ci: bump actions/upload-pages-artifact from 3 to 5#20
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…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/upload-pages-artifact](https://github.com/actions/upload-pages-artifact) from 3 to 5. - [Release notes](https://github.com/actions/upload-pages-artifact/releases) - [Commits](actions/upload-pages-artifact@v3...v5) --- updated-dependencies: - dependency-name: actions/upload-pages-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
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Bumps actions/upload-pages-artifact from 3 to 5.
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fc324d3Merge pull request #139 from Tom-van-Woudenberg/patch-1fe9d4b7Merge branch 'main' into patch-10ca1617Merge pull request #137 from jonchurch/include-hidden-files57f0e84Update action.yml4a90348v7 --> hash56f665aUpdate upload-artifact action to version 7f7615f5Addinclude-hidden-filesinput7b1f4a7Merge pull request #127 from heavymachinery/pin-sha4cc19c7Pinactions/upload-artifactto SHA2d163beMerge pull request #107 from KittyChiu/mainDependabot 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
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