Bound Variovorax causal graph and correct strain-aware census (batch 43)

[realmarcin]

Scope

Closes #1471. Closes #1472.

Three existing Variovorax nodes retained and renamed; both unsupported downstream arrows removed. Compartment DNA enrichment is relative, resource competition remains HYPOTHESIZED, and the separate PMI12_01353 deletion/root-CFU assay belongs only to canonical CF313. No priority effects, interstrain facilitation, universal pathway sufficiency or demonstrated whole-panel mediation. The existing L-fucose grounding is reused; exact canonical preferred names prevent genus-only ambiguity. No new graph structure or Edison/provider spend.

Correct the separate connectivity survey's shared-CURIE overcredit by reusing the already strain-aware readiness resolver. Production auditor/ranker semantics are unchanged. Both algorithms were measured on both corpus versions: legacy baseline/current solely-community credit 1219/1191, corrected baseline/current 1222/1221. The biological scope change credits exactly one strain, not all 28. Mixed scope changes 124 to 125; other bounds unchanged. Preserve synthetic auditor canaries and add exact live CF313 coverage. Historical outputs remain unchanged but are no longer presented as exact strain-resolved counts; README documents the correction.

Verification And Output Records

445 passed in 176.93s (0:02:56); five new focused regressions. Schema, strict, terms, references and history checks pass. All 44 snippets match cached text. The CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage #476 remains incomplete, and textual matching does not establish scientific support or independent provenance.

Both-root pre-paper baseline retained. Zero graph errors; all 33 existing network warnings unchanged. 459 other records, all 920 caches and non-graph raw blocks preserved. Repeat render deterministic; all 456 published pages checked for exact node/edge descriptions. Participant registry 189 to 190. No browser screenshot review claimed.

One draft absolute-read-abundance phrase was corrected to normalized-read abundance during self-review. The initial run passed 445 tests but failed Ruff on two test-style issues; those were fixed and fresh complete validation ran on final bytes. The initial run is archived with hashes and actual failure output. A local dedup path typo was corrected before conclusions. Actual outputs and limitations are committed in reports/causal_graph_review, batch43.

Actual post-commit just check-docs-current exited 0 with a clean tree, log SHA256 234baf5d49cb6fccc29c40d4dfcb6b271192815f3bbc9654b7df8438efbda680.

Whole original record and complete cached primary main body/Methods/captions read. Stale abstract_only front matter is disclosed, not silently rewritten. Public PMC access presented reCAPTCHA; no bypass. No figures, separate supplements, raw data, code, complementation or whole-panel mutant-replacement verification claimed. Non-graph metadata is preserved, not certified. The UFMP and GOM candidates remain pending.

Source-based self-adversarial review, not independent approval. Broader #524 remains open.

Corpus: 164 reviewed / 284 pending / 12 needs_research, across 460 records. Full-corpus completion is not claimed.

Dependency

Draft depends on #1470. Do not merge into the topic parent. Require eligible exact-head checks and the protected main queue after parents merge; move dependents before deleting merged branches.

[realmarcin]

Source-based self-adversarial review at exact head c106450; not independent approval.

Issues #1471/#1472 addressed after primary-text, code, full diff and output review.

Three existing Variovorax nodes retained and renamed; both unsupported downstream arrows removed. Compartment DNA enrichment is relative, resource competition remains HYPOTHESIZED, and the separate PMI12_01353 deletion/root-CFU assay belongs only to canonical CF313. No priority effects, interstrain facilitation, universal pathway sufficiency or demonstrated whole-panel mediation. The existing L-fucose grounding is reused; exact canonical preferred names prevent genus-only ambiguity. No new graph structure or Edison/provider spend.

Correct the separate connectivity survey's shared-CURIE overcredit by reusing the already strain-aware readiness resolver. Production auditor/ranker semantics are unchanged. Both algorithms were measured on both corpus versions: legacy baseline/current solely-community credit 1219/1191, corrected baseline/current 1222/1221. The biological scope change credits exactly one strain, not all 28. Mixed scope changes 124 to 125; other bounds unchanged. Preserve synthetic auditor canaries and add exact live CF313 coverage. Historical outputs remain unchanged but are no longer presented as exact strain-resolved counts; README documents the correction.

445 passed in 176.93s (0:02:56); five new focused regressions. Schema, strict, terms, references and history checks pass. All 44 snippets match cached text. The CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage #476 remains incomplete, and textual matching does not establish scientific support or independent provenance.

Both-root pre-paper baseline retained. Zero graph errors; all 33 existing network warnings unchanged. 459 other records, all 920 caches and non-graph raw blocks preserved. Repeat render deterministic; all 456 published pages checked for exact node/edge descriptions. Participant registry 189 to 190. No browser screenshot review claimed.

One draft absolute-read-abundance phrase was corrected to normalized-read abundance during self-review. The initial run passed 445 tests but failed Ruff on two test-style issues; those were fixed and fresh complete validation ran on final bytes. The initial run is archived with hashes and actual failure output. A local dedup path typo was corrected before conclusions. Actual outputs and limitations are committed in reports/causal_graph_review, batch43.

Actual post-commit just check-docs-current exited 0 with a clean tree, log SHA256 234baf5d49cb6fccc29c40d4dfcb6b271192815f3bbc9654b7df8438efbda680.

Whole original record and complete cached primary main body/Methods/captions read. Stale abstract_only front matter is disclosed, not silently rewritten. Public PMC access presented reCAPTCHA; no bypass. No figures, separate supplements, raw data, code, complementation or whole-panel mutant-replacement verification claimed. Non-graph metadata is preserved, not certified. The UFMP and GOM candidates remain pending.

Source-based self-adversarial review, not independent approval. Broader #524 remains open.

Protected main merge and full-corpus completion remain pending.

[github-actions]

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, 33 warning across 13 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)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 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]

Self-adversarial review refreshed at exact head 5b0b555a45aa07071a1e9865f46a37842d9ab27e
after protected main merge of #1323. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 c7868c10e36584e6dd930681a32619e16748a0ba
after protected main merge of #1328. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 d175d9fb2ad77883bd2ff761c18349cdf9b9b9d0
after protected main merge of #1334. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 4df839e08f04ebbc72615cd3611828f5ba8ad82d
after protected main merge of #1339. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 631524195da3a1e15b614c6a0a62d4f46377fe0d
after protected main merge of #1346. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 2b7aba0e2d89092e7febc07a90babb04583c4943
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 8a8cfe3dfa9d33dccfae2f64fea8b7d891a9c2c3
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 92a55c0de17232e3032e43e3f7e13c7023656126.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 integration review at exact head 38a9aafb8356b10f8d9ba379a99b0a812eae0957. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 8a8cfe3dfa9d33dccfae2f64fea8b7d891a9c2c3, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head c1467fb4af5eaa0be539d010a5b208146efc5207
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree a840ce5caae2164ea02c4ad2ae1efa940406a338.
The batch-owned binary patch is byte-identical
(SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d); 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 governance integration review at exact head ba8b643e3b40c0483110bad8dc86f5bc0a01bbe5. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head c1467fb4af5eaa0be539d010a5b208146efc5207, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at 73f3907747db63597b36430a64e4ac979c696430.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 853d59289d52b14547905d16ea264a31580ae3d0f95017246c5df69a6fa09f4d.
Tree 0df0cd79e6dfc7e86ea672da6408a04df7ff47b0 matches the independently computed clean merge.
Compared with historical tree c69aec43593ae3bb8b0be54b8f606ceed5837077, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head bcd937cb7cd7121fce4af64a776ccadd850f48a4 was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.