Feat/stipple typed studies UI - #73
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hyperpolymath wants to merge 92 commits into
Closed
hyperpolymath wants to merge 92 commits into
hyperpolymath wants to merge 92 commits into
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… a better place one less R module at a time.
…nd working cutadapt -> vsearch-dada merge on default settings.
…for DADA2 and VSEARCH
… of previously run stages. Created a versatile project structure.
….it was getting messy and altogether not worth it for now.
…ing of reads bug.
Squashed replacement for #6, which became undiffable after a history rewrite on the fork severed its merge base. Why this PR exists ------------------ PR #6 was opened from `hyperpolymath:main`. That branch was subsequently rewritten with git-filter-repo to strip ~260 MiB of dead blobs (committed node_modules, a long-gone `web/` directory, and three raw FASTQ pools that no longer exist in the working tree): 269.35 MiB -> 9.23 MiB, ~96.6% reclaimed, with the HEAD tree byte-identical at every stage. The rewrite renamed every commit. GitHub resolves a merge base by SHA, so none of the commits #6 shared with upstream matched afterwards and the base collapsed to the repository's "Initial commit" of 2026-01-30. #6 therefore reported 338 files / +65,566 / -22 - not new work, just the whole tree diffed from January - and went CONFLICTING, which meant it ran no checks at all. That is unrecoverable: the pre-rewrite head is readable through the API but is on no ref, so `upload-pack` refuses to serve it. What this PR is --------------- One commit whose tree is byte-identical to `hyperpolymath:main` (tree 80269dd), applied on top of this repository's current `main` (ecefb1c). The diff is 319 files / +23,681 / -6,076 and is reviewable as a normal change. Per-commit granularity from the original 66 commits is lost; the content is identical. Happy to split this into reviewable parts if you would prefer that. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm Signed-off-by: Jonathan D.A. Jewell <jonathan.jewell@gmail.com>
…ntain permissions' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>
…ntain permissions' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>
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Important Review skippedToo many files! This PR contains 328 files, which is 228 over the limit of 100. To get a review, reduce the PR to 100 files or fewer by splitting it into smaller PRs or changing its base branch. Upgrade to a paid plan to raise the limit. Usage-priced reviews support at most 300 files. ⚙️ Run configurationConfiguration used: Organization UI Review profile: ASSERTIVE Plan: Advanced Run ID: ⛔ Files ignored due to path filters (10)
📒 Files selected for processing (328)
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Triaged 2026-09-26 (Arena backlog sweep). Closing as a wrong-base duplicate — the live version of this work is JoshuaJewell#7, where this exact branch ( Why this PR cannot work here:
Nothing is lost: the branch is untouched, parent #7 stays open, and a proposed split of that 319-file change into reviewable stacked PRs is being prepared. Reopen if you disagree. |
hyperpolymath
added a commit
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Sep 26, 2026
…67 archive (#76) ## Summary Triages the notification backlog (see `docs/triage/2026-09-26-notification-backlog.md`). Docs + tooling only; no application-logic changes. **Already done alongside (not in this diff):** - Closed fork #73 as a wrong-base duplicate of parent #7 (same branch, clean upstream). - Owner merged fork #75 mid-triage → fork #20 auto-closed. Post-merge verification still owed once CI runs. - Deleted stale branch `arena/01a0db67` at owner's request after archiving it here. ## Changes - `docs/triage/2026-09-26-notification-backlog.md` — every open PR/issue on fork + parent triaged; CI outage diagnosed (file-based workflows `startup_failure` repo-wide since 2026-09-25 22:19 UTC; settings/platform-side, owner steps in runbook). - `docs/triage/pr7-split/` — parent #7's 319-file change as 14 disjoint stacks (`STACKS.md` review guide, `RUNBOOK.md` with merge-as-is vs stacked-PRs options, `make-stacks.sh` regenerates + verifies: disjoint, full coverage, sequential apply reproduces the branch tree exactly). - `docs/triage/db67-rescue/` — archived deleted branch as a verified byte-exact patch + restore instructions. - `.gitignore` — track `docs/triage/`, ignore derived 4.5 MB stack patches. ## Verification - `scripts/check-spdx.sh`: OK (new .md/.sh carry fork-series headers). - Format essentials (LF, final newline, no trailing WS in non-prose): clean. - `make-stacks.sh`: 14 stacks, disjoint, cover all 319 files, reproduce branch tree exactly. - `db67-rescue/deleted-branch.patch`: recreates the deleted branch tree exactly. ## Note on CI File-based workflows cannot start repo-wide right now (the outage diagnosed in the report), so expect `startup_failure` — unrelated to this docs-only change. Re-run once the owner fixes Actions. --------- Co-authored-by: hyperpolymath <6759885+hyperpolymath@users.noreply.github.com>
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Summary
Base check
hyperpolymath/MetaManifold-WebUI:main(not the upstreamparent; application changes go to
JoshuaJewell/MetaManifold-WebUI)Changes
Engineering checklist
Required
bun run checkpasses (frontend/: typecheck 0 errors, tests,benchmarks)
scripts/check-spdx.sh/check-format.sh/check-lint.shpass(advisory in CI — does not block merge)
CONTRIBUTING.md; advisory in CI)NOTICEexplainsthe authorship rule)
.env, or sequencing data includedAs applicable
CHANGELOG.mdupdated for user/developer-visible changesdocs/types/architecture.mdupdated if type boundaries moveddocs/testing/coverage.mdupdated if test coverage moveddocs/reproducibility.mdupdated if environment requirements changedTesting