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Correct graph participant identities and active lineage (batches126-128) - #1975
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Source-based self-adversarial review at b67230b18333580f43b58cb916714704247dc1f9; not independent approval.
Reviewed the focused diff against the indexed primary Introduction. Actual-system LC1 identity is now supported, but full Methods/Table1/supplement access and isolated encapsulation mediation are not claimed. Three nodes/two arrows remain; the record remains needs_research. Four mutation probes enforce the retained limits, and the historical ledger has an explicit hash-linked successor.
212 selected tests passed; all18 recorded gates and postcommit docs-current completed within the documented warning exceptions. See reports/causal_graph_review/adversarial-review-20261008-batch126.yaml and its validation report. #1860 remains OPEN for medium and mediation questions.
Lifecycle: GitHub rejected native-stack admission at100PRs with HTTP422. This dependent PR is reviewed but NOT registered in stack1973. Wait for protected merge to free capacity and verify any cascading head changes before admission. Do not merge into the topic parent or delete branches prematurely.
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Source-based self-adversarial review at 57b17a7c3116feae7b6d7deefa9c54680c0ae816; not independent approval.
Reviewed the incremental spring repair and retained batch126 changes against the PR base 6f062d2eb68fedab336b700c758cd21622fabbb6. TableS4 explicitly supports genus Thiothrix with blank species. Official NCBI genus1030 is used in the roster and both links. The source-specific GTDB assignment is pinned with provenance, not a fabricated current crosswalk vote. Beggiatoa classification and CPR cell/host/metabolic identity remain unresolved; #1841 and #1860 stay OPEN, including after this partial repair merges.
319 passed, 17 skipped in 423.72s (0:07:03). Eight focused batch127 tests include five mutation probes; batch126 tests remain in the selected suite. All18recorded gates plus postcommit docs-current passed within documented cache/network-warning limits. Full historical suite and full-repo lint/mypy not rerun. See batch127 and batch126 review/validation records under reports/causal_graph_review/.
Native100heads remain unchanged. This is a normal follow-up commit on the existing non-native PR1975, not a new PR or renewed stack-admission attempt. Protected-main merge and branch cleanup remain unfinished.
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 at 52e905def8367ffccf9179af7337e6f80710dd4d.
Batch128 corrects the corpus hierarchy regression found in CI: only the active Thiothrix phylum name is normalized to Pseudomonadota. Original Proteobacteria source quotations, all caches, genus identity, nodes and arrows are unchanged. #1978 is addressed pending protected-main merge. #1979 is addressed by the verified archival tag review-provenance/20261009-batch128, which retains the reviewed source through squash merge and branch cleanup.
246 focused tests passed; 17 external-crosswalk-dependent cases skipped. The unchanged whole-corpus hierarchy test and four mutation probes pass. Schema, strict, terms, references, snippets, history, inventory, network and deterministic rendering checks passed within recorded warning/cache limits; postcommit docs-current passed. Full local suite did not complete: pytest-cov and UMAP were missing, then locked isolated dependency installation failed building llvmlite. These failures are retained, not counted as passes. Exact-head and merge-group CI remain required.
Before review | After review | Structured after YAML | Validation | Provenance proof
This is a scoped self-adversarial review, not independent approval or whole-record scientific certification. Prior batches126-127 remain partial identity repairs: #1841 and #1860 stay open, both records stay needs_research, and no new topology or Edison submission was needed. The root PR's existing protected queue request is separate from this non-native child. No topic-parent merge, bypass or branch deletion is claimed.
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Exact-head self-adversarial integration review at 253544137c655443aaf270672f6c724db8d5b6c5 after the protected root merge. Not independent approval.
GitHub merged #1363 to ae197198aebf9d365cc6e5b15c164fffe112fd3e and rebased 99 native dependents. Every native PR's own binary patch was checked against its previously reviewed patch and is byte-identical. Only this non-native child's three commits were locally replayed onto 015fce4d2653160cf1128cd3894aa0babe048d04. Its complete own patch is also byte-identical (SHA256 337a6a1bec023b4d0834143fd952be8a7a74e5badb518e4b822269c1426a1269), and the cumulative tree equals the clean main integration tree b7d89808adba75fc18f78e6217810030f37ff8d4.
All 460 canonical records, 924 caches, and the structured review bundles match their pre-rebase bytes. The after-review's attested inputs still match; its source base remains available under archival tag review-provenance/20261009-batch128. Main's newly adopted structured-review gate passes, as do 50 focused rebase regression/contract tests and post-rebase docs-current. The earlier 246-pass/17-skip validation remains applicable to unchanged target bytes. Full local tests remain unavailable for the documented dependency-build reason; no old-head CI result is promoted to this head.
After review Markdown | Authoritative YAML
Issues #1978 and #1979 are addressed pending protected main merge; #1841 and #1860 remain research gaps. This PR remains non-native and must not merge into its topic parent. Root branch cleanup is complete; other branch deletions and the full chain's merge remain unfinished. New exact-head CI is required.
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Latest Integration Review
Exact-head self-adversarial integration review at
253544137c655443aaf270672f6c724db8d5b6c5after the protected root merge. Not independent approval.GitHub merged #1363 to
ae197198aebf9d365cc6e5b15c164fffe112fd3eand rebased 99 native dependents. Every native PR's own binary patch was checked against its previously reviewed patch and is byte-identical. Only this non-native child's three commits were locally replayed onto015fce4d2653160cf1128cd3894aa0babe048d04. Its complete own patch is also byte-identical (SHA256337a6a1bec023b4d0834143fd952be8a7a74e5badb518e4b822269c1426a1269), and the cumulative tree equals the clean main integration treeb7d89808adba75fc18f78e6217810030f37ff8d4.All 460 canonical records, 924 caches, and the structured review bundles match their pre-rebase bytes. The after-review's attested inputs still match; its source base remains available under archival tag
review-provenance/20261009-batch128. Main's newly adopted structured-review gate passes, as do 50 focused rebase regression/contract tests and post-rebase docs-current. The earlier 246-pass/17-skip validation remains applicable to unchanged target bytes. Full local tests remain unavailable for the documented dependency-build reason; no old-head CI result is promoted to this head.After review Markdown | Authoritative YAML
Issues #1978 and #1979 are addressed pending protected main merge; #1841 and #1860 remain research gaps. This PR remains non-native and must not merge into its topic parent. Root branch cleanup is complete; other branch deletions and the full chain's merge remain unfinished. New exact-head CI is required.
Earlier Repair Details
Summary And Verification
Batch128 corrects the corpus hierarchy regression found in CI: only the active Thiothrix phylum name is normalized to Pseudomonadota. Original Proteobacteria source quotations, all caches, genus identity, nodes and arrows are unchanged. #1978 is addressed pending protected-main merge. #1979 is addressed by the verified archival tag
review-provenance/20261009-batch128, which retains the reviewed source through squash merge and branch cleanup.246 focused tests passed; 17 external-crosswalk-dependent cases skipped. The unchanged whole-corpus hierarchy test and four mutation probes pass. Schema, strict, terms, references, snippets, history, inventory, network and deterministic rendering checks passed within recorded warning/cache limits; postcommit docs-current passed. Full local suite did not complete: pytest-cov and UMAP were missing, then locked isolated dependency installation failed building llvmlite. These failures are retained, not counted as passes. Exact-head and merge-group CI remain required.
Before review | After review | Structured after YAML | Validation | Provenance proof
This is a scoped self-adversarial review, not independent approval or whole-record scientific certification. Prior batches126-127 remain partial identity repairs: #1841 and #1860 stay open, both records stay needs_research, and no new topology or Edison submission was needed. The root PR's existing protected queue request is separate from this non-native child. No topic-parent merge, bypass or branch deletion is claimed.
Depends on #1974. Keep research issues open. Do not merge this PR into its topic parent.