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Commits on Jan 15, 2026

• Update publish workflows and add TestPyPI index config

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• Revert "Update GitHub Actions for publish and test-publish"

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• Update GitHub Actions for publish and test-publish

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• Remove smoke tests from publish workflows

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• Bump version to 2.2.1

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• Merge pull request #98 from EnzymeML/fix-numpy-dep

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• Remove legacy integration test for EnzymeML v1

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• Update Python version and dependency constraints in uv.lock

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• Update minimum Python version to 3.11

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• Update mdmodels dependency version

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• Refactor ChEBI fetcher to use search API and update tests

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Commits on Jan 13, 2026

• Add documentation section to README

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• Merge branch 'update-docs'

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• Update docs workflow to trigger on main branch

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• Update workflow name to 'Build and deploy Astro docs'

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• Add spacing after checkout step in docs workflow

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• Update deployment environment name in docs workflow

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• Fix EnzymeML Suite image path in documentation

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• Add COPASI installation instructions to docs

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• Use --all-groups in uv sync for test workflows

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• Add copasi-basico and python-copasi to dependencies

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• Update docs.yml

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• Add @pytest.mark.remote to integration fetcher tests

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• Replace requests with httpx in fetcher modules

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• Migrate to PEP 621 pyproject.toml and add uv.lock

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• Add initial documentation site with Starlight

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• Remove documentation and example files from docs directory

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• Revamp CI workflows: add docs, remote tests, switch to uv

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Commits on Dec 8, 2025

• Merge pull request #95 from EnzymeML/94-fetch-rhea-for-23-butanediol-dehydrogenase-fails

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• Refactor ChEBI models to ignore extra fields

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Commits on Nov 15, 2025

• Merge pull request #93 from EnzymeML/fix-thinlayer-imports

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Commits on Nov 14, 2025

• Fix PySCeS and Copasi thinlayer imports

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Commits on Oct 14, 2025

• Merge pull request #90 from EnzymeML/86-thinlayerpysces-proteins-not-updated-during-simulation

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• Refactor species initialization in InitMap

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Commits on Oct 9, 2025

• Preserve species referenced in equations during filtering

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