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Correct Geobacter-Pseudomonas direction and bound competition (batch47) - #1486
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Source-based self-adversarial review at exact head 9174d5c; not independent approval.
Issue #1485 addressed after primary-text, graph/test-diff and actual-output review.
Correct the existing Geobacter-Pseudomonas formate/fumarate graph after whole-record and primary-source review:
- Correct the inferred electron donor direction to Pseudomonas-to-Geobacter using canonical endpoints and the explicit 2020 Results interpretation.
- Preserve positive omcZ/omcS growth impairment and phz-mutant growth evidence, not protein association alone. Keep SYNTROPHY in the transfer node and mark its growth-enabling arrow PARTIAL rather than claim an exclusive transfer route.
- Remove the serial-transfer chronology arrow. Represent observed growth and adaptation with explicit community participants; distinguish dominance, sequence variants and protein changes from unproven competition, killing, variant causality or complete partner independence.
- Represent added commercial PHZ-1-CA inhibitory response without asserting endogenous Pseudomonas pressure. It was below detection in cocultures and did not select the tested variants. Other mediators remain unresolved.
- Correct experimental SWATH-MS and sequencing classifications. Preserve later HybA/FdnG observations as bounded adaptation context, not measured flux or an invented route-to-dominance link. Record the source's MIC-duration discrepancy without silently choosing a duration.
All four nodes retained; two arrows to one. No new causal structure or paid Edison job for this existing-structure repair.
466 passed in 189.53s (0:03:09); five new focused tests. Schema, strict, term, reference, snippet and history checks pass. All 24 snippets match unchanged caches. Text matching is not scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091), and selected-cache provenance (#1362) remain limitations.
Both-root pre-source baseline retained. Zero structural errors; all 34 existing network warnings unchanged. All 459 other records, 920 caches, taxonomy, non-graph raw blocks and prior histories preserved, not certified.
Actual census: community-level records 388 to389, mixed125 to126, taxa1496 to1498; community-level-only263 and solely-credited1223 unchanged. Registry194 to195. Only the corresponding mixed upper bound increases by one, with the issue rationale; other bounds and production logic are unchanged. Repeat renders deterministic; exact descriptions parser-checked across456 pages without a browser screenshot claim.
Actual post-commit just check-docs-current exited0 with a clean tree; log SHA256 fb10d29e368c7a19363c2fde4dafa56b4643da49de62b78859b1550ca86fae67.
Whole374-line record and every original node/arrow reviewed. Complete2018 primary abstract and complete cached2020 primary main text/Methods/Tables1-2/embedded captions read. The2018 full text was unavailable. No figure images, separate supplements, raw data or analysis code audited; failed PDF screenshots are not claimed as inspection.
Decisions, actual outputs/digests, scope and limitations are committed under reports/causal_graph_review, batch47. Source-based self-adversarial review, not independent approval.
Protected main merge and full-corpus completion remain pending.
Network integrity findingsWarnings 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. The full report is attached to the workflow run as an artifact. |
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Self-adversarial review refreshed at exact head ac6248a1b9885752187aba734fff4d59146a5ba6
after protected main merge of #1334. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a74ac965aa5a120b2f5c585c6ba42d1a452e5cef.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial review refreshed at exact head 504a4c4e537078f392304cf43fb8494058da56e1
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a74ac965aa5a120b2f5c585c6ba42d1a452e5cef.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial review refreshed at exact head 93e4d4d3234b26faa9535ad70799c07ca9c44844
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a74ac965aa5a120b2f5c585c6ba42d1a452e5cef.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial review refreshed at exact head 80fccd29c667515745434bf6b4c106df2901bcdf
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a74ac965aa5a120b2f5c585c6ba42d1a452e5cef.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial review refreshed at exact head 09a360119c57e3b1a262f2127772e92d354f81e6
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree a74ac965aa5a120b2f5c585c6ba42d1a452e5cef.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial integration review at exact head c6d1f17f12ed8e6131ad0c2dbc5a8541a44766bd. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 09a360119c57e3b1a262f2127772e92d354f81e6, 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 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d). 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.
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Self-adversarial review refreshed at exact head bde849afaf99802409856cef83a9f1b54ccf3dbc
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 02a3ce0e0a743ffbe92a68831e7fd32129db55ca.
The batch-owned binary patch is byte-identical
(SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d); 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.
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Self-adversarial governance integration review at exact head 8758468cb0a11caeb6e7476122898c0107b0370c. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head bde849afaf99802409856cef83a9f1b54ccf3dbc, 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 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d). 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.
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Exact-head self-adversarial restack review at 3e8d8a5c66685aa3c83cdef45e25798b46779f1f.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 253fff8565acd0445226fe14092547e6b44f354f3cc59019209f7ab0eae6186d.
Tree 2e7dfd8225e7356170b5d563f002f21ca39a9ee4 matches the independently computed clean merge.
Compared with historical tree 8162ad5fd1cca169095ee76b36f330fb0e27d091, 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.
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Superseded by the protected cumulative merge #1975 at 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. |
1 participant
Scope
Closes #1485.
Correct the existing Geobacter-Pseudomonas formate/fumarate graph after whole-record and primary-source review:
All four nodes retained; two arrows to one. No new causal structure or paid Edison job for this existing-structure repair.
Verification And Output Records
466 passed in 189.53s (0:03:09); five new focused tests. Schema, strict, term, reference, snippet and history checks pass. All 24 snippets match unchanged caches. Text matching is not scientific support or independent provenance. CLI Total checks:0 means no reported issues, not no executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091), and selected-cache provenance (#1362) remain limitations.
Both-root pre-source baseline retained. Zero structural errors; all 34 existing network warnings unchanged. All 459 other records, 920 caches, taxonomy, non-graph raw blocks and prior histories preserved, not certified.
Actual census: community-level records 388 to389, mixed125 to126, taxa1496 to1498; community-level-only263 and solely-credited1223 unchanged. Registry194 to195. Only the corresponding mixed upper bound increases by one, with the issue rationale; other bounds and production logic are unchanged. Repeat renders deterministic; exact descriptions parser-checked across456 pages without a browser screenshot claim.
Actual post-commit just check-docs-current exited0 with a clean tree; log SHA256 fb10d29e368c7a19363c2fde4dafa56b4643da49de62b78859b1550ca86fae67.
Whole374-line record and every original node/arrow reviewed. Complete2018 primary abstract and complete cached2020 primary main text/Methods/Tables1-2/embedded captions read. The2018 full text was unavailable. No figure images, separate supplements, raw data or analysis code audited; failed PDF screenshots are not claimed as inspection.
Decisions, actual outputs/digests, scope and limitations are committed under reports/causal_graph_review, batch47. Source-based self-adversarial review, not independent approval.
Corpus:169 reviewed /277 pending /14 needs_research across460 records. Full-corpus completion is not claimed. Knowledge gaps within this bounded graph remain explicit.
Dependency
Draft depends on #1484. Do not merge into the topic parent. Require eligible exact-head checks and the protected main queue after parent merges; move dependents before deleting merged branches.