Repository navigation
Qualify graph mechanisms and withhold unverified subset attribution (batch103) - #1815
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 f3f972b; not independent approval.
-
Retain genome-predicted supplier capacity and explicitly hypothesized reservoir replenishment, without categorical cross-feeding.; Retain context-dependent composition responses to added corrinoids without niche-partitioning attribution.; Retain the measured soil-associated pool, distinguish accessibility from abundance, and qualify its proposed buffering effect.
-
Withhold four parent-SRC1 nodes from an unverified subset identity; retain needs_research and source-grounded identity discussion.
-
Retain relative composition fidelity with statistical, context and source-consistency limits; remove facilitation.; Preserve positive live-treatment host biomass results without mutualism or field-efficacy claims.; Retain host transcript/metabolite responses while withholding unproven flavonoid mediation.
-
Retain cross-site community composition association without categorical niche partitioning or controlled restoration causality.; Retain archaeal gene/flux evidence and bounded substrate-response support without syntrophic feedback or field flux apportionment.; Retain bacterial pathway potential with canonical scope, non-exclusivity and explicitly inferred contribution, not cross-feeding.; Retain salinity/sulfate covariation without a competition or causal sulfate claim.
-
Whole original target records and every changed graph/discussion diff reviewed. Every original node/direction has a disposition. Retain10of14nodes and both original directions asHYPOTHESIZED; withhold4unverified-subset nodes;8renames. No new node/direction/provider spend.
-
Challenge removal versus lost evidence: corrinoid retains producer inference, measured pool and amendment responses; SRC2v4 retains composition/host biomass/flavonoid responses; salt pond retains associations and methanogenesis activity support. SRC1 parent observations are not rejected: attribution to an unverified subset is withheld pending identity1813, not replaced by another formulation.
-
Corrinoid: keep the full prediction qualifier, distinguish native predominantlycobalamin reservoir from diverse amendments, and distinguish total abundance from bioavailability. Producer release/replenishment and reservoir buffering are model hypotheses, not measured flux or isolated stability mechanisms. Both original directions are retained with these explicit limits; no new graph extension.
-
SRC1: the cached/fresh abstract does not identify the claimed16-20member subset. Indexed primary introduction and independently retrievedSRC2paper identify57member parent. Do not silently rename the record, assert absence of any subset globally, reintroduce removed assay-order arrows, assign reciprocal benefit, or interpret lignin correlation as mediation. Identity remainsneeds_research; no subset formulation is invented.
-
SRC2v4: relative compositional fidelity is not equivalence or universal stability. Source text/Fig2caption inconsistency is disclosed; no raw-data adjudication claimed. Preserve host biomass response without microbial fitness signs or field efficacy. Host flavonoid response does not establish recruitment/colonization or growth mediation; within-treatment correlations were nonsignificant. Prior782-790fixes remain. No new growth, colonization, infection or genetic-design procedures.
-
Salt pond: cross-site association is not an isolated restoration effect or niche partitioning. Gene/flux correlation is not syntrophic feedback or cross-feeding. Microcosm methylated-substrate responses support activity but do not apportion field flux or identify partner feedback. The explicitly bacterial node does not claim exclusivity; archaealphnJis acknowledged. Canonical participants use identity-only copies. Statistical tools are primary-method-supported, with no guessed versions. Prior652treatment separation remains.
-
Sixteen graph and four discussion quotations match fresh primary text and unchanged caches. SRC1 complete text was not independently persisted/read; other source-read spans are explicitly bounded. No figure pixels, raw data or supplementary files reviewed. Large caches not read exhaustively; literal matching is not entailment or whole-record certification. No new cache imports or validator exceptions.
-
Four guarded writes/four append-only histories;456otherrecords/all923caches and all prior history/decision files byte-identical. Taxonomy and non-graph raw blocks preserved, not recertified. WithholdingSRC1 removes oneCL-onlyrecord and six broadly credited taxa from the census; salt-pond participant scopes are added. No census-threshold, schema, runtime or audit-rule changes.
-
Eight focused tests and935combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. Network equals baseline56warnings/zero structural defects. Deterministic rendering and HTML parser cover456pages/1378descriptions/557arrows, not screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
-
Repairs1809-1812 addressed and remainopen until protected-main merge; identity1813/non-graph1814 remainopen. Licensegate949, loader1703, DOIcache1091 and denied/unansweredEdison scopes not certified or resolved. Self-review is not independent approval; no artificialCI, protection bypass or premature cleanup.
-
Corpus327reviewed/84pending/49needs_research is not completion. Postcommit docs-current and exact-head publication require separate receipts and are not preasserted here.
935 passed in 299.74s (0:04:59); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated.41 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All20reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
Ten of fourteen nodes remain, with eight renames; both original corrinoid directions remain explicitly hypothesized. All four targets changed;456otherrecords, all923caches, taxonomy and non-graph raw blocks preserved. Corpus327reviewed/84pending/49needs_research. Network56existingwarnings/zero structural defects. Salt pond gains scoped participant identities. Withholding the unverified SRC1 graph removes one community-level-only record and six broadly credited taxa from the census; thresholds unchanged.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 edd30f403234f4626e4016e7372a76a6378c3ec91ffedf8ad021ec2c52db76a2. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
SRC1 independent evidence is abstract-bounded plus indexed primary identity leads; its exact subset remains unverified. Other sources have bounded primary main-text coverage with explicit supplementary/figure/raw-data limits. No new topology or Edison spend. Identity1813 and non-graph1814 stay open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
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. |
ca28c79 to
7023b96
Compare
f3f972b to
56b8c11
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Exact-head self-adversarial restack review at 56b8c117d428207ad722c5755fd154efd0b40b84.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 9d5a49cd928ec5144ffe7a06947444fcf535fa9f15c24852e75998951c655995.
Tree a9af5dbbbc28c8b39c3d470c3fdf52d282daaacc matches the independently computed clean merge.
Compared with historical tree 8df37053642affeb8e07c787cbdec57fe1edfb7c, 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.
56b8c11 to
5533fc1
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 #1809.
Closes #1810.
Closes #1811.
Closes #1812.
Identity #1813 and non-graph #1814 remain open.
Adversarial Review
Verification And Output Records
935 passed in 299.74s (0:04:59); eight new focused tests. Four full-record schema, strict, ontology-term, reference and snippet checks passed; four append-only histories validated.41 recorded gate outputs/digests. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked. Explicit-runtime non-incremental mypy passed. All20reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
Ten of fourteen nodes remain, with eight renames; both original corrinoid directions remain explicitly hypothesized. All four targets changed;456otherrecords, all923caches, taxonomy and non-graph raw blocks preserved. Corpus327reviewed/84pending/49needs_research. Network56existingwarnings/zero structural defects. Salt pond gains scoped participant identities. Withholding the unverified SRC1 graph removes one community-level-only record and six broadly credited taxa from the census; thresholds unchanged.
Decisions, provenance, validation and self-adversarial review are committed under reports/causal_graph_review, with four append-only history records. Postcommit docs-current passed clean, SHA256 edd30f403234f4626e4016e7372a76a6378c3ec91ffedf8ad021ec2c52db76a2. Deterministic rendering and HTML parser checks are not screenshots. Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
SRC1 independent evidence is abstract-bounded plus indexed primary identity leads; its exact subset remains unverified. Other sources have bounded primary main-text coverage with explicit supplementary/figure/raw-data limits. No new topology or Edison spend. Identity1813 and non-graph1814 stay open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Source Limits
Dependency
Draft depends on #1808. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.