Run Decapodes simulation via Julia kernel in Jupyter

packages/algjulia-service/.gitignore

@@ -0,0 +1,24 @@
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

packages/algjulia-service/Project.toml

@@ -0,0 +1,33 @@
+name = "AlgebraicJuliaService"
+uuid = "9ecda8fb-39ab-46a2-a496-7285fa6368c1"
+license = "MIT"
+authors = ["CatColab team"]
+version = "0.1.0"
+
+[deps]
+ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
+CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
+Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
+DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+
+[compat]
+ACSets = "0.2.21"
+ComponentArrays = "0.15"
+Decapodes = "0.5.6"
+DiagrammaticEquations = "0.1.7"
+Distributions = "0.25"
+GeometryBasics = "0.4"
+JSON3 = "1"
+LinearAlgebra = "1"
+MLStyle = "0.4"
+OrdinaryDiffEq = "6"
+StaticArrays = "1"

packages/algjulia-service/README.md

@@ -0,0 +1,35 @@
+# AlgebraicJulia Service
+
+This small package makes functionality from
+[AlgebraicJulia](https://www.algebraicjulia.org/) available to CatColab,
+intermediated by a Julia kernel running in the [Jupyter](https://jupyter.org/)
+server. At this time, only a
+[Decapodes.jl](https://github.com/AlgebraicJulia/Decapodes.jl) service is
+provided. Other packages may be added in the future.
+
+## Setup
+
+1. Install [Julia](https://julialang.org/), say by using
+[`juliaup`](https://github.com/JuliaLang/juliaup)
+2. Install [Jupyter](https://jupyter.org/), say by using `pip` or `conda`
+3. Install [IJulia](https://github.com/JuliaLang/IJulia.jl), which provides the
+   Julia kernel to Jupyter
+
+At this stage, you should be able to launch a Julia kernel inside a JupyterLab.
+
+Having done that, navigate to this directory and run:
+
+```sh
+julia --project -e 'import Pkg; Pkg.instantiate()'
+```
+
+## Usage
+
+Navigate to this directory and run:
+
+```sh
+jupyter server --IdentityProvider.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173"
+```
+
+While the Jupyter server is running, the AlgebraicJulia service will be usable
+by CatColab served locally.

packages/algjulia-service/src/AlgebraicJuliaService.jl

@@ -0,0 +1,6 @@
+module AlgebraicJuliaService
+
+include("kernel_support.jl")
+include("decapodes.jl")
+
+end