Fix the stale merge_compartments note left behind on 16.4 - #48
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8f0430a regenerated this section's output blocks after the submodule bump but left the prose beneath them describing the old behaviour. Two things were wrong. The admonition's header line was deleted while its indented body stayed, so the paragraphs rendered as a code block rather than a note. The text itself no longer matched the output above it. It said "of the 11 reactions it drops above, only 3 are genuine transports" where the example now prints 3, and "until the fix ships" after the fix had shipped: SysBioChalmers/raven-toolbox#96 is merged and is in the tracked commit. Replaced with a note that explains what the two tabs actually show -- both end at 50 reactions, RAVEN reporting 0 removals and raven-toolbox 3, because RAVEN's deletedRxns counts only the deleteRxnsWithOneMet path, which is off by default. The exchange-deletion bug is recorded in the past tense, with the PR that fixed it.
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Found while pulling after #46 — this is exactly the drift
#41 warns about, already live
on
main.8f0430aregenerated 16.4's output blocks after the submodule bump, but theprose beneath them still described the old behaviour. Two problems:
1. It rendered as a code block. The
!!! dangerheader line was removed andits indented body left behind, so three paragraphs of prose showed up as
preformatted text.
2. It contradicted the output directly above it. The text said "of the 11
reactions it drops above, only 3 are genuine transports" — the example now prints
3 — and "until the fix ships", when
raven-toolbox#96 is
merged and present in the tracked commit
173131d1. A reader would have beentold the Python tab was broken while looking at output showing it is not.
What it says now
A note explaining what the two tabs really show: both end at 50 reactions,
but RAVEN reports 0 removals and raven-toolbox 3 (
CAT2,CO2TRANS,ShuttleX). Same three reactions either way — RAVEN clears them when it removesreactions the merge left empty, and its
deletedRxnscounts only what thedeleteRxnsWithOneMetpath deleted, which is nothing while that flag isfalseby default. The exchange-deletion bug is recorded in the past tense with the PR
that fixed it.
Verified: the built page now renders an admonition rather than a code block, and
check_names.pyis clean (deletedRxnsallow-listed as a variable).Worth noting for #41
The examples themselves were fine — CI has been green because
--updatealreadycorrected the numbers. It is the surrounding prose that went stale, which nothing
checks. That is the part of the regeneration that needs a person, and this is a
concrete instance of it.