Repository navigation
Bound HAMBI, Hanford and C6 community causal claims (batch50) - #1496
realmarcin wants to merge 1 commit into
Conversation
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Source-based self-adversarial review at exact head fbd0ad0; not independent approval.
Issues #1493, #1494 and #1495 addressed.
-
Bound controlled carbon-state outcomes and competitive-sorting interpretation.
-
Separate aquifer guild inference from measured flux and remove two unsupported causal arrows.
-
Bound bulk chemical removal and post-irradiation community recovery.
-
Whole three records and all six original nodes/two arrows reviewed. HAMBI/C6 complete cached main texts, Methods and embedded captions read; C6 main Tables1-3 read. Hanford complete primary abstract and selected local excerpts only. No original figure images, supplements, raw data or code audited.
-
HAMBI controlled carbon-dependent composition shifts remain positive SUPPORT/IN_VITRO observations. The authors' OD-scaled analysis is retained, not dismissed as purely compositional. Competitive sorting remains an interpretation; ancestral monoculture traits and pH associations do not selectively demonstrate the mediator or alternative within-condition stable states.
-
HAMBI keeps all16 canonical input strains, including taxa not dominant at endpoints. Do not infer persistence/extinction from the roster. R2A is a limited resource-complexity proxy; no universal conclusion about complexity or new trait/pH arrow is added.
-
Hanford preserves field observations and the authors' hydrologic structuring interpretation. Remove two arrows that imply community-to-flux and flux-to-depth causal directions. Putative guild annotation is distinct from measured metabolism, and environmental nitrate/uranium is not interspecies exchange.
-
The Hanford cache says full_text but contains selected snippets; this was not misreported as complete primary-body review. PMC CAPTCHA was not bypassed. Broad four-taxon participants are an incomplete subset, not resolved physiological guilds; no new top-down-control/predation mechanism was invented from the abstract proposal.
-
Self-adversarial review found that the selected Hanford guild sentence did not retain its spatial comparator. Removed the contact/redox-transition attribution, renamed the node to neutral depth-stratified sampling context and repaired its anchor and ledger. Prior actual checks were archived as superseded; every verification command was rerun against final text. No history or cache was erased.
-
C6 retains the positive reported94.41/85.56/37.64percent 24-hour biofilm benchmark. Rich AS medium, bulk COD and chemical disappearance do not establish mineralization or reciprocal fitness. Table2 ammonia production is distinct from isolate-level ammonia removal.
-
C6 retains all6 strain labels, including two pairs sharing taxon CURIEs. Bulk post-irradiation recovery during medium renewal does not prove every-strain survival, unchanged composition or an EPS/quorum-sensing mechanism. Nonsignificance is not formal equivalence, and suspended-culture recovery timing is not substituted for biofilm timing.
-
Self-review corrected the issue1495 wording: the original record already said not significantly changed. That was not an unqualified no-effect assertion. These statistical and mineralization statements are explicit boundaries, not claims that the original graph asserted every excluded mechanism. The scientific record required no further correction.
-
C6 main-text50mg/L versus Fig4-caption100mg/L irradiation feed remains explicitly unresolved. The earlier review's chosen non-graph concentration is preserved without recertification. Existing gap author/date/evidence remain, with both nodes anchored; no duplicate gap or history deletion.
-
Inspected all record diffs and focused test assertions. Six nodes retained, two arrows removed, three guarded writes and append-only history artifacts. All457 other records and920 caches preserved. Canonical taxonomy and other non-graph raw blocks unchanged. Three participant registry entries added; measured connectivity census unchanged, no production matching or census-bound change.
-
Actual schema, strict, terms, references, snippets, rank and history gates passed. Network equals baseline with34 prior findings and zero structural defects. Deterministic repeat renders and exact descriptions across456 pages parser-checked, not browser screenshots. Actual post-commit docs-current remains a separate publication gate.
-
Dedup checked803 all-state issue titles/bodies and19 ignored/hidden local files, not every comment/PR review. Existing1059/1060/1007 are closed non-graph repairs;1095 remains an unrelated open writer-audit issue. Issues1493/1494/1495 stay open until protected main merge. Source-based self-adversarial review is not independent approval.
484 passed in 196.51s (0:03:16); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 63 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All six nodes retained and two unsupported Hanford arrows removed. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. Three participant registry entries added; no census-bound or production matching change.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 30470ed6337306eaea39636fbf672e78d2ad8b8e592b776cdf39fa26866c7ea1.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch50. Not independent approval. Corpus176 reviewed /270 pending /14 needs_research, not complete.
Protected main merge remains 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. |
5d6f2a6 to
f654e44
Compare
fbd0ad0 to
c9daec9
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head c9daec995c8909da36ea5df0da0e6b4eb20f416c
after protected main merge of #1339. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree f87fe4da5384c18d2d7f6d390a9d1f4c185a735f.
The batch-owned binary patch is byte-identical
(SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb); 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.
c9daec9 to
f357ed2
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head f357ed253ac130cf21e71b2795be383d1e89cc07
after protected main merge of #1346. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree f87fe4da5384c18d2d7f6d390a9d1f4c185a735f.
The batch-owned binary patch is byte-identical
(SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb); 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.
f357ed2 to
3874623
Compare
5e24edd to
24731bb
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head 387462365c3621d365294591567ba91be89999e8
after protected main merge of #1350. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree f87fe4da5384c18d2d7f6d390a9d1f4c185a735f.
The batch-owned binary patch is byte-identical
(SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb); 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.
3874623 to
9768606
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head 97686067d6049427cabae945b76a044cc54b6bca
after protected main merge of #1355. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree f87fe4da5384c18d2d7f6d390a9d1f4c185a735f.
The batch-owned binary patch is byte-identical
(SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb); 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.
9768606 to
69a7b20
Compare
4d5d624 to
62e2d72
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial integration review at exact head 69a7b20dd96f5ce67fa0cc07bd41c1939bfe487e. Not independent approval.
Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 97686067d6049427cabae945b76a044cc54b6bca, 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 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb). 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.
62e2d72 to
a521f49
Compare
69a7b20 to
7c4fe56
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head 7c4fe5658e5061df9dabdd3de02a879b25df4057
after protected main merge of #1361. This is not independent approval.
The entire tree remains identical to the preceding reviewed tree 3e3f28e41803932998f908c0f19c1bdb5ff4df7e.
The batch-owned binary patch is byte-identical
(SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb); 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.
a521f49 to
a009afc
Compare
7c4fe56 to
3a9720d
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial governance integration review at exact head 3a9720d03838b81bc542aa214162b717f0ee1cc1. This is a COMMENT, not independent approval.
Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 7c4fe5658e5061df9dabdd3de02a879b25df4057, 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 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb). 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.
3a9720d to
52ab1b1
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Exact-head self-adversarial restack review at 52ab1b197a7dcc0949a10812055718ab930f4410.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 8e88fabb749ba3a13aa38deab69b40064ec436db0d1cfb33039b72049a8d3ffb.
Tree cb052e5cc3fa05c68139b471a461fc3c314bee71 matches the independently computed clean merge.
Compared with historical tree 86382b2b3b7f2955d6316215350cccd8b535ca90, 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.
52ab1b1 to
d8f14f8
Compare
|
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 #1493. Closes #1494. Closes #1495.
Adversarial Review
Verification And Output Records
484 passed in 196.51s (0:03:16); six new focused tests. Schema, strict, term, reference, snippet and history gates pass. 63 snippets match unchanged caches. Text matching is not independent provenance or scientific support. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.
All six nodes retained and two unsupported Hanford arrows removed. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and920 caches preserved, not certified. Measured connectivity census unchanged. Three participant registry entries added; no census-bound or production matching change.
Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 30470ed6337306eaea39636fbf672e78d2ad8b8e592b776cdf39fa26866c7ea1.
Source decisions, actual validation outputs/digests and self-adversarial review committed under reports/causal_graph_review, batch50. Not independent approval. Corpus176 reviewed /270 pending /14 needs_research, not complete.
Dependency
Draft depends on #1492. Do not merge into the topic parent. Require eligible exact-head CI and the protected main queue after parent merges. Move dependents before deleting merged branches. No Edison job or provider spend for this existing-structure repair.