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docs: add public figures/data assets under MIT; scaffold docs & templates
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‎.gitattributes‎

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*.png filter=lfs diff=lfs merge=lfs -text
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*.jpg filter=lfs diff=lfs merge=lfs -text
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*.pdf filter=lfs diff=lfs merge=lfs -text
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*.csv filter=lfs diff=lfs merge=lfs -text
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*.xlsx filter=lfs diff=lfs merge=lfs -text
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assets/figures/*.png filter=lfs diff=lfs merge=lfs -text
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assets/figures/*.pdf filter=lfs diff=lfs merge=lfs -text
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data/raw/*.xlsx filter=lfs diff=lfs merge=lfs -text

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: File a bug
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---
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**Describe the bug**
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**Steps to reproduce**
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**Expected behavior**
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**Environment (OS, MATLAB/Octave version)**
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**Additional context**

‎.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
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---
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**Problem**
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**Proposed solution**
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**Alternatives**
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**Additional context**

‎.github/workflows/docs.yml‎

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name: Docs & links
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on: [push, pull_request]
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jobs:
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check:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: List docs
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run: ls -R docs

‎.gitignore‎

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# MATLAB / Octave
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*.asv
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*.mex*
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*.mltbx
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*.mat
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*.m~*
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*.slxc
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*.slprj/
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*.autosave
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# OS / editors
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.DS_Store
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Thumbs.db
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.vscode/
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.idea/
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*.log
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# Python venvs if you add wrappers later
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.venv/
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__pycache__/
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*.pyc

‎CITATION.cff‎

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cff-version: 1.2.0
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title: "ChromoSim: Ion-Exchange Column Simulator"
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version: "0.1.0"
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message: "If you use ChromoSim, please cite this record."
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authors:
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- family-names: "Mironov"
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given-names: "Bogdan"
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orcid: "https://orcid.org/0009-0008-2866-5529"
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license: MIT
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repository-code: "https://github.com/<your-username>/ChromoSim"
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keywords: [chromatography, ion-exchange, mechanistic-model, simulation]

‎CODE_OF_CONDUCT.md‎

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# Code of Conduct
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We are committed to a welcoming and inclusive environment.
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We follow the Contributor Covenant: https://www.contributor-covenant.org/version/2/1/code_of_conduct/

‎CONTRIBUTING.md‎

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# Contributing to ChromoSim
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Thanks for your interest! Please open an issue to propose features/bugs.
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- Fork → branch → PR with clear title and description.
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- Keep assets small; use Git LFS for figures/data.
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- Add/update examples and docs when changing user-facing behavior.

‎README.md‎

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# ChromoSim
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1D ion-exchange chromatography column simulator (mechanistic; multi-species; gradient; FPLC-style outputs)
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**ChromoSim** is a general, mechanistic simulator for ion-exchange chromatography
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(anionic or cationic). It models 1D convection–dispersion with competitive binding
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and supports user-defined affinity maps (e.g., surface-potential dependent) or
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constant-affinity protein models.
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## Highlights
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- Multi-species breakthrough & in-column heatmaps
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- FPLC-style output (mL / pseudo-mAU) with %B overlay
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- Fast stiff-ODE integration with sparse Jacobian
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- Works for proteins, nanoparticles, EVs (by configuration)
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## Repo layout
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- `src/` library code (added later)
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- `examples/` runnable demos (added later)
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- `assets/` figures/schematics (MIT-licensed)
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- `data/` small demo data (LFS)
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- `docs/` user docs & images
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- `tests/` lightweight checks
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## Quick start
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Examples and core library will be added in v0.1.0.
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For now, see `docs/` for the modeling overview.
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## License
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MIT for code and assets.

‎docs/faq/faq.md‎

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# FAQ
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**Q: Can I use ChromoSim for cation-exchange?**
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A: Yes—configure the affinity map accordingly and use cation-exchange parameters.
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**Q: How big can my figures/data be?**
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A: Use Git LFS. Keep single files <50 MB where possible.

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