Review GenX, compost and wheat-straw causal graphs (batch 23) by realmarcin · Pull Request #1350 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T02:12:30Z

Summary

Source-review Community G GenX, composting SynCom and tripartite wheat-straw graphs.
Retain all eight nodes and four arrows, with six exact renames and bounded omics interpretations. No new structure or Edison spend.
Preserve positive chemical, compost and shaking-speed outcomes without unsupported competition, establishment, partner transfer or enzyme mediation.
Add three knowledge gaps, three append-only histories, eight focused regressions, review records and regenerated pages.

Closes #1347. Closes #1348. Closes #1349. Existing #746/#524 remain open.

Validation

All 30 local checks completed; 278 passed in 291.48s (0:04:51).
Rights: 3 passed in 2.55s.
53 MATCH snippets; all other classes zero.
Zero structural/network errors; 25 existing warnings unchanged.
42 unrelated YAML blocks and six tracked cache artifacts byte-preserved.
Two identical full renders and exact parsed node/edge description coverage.
Before/after both-root census: same 460 records, 389 with community scope, 122 mixed records and 1499 community-credited taxa; solely community-credited taxa 1218 -> 1220. No sentinel bounds or registry changes.
Stacked coverage: 118 reviewed, 339 pending, 3 needs research. Not corpus completion.

Review Limits

Source-based self-adversarial review, not independent approval. Two complete primary bodies and four additional abstracts reviewed; 2020 author PDF failed after cover/abstract/early Introduction. No full Methods/Results claim for that paper. No visual images or supplementary files inspected, and no copyrighted full body added. Unrelated metadata preserved, not certified.

Stacked on batch22 PR #1346. Do not merge into the 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 merged branches only after dependents move. The stack already includes the merged history-base CI fix.

realmarcin

Source-based self-adversarial review at exact head ee38b8f0a6166f3d56dbf9ec07ac3afbabe2d1eb, not independent approval.

Addressed #1347, #1348 and #1349. All eight nodes and four arrows retained, with six exact renames and no new structure. Relative profiles are not reciprocal competition or proven degrader functions; metagenomic potential is not enzyme activity; transcript roles do not establish directed transfer, exclusive vitamin donation or selective mediation. Preserve the positive chemical, compost and shaking-speed outcomes and the unfavorable fungal monoculture comparison.

All 30 local gates pass: 278 passed in 291.48s (0:04:51); 53 MATCH snippets and zero other classes; 3 passed in 2.55s; 42 unrelated raw blocks and six 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. Both-root census verifies unchanged connected taxa and mixed record counts, with solely community-credited taxa 1218 -> 1220. No sentinel or participant-registry edits.

Committed decision/adversarial/validation records bind all nodes, arrows and record/cache hashes. Two primary main bodies and four additional abstracts reviewed; 2020 author PDF access failed after partial reading, so no full-body claim. No visual images/supplement files inspected or copyrighted full body added. Unrelated metadata not certified; #746/#524 remain open. Stacked coverage 118/460 reviewed, not corpus completion.

Required CI and protected main queue remain mandatory. Do not merge into the topic parent. The history-base CI fix is already included in this stack.

github-actions · 2026-10-06T02:31:23Z

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 c6301accc464db4063290a84fca8b1e1592618f8 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: 95e58eb0e0ff670ac067307b34c28252b37139bd482240a58c75cff84667d348. New whole-tree SHA: 1faa7671682a96c1a5ffb34570ee0e5abedde69c. 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 3bf947900491e17eb79b95882e425fb4901c6b1c
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 abd5d13ceb1b9905fe1be19111934584cad55b77
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 2db69594dc9d6aa1e8570feb37a368fc655e1559
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 b881157535ac90167cfc867e1eeb454c38c4c80d
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 9c819ad638841906850c9869ac86bdf37de6aaec
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 aff15721f2f0c3afe4920956eda6431f542b5b66
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 dd1ab003ee849fd1faafacea270ae667e16e841a
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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 e10315c67527685d9c15d64d04d2ae9d1d996c2d
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 1faa7671682a96c1a5ffb34570ee0e5abedde69c.
The batch-owned binary patch is byte-identical
(SHA-256 c0e53c57c6c201eff6da0463766305a4966e00fb2a2b3d5fb51de34d2797e864); 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.