SciML/Catalyst.jl

add common mistakes documentation

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#1,316 opened on Aug 8, 2025

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good first issue

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Description

There are certain mistakes / misunderstandings that seem to commonly arise for newer users. We should add a common mistakes page and link it prominently from the tutorials.

Examples include

  1. Using @species and @parameters outside of @reaction_network and not understanding that these are actually completely unconnected.
  2. Similarly for defining t outside of @reaction_network.
  3. Using interpolation when it isn't needed (or if it is needed not using it sufficiently in that interpolation of only expressions but not external variables/species ends up being used which is like point 1. above).
  4. Callback and VariableRateJump saving controls, see https://discourse.julialang.org/t/memory-issues-for-long-ssa-simulations-with-mass-action-jumps/133530

Contributor guide

Research direction
Review the existing tutorials and documentation structure in the Catalyst.jl repository. Identify where to add a common mistakes page and link it prominently from tutorials. Compile the examples given and any additional common pitfalls from community discussions.
Tech stack
julia
Domain
documentation
Issue type
Documentation
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
1
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitJulia basics
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
90