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MAINT: implement updates from formatters
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docs/usage/reaction.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.12"
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"version": "3.13.15"
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}
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},
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"nbformat": 4,

docs/usage/visualize_mermaid.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.undefined"
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"version": "3.13.15"
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}
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},
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"nbformat": 4,

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