Frontend v1.2.0

Bug Fixes

• Address whole-branch review findings (frontend) (campaigns)
• Keep the stage criterion readout select inside its column (screen-campaign)
• Top-align the stage criterion row labels (screen-campaign)
• Surface domain error messages in toasts; verdict chip on its own line (frontend)
• Filter-bar separator, compound column width, dead source DTOs (screen-campaign)
• Compound activity tab shows reported endpoints for curve-less dose-response readouts (activity)
• Colliding stage_name is an advisory, not a block (screen-campaign)
• Bulk gestures act only on rows the chip filter shows (screen-campaign)
• StageKind aliases the generated enum (screen-campaign)
• Depict renders again, and every campaign write answers 204 (api)
• Reopening the delete dialog refetches, and blocked deletes stay accessible (admin)
• Unique wells in the plate trace, no filter, warm surface (login)
• Library rows use the 14px list size like every other list (protocols)
• Clear every fixable high and critical Trivy finding (security)

Features

• Structure role in the summary wizard; both import wizards render the shared result vocabulary (frontend)
• Regenerate FE types for hit stages, drop retired hit/signature/publish fields (campaigns)
• Hit stages section and stage editor (frontend) (campaigns)
• Stage lens — outcome chips, cell verdicts, Stage column, override popover (campaigns)
• Close/reopen dialogs, header, stages preview, save-as-stage (screen-campaign)
• Compact readout chips, funnel stage tiles, per-protocol colors (screen-campaign)
• Tags as a compact chip row under the description (screen-campaign)
• Colored sidebar icons carried into page headers; persist sidebar collapse (nav)
• Refuse direct entry onto calculated readouts across summary, plate and bulk paths (screening)
• Compound page and search fall back to reported endpoints for dose-response columns; reported markers (activity)
• Manual stages, pending outcome, bulk promote/demote and bulk remove (screen-campaign)
• Summary-driven campaign list with status filter, stage parent on import dialogs, readout reorder (screen-campaign)
• Per-readout "resolve from all runs" opt-out (screen-campaign)
• Page and filter a campaign's results server-side (campaigns)
• Offer the maximum common substructure as a core, never pick it (sar)
• Let the results filter take several outcomes (campaigns)
• Show a campaign's libraries and what it left unread (campaigns)
• Show hits per stage under each library's coverage bar (campaigns)
• Hold back the per-library stage lines in cellar's UI (campaigns)
• Hide the Libraries section itself, not just its stage lines (campaigns)
• A draft's creator may delete it, and no delete while anything still uses it (protocols)
• Force-delete dialog lists what blocks or changes, and won't submit a blocked delete (admin)
• Lime accent from the product site, flat logo mark (theme)
• Live screening plate with a glowing dose-response hit (login)

Refactor

• Drop decision UI; notes column; stage picker for add-from-campaign (screen-campaign)
• Export isReportedEndpoint so the grid's own line is tested (campaigns)
• Render the shared chart core, drop the local copy (dose-response)

Backend v1.2.0

Bug Fixes

• Import result counts are required on the wire (screening)
• Report the compound ref too when both refs miss (both importers) (screening)
• Structure fallback applies to compound-only rows; import total_rows regression test (screening)
• Serialize number minting per workspace; surface constraint violations as 409 (registration)
• Enforce one live molecule per InChIKey per workspace in the database (registration)
• Remove per-cell hit call and per-readout hit threshold (campaigns)
• Address whole-branch review findings (backend) (campaigns)
• Require notes key on PATCH, normalise blank notes to NULL (campaigns)
• Single-row readout create follows the run's shape (screening)
• Curve-class filter on add-from-runs applies to curves only, not endpoint fallbacks (campaigns)
• Compound activity tab shows reported endpoints for curve-less dose-response readouts (activity)
• Reported-endpoint fallback reads well-less rows only (activity)
• Add-from-runs preview and commit share one candidate resolver (campaigns)
• Drc reported-endpoint fallback only fires on unscoped columns (search)
• Refuse the summary header preview onto a welled run (screening)
• Empty result_ids on bulk-remove is a 422 (campaigns)
• Break display_order ties on id; tighten stage/bulk-remove DTOs (campaigns)
• Campaign records its seed runs; resolution scope is per channel protocol (campaigns)
• Depict renders again, and every campaign write answers 204 (api)
• An ND that came off a curve is a miss, not untested (campaigns)
• A reported endpoint keeps its qualifier and fills only its own intercept (campaigns)
• A censored value that can't prove a criterion is a miss (campaigns)
• A reported ">=40" stays censored instead of reading as 40 (campaigns)
• Apply every null before any delete so id-only references stay FK-safe (admin)
• Clear every fixable high and critical Trivy finding (security)

Documentation

• Correct rule-module docstrings and record final-review findings (admin)

Features

• STRUCTURE role on the summary-import mapping + SMILES header inference (screening)
• Summary planner falls back to SMILES when the identifier misses; per-row unmatched_compounds (screening)
• Summary preview/import resolve by structure on identifier miss; import result carries the shared vocabulary (screening)
• One result vocabulary for import preview/import responses; structure on the summary mapping (screening)
• Plate preview/import speak the shared result vocabulary; rows_skipped on the plate preview (screening)
• Add hit-stage value objects and shared compare() (campaign)
• Wire hit stages and overrides into the Campaign aggregate (campaign)
• Pure stage evaluator (evaluate_stages, tally_stage_counts) (campaigns)
• ORM models, repository mapping, and migration 074 for hit stages (campaigns)
• Soft close — drop signature/collection, add reopen (campaigns)
• Migration 075 — drop retired hit/publish columns (campaigns)
• Published JSON gains stages and per-result stage outcomes (campaigns)
• Stage use cases, routes, and DTOs (campaigns)
• Stage_name on run import and mirror protocol (campaigns)
• Stage override use case, DTOs, and API routes (campaigns)
• Refuse direct entry onto calculated readouts across summary, plate and bulk paths (screening)
• One run, one shape — refuse summary import onto welled runs and plate paths onto well-less runs (screening)
• Dose-response channels fall back to reported endpoint rows when no curve survives QC (campaigns)
• Compound page and search fall back to reported endpoints for dose-response columns; reported markers (activity)
• Manual stage kind with a pending outcome (campaigns)
• Bulk stage overrides and bulk row removal (campaigns)
• Parent_stage_id and get-or-create on the stage_name paths (campaigns)
• Stage counts on the draft read, summary endpoint, list summaries with status filter; viewer gate, channel reorder, stable result order (campaigns)
• Resolution honours the campaign's source runs, with a per-readout opt-out (campaigns)
• Maximum common substructure over a supplied molecule set (sar)
• Page and filter a campaign's results server-side (campaigns)
• Offer the maximum common substructure as a core, never pick it (sar)
• Let the results filter take several outcomes (campaigns)
• Name the libraries a campaign screened, and how much it read (campaigns)
• Count each library's compounds through the campaign's stages (campaigns)
• A draft's creator may delete it, and no delete while anything still uses it (protocols)
• Cascade rules express references with or without a column (admin)
• One exhaustive plan walk behind force-delete preview and execute (admin)
• Tier-1 hard delete refuses on cascade-rule references too (admin)
• Force delete refuses on campaigns and import templates, removes flags and attachments (admin)
• Molecule force delete refuses while its data or open work remains (admin)
• Export/import a full local environment as a bundle (replication)

Refactor

• Remove per-result decisions; notes-only edit; add-from-campaign filters by stage (campaigns)

Tests

• Reformat API test helpers after merge (campaigns)
• Drop stale CV- registration-prefix assertion (molecules)
• Bulk upsert writes a well-bound row on a welled run (screening)
• Cover the bulk routes' reason and closed-campaign guards (campaigns)
• Guard that every id reference says what a force delete does to it (admin)
• Guard tests only count rules that actually stop an FK violation (admin)

Frontend v1.1.0

Bug Fixes

• Unit affordance, stale seed shape, and null-sort fixes on the any-protocol UI (search)
• Pre-merge review follow-ups on preview, wizard forecast, and storage probe

Build & CI

• Duar SDKs 1.0.0 -> 1.3.0; refresh all in-range Python and npm deps (deps)

Features

• "Any protocol" activity criterion — curve class + potency cutoff across all protocols (search)
• Derive the any-protocol where-picker from every protocol's measurements (search)
• Any-protocol rows use the derived measurement catalog (search)
• 'Active in' results column for any-protocol searches; matched protocols expand in the detail sheet (search)
• Surface summary-import attachment and molecule provenance (frontend)
• Bulk-registration preview forecasts what each row will do (frontend)

Backend v1.1.0

Bug Fixes

• Tenant-scope + normalization-layer fixes on the any-protocol activity query (search)
• Review follow-ups on the declared disclosure date (disclosure)
• Every file write hangs off STORAGE_ROOT; refuse to boot prod off a volume (storage)
• Pre-merge review follow-ups on preview, wizard forecast, and storage probe

Build & CI

• Duar SDKs 1.0.0 -> 1.3.0; refresh all in-range Python and npm deps (deps)

Features

• "Any protocol" activity criterion — curve class + potency cutoff across all protocols (search)
• Any-protocol dr_curve conditions accept an intercept_key (IC50/EC90 across protocols, µM) (search)
• Any-protocol readout_data conditions match readout-defs by normalized name + unit (search)
• 'any' activity column — per-protocol DR entries, native units, best first (search)
• 'any' column adds readout entries for readout groups named in the criterion (search)
• 'any' activity column exports as one 'Active in' text column (export)
• Attach the raw upload to the run on summary import (screening)
• Scientist_name on POST /molecules, persisted on the molecule (registration)
• Settable disclosure_date on POST /disclosures (disclosure)
• Declared disclosure_date through POST /molecules (registration)
• Shared classifier + advisory POST /molecules/preview-registration (registration)
• Refuse to start against a database that is not at this image's migration head (ops)

Tests

• Any-protocol intercept-key and readout-name searches against Postgres (api)

Frontend v1.0.0

Bug Fixes

• Close frontend-backend gap — all APIs now have UI coverage
• Review fixes — remove ghost operator field, guard log10(0), fix retire reason type (S31-S32)
• Replace UUID text inputs with compound/batch selectors (GF04)
• Add CSV template downloads and use human-readable columns in imports
• Serve RDKit WASM from public/ — fixes streaming compile error (GF02)
• Show error states instead of infinite skeletons when backend is down
• Dynamic CSV templates — protocol-aware readout, multi-ID compounds
• Show multiple custom_id columns in CSV template
• Readout data table shows compound names and measurement names, not UUIDs
• Pivot readout data table — definitions as columns, one row per compound
• Root-cause fixes — server-side identifier resolution, search-based selector
• Replace window.location.href/history.back with Next.js router
• Add storage location dropdown to create sample dialog
• Replace raw UUID inputs with entity selectors (S26)
• Replace empty-string SelectItem values with sentinel strings
• Replace UUID displays with entity names + fix assign 401
• Eliminate all UUID displays from new inventory UI
• Add link to manage synthesis routes from Start dialog
• Redesign shipment creation with compound-first workflow
• Widen dialogs globally — default max-w-2xl (672px)
• Search results — emerald colors + structure depiction cards
• Stringify nested objects in Excel export to prevent [object Object] (export)
• Reset editorOpen state in form reset functions, remove redundant cast
• Enlarge structure thumbnails in compound list (40px → 80px)
• Replace empty string SelectItem values with sentinel in plate components
• Enlarge well mapping dialog + add import template management UI
• Well mapping dialog — 80vw/85vh, CSV paste/upload, download template
• Resolve UUID displays to human-readable names in plate UI
• Well mapping dialog — ResizeObserver-based square cell grid
• CustomInstance FormData support + clarify import wizard purpose
• Import wizard end-to-end — type alignment, UoW, FormData upload
• Move useCallback above early returns in CollectionDetail
• Remove stray 's' from API endpoint URLs (attachment)
• Replace UUID input with MemberSelector search-by-name (project-scoping)
• Vault mapper field names, pagination, dialog scroll, and caching
• Map external description/category, fix 204 JSON parse, pagination
• Ontology annotation PUT sends 'slot' not 'slot_name'
• Ontology_annotations is a dict not array on Protocol type
• Add cascade selection guidance to inventory dashboard (ui)
• Use Zustand store for breadcrumb overrides instead of context (ui)
• Only make breadcrumb segments clickable if page exists (ui)
• Restore Saved Searches to sidebar navigation (ui)
• Show compound names in dose-response chart legend and cards (ui)
• Add Edit Points toggle, compound names on constraints, round IC50 values (ui)
• Guard against undefined plateMap.wells in run data panel (ui)
• Make readout_data molecule_id/batch_id nullable in API + frontend
• Validate batch amount required when include batch is toggled on
• Resolve chemist UUID to display name on batch detail page
• Review fixes — zero-value data points, shared helper, actual top/bottom, sorted query key
• Excel export now uses getCellValue to respect valueGetter columns
• Readout data table shows per-well rows for dose-response data
• Excel export — plain headers, CV ID in Compound, custom-only synonyms
• Excel export fills existing Structure/Curve columns with images
• Marker toggle label uses actual curve type (IC50/EC50/Ki/etc)
• Restore integration client naming — only docs/commits are sanitized
• Clean up collection criterion types and unused imports in search form
• Search revamp frontend bugs — protocol columns, 4PL div-by-zero, config safety, cursor jumps
• Code review fixes — updated_at propagation, null visibility, grid selection sync, hook lift
• Replace hardcoded colors with semantic design tokens
• Simplify ProtocolSection — remove dead dropdowns, unify readout/curve selector
• Wire protocol and/or conjunctions to actual search query
• DR chart not rendering — raw_data keys were concentration/response, not x/y
• Persist protocol conjunctions in saved searches + support mixed AND/OR
• Remove placeholder tabs, fix scroll, open detail in new tab
• Saved search loading stuck on skeleton — remove handleSearch from useEffect deps
• Derive protocol curve types from readout definitions instead of hardcoding
• Restore lost backend changes + commit all pending work
• Restore DR curve plots in search results grid
• Breadcrumb trail system — fix duplicate Protocols and missing protocol on runs
• Remove AG Grid Enterprise rowGroup from collection list
• Disclosure mode uses disclosure endpoint, not registration
• Add disclosure provenance fields + confirmation before submit
• Remove explicit Content-Type for FormData + fix status poll URL
• Saved-search load stuck on skeleton — inline mutation (search)
• Infinite loop from mutation deps in reset() (run-import-wizard)
• Upgrade confidence to High when header exactly matches a readout-def name (import-wizard)
• Widen dialog so the mapping table fits without horizontal scroll (import-wizard)
• Widen all protocol-related dialogs to remove horizontal scroll (protocol-ui)
• Accept signal + nullable params in customInstance (frontend)
• Reliably pre-load SMILES into Ketcher edit dialog (chemistry)
• Re-resolve preview when chemist refines column mapping (screening)
• Readable amber text on light mode for run import panels (ui)
• Disclosure path sets batch_skipped=false (types)
• Place campaigns route under existing [id] segment (fe)
• Persist result notes from decision panel
• Show registration_number in compound-list pane (fe)
• Use backend enum values for source_kind (fe)
• Align all campaign enums with backend StrEnum values (fe)
• Never display UUIDs to users — breadcrumbs, sources, fallbacks (fe)
• Edit-channel popover — add hit threshold, hide non-editable fields, tidy QC (fe/campaign)
• Radix Select rejects empty-string item values — use "none" sentinel (fe/campaign)
• Require projectId on add-dialogs (spec contract) (fe/campaign)
• SourcesSection empty-state + SourceEntry + remove callback (fe/campaign)
• MeasurementToActivity readout uses replicate_count for point count (fe/campaign)
• Re-export useCampaignCurves + tighten enabled guard (fe/campaign)
• Final review polish + Phase 5 handoff update (fe/campaign)
• +Channel popover pre-fills hit criteria from protocol recommendations (fe/campaign)
• Friendly run label in Sources — protocol name + run date instead of UUID prefix (campaign)
• Show channel unit on hit threshold + spell out the comparison (campaign/import)
• Explicit Save / Cancel buttons on the description editor (campaign)
• Description itself is the edit target — drop the corner-floating pencil (campaign)
• Decision popover only saves on Save — no more auto-save mid-edit (campaign)
• Published collection uses campaign name + sign-time publish toggle (campaign/close)
• Closed-meta line resolves user name and hides signature UUID (campaign)
• Fold "N results" into the filter bar, drop the empty toolbar row (campaign)
• Drop TautomerEnumerator + populate stereo classification; rename chem_vault → cellar (registration)
• Address Phase 1 code review feedback (shared)
• Address Phase 2 review — migrate inventory-dashboard tabs, fix lifecycle variant (frontend)
• Drop redundant server-state sync into Zustand store (registration)
• Replace state-sync effects with derived values (frontend)
• Replace imperative DOM/window APIs with proper React patterns (frontend)
• Handle PageResult shape in bespoke list hooks + regen api (frontend)
• IC90/EC90 marker Y position needs level/100 (screening)
• Detail drawer Selected Protocols card missing on DR rows (search)
• Multi-intercept channels — proper cells, hits, labels (campaign)
• Closed view defaults filter to Selected only (campaign)
• ND / >max cells sort to where a chemist expects them (screening)
• Grid value cell renders ND uppercase, tooltip + sort honest (campaign)
• Download via authed fetch — drops the bearer token (export)
• Ready toast — Download action + close icon, no stale Cancel (export)
• V1 smoke — card grid ref timing + dup heading + table density (collections)
• Expose is_frozen + derived_from_campaign_id on API (collections)
• Split-pane layout — string sizes (percent) + explicit height (scaffold-tree)
• Drop SMILES text + bump thumbnail to 80px (scaffold-tree)
• See the FULL collection, not just the visible page (scaffold-tree)
• Relax pagination cap for {type:'collection'} queries (search)
• Split handoffs into prepare + fire effects to fix soft-nav stale-mutation bug (search)
• Cluster-map sends collectionId XOR moleculeIds (was sending both) (sar)
• Cluster scatter hover shows reg_number/name, not UUID (sar)
• Picker/N/threshold changes wait for Diversify, no auto-refetch (sar)
• Lasso uses Plotly's selected points directly + lasso wins over reps (sar)
• Lasso resolves IDs via pointNumber index; SVG trace ≤5K (scattergl selection unreliable) (sar)
• Star markers use amber fill (SVG scatter ignored the transparent fill) (sar)
• Star fill = cluster color (per-rep chemotype palette + dark outline) (sar)
• Star size 18→12 (closer to base dot size; thinner outline) (sar)
• Polling reads {result,job} shape from GET (was treating it as flat UmapJobDto, never recognized ready) (sar)
• NO_SCAFFOLD bucket falls back to in-memory filter (not exact_match_in) (sar)
• DR point counter reflects all exclusion sources (screening)
• Align FE/BE idx domain for DR point editing (screening)
• Collection-import wizard UX — loading state + breadcrumb + row input + top commit button (frontend)
• Stop UMAP cluster poll storm + bound selection pane (sar_analysis)
• Bulk-registration summary renders its results (chemical_registration)
• Lasso resolves ids via data-space polygon (scatter + scattergl) (sar_analysis)
• Keep 'Diversify...

Frontend v0.1.0

Bug Fixes

• Close frontend-backend gap — all APIs now have UI coverage
• Review fixes — remove ghost operator field, guard log10(0), fix retire reason type (S31-S32)
• Replace UUID text inputs with compound/batch selectors (GF04)
• Add CSV template downloads and use human-readable columns in imports
• Serve RDKit WASM from public/ — fixes streaming compile error (GF02)
• Show error states instead of infinite skeletons when backend is down
• Dynamic CSV templates — protocol-aware readout, multi-ID compounds
• Show multiple custom_id columns in CSV template
• Readout data table shows compound names and measurement names, not UUIDs
• Pivot readout data table — definitions as columns, one row per compound
• Root-cause fixes — server-side identifier resolution, search-based selector
• Replace window.location.href/history.back with Next.js router
• Add storage location dropdown to create sample dialog
• Replace raw UUID inputs with entity selectors (S26)
• Replace empty-string SelectItem values with sentinel strings
• Replace UUID displays with entity names + fix assign 401
• Eliminate all UUID displays from new inventory UI
• Add link to manage synthesis routes from Start dialog
• Redesign shipment creation with compound-first workflow
• Widen dialogs globally — default max-w-2xl (672px)
• Search results — emerald colors + structure depiction cards
• Stringify nested objects in Excel export to prevent [object Object] (export)
• Reset editorOpen state in form reset functions, remove redundant cast
• Enlarge structure thumbnails in compound list (40px → 80px)
• Replace empty string SelectItem values with sentinel in plate components
• Enlarge well mapping dialog + add import template management UI
• Well mapping dialog — 80vw/85vh, CSV paste/upload, download template
• Resolve UUID displays to human-readable names in plate UI
• Well mapping dialog — ResizeObserver-based square cell grid
• CustomInstance FormData support + clarify import wizard purpose
• Import wizard end-to-end — type alignment, UoW, FormData upload
• Move useCallback above early returns in CollectionDetail
• Remove stray 's' from API endpoint URLs (attachment)
• Replace UUID input with MemberSelector search-by-name (project-scoping)
• Vault mapper field names, pagination, dialog scroll, and caching
• Map external description/category, fix 204 JSON parse, pagination
• Ontology annotation PUT sends 'slot' not 'slot_name'
• Ontology_annotations is a dict not array on Protocol type
• Add cascade selection guidance to inventory dashboard (ui)
• Use Zustand store for breadcrumb overrides instead of context (ui)
• Only make breadcrumb segments clickable if page exists (ui)
• Restore Saved Searches to sidebar navigation (ui)
• Show compound names in dose-response chart legend and cards (ui)
• Add Edit Points toggle, compound names on constraints, round IC50 values (ui)
• Guard against undefined plateMap.wells in run data panel (ui)
• Make readout_data molecule_id/batch_id nullable in API + frontend
• Validate batch amount required when include batch is toggled on
• Resolve chemist UUID to display name on batch detail page
• Review fixes — zero-value data points, shared helper, actual top/bottom, sorted query key
• Excel export now uses getCellValue to respect valueGetter columns
• Readout data table shows per-well rows for dose-response data
• Excel export — plain headers, CV ID in Compound, custom-only synonyms
• Excel export fills existing Structure/Curve columns with images
• Marker toggle label uses actual curve type (IC50/EC50/Ki/etc)
• Restore integration client naming — only docs/commits are sanitized
• Clean up collection criterion types and unused imports in search form
• Search revamp frontend bugs — protocol columns, 4PL div-by-zero, config safety, cursor jumps
• Code review fixes — updated_at propagation, null visibility, grid selection sync, hook lift
• Replace hardcoded colors with semantic design tokens
• Simplify ProtocolSection — remove dead dropdowns, unify readout/curve selector
• Wire protocol and/or conjunctions to actual search query
• DR chart not rendering — raw_data keys were concentration/response, not x/y
• Persist protocol conjunctions in saved searches + support mixed AND/OR
• Remove placeholder tabs, fix scroll, open detail in new tab
• Saved search loading stuck on skeleton — remove handleSearch from useEffect deps
• Derive protocol curve types from readout definitions instead of hardcoding
• Restore lost backend changes + commit all pending work
• Restore DR curve plots in search results grid
• Breadcrumb trail system — fix duplicate Protocols and missing protocol on runs
• Remove AG Grid Enterprise rowGroup from collection list
• Disclosure mode uses disclosure endpoint, not registration
• Add disclosure provenance fields + confirmation before submit
• Remove explicit Content-Type for FormData + fix status poll URL
• Saved-search load stuck on skeleton — inline mutation (search)
• Infinite loop from mutation deps in reset() (run-import-wizard)
• Upgrade confidence to High when header exactly matches a readout-def name (import-wizard)
• Widen dialog so the mapping table fits without horizontal scroll (import-wizard)
• Widen all protocol-related dialogs to remove horizontal scroll (protocol-ui)
• Accept signal + nullable params in customInstance (frontend)
• Reliably pre-load SMILES into Ketcher edit dialog (chemistry)
• Re-resolve preview when chemist refines column mapping (screening)
• Readable amber text on light mode for run import panels (ui)
• Disclosure path sets batch_skipped=false (types)
• Place campaigns route under existing [id] segment (fe)
• Persist result notes from decision panel
• Show registration_number in compound-list pane (fe)
• Use backend enum values for source_kind (fe)
• Align all campaign enums with backend StrEnum values (fe)
• Never display UUIDs to users — breadcrumbs, sources, fallbacks (fe)
• Edit-channel popover — add hit threshold, hide non-editable fields, tidy QC (fe/campaign)
• Radix Select rejects empty-string item values — use "none" sentinel (fe/campaign)
• Require projectId on add-dialogs (spec contract) (fe/campaign)
• SourcesSection empty-state + SourceEntry + remove callback (fe/campaign)
• MeasurementToActivity readout uses replicate_count for point count (fe/campaign)
• Re-export useCampaignCurves + tighten enabled guard (fe/campaign)
• Final review polish + Phase 5 handoff update (fe/campaign)
• +Channel popover pre-fills hit criteria from protocol recommendations (fe/campaign)
• Friendly run label in Sources — protocol name + run date instead of UUID prefix (campaign)
• Show channel unit on hit threshold + spell out the comparison (campaign/import)
• Explicit Save / Cancel buttons on the description editor (campaign)
• Description itself is the edit target — drop the corner-floating pencil (campaign)
• Decision popover only saves on Save — no more auto-save mid-edit (campaign)
• Published collection uses campaign name + sign-time publish toggle (campaign/close)
• Closed-meta line resolves user name and hides signature UUID (campaign)
• Fold "N results" into the filter bar, drop the empty toolbar row (campaign)
• Drop TautomerEnumerator + populate stereo classification; rename chem_vault → cellar (registration)
• Address Phase 1 code review feedback (shared)
• Address Phase 2 review — migrate inventory-dashboard tabs, fix lifecycle variant (frontend)
• Drop redundant server-state sync into Zustand store (registration)
• Replace state-sync effects with derived values (frontend)
• Replace imperative DOM/window APIs with proper React patterns (frontend)
• Handle PageResult shape in bespoke list hooks + regen api (frontend)
• IC90/EC90 marker Y position needs level/100 (screening)
• Detail drawer Selected Protocols card missing on DR rows (search)
• Multi-intercept channels — proper cells, hits, labels (campaign)
• Closed view defaults filter to Selected only (campaign)
• ND / >max cells sort to where a chemist expects them (screening)
• Grid value cell renders ND uppercase, tooltip + sort honest (campaign)
• Download via authed fetch — drops the bearer token (export)
• Ready toast — Download action + close icon, no stale Cancel (export)
• V1 smoke — card grid ref timing + dup heading + table density (collections)
• Expose is_frozen + derived_from_campaign_id on API (collections)
• Split-pane layout — string sizes (percent) + explicit height (scaffold-tree)
• Drop SMILES text + bump thumbnail to 80px (scaffold-tree)
• See the FULL collection, not just the visible page (scaffold-tree)
• Relax pagination cap for {type:'collection'} queries (search)
• Split handoffs into prepare + fire effects to fix soft-nav stale-mutation bug (search)
• Cluster-map sends collectionId XOR moleculeIds (was sending both) (sar)
• Cluster scatter hover shows reg_number/name, not UUID (sar)
• Picker/N/threshold changes wait for Diversify, no auto-refetch (sar)
• Lasso uses Plotly's selected points directly + lasso wins over reps (sar)
• Lasso resolves IDs via pointNumber index; SVG trace ≤5K (scattergl selection unreliable) (sar)
• Star markers use amber fill (SVG scatter ignored the transparent fill) (sar)
• Star fill = cluster color (per-rep chemotype palette + dark outline) (sar)
• Star size 18→12 (closer to base dot size; thinner outline) (sar)
• Polling reads {result,job} shape from GET (was treating it as flat UmapJobDto, never recognized ready) (sar)
• NO_SCAFFOLD bucket falls back to in-memory filter (not exact_match_in) (sar)
• DR point counter reflects all exclusion sources (screening)
• Align FE/BE idx domain for DR point editing (screening)
• Collection-import wizard UX — loading state + breadcrumb + row input + top commit button (frontend)
• Stop UMAP cluster poll storm + bound selection pane (sar_analysis)
• Bulk-registration summary renders its results (chemical_registration)
• Lasso resolves ids via data-space polygon (scatter + scattergl) (sar_analysis)
• Keep 'Diversify...

Backend v1.0.0

Bug Fixes

• Green up backend lint, unit, and integration jobs (ci)

Tests

• Remove tautological tests that only echo source literals

Bug Fixes

• User preferences — proper DDD layers, no architecture violations
• Security + architecture review — 8 findings resolved
• Architectural review — 7 findings resolved
• Architectural review — 3 findings resolved
• Architectural review — workspace isolation, DDD, security (11 findings)
• Protocol versioning — parent stays active until new version published
• Root-cause fixes — server-side identifier resolution, search-based selector
• Correct model import paths in dashboard route and disclosure repo
• Schema hardening + disclosure/merge atomicity
• Skip name-to-identifier promotion for auto-generated names
• Add missing guard checks across use cases
• Lazy Sentinel init so interface layer imports don't crash
• Replace None auth fallback with reject-all stub
• Replace UUID displays with entity names + fix assign 401
• Architectural review — workspace isolation + persistence gaps
• Columns type to dict[str, Any], add_molecules/remove_molecules return int (research-org)
• Clean architecture fix — move query composer to infra, add repo method (search)
• Find_collections_containing returns Collection objects per Protocol
• Rename protocol_id/run_id to project_id/template_id on RegisteredPlate
• Add batch validation on MapWells + PlateTemplate delete guard
• MapWells accepts batch numbers (CV-00001-001), not just UUIDs
• Import wizard end-to-end — type alignment, UoW, FormData upload
• Rename AddMoleculesBody.refs → references to match frontend contract
• Add UoW to list use cases — missing async context manager (t10)
• Clean architecture violations in vault import — move errors to app layer, catch timeout
• Correct WorkspaceSettings types and vault import use case UoW handling
• Handle legacy {} values in workspace_settings columns
• Vault mapper field names, pagination, dialog scroll, and caching
• Map external description/category, fix 204 JSON parse, pagination
• Filter external calculation outputs, map description/category, fix 204
• Move PlateFormat to shared kernel to fix bounded context independence
• Show compound names in dose-response chart legend and cards (ui)
• Clamp R² to [0, 1] in both fitting passes (infra)
• Make readout_data molecule_id/batch_id nullable in API + frontend
• Batch numbering uses molecule reg number prefix (CV-00001-001)
• Serialize recommended_hit_criteria in ProtocolResponse
• Remove is_computed filter + add n/sd to numeric readout aggregation
• Review fixes — zero-value data points, shared helper, actual top/bottom, sorted query key
• Fit-curves endpoint calls FitDoseResponseCurves directly
• Activity summary includes compounds with DR curves but no readout data
• Normalize top > bottom in curve fitter output
• Compute R² and classify before top/bottom swap in curve fitter
• Commit UoW after fitting curves in standalone mode
• Excel export — plain headers, CV ID in Compound, custom-only synonyms
• Restore integration client naming — only docs/commits are sanitized
• Code review fixes — updated_at propagation, null visibility, grid selection sync, hook lift
• DR chart not rendering — raw_data keys were concentration/response, not x/y
• Restore lost backend changes + commit all pending work
• Wire GetMoleculeActivityDetail in DI container and dependencies
• Update CDD client docstring, add param validation, fix type hint
• Register get_sync_watermark activity in Temporal worker
• Register ListCddMoleculeImports and ForceFailCddMoleculeImport in DI container
• Parse cdd_modified_at ISO string to datetime before DB insert
• Correct Mapped type hints for DateTime columns on CddMoleculeImportModel
• Detect crashed workflows in status endpoint, graceful cancel for terminated
• Sync crashed workflow status to DB to prevent UI infinite loop
• Disclosure FK violation + add missing merge side effects
• Mark_conflict keyword arg + add find_by_id_in_workspace to Protocol
• Restore saved-search write-back on first page (execute-search)
• Add missing updated_at column to compound_flags (db)
• Wrap PreviewRunFile in UoW context (import-run-file)
• Unwrap RegistrationNumber + case-insensitive identifier match (import)
• Write readouts for control wells; unblocks plate normalization (import)
• Hydration regression + invariant boundaries + drop legacy normalization kwarg (protocols)
• FitOverrides + versioning carry-forward all DR config fields (screening)
• Scope inbound-ref and cascade engine queries by workspace_id (cascade)
• Write audit operation inside the deletion transaction (admin)
• Morgan similarity must pass Python-computed bytes via bfp_from_binary_text (persistence)
• Drop mol_adjust_query_properties from substructure path (persistence)
• Drop typed bindparam on SMARTS/SMILES query strings (persistence)
• SQL-level CAST to cstring + execute-tier regression tests (search)
• Apply professional mode descriptions to MODE_DEFAULTS (domain)
• Re-resolve preview when chemist refines column mapping (screening)
• Preserve config writes when patching create_batch_on_duplicate together (data-sources)
• Correct NotFoundError signature in Collection guards (persistence)
• Tighten close-campaign tests and import hygiene (application)
• Tidy get_published_campaign dead paths (application)
• Preserve measurement id on re-resolve (application)
• Persist result notes from decision panel
• Handle nested per-plate z_prime shape in qc_metrics JSONB (campaign)
• Match find_by_ids signature convention + drop fixture commit (be/screening)
• Rely on Pydantic for batch cap + document non-enrichment (be/dose-response)
• Condense raw_data to {x,y} in curves:batch (be/dose-response)
• Include curve_class in DR candidates so the curve-class chip filter actually works (campaign/import)
• Published collection uses campaign name + sign-time publish toggle (campaign/close)
• Drop TautomerEnumerator + populate stereo classification; rename chem_vault → cellar (registration)
• Multi-intercept channels — proper cells, hits, labels (campaign)
• Tighten ExportJob state-machine guards + Protocol typing (domain)
• Commit UoW transactions in RenderExport state transitions (export)
• Replace inline container access in download route with PrepareExportDownload use case (export)
• Build columns in total_count() so the renderer sees them (export)
• Use parent drc token for activity lookups (cell values + sparklines) (export)
• Expose is_frozen + derived_from_campaign_id on API (collections)
• Backfill script must eagerly import sibling model modules (scaffold-tree)
• Emit clean ring-only scaffolds, parent=simpler (scaffold-tree)
• See the FULL collection, not just the visible page (scaffold-tree)
• Relax pagination cap for {type:'collection'} queries (search)
• UmapJobRepository takes UoW + alembic env.py imports for sar_analysis models (sar)
• Test_find_cached_misses_past_ttl — use unique ids_hash to avoid cross-test cache collision (sar)
• Morgan FP decode uses CreateFromBitString (was passing bytes to CreateFromBinaryText) (sar)
• Refit endpoint honors disable_auto_outliers flag (screening)
• Migration 041 preserves concentration+response payload (screening)
• Refit audit reason + audit-rollback atomicity test (screening)
• Next_batch_number uses MAX-tail regex, accepts width (inventory)
• Backfill script — use database_url + pool_pre_ping (matches sibling) (scripts)
• Immutable candidates tuple + has_identifier/empty-outcomes tests (research_org)
• Guard uow.commit + tests for not-found + TTL (research_org)
• BulkAddToCollection populates molecule_name on resolved outcomes (research_org)
• Dedup summary-import items by key (last-wins) + normalize errors (screening)
• Return 422 for malformed summary-import mapping (api)
• Summary import resolves compound_ref by identifier (mirrors plate path) (screening)
• Resolve code-review findings on kvt branch (tagging,screening)
• Move tag-browse read protocol to the application layer (arch)
• 422 on explicit-null type in collection PATCH (research-org)
• 404 on unknown target links + audit events + light guards (screening)
• Block deleting in-use targets (RESTRICT + 409) (screening)
• Resolve targets in the same transaction as reads + scope link queries (screening)
• Mutation responses carry targets like GET (screening)
• Forbid unknown fields on protocol create/update bodies (screening)
• Enforce workspace tenant guard in every application use case (security)
• Workspace-scope tag-link repoint (defence-in-depth) (security)
• Single workspace-first unique index on favorites (personalization)
• Require_same_user guard on favorite use cases (personalization)
• Idempotent favorite insert + drop dead dispatcher wiring (personalization)
• Per-project SQL cap on scope-stats member ids (projects)
• Owner-side workspace scope on target filter subquery (campaigns)
• Serialize curve excluded_points to dicts in activity-detail (screening)
• Guard decomposer translate loop + cover multi-Rgroup and mid-sequence unmatched (sar)
• Surface no-SMILES molecules as unmatched; ruff format (sar)
• Install cellar project in backend image so it boots (docker)
• Fan out synonym mirrors on batches created during import (inventory)
• Scope activity-projection find_cached by workspace_id (defense-in-depth) (sar)
• Validate projection ownership in /rows (defense-in-depth) (sar)
• Resolve design-7 code-review findings (lifecycle, heatmap, grid, efficiency) (sar)
• Log status_code=None (not 0) on pre-response crash; +health/client_ip tests (logging)
• Source environment from APP_ENV to match deployment (version)
• Conservative is_run_candidate + immutable VO fields + remove name_floor knob (screening)
• Unify free-text facet normalization + canonical type labels in name suggestion + seam tests (screening)
• Persist protocol facets atomically at create + type ontology-term boundary (screening)
• _AuthShim satisfies widened AuthContext (org_id/org_slug) (b...

Backend v0.1.0

Bug Fixes

• User preferences — proper DDD layers, no architecture violations
• Security + architecture review — 8 findings resolved
• Architectural review — 7 findings resolved
• Architectural review — 3 findings resolved
• Architectural review — workspace isolation, DDD, security (11 findings)
• Protocol versioning — parent stays active until new version published
• Root-cause fixes — server-side identifier resolution, search-based selector
• Correct model import paths in dashboard route and disclosure repo
• Schema hardening + disclosure/merge atomicity
• Skip name-to-identifier promotion for auto-generated names
• Add missing guard checks across use cases
• Lazy Sentinel init so interface layer imports don't crash
• Replace None auth fallback with reject-all stub
• Replace UUID displays with entity names + fix assign 401
• Architectural review — workspace isolation + persistence gaps
• Columns type to dict[str, Any], add_molecules/remove_molecules return int (research-org)
• Clean architecture fix — move query composer to infra, add repo method (search)
• Find_collections_containing returns Collection objects per Protocol
• Rename protocol_id/run_id to project_id/template_id on RegisteredPlate
• Add batch validation on MapWells + PlateTemplate delete guard
• MapWells accepts batch numbers (CV-00001-001), not just UUIDs
• Import wizard end-to-end — type alignment, UoW, FormData upload
• Rename AddMoleculesBody.refs → references to match frontend contract
• Add UoW to list use cases — missing async context manager (t10)
• Clean architecture violations in vault import — move errors to app layer, catch timeout
• Correct WorkspaceSettings types and vault import use case UoW handling
• Handle legacy {} values in workspace_settings columns
• Vault mapper field names, pagination, dialog scroll, and caching
• Map external description/category, fix 204 JSON parse, pagination
• Filter external calculation outputs, map description/category, fix 204
• Move PlateFormat to shared kernel to fix bounded context independence
• Show compound names in dose-response chart legend and cards (ui)
• Clamp R² to [0, 1] in both fitting passes (infra)
• Make readout_data molecule_id/batch_id nullable in API + frontend
• Batch numbering uses molecule reg number prefix (CV-00001-001)
• Serialize recommended_hit_criteria in ProtocolResponse
• Remove is_computed filter + add n/sd to numeric readout aggregation
• Review fixes — zero-value data points, shared helper, actual top/bottom, sorted query key
• Fit-curves endpoint calls FitDoseResponseCurves directly
• Activity summary includes compounds with DR curves but no readout data
• Normalize top > bottom in curve fitter output
• Compute R² and classify before top/bottom swap in curve fitter
• Commit UoW after fitting curves in standalone mode
• Excel export — plain headers, CV ID in Compound, custom-only synonyms
• Restore integration client naming — only docs/commits are sanitized
• Code review fixes — updated_at propagation, null visibility, grid selection sync, hook lift
• DR chart not rendering — raw_data keys were concentration/response, not x/y
• Restore lost backend changes + commit all pending work
• Wire GetMoleculeActivityDetail in DI container and dependencies
• Update CDD client docstring, add param validation, fix type hint
• Register get_sync_watermark activity in Temporal worker
• Register ListCddMoleculeImports and ForceFailCddMoleculeImport in DI container
• Parse cdd_modified_at ISO string to datetime before DB insert
• Correct Mapped type hints for DateTime columns on CddMoleculeImportModel
• Detect crashed workflows in status endpoint, graceful cancel for terminated
• Sync crashed workflow status to DB to prevent UI infinite loop
• Disclosure FK violation + add missing merge side effects
• Mark_conflict keyword arg + add find_by_id_in_workspace to Protocol
• Restore saved-search write-back on first page (execute-search)
• Add missing updated_at column to compound_flags (db)
• Wrap PreviewRunFile in UoW context (import-run-file)
• Unwrap RegistrationNumber + case-insensitive identifier match (import)
• Write readouts for control wells; unblocks plate normalization (import)
• Hydration regression + invariant boundaries + drop legacy normalization kwarg (protocols)
• FitOverrides + versioning carry-forward all DR config fields (screening)
• Scope inbound-ref and cascade engine queries by workspace_id (cascade)
• Write audit operation inside the deletion transaction (admin)
• Morgan similarity must pass Python-computed bytes via bfp_from_binary_text (persistence)
• Drop mol_adjust_query_properties from substructure path (persistence)
• Drop typed bindparam on SMARTS/SMILES query strings (persistence)
• SQL-level CAST to cstring + execute-tier regression tests (search)
• Apply professional mode descriptions to MODE_DEFAULTS (domain)
• Re-resolve preview when chemist refines column mapping (screening)
• Preserve config writes when patching create_batch_on_duplicate together (data-sources)
• Correct NotFoundError signature in Collection guards (persistence)
• Tighten close-campaign tests and import hygiene (application)
• Tidy get_published_campaign dead paths (application)
• Preserve measurement id on re-resolve (application)
• Persist result notes from decision panel
• Handle nested per-plate z_prime shape in qc_metrics JSONB (campaign)
• Match find_by_ids signature convention + drop fixture commit (be/screening)
• Rely on Pydantic for batch cap + document non-enrichment (be/dose-response)
• Condense raw_data to {x,y} in curves:batch (be/dose-response)
• Include curve_class in DR candidates so the curve-class chip filter actually works (campaign/import)
• Published collection uses campaign name + sign-time publish toggle (campaign/close)
• Drop TautomerEnumerator + populate stereo classification; rename chem_vault → cellar (registration)
• Multi-intercept channels — proper cells, hits, labels (campaign)
• Tighten ExportJob state-machine guards + Protocol typing (domain)
• Commit UoW transactions in RenderExport state transitions (export)
• Replace inline container access in download route with PrepareExportDownload use case (export)
• Build columns in total_count() so the renderer sees them (export)
• Use parent drc token for activity lookups (cell values + sparklines) (export)
• Expose is_frozen + derived_from_campaign_id on API (collections)
• Backfill script must eagerly import sibling model modules (scaffold-tree)
• Emit clean ring-only scaffolds, parent=simpler (scaffold-tree)
• See the FULL collection, not just the visible page (scaffold-tree)
• Relax pagination cap for {type:'collection'} queries (search)
• UmapJobRepository takes UoW + alembic env.py imports for sar_analysis models (sar)
• Test_find_cached_misses_past_ttl — use unique ids_hash to avoid cross-test cache collision (sar)
• Morgan FP decode uses CreateFromBitString (was passing bytes to CreateFromBinaryText) (sar)
• Refit endpoint honors disable_auto_outliers flag (screening)
• Migration 041 preserves concentration+response payload (screening)
• Refit audit reason + audit-rollback atomicity test (screening)
• Next_batch_number uses MAX-tail regex, accepts width (inventory)
• Backfill script — use database_url + pool_pre_ping (matches sibling) (scripts)
• Immutable candidates tuple + has_identifier/empty-outcomes tests (research_org)
• Guard uow.commit + tests for not-found + TTL (research_org)
• BulkAddToCollection populates molecule_name on resolved outcomes (research_org)
• Dedup summary-import items by key (last-wins) + normalize errors (screening)
• Return 422 for malformed summary-import mapping (api)
• Summary import resolves compound_ref by identifier (mirrors plate path) (screening)
• Resolve code-review findings on kvt branch (tagging,screening)
• Move tag-browse read protocol to the application layer (arch)
• 422 on explicit-null type in collection PATCH (research-org)
• 404 on unknown target links + audit events + light guards (screening)
• Block deleting in-use targets (RESTRICT + 409) (screening)
• Resolve targets in the same transaction as reads + scope link queries (screening)
• Mutation responses carry targets like GET (screening)
• Forbid unknown fields on protocol create/update bodies (screening)
• Enforce workspace tenant guard in every application use case (security)
• Workspace-scope tag-link repoint (defence-in-depth) (security)
• Single workspace-first unique index on favorites (personalization)
• Require_same_user guard on favorite use cases (personalization)
• Idempotent favorite insert + drop dead dispatcher wiring (personalization)
• Per-project SQL cap on scope-stats member ids (projects)
• Owner-side workspace scope on target filter subquery (campaigns)
• Serialize curve excluded_points to dicts in activity-detail (screening)
• Guard decomposer translate loop + cover multi-Rgroup and mid-sequence unmatched (sar)
• Surface no-SMILES molecules as unmatched; ruff format (sar)
• Install cellar project in backend image so it boots (docker)
• Fan out synonym mirrors on batches created during import (inventory)
• Scope activity-projection find_cached by workspace_id (defense-in-depth) (sar)
• Validate projection ownership in /rows (defense-in-depth) (sar)
• Resolve design-7 code-review findings (lifecycle, heatmap, grid, efficiency) (sar)
• Log status_code=None (not 0) on pre-response crash; +health/client_ip tests (logging)
• Source environment from APP_ENV to match deployment (version)
• Conservative is_run_candidate + immutable VO fields + remove name_floor knob (screening)
• Unify free-text facet normalization + canonical type labels in name suggestion + seam tests (screening)
• Persist protocol facets atomically at create + type ontology-term boundary (screening)
• _AuthShim satisfies widened AuthContext (org_id/org_slug) (backend)
• Only own org (or admin) may set plate owner_org_id (backend)
• Enforce private-org visibility on children/export/read-model/writes (ba...