Make docker#2

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Melclic wants to merge 7 commits intomainfrom

Commits on Oct 2, 2025

ENH: fixed the reaction parsing from metanetx

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Commits on Oct 13, 2025

ENH: switched the taxonomy id to be at a lower levek

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Commits on Oct 14, 2025

ENH: working nextflow workflows

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Commits on Oct 15, 2025

ENH: the pubchem search includes xref and lowest CID based on int for multiple hits

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Commits on Oct 18, 2025

ENH: added pubchem xref search

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Commits on Nov 11, 2025

ENH: still working on it

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Commits on Dec 4, 2025

ENH: small changes

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