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port code from private project
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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**Minimal Working Example**
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Please provide a piece of code that leads to the bug you encounter.
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If the code is **runnable**, it will help us identify the problem faster.
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**Package versions**
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Please provide the versions you use. To do this, run the code:
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```julia
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using Pkg
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Pkg.status([
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"Package1", "Package2"]; # etc.
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mode = PKGMODE_MANIFEST
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)
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```

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the feature you'd like to have**
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**Cite scientific papers related to the feature/algorithm**
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**If possible, sketch out an implementation strategy**

‎.github/workflows/CompatHelper.yml

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name: CompatHelper
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on:
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schedule:
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- cron: '00 * * * *'
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jobs:
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CompatHelper:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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julia-version: [1]
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julia-arch: [x86]
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os: [ubuntu-latest]
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steps:
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- uses: julia-actions/setup-julia@latest
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with:
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version: ${{ matrix.julia-version }}
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- name: Pkg.add("CompatHelper")
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run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
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- name: CompatHelper.main()
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: julia -e 'using CompatHelper; CompatHelper.main()'

‎.github/workflows/TagBot.yml

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name: TagBot
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on:
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issue_comment:
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types:
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- created
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workflow_dispatch:
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jobs:
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TagBot:
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if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
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runs-on: ubuntu-latest
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steps:
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- uses: JuliaRegistries/TagBot@v1
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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ssh: ${{ secrets.DOCUMENTER_KEY }}

‎.github/workflows/ci.yml

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name: CI
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on:
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pull_request:
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branches:
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- main
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- '**' # matches every branch
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push:
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branches:
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- main
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tags: '*'
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jobs:
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test:
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name: Tests, Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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version:
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- '1'
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os: [ubuntu-latest] # adjust according to need, e.g. os: [ubuntu-latest] if testing only on linux
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arch:
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- x64
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steps:
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# Cancel ongoing CI test runs if pushing to branch again before the previous tests
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# have finished
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- name: Cancel ongoing test runs for previous commits
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uses: styfle/[email protected]
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with:
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access_token: ${{ github.token }}
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# Do tests
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- uses: actions/checkout@v2
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.version }}
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arch: ${{ matrix.arch }}
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- uses: actions/cache@v1
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env:
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cache-name: cache-artifacts
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with:
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path: ~/.julia/artifacts
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key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
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restore-keys: |
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${{ runner.os }}-test-${{ env.cache-name }}-
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${{ runner.os }}-test-
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${{ runner.os }}-
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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-runtest@v1
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- uses: julia-actions/julia-processcoverage@v1
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- uses: codecov/codecov-action@v1
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with:
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file: lcov.info

‎.github/workflows/doccleanup.yml

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name: Doc Preview Cleanup
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on:
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pull_request:
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types: [closed]
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jobs:
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doc-preview-cleanup:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout gh-pages branch
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uses: actions/checkout@v2
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with:
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ref: gh-pages
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- name: Delete preview and history + push changes
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run: |
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if [ -d "previews/PR$PRNUM" ]; then
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git config user.name "Documenter.jl"
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git config user.email "[email protected]"
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git rm -rf "previews/PR$PRNUM"
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git commit -m "delete preview"
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git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
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git push --force origin gh-pages-new:gh-pages
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fi
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env:
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PRNUM: ${{ github.event.number }}

‎.github/workflows/documentation.yml

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name: Documentation
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on:
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push:
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branches:
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- main
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tags: '*'
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pull_request:
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jobs:
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build:
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permissions:
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contents: write
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: julia-actions/setup-julia@v1
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with:
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version: '1'
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- name: Install dependencies
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run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
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run: julia --project=docs/ docs/make.jl

‎Project.toml

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name = "ProcessBasedModelling"
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uuid = "ca969041-2cf3-4b10-bc21-86f4417093eb"
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authors = ["Datseris <[email protected]>"]
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version = "0.1.0"
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[deps]
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ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
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Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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[compat]
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ModelingToolkit = "8.73"
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Reexport = "1.2"

‎README.md

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# ProcessBasedModelling.jl
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# ProcessBasedModelling.jl
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[![docsdev](https://img.shields.io/badge/docs-dev-lightblue.svg)](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/ProcessBasedModelling/dev/)
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[![docsstable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/ProcessBasedModelling/stable/)
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[![Paper](https://img.shields.io/badge/Cite-DOI:10.1063/5.0159675-purple)](https://arxiv.org/abs/2304.12786)
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[![CI](https://github.com/JuliaDynamics/ProcessBasedModelling.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/ProcessBasedModelling.jl/actions?query=workflow%3ACI)
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[![codecov](https://codecov.io/gh/JuliaDynamics/ProcessBasedModelling.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaDynamics/ProcessBasedModelling.jl)
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[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/ProcessBasedModelling)](https://pkgs.genieframework.com?packages=ProcessBasedModelling)
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ProcessBasedModelling.jl is an extension to [ModelingToolkit.jl](https://docs.sciml.ai/ModelingToolkit/stable/) (MTK).
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It is an alternative framework to MTK's
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native component-based modelling, but, instead of components, there are "processes".
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This modelling approach is useful in the modelling of physical/biological/whatever systems, where each variable corresponds to particular physical concept or observable and there are few (or any) duplicate variables to make the definition of MTK "factories" worthwhile.
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In many modelling scenarios this follows the line of reasoning in the researcher's head.
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Beyond this reasoning style, the biggest strength of ProcessBasedModelling.jl is the informative errors it provides regarding incorrect/incomplete equations. When building the MTK model via ProcessBasedModelling.jl the user provides a vector of "processes": equations or custom types that have a well defined and single left-hand-side variable.
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This allows ProcessBasedModelling.jl to achieve the following:
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1. Iterates over the processes and collects _new_ variables that have been introduced by a provided process but do not themselves have a process assigned to them.
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2. For these collected "process-less" variables:
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- If there is a default process defined, it incorporates this one into the model
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- If there is no default process but the variable has a default value, it equates the variable to a _parameter_ that has the same default value and throws an informative warning.
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- Else, it throws an informative error saying exactly which originally provided variable introduced this new "process-less" variable.
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3. Also throws an informative error if a variable has two processes assigned to it (by mistake).
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In our experience, and as we also highlight explicitly in the online documentation, this approach typically yields simpler, less ambiguous and more targeted warning/error messages than the native MTK one's, leading to faster identification and resolution of the problems with the composed equations.
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ProcessBasedModelling.jl is particularly suited for developing a model about a physical/biological/whatever system and being able to try various physical "rules" (couplings, feedbacks, mechanisms, ...) for a given physical observable efficiently.
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This means switching arbitrarily between different processes that correspond to the same variable.
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Hence, the target application of ProcessBasedModelling.jl is to be a framework to develop field-specific libraries that offer predefined processes without themselves relying on the existence of context-specific predefined components. An example usage is in [EnergyBalanceModels.jl](https://github.com/JuliaDynamics/EnergyBalanceModels.jl).
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Besides the informative errors, ProcessBasedModelling.jl also
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1. Provides a couple of common process subtypes out of the box to accelerate development of field-specific libraries.
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2. Makes named MTK variables and parameters automatically, corresponding to parameters introduced by the by-default provided processes. This typically leads to intuitive names without being explicitly coded, while being possible to opt-out.
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3. Provides some utility functions for further building field-specific libraries.
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See the documentation online for details on how to use this package as well as examples highlighting its usefulness.

‎docs/Project.toml

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[deps]
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CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
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DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
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DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
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ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"

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