Review coculture and crucian carp causal graphs (batch 24) by realmarcin · Pull Request #1355 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T02:40:11Z

Summary

Source-review Cordyceps-Malbranchea, succinate coculture and crucian carp SynCom graphs.
Repair two records; record one byte-unchanged review. Retain eight nodes/four arrows with four exact renames. No new structure or Edison spend.
Preserve positive intervention outcomes while qualifying electron/flux and host immune/barrier mediation.
Add two focused gaps, two append-only histories, seven regressions, review outputs and regenerated pages.

Closes #1351. Closes #1352. Separate metadata followups #1353/#1354 remain open.

Validation

All 29 local gates completed; 285 passed in 190.25s (0:03:10).
Rights: 3 passed in 1.56s.
24 MATCH snippets; all other classes zero.
Zero structural/network errors; 25 existing network warnings unchanged.
36 unrelated raw YAML blocks and three tracked caches byte-preserved.
Two identical full renders and exact parsed description coverage.
Both-root census unchanged except solely community-credited taxa 1220 -> 1221, reflecting corrected Shewanella scope. No registry/sentinel changes.
Stacked coverage: 121 reviewed, 336 pending, 3 need research. Copper and Coscinodiscus remain pending.

Review Limits

Source-based self-adversarial review, not independent approval. Complete fish primary main body/captions and complete abstracts for both cocultures read. No accessible full publisher body for the cocultures, and no figure images or supplementary files inspected. No full copyrighted body added. Unrelated metadata preserved, not certified.

Stacked on batch23 PR #1350. Do not merge into a topic parent or bypass checks. After protected parent merges, restack the owned commit, retarget to main, refresh exact-head review and use the protected queue. Delete a merged branch only after dependents move. The stack already includes the merged history-base CI fix.

realmarcin

Source-based self-adversarial review at exact head 2eb1818f3d94f9420099a991136254501b543891, not independent approval.

Addressed #1351/#1352; separate metadata followups #1353/#1354 remain open. Three records reviewed: two graph repairs and one byte-unchanged Cordyceps decision. All eight nodes/four arrows retained with four exact renames and no new structure or Edison spend.

Preserve positive parent/K1, additive, lactate-deletion and fish challenge outcomes without promoting transcripts into traced flux, riboflavin into demonstrated partner donation, or immune/barrier markers into selective mediation. IgA is a pathway annotation; barrier genes are transcript measurements; DAO is ambiguous. SynCom survival and calibrated qPCR pathogen DNA loads remain separate from FMT, relative 16S and viable CFU.

All 29 local gates pass: 285 passed in 190.25s (0:03:10); 24 MATCH snippets and zero other classes; 3 passed in 1.56s; 36 unchanged raw blocks and three tracked caches byte-preserved. Two identical full renders and exact parsed description coverage. Actual post-commit just check-docs-current passed and left the tree clean. Solely community-credited taxa change 1220 -> 1221 after correcting Shewanella scope; other census counts and sentinels remain unchanged.

Decision/adversarial/validation records bind all nodes, arrows and record/cache hashes. Complete fish main body/captions and two complete coculture abstracts reviewed; no full publisher body available for the latter. No figure images or supplementary files inspected; no copyrighted full body added. Stacked coverage 121/460, not completion. Copper and Coscinodiscus remain pending.

Required CI and protected main queue remain mandatory. Do not merge into a topic parent. The merged history-base CI fix is already included.

github-actions · 2026-10-06T02:51:40Z

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 25 warning across 10 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

realmarcin

Source-based self-adversarial review refreshed at exact head 041364c50372ed68007839167fd3ce523bb218fd after integrating merged website PR #1303 (a937575f88ab11ff74683a8902fe13fd80c96165). Not independent approval.

The website merge conflicted only in the parent generated browser page; it was regenerated from the merged renderer and preserved KB. Each dependent owned commit was then rebased, generated pages refreshed, and actual post-commit just check-docs-current run successfully in every worktree. All branches were pushed atomically with exact leases.

Every non-document blob is verified identical to its previously reviewed version except the nine exact upstream website files. This includes unchanged scientific records, taxa, caches, histories, review ledgers and batch-owned regression code. Non-document manifest SHA-256: c5a0e18498fdc5f2911e5470dae56dde85b4d9bff341d38193e2df8a782289c6. New whole-tree SHA: b8123c25f9b2ff07de163c75eacacd635d39dce8. Whole-tree equality to the previous head is NOT claimed because upstream rendering changed.

The parent integration-focused tests passed. The final combined stack suite, including all batch regressions, site/link tests, corpus/network checks, reference-validator canaries and publication-rights tests, reports: 302 passed in 223.43s (0:03:43). All twelve worktrees passed actual docs-current. Batch-specific scientific/access limitations remain as recorded; batch25 still explicitly retains three primary-verified Results quotes absent from its abstract-only cache, not a passed reference gate.

The decision, adversarial-review and validation files remain historical source-review provenance. Required CI must pass at this new head and the protected main queue remains mandatory. Do not merge a child into a topic parent; delete merged branches only after their dependents move.

realmarcin

Self-adversarial review refreshed at exact head ea372c759fe42b06c6bd667120beafa2727d082f
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head 9615b423a55ccf3dab49066111e66770bd7fadeb
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head 9b5e033264f407ee85803cdfeb66dd56aeade292
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head c387b8e1711617605c529bf3843fad7e1f55aec4
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head d4689ca789c8da87fd0434e53a85e97a6d87fbfc
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head a46eae176e066b9394efef9c88afba17452b60fa
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

realmarcin

Self-adversarial review refreshed at exact head f37bc90c182c93c3f30799a05819819dc67cb02b
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree b8123c25f9b2ff07de163c75eacacd635d39dce8.
The batch-owned binary patch is byte-identical
(SHA-256 7680b19e2883db238523f958732ac78a60ac8f6e5232f2b4c19a4170e794ac10); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.