Repository navigation
Bound marine aggregation, transcript responses and helper hypotheses (batch113) - #1887
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 553707b; not independent approval.
-
Preserve the positive 2011 aggregation phenotype and the 2014 null effect without universal dependence or colonization typing.; Replace TEP cross-feeding with an assay-bounded polymer outcome and qualify the existing aggregation direction.; Preserve mutant attachment evidence but distinguish bacterial attachment from diatom benefit and downstream mediation.; Keep the existing sinking/export interpretation, remove niche-partitioning typing and separate measurements from extrapolation.
-
Retain a putative recognition response without colonization typing or a restatement arrow to other transcript changes.; Preserve supported organic-carbon feeding, grade metabolite evidence and remove the shared-substrate-to-transcript arrow.; Retain the chitin/lipid response as transcription, not reverse cross-feeding; preserve the separate B12 growth-benefit boundary.
-
Represent colony association without commensal neutrality or a habitat-setting arrow; distinguish laboratory and field identities.; Bound helper functions to hypotheses, preserve ROS compound/process grounding and correct the B12 direction and facultative-use distinction.; Retain field coexpression without cross-feeding typing or exact IMS101 attribution; narrow connectivity to the supported guild.
-
Every original node and direction has a disposition: ten nodes retained, six renamed, two existing directions qualified and four unsupported arrows removed. No new topology. Renamed targets and discussion anchors resolve exactly.
-
Overcorrection check: preserve positive 2011 aggregation, mutant attachment impairment, diatom-supported Ruegeria growth, the 2017 B12-limited growth rescue and conserved Trichodesmium association. Qualification does not erase observed benefits.
-
HP15: later null bacterial effects on total TEP, aggregate volume and the size-sinking relation constrain universal claims. Aggregate-free-water TEP and total TEP are different endpoints. Inactivation did not produce uniformly zero aggregation and may change surface chemistry. The caption documents chitin fibres, not all TEP chemistry or feeding. The two retained arrows remain conditional or hypothetical; ocean export is an extrapolation.
-
Ruegeria: recognition is inferred from gene homology and transcription, not a colonization benefit. Chitin/lipid transcription is not reverse feeding. Neither removed arrow demonstrates mediation. Structured 2020 Table 1 cells distinguish DMSP/GlcNAc expression from proline/guanosine net drawdown; neither is a traced compound-specific flux. Separate pair cultures are not a mixed consortium.
-
B12 check: the 2017 growth rescue must not be erased by later L1 assay results or substituted for the chitin node. Missing topology remains #1883 and needs_research. One authorized real invocation stopped at authentication before submission. No report, task or spend is claimed; previously denied scopes were not retried.
-
Trichodesmium: association is not commensal neutrality and genomic complementarity is not mutualistic fitness. The 2017 mechanism figure is a model; siderophore and DMSP measurements do not prove full interpartner fluxes. Proposed B12 provision runs host-to-epibiont, with facultative use in the 2017 genome. Preserve #297 ROS compound/process distinctions and proposed iron chemistry without treating Fe(II) as generic iron. Remove the two unsupported explanatory arrows.
-
Field identity: the 2018 host was not demonstrated to be IMS101, and Alteromonas genus transcripts are not automatically A. macleodii. The field node credits only the canonical microbiome guild. Laboratory association retains the canonical pair. Non-graph identity and medium issues remain #1886 and #765; restricted publication bodies are not restored.
-
Source scope: three fresh extracted main bodies, three complete primary PDF text extractions and selected figure images were reviewed. Diel main text came from existing curator text; chemotaxis is abstract-bounded and MEPS remains caption-only after HTTP 401. Of 24 quotations, 23 match fresh primary text and one matches the existing caption. No new publication bodies or caches. Supplements, raw data and other figure pixels were not reviewed.
-
Three guarded records and append-only histories preserve 457 other records, 923 caches, all non-graph blocks and prior history/decision artifacts. Two explicit participant-list users are added to the exact test expectation. Census remains 412 community-level, 136 mixed, 276 community-only, 1563 taxa and 1273 solely credited. Connectivity logic and share guards are unchanged.
-
Five real in-memory control/mutation/restored-control probes reject TEP feeding, proven attachment mediation, reverse transcript feeding, genomic SUPPORT inflation and exact IMS101 field attribution. Actual mutations and rejecting assertions are recorded. Canonical hashes are unchanged; probes are not counted as additional pytest tests.
-
Ten focused tests and 1024 combined regressions pass. All three edited records pass schema, strict, terms, full-record references, snippets and history checks. The 56 network warnings are unchanged, with zero structural defects. Deterministic rendering and exact HTML descriptions cover 456 pages, 1366 nodes and 531 arrows, not UI screenshots. Full-corpus snippets remain informational. Local reference passes are not Linux certification.
-
Repairs #1880-#1882 await protected-main merge; research #1883 and metadata #1884-#1886 remain open. Self-review is not independent approval. Exact-head publication and postcommit docs-current are separate gates. Root CI blocker #1836 is not bypassed and dependent branches are not deleted.
-
Corpus: 364 reviewed, 42 pending and 54 needs_research across 460 records. The overall goal remains incomplete.
1024 passed in 306.57s (0:05:06); ten focused tests and five real in-memory mutation probes. All three edited records pass schema, strict, term, full-record reference, local-snippet and history checks. 34 validation outputs retain commands, output tails and log digests. All 457 other records, 923 caches and non-graph blocks are unchanged.
Ten nodes remain, six renamed; two qualified HP15 directions remain and four unsupported arrows are removed. Twenty-three of 24 graph/discussion quotations match fresh primary text; one is an existing caption-only quote. Three fresh extracted primary main bodies and three complete primary PDF text extractions were read, with selected PDF figures inspected. Diel full text was read from existing curator text; chemotaxis is abstract-bounded and MEPS access remained HTTP 401. No publication bodies or PDFs were added. Separate supplements/raw data were not reviewed.
Corpus:364 reviewed,42 pending,54 needs_research;56 unchanged network warnings and zero structural defects. Connectivity census is unchanged. Rendering is deterministic with exact HTML-description coverage, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 696de3d850c7affed96f7be6f95ab2e509d3ac5c07ff48a564b063be66938eda. Local reference passes are macOS,not Linux certification; full-corpus snippet results are informational,not clean-corpus certification.
Ruegeria remains needs_research for its distinct B12 growth-support extension (#1883). The dry run completed; the authorized real invocation stopped in load_api_key before client creation. No provider submissions or credits spent. This is not an Edison report or completed extension. Metadata follow-ups #1884-#1886 remain open.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. This COMMENT is self-review,not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI,protection bypass or premature branch deletion.
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. |
7a92057 to
5238663
Compare
553707b to
2d8312a
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Self-adversarial review refreshed at exact head 2d8312a after propagating the real CI correction #1899. Not independent approval.
Original head: 553707b. Current parent: 5238663. Only tests/test_datamodel.py changes in the tree for batches109-114; batch115's whole tree is unchanged. Scientific records, prior histories/decisions, caches, renderings and all other files are byte-identical to the respective reviewed trees. Each batch-owned patch excluding this test is byte-identical (SHA256 a440684fe9686d9f56d9d4f92e393e18fe9deea019871989c370395988623ec9).
The stale smoke test now requires the reviewed source and target names, resolving target, canonical pairwise taxa, qualified sucrose mediation and both SUPPORT/PARTIAL evidence. No graph was reverted or test skipped. The batch115 CI artifact records the original failed strict run, reproduction, 24 related test passes and seven rejecting counterfactual probes.
Fresh tests at this head: ............. [100%]
13 passed in 20.36s
Test log SHA256: 59aec18700e033954f9d007155724a12eeadb408ede839d2334ae50cede9c07a. Fresh docs-current passed with a clean worktree; log SHA256 696de3d850c7affed96f7be6f95ab2e509d3ac5c07ff48a564b063be66938eda.
The propagation-pending entries in batch115's immutable publication report describe the earlier publication state; this exact-head review records the subsequent propagation. Focused tests are not a new full-suite pass. Real exact-head protected CI remains required; #1836 independently blocks the upstream root PR. #1899 remains open until protected-main integration. No artificial CI, protection bypass, merge or branch deletion was performed.
2d8312a to
3471c93
Compare
5238663 to
271b022
Compare
realmarcin
left a comment
realmarcin
left a comment
There was a problem hiding this comment.
Exact-head self-adversarial restack review at 3471c936fa30e31efb65c677ef4f60dc4d5ea889.
COMMENT, not independent approval.
The batch-owned binary patch remains byte-identical:
SHA-256 a440684fe9686d9f56d9d4f92e393e18fe9deea019871989c370395988623ec9.
Tree 3904cdb206e506e02c0b126f9c90fcd67406e143 matches the independently computed clean merge.
Compared with historical tree a9d128bafbfc0199bd7823779a45a70ea37d3b5b, 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.
3471c93 to
5520158
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 #1880.
Closes #1881.
Closes #1882.
Research #1883 and metadata #1884-#1886 remain open.
Adversarial Review
Verification And Output Records
1024 passed in 306.57s (0:05:06); ten focused tests and five real in-memory mutation probes. All three edited records pass schema, strict, term, full-record reference, local-snippet and history checks. 34 validation outputs retain commands, output tails and log digests. All 457 other records, 923 caches and non-graph blocks are unchanged.
Ten nodes remain, six renamed; two qualified HP15 directions remain and four unsupported arrows are removed. Twenty-three of 24 graph/discussion quotations match fresh primary text; one is an existing caption-only quote. Three fresh extracted primary main bodies and three complete primary PDF text extractions were read, with selected PDF figures inspected. Diel full text was read from existing curator text; chemotaxis is abstract-bounded and MEPS access remained HTTP 401. No publication bodies or PDFs were added. Separate supplements/raw data were not reviewed.
Corpus:364 reviewed,42 pending,54 needs_research;56 unchanged network warnings and zero structural defects. Connectivity census is unchanged. Rendering is deterministic with exact HTML-description coverage, not UI screenshot certification. Postcommit docs-current passed clean; log SHA256 696de3d850c7affed96f7be6f95ab2e509d3ac5c07ff48a564b063be66938eda. Local reference passes are macOS,not Linux certification; full-corpus snippet results are informational,not clean-corpus certification.
Ruegeria remains needs_research for its distinct B12 growth-support extension (#1883). The dry run completed; the authorized real invocation stopped in load_api_key before client creation. No provider submissions or credits spent. This is not an Edison report or completed extension. Metadata follow-ups #1884-#1886 remain open.
Decision ledger, provenance, validation, three append-only histories and self-adversarial review are committed. This COMMENT is self-review,not independent approval. Root blocker #1836 remains subject to real protected checks; no artificial CI,protection bypass or premature branch deletion.
Dependency
Draft depends on #1879. Do not merge into the topic parent. Require actual exact-head checks through protected main. Move dependents before deleting parent branches.