Initial commit

Author: edkerk

.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+*.egg
+build/
+dist/
+.pytest_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# Virtual envs
+.venv/
+venv/
+env/
+
+# Editor / OS
+.vscode/
+.idea/
+.DS_Store
+Thumbs.db
+
+# Tooling caches
+.claude/
+
+# Local data
+*.pkl
+*.cache

README.md

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+# raven-python
+
+The Python counterpart of the
+[RAVEN Toolbox 2](https://github.com/SysBioChalmers/RAVEN) (MATLAB), built on
+[cobrapy](https://github.com/opencobra/cobrapy).
+
+`raven-python` covers de-novo reconstruction (KEGG + protein homology),
+context-specific model extraction (`tINIT` / `ftINIT`), metabolic-task
+validation, gap-filling, omics ingestion, sub-cellular localisation, model
+manipulation, and YAML / SIF / Excel I/O — preserving the established RAVEN
+workflows in a Python-native form.
+
+This `main` branch is intentionally empty. Development happens on the
+`develop` branch via a series of feature branches; see the open and merged
+pull requests for the current state of the port.