ci: bump actions/deploy-pages from 4 to 5#19
Open
dependabot[bot] wants to merge 22 commits into
Open
Conversation
…rden saves BLAST modal — new "Online BLAST / HMM" tab: - NCBI BLAST (blastn/blastp/blastx/tblastn/tblastx) + EBI HMMER hmmscan vs Pfam, results in scrollable tables with enriched detail panes (family/hit descriptions, Pfam clan + InterPro links, NCBI lookup). - Query from the textbox, a whole library plasmid, or a feature (CDS auto-translated for protein programs); live keep-alive heartbeat + cancel; query refused above NCBI's length limits so the server can't reject the job. Universal save-to-library flow: - NamePlasmidModal gains an opt-in collection picker; new shared _commit_library_entry_to_collection helper (atomic, under _cache_lock, collision-renames name with " COPY" / id with "_N", mirrors the active library). Constructor (MoClo/GB), Gibson (now prompts instead of auto- naming), Traditional cloning, and the PCR amplicon all let the user choose name + collection — linear fragment or circular plasmid alike. - Fix: the PCR amplicon default name no longer forces underscores into the library row. Help + diagnostics: - ? help modal reorganised — Navigation (panel/viewport keys) first, then editing, files, tools, toolbar menus, diagnostics; stale/missing entries corrected. - Alt+D UI snapshot now captures the live mouse position + every open element (all stacked screens), not just the top one. Hardening: - Parts-bin read-modify-save (Constructor persist, New Part, Load Parts) now holds _cache_lock across read->insert->save, closing a cross-group drop-a-row race. Tests: new test_online_blast + test_universal_save; full suite green. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Correctness: mutagenesis "modified outer" primer must span the mutant codon (else it amplified wild-type); verification-report variant frame for axis=query diffs; alignment coverage clamp; traditional-clone origin-wrap features preserved; corrupt custom_enzymes.json no longer crashes import; linear negative-cut restriction guards; Gibson fragment-0 homology-arm validation. Data integrity: _h_delete_experiment_project + _h_bulk_import_folder do their RMW under _cache_lock; _delete_experiment_attach_dir + _cleanup_pressed_files routed through the L2 delete gate. Security: control-byte strip on remote BLAST/HMM hit text + agent-API gel/experiment/grammar/part/primer/feature fields; shared hardened URL opener refuses https->http redirect downgrade (PyPI + HMM-DB); NCBI BLAST poll tolerates transient 5xx + deletes the RID on any abort; HMM version-check content-type guard. UI: --no-splash now runs the post-splash gate (What's New + last_seen); 5 modal-open deepcopy paths -> readonly iterators; settings-save failure notifies. Completeness (built/wired by hand): protein-motif editor New/Delete; codon-table TSV paste import; ORF finder + manual feature grouping wired to entry points; parts-bin + HMM-database agent endpoints. Docs: CHANGELOG [Unreleased], features.md, agent-api.md, README, [PREFS] list + [INV-85], CLAUDE.md sacred-#2 prose. Tests: +32 new (codon TSV, motif editor, agent endpoints) + updated mutagenize/alignment/move-copy. Full suite green: 4347 passed, 5 skipped. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
10-agent read-only audit; every finding verified against the code before action. No version bump (not a release). Data integrity: _safe_save_json re-raises fsync failures and refuses to overwrite an unreadable prior file; library add/delete/rename workers persist the authoritative cache (closes the cross-group out-of-order write race); agent delete/set-status/add + add_entry RMWs now hold _cache_lock [INV-74]. Privacy: F9 bundle events_summary scrubbed at the _extract_recent_events chokepoint [INV-38]. Security: online BLAST/HMM clan/type/link control-strip + literal-render table cells + hardened url opener + version-check gzip-bomb cap; agent experiment/gel free-text strips; PyPI version-metadata guard + override URL credential redaction. Robustness: app-wide @on(Worker.StateChanged) error net; import-time data-dir crash guard; leading-dash CLI arg rejected; corrupt custom-enzyme skipped in digest; Gibson RNA U->T. Correctness: honor /transl_table for non-standard genetic codes (mito/Mycoplasma) — correct protein + no false premature-stop glyph. Completeness: restore "Transfer annotations from..." File-menu entry. UI: rename Mutagenize menu -> "Mutato". Docs: README rewritten (human-friendly summary + workhorse section + menu-by-menu tour, RC status badge); CHANGELOG [1.0.0] narrative; [INV-86]; keybindings/features/CLAUDE pointers refreshed. Tests: TestSweep30SafeSaveJson, TestAuthoritativeLibrarySnapshot, TestTranslTableNonStandard. Full suite green (4,359 passed, 5 skipped). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
_index_usage_worker now captures self.app at thread entry so its result callback can't hit NoActiveAppError when the user navigates during the ~3 s scan (smoke-found 2026-05-28, session 3a963157). Replace the stale README screenshot with a current capture (post-Mutato menu bar). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
docs.yml builds the Material site (strict) and publishes to Pages on push to master (+ manual dispatch). mkdocs.yml: exclude dev-internal invariants.md + subsystems.md from the public site (subsystems' raw regexes break mkdocs's HTML pass), point the Project nav at GitHub, add a Supported-terminals page. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
…coverage Logger: the rotating file handler now uses errors="backslashreplace" so a code point utf-8 can't encode — e.g. a lone surrogate os.fsdecode yields for an undecodable filename under a non-UTF-8 locale (LANG=C, exotic terminals) — is escaped in the log instead of being silently dropped with a stderr traceback that corrupts the live Textual TUI. Covers every log path (_log_event payloads + raw _log.* with OS-derived strings). Tests: event-logger encoding robustness (3); _iupac_pattern's non-IUPAC ValueError contract; _rebuild_record_with_edit wrap origin-edge inserts (bp 0 / bp total) + no-record guard + replace-overhang + fully-consumed- wrap drop — bringing all 7 sacred biology primitives to full line coverage. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
v1.0.3's `git add -A` swept in TechSupport/user1.png + user2.png. That folder is the maintainer's local drop for user bug-report screenshots, not repo content. Untrack the PNGs (kept on disk) and ignore the folder so future releases don't re-commit it. PyPI artifacts were unaffected — the package never shipped these. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Bumps [actions/deploy-pages](https://github.com/actions/deploy-pages) from 4 to 5. - [Release notes](https://github.com/actions/deploy-pages/releases) - [Commits](actions/deploy-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/deploy-pages dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
dependabot
Bot
added
dependencies
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Bumps actions/deploy-pages from 4 to 5.
Release notes
Sourced from actions/deploy-pages's releases.
... (truncated)
Commits
cd2ce8fMerge pull request #404 from salmanmkc/node24bbe2a95Update Node.js version to 24.x854d7aaMerge pull request #374 from actions/Jcambass-patch-1306bb81Add workflow file for publishing releases to immutable action packageb742728Merge pull request #360 from actions/dependabot/npm_and_yarn/npm_and_yarn-513...7273294Bump braces in the npm_and_yarn group across 1 directory963791fMerge pull request #361 from actions/dependabot-friendly51bb29dMake the rebuild dist workflow safer for Dependabot89f3d10Merge pull request #358 from actions/dependabot/npm_and_yarn/non-breaking-cha...bce7355Merge branch 'main' into dependabot/npm_and_yarn/non-breaking-changes-99c12deb21Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
@dependabot rebase.Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR:
@dependabot rebasewill rebase this PR@dependabot recreatewill recreate this PR, overwriting any edits that have been made to it@dependabot show <dependency name> ignore conditionswill show all of the ignore conditions of the specified dependency@dependabot ignore this major versionwill close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this minor versionwill close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this dependencywill close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)