Review copper heap and Coscinodiscus causal graphs (batch 25) by realmarcin · Pull Request #1361 · CultureBotAI/CommunityMech

realmarcin · 2026-10-06T03:07:38Z

Summary

Source-review Copper heap leaching and Coscinodiscus synthetic-community graphs.
Repair two records; retain ten nodes/ten arrows with seven exact renames, two gaps and two append-only histories. No new structure or Edison spend.
Preserve real oxidation/leaching, nutrient supplementation and partner-specific growth outcomes while qualifying flux, transfer, fitness signs and model scope.

Closes #1356. Closes #1357. Closes #1360. Separate metadata followups #1358/#1359 remain open.

Validation

23 initial local commands plus 4 remediation commands completed. The initial full suite had 292 passed and one stale census-ceiling failure; the complete rerun now has 293 passed in 187.32s (0:03:07). Rights: 3 passed in 1.93s. One documented reference-check failure remains.
46 MATCH and exactly 3 MISMATCH snippets; other classes zero. The three short primary Results quotes were read in the publisher preview but are absent from the abstract-only cache. Reference validator exit 1 and diagnostics are preserved; this gate is NOT reported passed. Existing 97 evidence snippets remain unverifiable, effectively all on closed-access sources #596 remains open.
Zero structural/network errors; 25 existing network warnings unchanged.
27 unrelated raw YAML blocks and eight cache artifacts byte-preserved.
Two identical full renders and exact parsed node/arrow description coverage. Eight focused new regressions.
Canonical taxa and census total 1499 unchanged; two records become mixed-scope, solely community-credited taxa 1221 -> 1217 after intrinsic source corrections. Only the mixed-scope ceiling/comment changes (122 -> 124) under Account for Copper and Coscinodiscus mixed-scope census corrections #1360; other bounds and connectivity behavior unchanged.
Stacked coverage: 123 reviewed, 334 pending, 3 need research.

Review Limits

Source-based self-adversarial review, not independent approval. Four complete primary main bodies and three contextual abstracts read. No figure images or supplementary files inspected; OCR equations not visually verified. No new full copyrighted body or PDF added. Unrelated metadata preserved, not certified.

Stacked on batch24 PR #1355. 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 merged branches only after dependents move.

realmarcin

Source-based self-adversarial review at exact head 5f7e0faecd6486addf38d462234f7cb6067d29a4, not independent approval.

Addressed #1356/#1357/#1360; separate metadata followups #1358/#1359 remain open. Two records repaired; ten nodes/ten arrows retained with seven exact renames. No new graph structure or Edison spend.

Preserve real iron/sulfur oxidation, conditional copper extraction, pooled nutrient supplementation and partner-specific growth. Separate DNA/RNA field association from taxon-resolved flux, genus from exact species, BLASTP from DMSP consumption, pooled rescue from individual vitamin donation, and phase-specific model fit from universal absence of higher-order interactions. Chemical feedback remains conditional, not removed merely for being cyclic.

23 initial local commands plus 4 remediation commands completed. The initial full suite had 292 passed and one stale mixed-scope ceiling failure; after verifying the exact two-record delta, only the ceiling/comment changed from 122 to 124 and the full suite passed. The initial failure is preserved. One reference validator exit 1 remains, reporting exactly three primary-verified Results quotes absent from the abstract-only local cache. This gate is NOT passed; broad #596 stays open. No curated snippet was promoted to independent cache content. 293 passed in 187.32s (0:03:07); 3 passed in 1.93s; 46 MATCH and 3 documented abstract-cache MISMATCH snippets; 27 unchanged raw blocks and eight 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. Four intrinsic source corrections move solely community-credited taxa 1221 -> 1217 while total coverage remains 1499; two records become mixed-scope. Other census bounds, participant checks, connectivity behavior and registries are unchanged.

Decision/adversarial/validation records bind every node/arrow and record/cache hashes. Four complete primary main bodies plus three contextual abstracts read; no figure images, supplementary files or visual OCR equation verification. No new copyrighted full body/PDF. Stacked coverage is 123/460, not completion.

Required CI and protected main queue remain mandatory. Do not merge into a topic parent. Move dependents before deleting merged branches.

github-actions · 2026-10-06T03:08:09Z

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 e65a2deffbbcd6aa30fb5548c6866a59d426ee9c 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: 84c753bb910d4bf5070e53bc1f15e9f2da9be165389d1dba27c92f4e443d417d. New whole-tree SHA: 18e0b3c4ab7d222726060fa48750d7c598559688. 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 37d3d54646896b375fd245b07cfaddb1c43a87a9
after protected main merge of #1307. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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 5c65f1f504ff86a343cbb029eb261fd3f97aae4e
after protected main merge of #1312. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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 8f24d545e60a78687b55f320b14fcb8cf92c8528
after protected main merge of #1315. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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 090349e648f5c663eaffb59a08a4d8d88cf4a38a
after protected main merge of #1318. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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 b3be2ec110e46f1b568d4f40f981edc36ff879d4
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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 f202262e7436a174cce150b69017e0a81876f124
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 18e0b3c4ab7d222726060fa48750d7c598559688.
The batch-owned binary patch is byte-identical
(SHA-256 a0ab02f2bcd74031f646bac36fb73be3ad326f205542d94a0109ac0c7ca7c127); 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.