] MozillaCACerts_jll v2022.2.1
  [4536629a] OpenBLAS_jll v0.3.20+0
  [05823500] OpenLibm_jll v0.8.1+0
  [efcefdf7] PCRE2_jll v10.40.0+0
  [bea87d4a] SuiteSparse_jll v5.10.1+0
  [83775a58] Zlib_jll v1.2.12+3
  [8e850b90] libblastrampoline_jll v5.1.1+0
  [8e850ede] nghttp2_jll v1.48.0+0
  [3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.