Repository navigation
Bound soy community graphs and record unresolved sfSynCom identity (batch104) - #1822
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 5d8eb3b; not independent approval.
-
Preserve positive flavor measurements with exact experimental and comparator scope; remove the assembly node and unsupported niche-partitioning arrow.
-
Retain the inferred genotype pattern without mutualism, nitrogen flux or a genotype-to-phenotype arrow.; Preserve the observed composition shift while removing niche partitioning and unsupported mediator annotations.; Retain plant phenotype observations with table-based significance limits, pot context and no reciprocal-benefit attribution.
-
Withhold three strain/formulation-attributed sfSynCom nodes pending exact membership; retain needs_research and positive source observations in a bounded identity discussion.
-
Retain the two-taxon succession observation with canonical participant scope and qualified facilitation.; Preserve the dropout transcriptional response as indirect support for hypothesized nutrient exchange, with abstract-bounded provenance.
-
Whole original targets and every changed graph/discussion diff reviewed. All11originalnodes/6directions have dispositions: retain6nodes, remove5workflow/unverified-attribution nodes and all6directions, rename6nodes. No new topology or provider spend.
-
Challenge removal versus lost evidence: preserve the soy-sauce flavor measurements, chlorophyll genotype/composition/host observations and soymilk succession/dropout response. sfSynCom positive helper and consortium results remain in the discussion; only their mapping to the assumed three-microbe formulation is withheld, not the published results.
-
Soy sauce: experimental scheduling is not demonstrated ecological niche partitioning. Preserve laboratory comparator scope without universal optimum, industrial efficacy or recalculated ambiguous fold changes. Existing compact-table history899 unchanged; no operational enhancements added.
-
Chlorophyll: genotype-pattern interpretation leaves selection pressures unresolved. Relative composition and co-occurrence do not establish niche partitioning, cooperation or IAA/siderophore mediation. Host phenotype is not reciprocal microbial benefit or direct nitrogen flux. Table1 shares significance letters with both controls for the three named endpoints; retain higher reported means without blanket significant superiority. Pot soil provenance is not field deployment. Previous formulation-arrow removal remains.
-
sfSynCom: exact community membership and source identity of ordinal helper slots are unverified from the abstract, not disproven globally. Do not silently equate two mentioned helper strains with the complete final consortium, assign reciprocal pairwise benefit or import another formulation. Keep needs_research and identity1820 open; retain positive abstract observations with partial attribution support.
-
Soymilk: succession does not isolate directional facilitation; dropout-associated transcription indirectly supports the authors' nutrient-supply interpretation, not traced transfer or mediation of succession. Retain HYPOTHESIZED/PARTIAL qualifiers, abstract-bounded statistical provenance and two canonical identity-only succession participants. Do not invent tools, versions, exact compounds or recipient-specific exchange.
-
Nine graph and five discussion quotations match fresh primary text and unchanged caches. Primary body coverage is bounded for soy-sauce/chlorophyll (including extractedTable1); sfSynCom/soymilk independent evidence is abstract-only. HTTP403 access failures and lack of a PMCID are not proof that full texts or supporting details do not exist. No access bypass, cache imports, supplements/figure-pixel or raw-data certification.
-
Four guarded writes and four append-only histories;456otherrecords/all923caches and prior history/decision files byte-identical. Alias-linked non-graph evidence preserved. sfSynCom previously had only pairwise nodes, so removing that graph does not change the community-level census; soymilk's succession scope is narrowed without audit-rule or threshold changes.
-
Eight focused tests and943combined regressions pass. Four full-record schema/strict/term/reference/snippet checks and four histories validate. Network equals56baselinewarnings with zero structural defects. Deterministic rendering and exact HTML parser cover456pages/1373descriptions/551arrows, not screenshots. Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
-
Repairs1816-1819 addressed but remain open until protected-main merge. Identity1820/non-graph1821 remain open. Existing source-access, license949, loader1703, DOIcache1091, denied and unansweredEdison scopes are not silently resolved. No pathogen growth/colonization/infection optimization or genetic designs. Self-review is not independent approval; no artificial CI, protection bypass or premature cleanup.
-
Corpus330reviewed/80pending/50needs_research is not completion. Postcommit docs-current and exact-head publication require separate receipts, not preasserted here.
943 passed in 309.18s (0:05:09); 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. All14 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
Six of eleven nodes remain, with six renames; five workflow/unverified-attribution nodes and all six directions are removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus330reviewed/80pending/50needs_research. Network56existingwarnings/zero structural defects. Soymilk succession gains scoped participant identities; the community-level census and its thresholds are 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 cbfbc4abefbb964fc7485f54ef2519531008d22969d133f255d6bbdf007254cb. 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.
sfSynCom/soymilk independent evidence is abstract-bounded. Soy-sauce/chlorophyll primary body coverage is bounded, including chlorophyll Table1, not full methods/supplement/figure/raw-data certification. No new topology or Edison spend. Identity1820 and non-graph1821 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. |
5d8eb3b to
d54c82f
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Exact-head self-adversarial restack review at d54c82fae83a31d5f031d475da0f5c1f7fb3d4da.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 edaf85b744fe46e6530d692673279587b4cd8c65c09a4b525645a8b2b529706b.
Tree 596ee3d4e81000337301f41d3204051be9101626 matches the independently computed clean merge.
Compared with historical tree fb89729566c9f3cbbb9237c3fcbde18e7cf52e59, 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.
d54c82f to
cdea094
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 #1816.
Closes #1817.
Closes #1818.
Closes #1819.
Identity #1820 and non-graph #1821 remain open.
Adversarial Review
Verification And Output Records
943 passed in 309.18s (0:05:09); 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. All14 reviewed graph/discussion quotations match fresh primary text and existing caches; literal matching is not entailment.
Six of eleven nodes remain, with six renames; five workflow/unverified-attribution nodes and all six directions are removed. All four targets changed; 456 other records, all923 caches, taxonomy and non-graph raw blocks preserved. Corpus330reviewed/80pending/50needs_research. Network56existingwarnings/zero structural defects. Soymilk succession gains scoped participant identities; the community-level census and its thresholds are 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 cbfbc4abefbb964fc7485f54ef2519531008d22969d133f255d6bbdf007254cb. 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.
sfSynCom/soymilk independent evidence is abstract-bounded. Soy-sauce/chlorophyll primary body coverage is bounded, including chlorophyll Table1, not full methods/supplement/figure/raw-data certification. No new topology or Edison spend. Identity1820 and non-graph1821 stay open. This COMMENT is self-review, not independent approval. Protected-main merge remains required.
Source Limits
Dependency
Draft depends on #1815. Do not merge into the topic parent. Require exact-head checks and independent approval through protected main. Move dependents before deleting parent branches.