Changelog

Bug Fixes

• Restore feedback config fallback

Bug Fixes

• Pass feedback config to sidecar

Features

• Unify automatic widget recommendations (#172)
• Streamline import cockpit workflow
• Guide users before import uploads
• Show collection computation progress in sidebar
• Allow custom API export data source
• Streamline collection data outputs
• Refine collection data outputs
• Complete standard profile workflows
• Add standardized export profiles
• Improve API export auto-configuration
• Support auxiliary source review editing
• Add data source inspection tabs (#142)
• Improve index field selection
• Add workflow history details
• Add workflow history view
• Add list performance diagnostics
• Add workflow commands to palette
• Remember desktop view preferences
• Remember desktop route per project
• Improve site builder authoring workflow
• Persist site workbench preview state
• Add native desktop menu shell
• Refine desktop shell and export toggles
• Add source enrichment reset mode
• Add enrichment panel workflow
• Add script to revert Tauri updater manifest to a previous version
• Add AST-based plugin manifest extractor
• Redesign pipeline overview (#125)
• Migrate from ReadTheDocs to GitHub Pages
• Add landing teaser with Niamoto product mocks
• Add Niamoto marketing site plan with partner assets
• Improve index generator configuration workflow
• Build remotion product demo
• Wire Intro/Outro scenes and add TransitionLabels
• Add Acts 4-6 (Collections, Site Builder, Publish)
• Add UI components, cursor system, and Acts 1-3
• Bootstrap Remotion demo video project
• Unify desktop and app startup loaders
• Add desktop debug mode and feedback fallback
• Improve collections computation feedback
• Replace collection select with custom dropdown
• Restore collection selector in CollectionPanel toolbar
• Add logos for BHL and spatial providers
• Add spatial enrichment v1
• Add inaturalist rich enrichment
• Add BHL references enrichment
• Add shared name verifier for rich enrichers
• Add catalogue of life rich enrichment
• Expand enrichment provider integrations
• Redesign enrichment workspace
• Add multi-source enrichment workflow
• Surface enrichment progress on dashboard cards
• Add desktop update test harness
• Improve publish workspace and desktop window state
• Refine panel navigation and transitions
• Html2canvas-pro screenshot + enriched debug context
• Add in-app feedback system with CF Worker proxy
• Add page transition and card entrance animations
• Add 8 new theme presets
• Extend style categories and add theme fallback logic
• Tauri desktop release readiness (#65)
• Add collapsible widget list panel
• Merge Sources tab into Blocs as dialog overlay
• Add enriched collections overview with status cards
• Simplify API export UX for non-technical users (#61)
• Extend pre-import impact checks (#60)
• Add iOS and Android icon sets
• Replace logo with new N lettermark design
• Add release automation infrastructure (#58)
• Show live import progress events
• Stream auto-config analysis events
• Classify auxiliary stats sources separately
• Improve semantic relationship detection
• Integrate ML acquisition wave and retraining results
• Replace synthetic anonymous holdout with diversified real columns
• Retrained models on enriched gold set (2525 cols)
• Add niamoto-nc to gold set, fix basal_area merge
• Expand alias registry — 13 new concepts, 76.6% concept (+5.3)
• Multi-dataset eval suite — 418 cols, 7 datasets, 71% concept
• Full instance evaluation with annotations — 57 cols, alias 25% → ML 46% concept
• Retrain all models with cross-rank reciprocity features — ProductScore 79.25 → 80.04 (+0.79)
• Add fusion surrogate autoresearch runner
• Add product-oriented evaluation and surrogate fusion loop
• Complete Phase 3 — profiles, affordances, patterns, anomalies
• Concept taxonomy, enriched data, coarsened training (2231 cols)
• Add gold set builder, training scripts, and CLI metric
• Add alias registry, ml_mode API, and evaluation harness
• Add multi-platform deployment from GUI
• Add sidebar layout to Data, Groups and Publish modules
• Add pipeline status hooks, home page and staleness banner
• Simplify navigation, fix multi-lang export and map rendering
• Refactor footer as category-based sections with internal/external links
• Create niamoto-subset instance from niamoto-nc for fast testing
• Centre de notifications connecté aux jobs du pipeline
• Bouton transform dans GroupPanel + checkbox composite dans Build
• Ajouter group_by, endpoints active/last-run et job composite transform→export
• Ajouter JobFileStore + fix os.chdir() thread-unsafe
• Add shimmer loading skeleton with widget-type icons
• Add Plotly bundle splitting (core 1.3MB, maps 2.2MB)
• Migrate all preview components to unified engine and delete legacy queue
• Wire preview engine invalidation and migrate recipes (Phase 4)
• Add usePreviewFrame hook and shared preview components (Phase 3)
• Add unified preview engine (Phase 1)
• Add combined widget analysis previews
• Centralize table resolver and transform config models
• Full offline support for desktop application
• Enrich raster_stats and land_use with layer-select UI hints
• Add geographic layers API and LayerSelectField widget
• Add Phase 2.1 form widgets for transform configuration
• Add KeyValuePairsField and TagsField widgets with auto-detection
• Enrich Pydantic models with UI hints and fix Select.Item bug
• Use native macOS titlebar overlay instead of custom traffic lights
• Add multilingual support and i18n infrastructure
• Add MapRenderer service and fix layout preview issues
• Refactor index config with side panel editor and reusable preview
• Improve site preview navigation and widget suggestions
• Complete i18n migration for all UI components
• Enhance site builder with improved navigation and group preview
• Add x_label and y_label quick edit fields for axis customization
• Implement Option A hybrid layout with improved widget modal
• Add multi-field pattern detection for combined widgets
• Add drag-and-drop widget reordering and layout.order support
• Add specialized parameter editors and preview service
• Add unified widget recipe editor with wizard interface
• Enhance relation detection and support for class_object_field_aggregator
• Add index generator configuration and widget management
• Enhance desktop app with welcome screen, site config UI and layout editor
• Add advanced theme system with typography, shapes, and effects
• Replace bootstrap with intelligent widget suggestion system
• Integrate Tauri for desktop application support
• Add PyInstaller support and resource cascade system
• Remove hardcoded table references in showcase metrics
• Remove hardcoded entity references in data explorer and showcase
• Complete EntityRegistry v2 migration for stats and entities
• Add development tooling with instance context management
• Add intelligent onboarding wizard with auto-configuration
• Add transform-source-select widget with group context
• Migrate 11 transformers to entity-select widget
• Add dynamic entity-select widget and update config templates
• Migrate aggregation transformers to EntityRegistry
• Migrate 3 distribution transformers to EntityRegistry
• Migrate remaining 3 class_objects transformers to EntityRegistry
• Migrate categories_extractor and series_extractor class_objects transformers to EntityRegistry
• Migrate loaders to EntityRegistry and create refactoring tracking system
• Add environment variable substitution and plugin config validation
• Add partners section to TeamSection component with logos and descriptions
• Add PerspectivesSection component and integrate into showcase page fix: update Rich version in StackTechSection fix: include 'perspectives' in showcase store sections
• Implement pipeline management with tabs and shared state
• Add Cloudflare deployment functionality and integrate into the GUI
• Add API demo component and integrate into showcase page
• Add exports structure API endpoint and update UI components for directory visualization
• Add YAML configuration editor and backup functionality
• Update API documentation page and navigation structure
• Add Plotly.js and react-plotly.js for data visualization
• Update GUI documentation and improve language switcher component
• Implement enrichment preview functionality in Data Explorer
• Add package.json to repo for Docker builds
• Enhance showcase components with improved YAML configuration display and updated use case statistics
• Implement interactive showcase pages with real data pipeline integration
• Expose plugin param schemas for dynamic gui config
• Implement unified pipeline editor with ReactFlow
• Improve Transform interface and add pipeline specifications
• Implement hierarchical navigation and transform pipeline interface
• Add SQLite performance optimizations
• Update CLAUDE.md for development guidelines and commands; update permissions in settings.local.json; refine error handling in bar_plot and donut_chart widgets
• Enhance API enrichment with chained requests and improve GUI packaging
• Add support for binomial naming in TaxonomyImporter
• Enhance taxonomy name generation logic in TaxonomyImporter
• Introduce Tropicos enricher plugin for enhanced taxonomy data enrichment
• Enhance ShapeImporter and StatsLoader for improved feature handling and ID generation
• Introduce comprehensive GUI enhancements and CLI improvements
• Update CLI help message and initialization options
• Enhance interactive map functionality with Mapbox support
• Implement hierarchical shape support and enhancements
• Implement new Shape ID generation format in documentation and code
• Enhance geospatial extraction and interactive map functionality
• Enhance FieldAggregator to support JSON field access
• Add project initialization and metadata enhancements
• Integrate i18n support across components and add language switcher
• Enhance shape import functionality and configuration management
• Introduce faceted spinner and enhance circular progress component
• Enhance import process with progress tracking and new UI components
• Add table fields retrieval and enhance import field handling
• Enhance PlotImporter and import functionality
• Enhance ShapeProcessor to support group_id configuration
• Update documentation and configuration for multiple data sources
• Enhance ShapeProcessor to support group_id configuration
• Update documentation and configuration for multiple data sources
• Enhance StatsLoader to support dynamic key field lookup
• Enhance import functionality with progress tracking and hierarchy configuration
• Add support for multiple data sources in transformations
• Implement new import-v2 interface with enhanced functionality
• Introduce taxonomy hierarchy configuration and streamline import process
• Integrate httpx for enhanced API interactions and improve import functionality
• Enhance import wizard and API integration for improved data handling
• Add React-based GUI configuration interface for Niamoto
• Enhance export command output and improve plot importer functionality
• Enhance console output utilities
• Implement JSON API exporter and enhance data access utilities
• Enhance configuration file handling and directory setup
• Add screenshots to README and enhance data availability checks in widgets
• Enhance Tailwind CSS configuration and implement image gallery features
• Major documentation overhaul and database aggregator plugin
• Enhance template handling and CLI options in Niamoto
• Add run and stats commands to Niamoto CLI
• Integrate Tailwind CSS for enhanced styling and remove legacy assets
• Add bump2version to development dependencies
• Update dependencies and enhance project configuration
• Enhance widget tooltips and JSON parsing capabilities
• Refactor Plotly widgets to utilize shared utility functions for layout and rendering
• Enhance widget styling and structure for modern design
• Enhance InteractiveMapWidget with loading indicator and improved error handling
• Adjust positioning and rotation in ConcentricRingsWidget for improved label visibility
• Update ConcentricRingsWidget to use annotations for segment labels and percentages
• Add stacked area normalized transformation and concentric rings widget
• Enhance data transformation and radial gauge widget functionality
• Add gradient color generation to BarPlotWidget
• Enhance data transformation and bar plot widget functionality
• Enhance InteractiveMapWidget with TopoJSON support and optimize GeoJSON handling
• Enhance HtmlPageExporter with field selection and navigation data extraction
• Add auto-zoom capability and improve empty state handling in map and info grid widgets
• • improve test isolation and prevent config file creation during tests - simplify nested field handling by using existing _get_field_from_table method -improve JSON field handling and use temporary directories for tests
• Enhance taxonomy import to handle family and genus level entries with taxon IDs
• Add plugins command to list and inspect available plugins
• Add auto-color feature to bar plots and enhance hierarchical navigation tests
• Add auto-color generation for bar plots and simplify widget layout template
• Add map attribution toggle and improve progress tracking in HTML export
• Add hierarchical configuration support for plot imports
• Implement configurable top ranking plugin with direct, hierarchical and join modes
• Add hierarchical plot structure with nested set model support
• Improve hierarchical navigation with auto-scroll and enhanced styling
• Implement hierarchical navigation widget with Tailwind CSS styling
• Add PyPI token authentication support and release documentation
• Add PyPI token authentication support and release documentation
• Implement HTML page exporter with configurable widgets
• Major core refactoring, taxonomy implementation, and testing overhaul
• Add support for creating named fields from labels in MultiColumnExtractor
• Add 'nb_species' to plot information and improve value handling in templates and data extraction, redising the shape_index page
• Update links in forests, plots, and trees templates to point to index pages
• Refactor data import process to use ImporterService and improve error handling
• Enhance GitHub deployment with configurable user identity and improved branch handling
• Update page generator and template for improved data handling and localization
• Add index page generation for taxons, plots, and shapes; update navigation links
• Add Endemia logo to footer and index templates
• Enhance node opening functionality with smooth scrolling effect
• Add API taxonomy enricher and enhance plugin documentation
• Enhance plugin architecture and add direct reference loader

Performance

• Speed up import auto-configuration
• Optimize data explorer table rendering
• Lazy load collection previews
• Speed up reference field suggestions
• Streamline transform and export pipelines (#59)
• Add pytest-xdist parallel execution and mark slow benchmarks
• Batch fusion features in evaluate.py — ProductScore 14h → 42min
• Batch fusion feature extraction — training 5h → 15min, identical results
• Reduce binary size by 43% through dependency optimization

Bug Fixes

• Keep uv run checks frozen
• Preserve uv lock resolution options in releases
• Narrow import status badge variants
• Preserve export cancellation fallback
• Address PR review blockers
• Harden publish and import dashboard flows
• Gate desktop releases on sidecar startup
• Polish dark mode branding and sidebar state
• Tighten import file handling
• Harden import cockpit file matching
• Preserve duckdb resolution cutoff
• Stabilize desktop API auth client test
• Keep missing DuckDB read-only connections lazy
• Stabilize DuckDB access in GUI previews
• Eliminate pytest warnings
• Stabilize plugin loading and test cleanup
• Resolve high clawpatch findings
• Resolve clawpatch review findings
• Resolve clawpatch high findings
• Resolve clawpatch findings
• Close remaining clawpatch low findings
• Stabilize preview and overlay regressions
• Stabilize collection and index workflows
• Stabilize API route regressions
• Authorize desktop API requests
• Preserve profiler total row count
• Infer legacy top ranking mode
• Resolve spatial preview geometry
• Preserve group index generator fields
• Discover recipe widget schemas
• Align import v2 validation with model
• Validate relationship CSV inputs
• Escape BibTeX export values
• Offload enrichment preview loading
• Bound index suggestion record loads
• Enforce query result limits
• Preserve duplicate transform widgets
• Fail transform jobs for unknown groups
• Count hierarchical representatives from relation
• Preserve registry plugin type
• Translate standard compatibility errors
• Translate enrichment preview errors
• Mark publication stale after site config changes
• Offload smart auto configure
• Analyze spatial shape uploads
• Drop registered import tables
• Scope combined suggestions sources
• Translate enrichment config errors
• Honor configured spatial geometry fields
• Bound csv import uploads
• Hide non-transform job status
• Parse underscored entity map references
• Bound time series presence percentages
• Resolve repository ml models
• Aggregate duplicate class object rows
• Validate outlier export thresholds
• Reload desktop projects through native bridge
• Bound retained import jobs
• Validate stats validation rules
• Bound data explorer query limits
• Expose cli export jobs
• Validate dataset config updates
• Respect cleared preview fields
• Align import v2 schema contract
• Enforce export widget identifiers
• Load all recipe widget plugins
• Cancel export jobs
• Validate canonical transform lists
• Stream site file uploads
• Align index generator group lookup
• Read root transform source configs
• Limit feedback screenshot uploads
• Prefer explicit spatial coordinate columns
• Preserve import status setup errors
• Validate config updates before writing
• Bind transformer package exports
• Securely open exported files
• Write validation rules atomically
• Avoid leaking config file paths
• Validate backup config names
• Parameterize archive preview validation query
• Escape Rich markup in stats output
• Escape Rich markup in plugin listing
• Escape Rich markup in direct CLI errors
• Escape Rich markup in progress output
• Escape Rich markup in CLI output
• Block unsafe outbound test redirects
• Write source transform config atomically
• Use read-only table preview connection
• Open table preview database read-only
• Require auth for credential mutations
• Serialize API export target updates
• Escape formulas in outlier CSV exports
• Validate API export target paths
• Require auth for validation rule updates
• Serialize config scaffolding updates
• Serialize source config updates
• Share transform config write lock
• Serialize transform widget updates
• Avoid orphan recipe transforms
• Serialize collection metadata updates
• Write data content atomically
• Restrict data content writes
• Serve uploaded SVGs as attachments
• Create valid web export targets
• Validate widget dependency scripts
• Open template lookups read-only
• Scope recipe widget deletion
• Require desktop auth for import mutations
• Write bulk import config atomically
• Serialize index generator updates
• Constrain backup restore paths
• Stabilize pipeline history import snapshot
• Write config updates atomically
• Serialize reference config updates
• Quote Darwin Core group queries
• Merge enrichment updates with current data
• Validate Darwin Core query identifiers
• Resolve entity tables before querying
• Restrict derived column formulas
• Restrict custom formula evaluation
• Resolve archived test fixture paths
• Hide absolute export list paths
• Guard widget suggestions without project
• Preserve group index preview footers
• Quote dataset count tables
• Accept uppercase upload extensions
• Hide combined suggestion internals
• Hide backup filesystem paths
• Avoid GUI backup collisions
• Record JSON export metadata duration
• Register plugins with correct arguments
• Preserve benchmark logs
• Escape class object CSV paths
• Bound GBIF request timeouts
• Open entity reads read-only
• Limit BibTeX upload size
• Constrain saved source paths
• Restrict served project files
• Tolerate empty BibTeX fields
• Restrict API test targets
• Constrain site file listing paths
• Validate recipe plugin params
• Preserve static page extensions
• Limit extracted upload archives
• Preserve uploads on failed overwrite
• Preserve API export group settings
• Preserve unresolved widgets on reorder
• Return all recipe source columns
• Ignore invalid WKT in shape distribution
• Preserve deploy validation extras
• Validate dataset config shape
• Count dangling taxonomy orphans
• Paginate valid WKT map features
• Constrain configured source paths
• Escape render widget messages
• Restrict site file content access
• Stream terminal auto config events
• Reject concurrent import all jobs
• Validate current import config schema
• Preserve zero medians in validation stats
• Include max values in validation histograms
• Redact listed import job tracebacks
• Redact import job tracebacks
• Guard debug health error route
• Tolerate invalid WKT in coverage analysis
• Reject duplicate normalized CSV headers
• Preserve layout widget index identity
• Validate plugin compatibility requests
• Include datasets for reference-only recipes
• Reject colliding source uploads
• Limit source upload memory use
• Avoid backup filename collisions
• Preserve upper edge in smart bins
• Keep top ranking suggestion counts positive
• Resolve humboldt collection backing sources
• Filter horizontal bar zeros by value axis
• Handle zero-width contextual gauge ranges
• Render dictionary line plots with multiple y axes
• Constrain exporter output paths
• Sanitize leaflet map rendering
• Use advanced transform chain references
• Default static page context to none
• Escape widget container metadata
• Validate archived shapefile zip extraction
• Resolve archived debug script roots
• Run archived test helper from repo root
• Resolve dev script repository root
• Clean untracked autoresearch directories
• Preserve fusion surrogate cache on rebuild failure
• Handle help sections without index pages
• Validate template config before export update
• Surface geospatial source failures
• Honor geospatial registry id fields
• Copy semantic affordance sets
• Calculate edge density per area unit
• Align class object series by axis
• Round scalar gauge maximums upward
• Handle deployer unpublish network errors
• Reject disjoint relationship samples
• Project vector overlay feature areas
• Honor raster nodata metadata
• Convert table view data before empty check
• Mark uvloop as non-windows dependency
• Ignore invalid summary stat filters
• Convert summary stats data before empty check
• Handle plot import removal
• Resolve query db paths from repo root
• Use configured spatial preview dataset
• Preserve DuckDB mode during selects
• Substitute plain config env vars
• Expand configured database paths
• Tolerate partial UI builds
• Fail plugin manifest on syntax errors
• Validate aggregation SQL identifiers
• Sanitize markdown preview html
• Validate import v2 saves
• Quote entity route identifiers
• Constrain site uploads to files
• Constrain preview source paths
• Require desktop auth for project reload
• Block private URL health checks
• Use typed ecological transformer params
• Preserve nojekyll in GitHub API deploys
• Restrict file browser to project root
• Keep desktop auth token private
• Prevent docs help output deletion
• Avoid export cwd lock deadlock
• Preserve existing zip upload components
• Skip empty product holdouts
• Support validated query templates
• Honor adjacency hierarchy id field
• Validate loader SQL identifiers
• Enforce GUI API path containment
• Escape user values in CLI console output
• Clean MagicMock artifacts between tests
• Preserve unowned root databases in tests
• Export transformer suggestion model
• Match plugin structures by descriptor
• Support empty widget transform tables
• Honor top-level widget source
• Prompt for deployment credentials
• Fail pipeline on transform config errors
• Prevent silent CLI startup failures
• Use dropdown for export data sources
• Improve export labels and warning handling
• Harden generated exports and enrichment configs
• Harden standard profile exports and tooling
• Harden export profile fallbacks
• Render void html tags without children
• Address React Doctor UI findings
• Address enrichment review feedback
• Improve enrichment previews
• Stabilize enrichment jobs
• Scan full CSV during DuckDB imports
• Allow adding import files incrementally
• Handle missing data preview tables
• Prevent recipe editor crashes
• Stabilize index field editor
• Preserve markdown content on page switch
• Persist desktop route memory natively
• Prevent collections preview update loops
• Address site editor review feedback
• Restore export config path hook
• Place preview restore next to delete
• Keep desktop project context in sync
• Soften project switcher hover states
• Preserve static site path for html exports
• Pin codecov cli version
• Harden release staging flow
• Update rustls webpki lockfile
• Harden export and enrichment jobs
• Split codecov checks by coverage area
• Align vitest config typing
• Address enrichment polling review feedback
• Stabilize frontend coverage tests
• Install pnpm before node cache
• Refine enrichment workflow reliability and UX
• Stage plugin manifest during releases
• Polish export format wizard
• Stabilize index config preview and actions
• Honor taxon stats relation fields
• Avoid welcome screen flicker on desktop
• Avoid recreating missing desktop project dirs
• Use native macOS traffic light placement
• Stabilize create project button hover
• Remove stale docs toctree entry
• Stabilize table preview pagination
• Harden release artifact publishing
• Restore macos executable permissions
• Harden release automation flows
• Accept flattened macos release app artifacts
• Resolve frontend lint warnings
• Surface pipeline status failures in publish
• Restrict publish gate to fresh sites
• Fail closed while publish gate resolves
• Gate publish on site configuration
• Restore site setup for unconfigured sites
• Tighten site root detection
• Base site readiness on a real root page
• Keep default web exports empty
• Stop scaffolding a synthetic home page
• Remove default home injection from site config
• Consolidate release automation flow
• Pass updater signing password explicitly
• Pass updater signing key path to macos finalizer
• Resolve downloaded macos app bundle in release finalizer
• Finalize macos release artifacts after notarization
• Repair macos signing pipeline for tauri bundles
• Sign versioned python framework bundle
• Bundle-sign python framework entrypoints
• Resolve versioned python path dynamically
• Sign flattened macos python entrypoints
• Sign embedded Python frameworks in CI
• Codesign macOS sidecar binaries in CI
• Pre-import Apple signing certificate in CI
• Recheck connectivity on startup
• Include trained ml models in desktop bundles
• Align mac traffic lights vertically
• Allow accented project names in wizard
• Point help output to the new GitHub Pages docs URL
• Exclude internal design system from Sphinx build
• Avoid duplicate help_content entries in wheel
• Harden config suggestions and uv dev workflow
• Stabilize collection auto-detect and desktop tools
• Resolve site builder lint warning
• Polish demo video interactions
• Refine demo video transitions
• Bind geospatial extractor to runtime config
• Stabilize previews and GitHub Pages deployment
• Prevent desktop preview request storms
• Harden desktop connectivity and updates
• Disable in-app windows updates
• Reduce collections preview load on low-power devices
• Preserve collection tab navigation
• Tighten publish readiness flow
• Improve UI rendering smoothness
• Smooth import query refresh states
• Improve linux updater install flow
• Prevent duplicate update toasts
• Repair packaged desktop widgets and feedback
• Enable tauri devtools feature for desktop debug mode
• Clarify collection batch progress
• Clear stale widget suggestion caches after import
• Hide sidebar branding in desktop builds
• Force bash shell for Tauri build on Windows
• Resolve typescript errors across forms and views
• Ensure site configs include a home page
• Auto fit map previews to data
• Stabilize tauri dev startup
• Reduce redundant frontend polling
• Harden widget previews and config inference
• Harden tauri desktop runtime
• Resolve frontend context split regressions
• Harden desktop update and packaging flows
• Improve Windows desktop compatibility
• Disable Windows sidecar console for desktop builds
• Limit entity list to 15 items with max-height cap
• Polish enrichment workspace and preview
• Use native linux titlebar chrome
• Streamline widget detail preview and forms
• Correct language switcher paths in exports
• Harden desktop update relaunch flow
• Simplify theme picker cards
• Open preview in browser from desktop
• Stabilize gui import and publishing workflows
• Harden gui runtime diagnostics
• Improve widget and transformer form handling
• Tighten desktop settings behavior
• Recover offline indicator on reconnect
• Align widget previews and layout config
• Hide legends in layout overview miniatures via Plotly relayout
• Improve preview engine resilience and health endpoint
• Improve Tauri startup, updater UX, and collections UI
• Disable RUSTSEC issue creation and improve desktop startup
• Address user findings — form reset, cooldown enforcement, screenshot capture, error sanitization
• Address code review findings
• Refine mac desktop header alignment
• Restore dev hot reload workflow
• Wire theme polish review fixes
• Isolate scroll zones and harmonize tab headers
• Move collapse toggle to right, fix scrollbar and scroll issues
• Use i18n for relative time in collections overview
• Resolve tab mismatch, API settings access, and stale i18n keys
• Correct stale i18n keys and tab value mismatch
• Enforce canonical home page export
• Improve desktop startup recovery
• Add unittest to PyInstaller hidden imports
• Polish publish workflow panels
• Stabilize publish previews and history
• Harden import and widget flows
• Harden import summary navigation
• Stabilize gui startup context
• Preserve enrichment tab state in onboarding UI
• Make pyinstaller install portable in CI
• Restore binary build packaging
• Increase auto-configure job polling timeout for CI with xdist
• Add --clear flag to uv venv to handle cached virtualenv
• Use correct codecov-action v5 parameter name
• Skip subset benchmark tests in CI when instance unavailable
• Skip benchmark tests when subset instance is unavailable
• Translate api enrichment UI
• Support reference-only spatial widgets
• Restore map suggestions for coordinate fields
• Correct silver.yml ground-truth annotations for afrique dataset
• Broaden pre-commit large-file exclusion to cover ml/models/*.joblib
• Raise ML confidence threshold to 0.6 to prevent false positives
• Clean up stale paths and packaging after ml/ centralization
• Restore ml autoresearch and packaging entrypoints
• Skip pre-commit hooks in autoresearch runner commits
• Replace codex with claude cli in surrogate runner
• Defer stack validation in surrogate runner, add scope filter
• Harden surrogate autoresearch prompt
• Defer stack baseline in surrogate runner
• Address gpt-5.4 review — ship models, fix hierarchy ID, anonymous inference, coordinates
• Address codex review — align identifier namespace, geometry affordances, drop rapidfuzz
• Address P1 review findings — remove dead code and unsafe deserialization
• Add monaco-editor types as dev dependency
• Remove obsolete deploy CLI tests and fix SyntaxWarning
• Comprehensive i18n audit — replace all French fallbacks with English, fix namespace issues and add missing translation keys
• Add fixed seed to ML detector tests for cross-version reproducibility
• Remove duplicate legacy preview route that shadowed templates router
• Address PR #54 review comments (CI, build scripts, docs)
• Datetime serialization in job store and obsolete preview mount test
• Prevent duplicate toasts and wrong group name on transform completion
• Supprimer read_only=True des connexions DuckDB API
• Codex review #3 — conditional polling, strict types, i18n timeAgo
• Corrections revue Codex #2 — sécurité, i18n, robustesse
• Extraire les chaînes FR hardcodées vers i18n (sources + publish)
• Corrections revue Codex — filtrage job_type, progression monotone, polling reprise
• Résoudre le montage preview et les chemins relatifs export
• Resolve full export pipeline for taxons, plots, and shapes
• Ajouter skipif pour les tests dépendant des instances locales
• Corriger la génération de config des suggestions et les tests cassés
• Add html.escape() to all widget error messages and data interpolations
• Add padding to info_grid widget container
• Refresh button now bypasses browser cache and shows shimmer
• Categorical_distribution type coercion for YAML string categories
• Rewrite _render_entity_map and pass is_map=True to Plotly
• Series_extractor bar_plot field name mismatch and missing param forwarding
• Stabilize widget previews and shape scalar gauges
• Correct widget previews for entity and class_object sources
• Add minimal Tailwind classes and CSS chevron for navigation preview
• Remove CDN dependencies (Tailwind, Font Awesome) from previews
• Force iframe preview refresh after widget reorder
• Fix drag & drop snap-back and refresh layout after reorder
• Make request optional in preview_template for direct call from layout.py
• Exclude FastAPI-injected request parameter from signature test
• Fix TypeScript errors and preview refresh
• Finalize analysis transformer output and formatting
• Stabilize config scaffolding and import config access
• Formatting and remaining test updates for v1 config contract
• Handle inline content_markdown in static pages
• Update test assertions and mocks for recent changes
• Ensure gauge widget is proposed for all numeric columns
• Improve relation reference_key detection
• Handle identical values in distribution preview and fix binary counter
• Improve widget suggestions and fix geometry serialization errors
• Use working directory context for Config in GUI API
• Update tests for absolute database path and refine numeric/categorical detection
• Correct PyInstaller settings to prevent numpy and DLL corruption
• Replace Unicode arrows and bullets with ASCII, fix run command description
• Replace all Unicode emojis with cross-platform emoji() function
• Replace Unicode characters with ASCII-only for Windows compatibility
• Replace Unicode characters with ASCII in spec file
• Commit package-lock.json for reproducible builds
• Actually check directory emptiness before blocking init
• Improve init command path handling and error messages
• Restore working directory after init command
• Handle Windows paths in project name extraction
• Correct project path derivation in plugins command
• Remove hard dependency on uv tool
• Flatten Windows zip structure for easier extraction
• Correction de 13 bugs dans les plugins transformers et l'API smart_config
• Preserve large integer ID precision and load group_by dynamically
• Preserve large integer IDs precision in index generation
• Fix pytest collection and test database artifacts
• Update instance initialization to EntityRegistry v2 format
• Improve fallback logic for displaying configuration path or file in ImportDemo component
• Update file count logic to handle edge cases and reorder sections in showcase store
• Resolve CI/CD build issues with GUI dist directory
• Restore .gitkeep file for CI/CD builds
• Update Tropicos API name in enrichment configuration
• Improve API enrichment field translations
• Simplify publish script to handle GUI packaging properly
• Ensure GUI dist directory exists for CI/CD builds
• Resolve CI/CD build issue with GUI dist directory
• Correct caching logic in api_taxonomy_enricher
• Refine entity existence check in PlotImporter
• Update API URL and enhance drag-and-drop functionality in import wizard
• Prevent rendering of empty widgets in WidgetPlugin and RadialGaugeWidget
• Improve zoom level calculation in InteractiveMapWidget
• Update parent linking logic in TaxonomyImporter
• Update drag-and-drop cursor styles and hierarchy level descriptions
• Correct hierarchy level description in PlotHierarchyConfig component
• Standardize field naming in advanced options for import functionality
• Update bar plot widget to handle cases with no meaningful y-axis data
• Add ORDER BY clause to SQL queries in HtmlPageExporter for consistent result ordering
• Correct quotation marks in LICENSE and update Plotly version in pyproject.toml for Scattermap support; enhance README with instructions for managing multiple Niamoto installations
• Fix interactive map widget for all groups
• Enhance info panel rendering by adding support for external data sources and improving value checks
• Improve error handling in page generation and refactor UICN translation function in taxon index template

Refactoring

• Reduce UI dead code
• Prune unused UI code
• Add shell-neutral desktop bridge
• Replace screencast architecture with motion graphics foundation
• Compact desktop UI density
• Overhaul theme system — consolidate to 6 themes, unique fonts, offline fonts, font selector
• Unify collection transform state
• Reorganize sidebar navigation and header
• Stabilize frontend lint architecture
• Enforce frontend architecture boundaries
• Split site config hooks
• Lazy load monaco editors
• Standardize frontend data queries
• Consolidate frontend theme state
• Consolidate enrichment configuration workflow
• Add ARIA region labels to enrichment panel columns
• Replace enrichment config tabs with accordion sections
• Replace enrichment 2-col grid with 3-col ResizablePanelGroup
• Extract enrichment render helpers to separate file
• Extract useEnrichmentState hook from EnrichmentTab
• Polish publish preview copy and layout
• Improve collection layout overview
• Compact source cards with consistent icon-only actions
• Migrate shell components to theme-aware utilities
• Redesign sources dashboard workflow (#64)
• Site module UX revamp — unified view + first-launch experience (#63)
• Merge header and tabs into single compact toolbar
• Move pipeline status from banner to breadcrumb
• Flatten collections sidebar with status dots
• Rename Groups module to Collections in GUI
• Redesign sources workspace
• Simplify publish workflow
• Migrate geospatial I/O to pyogrio
• Remove publish.sh, move scripts to dev/, update docs for CI-based PyPI publish
• Clean up scripts directory, archive obsolete utilities
• Close ui architecture review findings
• Move home route into dashboard feature
• Finalize frontend feature architecture cleanup
• Simplify import flow react architecture
• Streamline reference enrichment flow
• Keep import workflow in context
• Polish import analysis flow
• Simplify import configuration review UX
• Remove misleading data quality dashboard score
• Move plotly-bundles to scripts/build/ and add CSS assets
• Harden and centralize auto-config rules
• Calibrate enriched reference classification
• Extract smart auto-config decision layer
• Centralize offline ML workspace under ml
• Simplify FK heuristic, delegate specific id types to alias registry
• Address P3 review findings
• Address P2 review findings
• Replace old pattern matching with alias registry, remove old MLColumnDetector
• Declarative registries, POST inline, smart entity selection (#55)
• Migrate deployers from services to plugins, add GUI deploy API with health check and unpublish
• Flatten sidebar navigation and remove Labs/Tools sections
• Delegate to TransformerService with shared code path
• Intégrer JobFileStore dans les routers transform et export
• Finalize preview engine — dead code removal, security hardening, ETag optimization
• Consolidate HTML wrappers, remove dead Plotly bundle, fix review findings
• Extract preview_utils and decouple engine from PreviewService
• Migrate hooks to React Query + debounce
• Optimize widget preview system performance
• Migrate npm to pnpm and update build scripts
• Update EntityKind types, config generator and components
• Harden routers, normalize YAML None values, migrate to table resolver
• Rename Index tab to Liste for better UX
• Reorganize components directory structure
• Reorganize routes and consolidate API structure
• Cleanup legacy code and reorganize components
• Separate data loading from transformation logic
• Prepare EntityRegistry v2 migration
• Improve geospatial data handling in GeospatialExtractor
• Unify source configuration structure across documentation and code
• Remove taxon estimation logic from OccurrencesStep and SummaryStep
• Streamline import wizard and remove deprecated components
• Standardize success and error indicators in console output
• Clean up imports and enhance progress tracking
• Simplify value formatting logic in RadialGaugeWidget
• Remove deprecated template compatibility test from IndexGenerator
• Update asset paths and enhance static page layout
• Modernize export system with configurable IndexGeneratorPlugin and reorganize templates │ │ │ │ - Add new IndexGeneratorPlugin for configurable index page generation with filtering, custom display fields, and multiple views │ │ - Update HtmlPageExporter to integrate new plugin with fallback to traditional generation │ │ - Add comprehensive configuration models for index generation (IndexGeneratorConfig, IndexGeneratorDisplayField, etc.) │ │ - Reorganize template structure: move legacy templates to niamoto-legacy/ folder for backward compatibility │ │ - Modernize base templates with Tailwind CSS v4, improved responsive design, and configurable theming │ │ - Update template references to use simplified paths (group_detail.html instead of _layouts/group_detail_with_sidebar.html)
• Improve plugin test reliability by reloading modules and fixing imports
• Consolidate plugin system mocking with contextmanager in tests
• Improve plugin test structure with mock registry helper and better error handling
• Migrate from mapbox to standard plotly map types and remove token requirement
• Optimize hierarchical navigation by loading data from external JS files
• Centralize config models and restructure tests
• Improve error handling, validation, and tests
• Improve plugin architecture with enhanced registry and tests
• Optimize test suite performance and fix environment test

Documentation

• Fix plugin registry docstring
• Refresh agent and GUI documentation
• Update institutional site wording
• Drop golden rule line from CLAUDE.md
• Add site markdown authoring plan
• Add site markdown authoring design
• Add site workbench preview plan
• Add site workbench preview design
• Add native menu shortcuts design
• Add desktop shell workbench trial design
• Add source enrichment reset design
• Add enrichment panel design spec
• Include release retrospective in docs toctree
• Add site builder empty-state implementation plan
• Add collection transform/export auto-config to ROADMAP
• Connect MCP server to local SLM fine-tuning and eval harness in ROADMAP
• Add Niamoto MCP server for AI-agent-driven instance setup to ROADMAP
• Add plugin platform overhaul (marketplace, R support, in-app creator) to ROADMAP
• Add desktop shell evaluation (Tauri vs Electron) to ROADMAP
• Move hosted Niamoto from not-planned to later in ROADMAP
• Add site builder empty-state design
• Link ROADMAP.md from README
• Add not-planned and contribute sections to ROADMAP.md
• Add Now/Soon/Later horizons to ROADMAP.md
• Add GBIF Challenge 2026 milestone to ROADMAP.md
• Add vision and recently shipped to ROADMAP.md
• Scaffold root ROADMAP.md
• Add ROADMAP.md implementation plan
• Add ROADMAP.md design spec
• Refresh README hero screenshots
• Refresh README visuals
• Rewrite contributing guide
• Reorganize and refresh desktop-first documentation (#123)
• Move DESIGN_SYSTEM.md to docs/ for project-wide visibility
• Add DESIGN_SYSTEM.md documenting the visual system
• Add motion graphics brainstorm and implementation plan
• Mark Phase 0+1 checkboxes as complete in demo video plan
• Add enrichment tab ux consolidation design
• Add spatial enrichment v1 design
• Add iNaturalist rich enrichment design
• Add BHL references enrichment design
• Add GN verifier shared design
• Add Catalogue of Life rich enrichment design
• Add demo video production plan
• Add GN-assisted TAXREF rich design
• Add Tropicos rich enrichment design
• Add GBIF rich enrichment implementation plan
• Add GBIF rich enrichment design
• Add desktop update harness design
• Add publish layout redesign spec
• Add sources mission control design
• Add publish ui simplification design
• Add ml model regeneration design
• Refine repository guidance for coding agents
• Rewrite gui documentation in english
• Update CHANGELOG for v0.9.0 release
• Fix CodeRabbit review findings — paths and changelog accuracy
• Reorganize ml detection knowledge base
• Add pertinence audit plan and update autoresearch programmes
• Add standards-based dataset acquisition plan
• Rename NiamotoOfflineScore → GlobalScore, remove CSV mention
• Add info tooltips to dashboard hero stat cards
• Update error patterns with fix status after session improvements
• Add workflow schema and improvement timeline to dashboard
• Add training & evaluation guide — complete workflow documentation
• Update dashboard and experiment doc with V5 results (77.5% concept)
• Rewrite ML detection dashboard with current data and new sections
• Remove archived obsolete documentation
• Translate all ML detection docs to English, rewrite index, fix cross-references
• Archive obsolete files and reorganize documentation structure
• Log retraining, ProductScore 80.04, batch optimization 20x, instance eval
• Log session 2026-03-19 — runner fixes, cross-rank gain, plateau
• Add integration status report, fix restore_paths for untracked files
• Rewrite overview for botanist audience
• Update roadmap with enriched dataset results
• Alléger le plan transform trigger + corrections revue Codex
• Ajouter les plans shapes config et transform trigger + jobs robustes
• Add preview architecture, API reference, and widget thumbnail guide
• Mark all acceptance criteria as validated
• Add architecture docs, v1 release plan and config contract
• Rewrite plugin dev guide with modern Pydantic patterns + update plan
• Add Phase 3.3 user documentation for transform widgets
• Add Phase 3.2 config simplification analysis (6 axes identified)
• Update plan - mark Phase 2.5 layers as completed
• Add comprehensive git tag management commands
• Reorganize and fix Sphinx documentation structure
• Reorganize documentation structure and add ML detection system
• Reorganize documentation structure and improve formatting
• Add API documentation for plugin system

Other

• Cover release lock resolution args
• Use PyPI Codecov CLI
• Snapshot fresh clawpatch review
• Harden clawpatch regression coverage
• Stabilize publication freshness check
• Cover fragmentation metric calculations
• Assert elevation profile calculations
• Isolate nested axis config mutations
• Restore plugin registry fixture state
• Assert pipeline option propagation
• Exercise layout preview delegation
• Make pattern matching checks collectable
• Enforce explicit schema fields
• Assert json api security guards
• Require template endpoint success
• Cover field aggregator registration
• Cover multi-group transform last run
• Cover plugin list registry types
• Cover index generator params groups
• Cover export widgets params groups
• Collect dev preview smoke scripts
• Cover read-only entity listing
• Fail plugin discovery regressions
• Fail stale plugin sample imports
• Preserve base test setup
• Fail on plugin discovery errors
• Tighten geospatial error contracts
• Isolate shape processor fixtures
• Assert import phase order
• Assert raw data error rendering
• Bump duckdb to 1.5.2
• Fix pnpm build approvals
• Avoid compatibility test module collision
• Untrack planning notes from gitignored dirs
• Gitignore skill working dirs (plans, brainstorms, superpowers, ideation)
• Archive internal planning docs and tidy AI-related tracking
• Fix collection block previews (#156)
• Update GitHub Actions to Node 24 (#143)
• Add file consistency pre-commit checks
• Enforce UI lint checks
• Ignore frontend coverage output
• Expand coverage baseline
• Strengthen enrichment regression coverage
• Sync plugin manifest and auto-regenerate via pre-commit
• Refresh release metadata
• Fail loudly instead of auto-committing blocked by branch rules (#130)
• Sync tauri cargo lock version
• Cover site builder readiness regressions
• Refine site readiness regressions
• Use Tailscale GitHub Action to reach Coolify on tailnet (#129)
• Add marketing-sync workflow (triggers niamoto-site redeploy)
• Initial .marketing/plugins.json
• Ignore local worktree and pnpm cache artifacts
• Wire Apple signing secrets into Tauri builds
• Sync release lockfiles
• Sync desktop planning and version metadata
• Remove retired design-system exclusions
• Add English desktop screenshots and dashboard polish
• Bump rustls-webpki to 0.103.12 (RUSTSEC-2026-0098)
• Apply rounded corners for Windows/Linux and macOS HIG padding
• Update lock files for v0.14.7
• Update uv.lock
• Update tauri lockfile version
• Desaturate herbier accent color — subtler stone tone
• Update uv.lock for 0.14.1
• Fix desktop project reload fixture
• Compact enrichment workspace layout
• Update lockfiles for 0.13.2
• Refresh uv.lock
• Drop macOS Intel matrix (macos-13 runner retired)
• Add macOS Intel and Linux arm64 to release builds
• Update tauri lockfile for 0.12.4
• Bump node to 22 for publish and binaries workflows
• Refresh safe dependencies
• Compact widget list items in collection panel
• Darken sidebar across all 10 themes
• Regenerate ml models for sklearn 1.8
• Pin pyinstaller and update desktop packaging
• Realign dependencies and raise minimum python to 3.12
• Replace battle test phases with focused import suites
• Clean unused ui public assets
• Add ablation runner and tune header convergence
• Macro-F1 0.3522 → 0.3527 (+0.05 pts)
• Macro-F1 0.3433 → 0.3522 (+0.89 pts)
• Macro-F1 0.3403 → 0.3433 (+0.30 pts)
• Macro-F1 0.3370 → 0.3403 (+0.33 pts)
• Macro-F1 0.2877 → 0.3068 (+1.91 pts)
• Macro-F1 0.3063 → 0.3257 (+1.9 pts)
• Macro-F1 0.3005 → 0.3063 (+0.6 pts)
• Macro-F1 0.2877 → 0.3005 (+1.3 pts)
• Macro-F1 0.5640 → 0.5641 (+0.01 pts)
• Macro-F1 0.5591 → 0.5640 (+0.49 pts)
• Macro-F1 0.5529 → 0.5591 (+0.62 pts)
• Macro-F1 0.5497 → 0.5529 (+0.32 pts)
• Macro-F1 0.5470 → 0.5497 (+0.27 pts)
• Macro-F1 0.5383 → 0.5470 (+0.87 pts)
• Macro-F1 0.5375 → 0.5383 (+0.08 pts)
• Macro-F1 0.5370 → 0.5375 (+0.05 pts)
• Macro-F1 0.5283 → 0.5370 (+0.87 pts)
• Macro-F1 0.4937 → 0.5283 (+3.46 pts)
• Macro-F1 0.4931 → 0.4937 (+0.06 pts)
• Macro-F1 0.4864 → 0.4931 (+0.67 pts)
• Macro-F1 0.4763 → 0.4864 (+1.01 pts)
• Macro-F1 0.4455 → 0.4763 (+3.08 pts)
• Macro-F1 0.3658 → 0.4455 (+7.97 pts)
• Update uv.lock for 0.8.1
• Sync tauri version to 0.7.5 and add it to bumpversion config
• Replace Rocket icon with Send and Menu with PanelLeft
• Redesign command palette with grouped layout and descriptions
• Upgrade GitHub Actions to Node.js 24 compatible versions
• Add preview engine tests and update layout tests
• Add e2e, data explorer, stats and service tests
• Add Phase 3.1 end-to-end tests for GUI config generation (30 tests)
• Add Phase 1.3 transform config validation tests (56 tests)
• Update npm dependencies to fix security vulnerabilities
• Remove macOS Intel build to save GitHub Actions quota
• Move Claude Code config files to gitignore
• Amélioration de la couverture de tests de 60% à 68%
• Upgrade minimum Python version from 3.10 to 3.11
• Fix test assertions and add auxiliary file cleanup
• Upgrade all dependencies to latest versions
• Remove old pipeline editor and dead import code
• Refactor code structure for improved readability and maintainability
• Update CHANGELOG for version 0.7.0 release
• Update versioning configuration and bump version to 0.7.0
• Update uv.lock to include upload times for package distributions and bump revision to 2
• Update shape import configuration and enhance testing
• Update version to 0.5.6, enhance installation and quickstart documentation, and refine configuration handling in tests. Added templates directory to documentation and improved export configuration assertions in tests.
• Update pyproject.toml for wheel packaging and modify README for asset links
• Update CHANGELOG.md
• Bump niamoto version from 0.4.2 to 0.5.0
• Remove config files and add config folder to gitignore
• Add requests-mock to dev dependencies and bump version to 0.4.2
• Enhance GitHub deployment tests with branch existence checks
• Fix commited mock files

Features

• Streamline import cockpit workflow
• Guide users before import uploads

Bug Fixes

• Preserve uv lock resolution options in releases
• Narrow import status badge variants
• Preserve export cancellation fallback
• Address PR review blockers
• Harden publish and import dashboard flows
• Gate desktop releases on sidecar startup
• Polish dark mode branding and sidebar state
• Tighten import file handling
• Harden import cockpit file matching
• Preserve duckdb resolution cutoff

Other

• Cover release lock resolution args
• Use PyPI Codecov CLI

Features

• Show collection computation progress in sidebar
• Allow custom API export data source
• Streamline collection data outputs
• Refine collection data outputs
• Complete standard profile workflows
• Add standardized export profiles

Performance

• Speed up import auto-configuration

Bug Fixes

• Stabilize desktop API auth client test
• Keep missing DuckDB read-only connections lazy
• Stabilize DuckDB access in GUI previews
• Eliminate pytest warnings
• Stabilize plugin loading and test cleanup
• Resolve high clawpatch findings
• Resolve clawpatch review findings
• Resolve clawpatch high findings
• Resolve clawpatch findings
• Close remaining clawpatch low findings
• Stabilize preview and overlay regressions
• Stabilize collection and index workflows
• Stabilize API route regressions
• Authorize desktop API requests
• Preserve profiler total row count
• Infer legacy top ranking mode
• Resolve spatial preview geometry
• Preserve group index generator fields
• Discover recipe widget schemas
• Align import v2 validation with model
• Validate relationship CSV inputs
• Escape BibTeX export values
• Offload enrichment preview loading
• Bound index suggestion record loads
• Enforce query result limits
• Preserve duplicate transform widgets
• Fail transform jobs for unknown groups
• Count hierarchical representatives from relation
• Preserve registry plugin type
• Translate standard compatibility errors
• Translate enrichment preview errors
• Mark publication stale after site config changes
• Offload smart auto configure
• Analyze spatial shape uploads
• Drop registered import tables
• Scope combined suggestions sources
• Translate enrichment config errors
• Honor configured spatial geometry fields
• Bound csv import uploads
• Hide non-transform job status
• Parse underscored entity map references
• Bound time series presence percentages
• Resolve repository ml models
• Aggregate duplicate class object rows
• Validate outlier export thresholds
• Reload desktop projects through native bridge
• Bound retained import jobs
• Validate stats validation rules
• Bound data explorer query limits
• Expose cli export jobs
• Validate dataset config updates
• Respect cleared preview fields
• Align import v2 schema contract
• Enforce export widget identifiers
• Load all recipe widget plugins
• Cancel export jobs
• Validate canonical transform lists
• Stream site file uploads
• Align index generator group lookup
• Read root transform source configs
• Limit feedback screenshot uploads
• Prefer explicit spatial coordinate columns
• Preserve import status setup errors
• Validate config updates before writing
• Bind transformer package exports
• Securely open exported files
• Write validation rules atomically
• Avoid leaking config file paths
• Validate backup config names
• Parameterize archive preview validation query
• Escape Rich markup in stats output
• Escape Rich markup in plugin listing
• Escape Rich markup in direct CLI errors
• Escape Rich markup in progress output
• Escape Rich markup in CLI output
• Block unsafe outbound test redirects
• Write source transform config atomically
• Use read-only table preview connection
• Open table preview database read-only
• Require auth for credential mutations
• Serialize API export target updates
• Escape formulas in outlier CSV exports
• Validate API export target paths
• Require auth for validation rule updates
• Serialize config scaffolding updates
• Serialize source config updates
• Share transform config write lock
• Serialize transform widget updates
• Avoid orphan recipe transforms
• Serialize collection metadata updates
• Write data content atomically
• Restrict data content writes
• Serve uploaded SVGs as attachments
• Create valid web export targets
• Validate widget dependency scripts
• Open template lookups read-only
• Scope recipe widget deletion
• Require desktop auth for import mutations
• Write bulk import config atomically
• Serialize index generator updates
• Constrain backup restore paths
• Stabilize pipeline history import snapshot
• Write config updates atomically
• Serialize reference config updates
• Quote Darwin Core group queries
• Merge enrichment updates with current data
• Validate Darwin Core query identifiers
• Resolve entity tables before querying
• Restrict derived column formulas
• Restrict custom formula evaluation
• Resolve archived test fixture paths
• Hide absolute export list paths
• Guard widget suggestions without project
• Preserve group index preview footers
• Quote dataset count tables
• Accept uppercase upload extensions
• Hide combined suggestion internals
• Hide backup filesystem paths
• Avoid GUI backup collisions
• Record JSON export metadata duration
• Register plugins with correct arguments
• Preserve benchmark logs
• Escape class object CSV paths
• Bound GBIF request timeouts
• Open entity reads read-only
• Limit BibTeX upload size
• Constrain saved source paths
• Restrict served project files
• Tolerate empty BibTeX fields
• Restrict API test targets
• Constrain site file listing paths
• Validate recipe plugin params
• Preserve static page extensions
• Limit extracted upload archives
• Preserve uploads on failed overwrite
• Preserve API export group settings
• Preserve unresolved widgets on reorder
• Return all recipe source columns
• Ignore invalid WKT in shape distribution
• Preserve deploy validation extras
• Validate dataset config shape
• Count dangling taxonomy orphans
• Paginate valid WKT map features
• Constrain configured source paths
• Escape render widget messages
• Restrict site file content access
• Stream terminal auto config events
• Reject concurrent import all jobs
• Validate current import config schema
• Preserve zero medians in validation stats
• Include max values in validation histograms
• Redact listed import job tracebacks
• Redact import job tracebacks
• Guard debug health error route
• Tolerate invalid WKT in coverage analysis
• Reject duplicate normalized CSV headers
• Preserve layout widget index identity
• Validate plugin compatibility requests
• Include datasets for reference-only recipes
• Reject colliding source uploads
• Limit source upload memory use
• Avoid backup filename collisions
• Preserve upper edge in smart bins
• Keep top ranking suggestion counts positive
• Resolve humboldt collection backing sources
• Filter horizontal bar zeros by value axis
• Handle zero-width contextual gauge ranges
• Render dictionary line plots with multiple y axes
• Constrain exporter output paths
• Sanitize leaflet map rendering
• Use advanced transform chain references
• Default static page context to none
• Escape widget container metadata
• Validate archived shapefile zip extraction
• Resolve archived debug script roots
• Run archived test helper from repo root
• Resolve dev script repository root
• Clean untracked autoresearch directories
• Preserve fusion surrogate cache on rebuild failure
• Handle help sections without index pages
• Validate template config before export update
• Surface geospatial source failures
• Honor geospatial registry id fields
• Copy semantic affordance sets
• Calculate edge density per area unit
• Align class object series by axis
• Round scalar gauge maximums upward
• Handle deployer unpublish network errors
• Reject disjoint relationship samples
• Project vector overlay feature areas
• Honor raster nodata metadata
• Convert table view data before empty check
• Mark uvloop as non-windows dependency
• Ignore invalid summary stat filters
• Convert summary stats data before empty check
• Handle plot import removal
• Resolve query db paths from repo root
• Use configured spatial preview dataset
• Preserve DuckDB mode during selects
• Substitute plain config env vars
• Expand configured database paths
• Tolerate partial UI builds
• Fail plugin manifest on syntax errors
• Validate aggregation SQL identifiers
• Sanitize markdown preview html
• Validate import v2 saves
• Quote entity route identifiers
• Constrain site uploads to files
• Constrain preview source paths
• Require desktop auth for project reload
• Block private URL health checks
• Use typed ecological transformer params
• Preserve nojekyll in GitHub API deploys
• Restrict file browser to project root
• Keep desktop auth token private
• Prevent docs help output deletion
• Avoid export cwd lock deadlock
• Preserve existing zip upload components
• Skip empty product holdouts
• Support validated query templates
• Honor adjacency hierarchy id field
• Validate loader SQL identifiers
• Enforce GUI API path containment
• Escape user values in CLI console output
• Clean MagicMock artifacts between tests
• Preserve unowned root databases in tests
• Export transformer suggestion model
• Match plugin structures by descriptor
• Support empty widget transform tables
• Honor top-level widget source
• Prompt for deployment credentials
• Fail pipeline on transform config errors
• Prevent silent CLI startup failures
• Use dropdown for export data sources
• Improve export labels and warning handling
• Harden generated exports and enrichment configs
• Harden standard profile exports and tooling
• Harden export profile fallbacks
• Render void html tags without children
• Address React Doctor UI findings

Refactoring

• Reduce UI dead code
• Prune unused UI code

Documentation

• Fix plugin registry docstring
• Refresh agent and GUI documentation
• Update institutional site wording
• Drop golden rule line from CLAUDE.md

Other

• Snapshot fresh clawpatch review
• Harden clawpatch regression coverage
• Stabilize publication freshness check
• Cover fragmentation metric calculations
• Assert elevation profile calculations
• Isolate nested axis config mutations
• Restore plugin registry fixture state
• Assert pipeline option propagation
• Exercise layout preview delegation
• Make pattern matching checks collectable
• Enforce explicit schema fields
• Assert json api security guards
• Require template endpoint success
• Cover field aggregator registration
• Cover multi-group transform last run
• Cover plugin list registry types
• Cover index generator params groups
• Cover export widgets params groups
• Collect dev preview smoke scripts
• Cover read-only entity listing
• Fail plugin discovery regressions
• Fail stale plugin sample imports
• Preserve base test setup
• Fail on plugin discovery errors
• Tighten geospatial error contracts
• Isolate shape processor fixtures
• Assert import phase order
• Assert raw data error rendering
• Bump duckdb to 1.5.2
• Fix pnpm build approvals
• Avoid compatibility test module collision
• Untrack planning notes from gitignored dirs
• Gitignore skill working dirs (plans, brainstorms, superpowers, ideation)
• Archive internal planning docs and tidy AI-related tracking

Other

• Fix collection block previews (#156)

Features

• Improve API export auto-configuration

Features

• Support auxiliary source review editing

Bug Fixes

• Address enrichment review feedback
• Improve enrichment previews
• Stabilize enrichment jobs
• Scan full CSV during DuckDB imports
• Allow adding import files incrementally
• Handle missing data preview tables
• Prevent recipe editor crashes
• Stabilize index field editor
• Preserve markdown content on page switch

Other

• Update GitHub Actions to Node 24 (#143)

Features

• Add data source inspection tabs (#142)

Bug Fixes

• Persist desktop route memory natively

Features

• Improve index field selection
• Add workflow history details
• Add workflow history view
• Add list performance diagnostics
• Add workflow commands to palette
• Remember desktop view preferences
• Remember desktop route per project

Performance

• Optimize data explorer table rendering

Bug Fixes

• Prevent collections preview update loops
• Address site editor review feedback

Features

• Improve site builder authoring workflow
• Persist site workbench preview state
• Add native desktop menu shell
• Refine desktop shell and export toggles

Bug Fixes

• Restore export config path hook
• Place preview restore next to delete
• Keep desktop project context in sync
• Soften project switcher hover states
• Preserve static site path for html exports
• Pin codecov cli version
• Harden release staging flow

Documentation

• Add site markdown authoring plan
• Add site markdown authoring design
• Add site workbench preview plan
• Add site workbench preview design
• Add native menu shortcuts design
• Add desktop shell workbench trial design

Other

• Add file consistency pre-commit checks
• Enforce UI lint checks

Features

• Add source enrichment reset mode
• Add enrichment panel workflow

Bug Fixes

• Update rustls webpki lockfile
• Harden export and enrichment jobs
• Split codecov checks by coverage area
• Align vitest config typing
• Address enrichment polling review feedback
• Stabilize frontend coverage tests
• Install pnpm before node cache
• Refine enrichment workflow reliability and UX
• Stage plugin manifest during releases

Documentation

• Add source enrichment reset design
• Add enrichment panel design spec

Other

• Ignore frontend coverage output
• Expand coverage baseline
• Strengthen enrichment regression coverage

Features

• Add script to revert Tauri updater manifest to a previous version

Bug Fixes

• Polish export format wizard
• Stabilize index config preview and actions
• Honor taxon stats relation fields
• Avoid welcome screen flicker on desktop
• Avoid recreating missing desktop project dirs
• Use native macOS traffic light placement
• Stabilize create project button hover
• Remove stale docs toctree entry
• Stabilize table preview pagination
• Harden release artifact publishing

Other

• Sync plugin manifest and auto-regenerate via pre-commit

Bug Fixes

• Restore macos executable permissions
• Harden release automation flows

Documentation

• Include release retrospective in docs toctree

Bug Fixes

• Accept flattened macos release app artifacts

Other

• Refresh release metadata
• Fail loudly instead of auto-committing blocked by branch rules (#130)

Features

• Add AST-based plugin manifest extractor

Bug Fixes

• Resolve frontend lint warnings
• Surface pipeline status failures in publish
• Restrict publish gate to fresh sites
• Fail closed while publish gate resolves
• Gate publish on site configuration
• Restore site setup for unconfigured sites
• Tighten site root detection
• Base site readiness on a real root page
• Keep default web exports empty
• Stop scaffolding a synthetic home page
• Remove default home injection from site config
• Consolidate release automation flow
• Pass updater signing password explicitly
• Pass updater signing key path to macos finalizer
• Resolve downloaded macos app bundle in release finalizer

Documentation

• Add site builder empty-state implementation plan
• Add collection transform/export auto-config to ROADMAP
• Connect MCP server to local SLM fine-tuning and eval harness in ROADMAP
• Add Niamoto MCP server for AI-agent-driven instance setup to ROADMAP
• Add plugin platform overhaul (marketplace, R support, in-app creator) to ROADMAP
• Add desktop shell evaluation (Tauri vs Electron) to ROADMAP
• Move hosted Niamoto from not-planned to later in ROADMAP
• Add site builder empty-state design
• Link ROADMAP.md from README
• Add not-planned and contribute sections to ROADMAP.md
• Add Now/Soon/Later horizons to ROADMAP.md
• Add GBIF Challenge 2026 milestone to ROADMAP.md
• Add vision and recently shipped to ROADMAP.md
• Scaffold root ROADMAP.md
• Add ROADMAP.md implementation plan
• Add ROADMAP.md design spec

Other

• Sync tauri cargo lock version
• Cover site builder readiness regressions
• Refine site readiness regressions
• Use Tailscale GitHub Action to reach Coolify on tailnet (#129)
• Add marketing-sync workflow (triggers niamoto-site redeploy)
• Initial .marketing/plugins.json

Bug Fixes

• Repair the macOS desktop signing and notarization pipeline, including post-build bundle finalization
• Include trained ML models in desktop bundles
• Recheck desktop connectivity on startup before surfacing offline failures

Refactoring

• Add a shell-neutral desktop bridge for desktop renderer integrations

Other

• Wire Apple signing secrets into Tauri builds
• Sync release lockfiles and release helper tooling
• Ignore local worktree and pnpm cache artefacts
• Refresh the local niamoto-release skill to match the tag-driven GitHub release flow

Features

• Redesign the desktop dashboard: horizontal pipeline bar, contextual quick actions, entity stats and recent activity feed

Bug Fixes

• Localize dashboard summary strings and activity type/status labels for non-French locales
• Tone down saturated backgrounds on the pipeline bar and make button subtitles legible on dark variants
• Drop the spurious "primary" highlight on the Import quick action

Other

• Validate /api/pipeline/history limit parameter (clamped to 1–100) and cover the endpoint with regression tests

Bug Fixes

• Allow accented project names in GUI wizard
• Point CLI help output to the new GitHub Pages docs URL
• Exclude internal design system from Sphinx build

Documentation

• Migrate from ReadTheDocs to GitHub Pages
• Refresh README hero screenshots
• Refresh README visuals
• Rewrite contributing guide

Other

• Remove retired design-system exclusions
• Add English desktop screenshots and dashboard polish

Features

• Embed public documentation inside the desktop app
• Refresh app about content with the new docs structure

Bug Fixes

• Harden config suggestions and uv dev workflow
• Avoid duplicate help_content entries in wheel (fixes PyPI 400 upload)

Documentation

• Reorganize and refresh project docs with a desktop-first layout
• Reboot structure for desktop-first refonte
• Add brainstorm and plan for documentation refonte

Refactoring

• Apply code review findings before shipping docs refonte
• Exclude superpowers/ from Sphinx and strip stale absolute paths
• Migrate section content to the desktop-first layout
• Refresh desktop-first README, style guide, and hero assets

Other

• Refresh lockfiles for docs toolchain

Bug Fixes

• Stabilize collection auto-detect and desktop tools

Other

• Bump rustls-webpki to 0.103.12 (RUSTSEC-2026-0098)

Features

• Add landing teaser with Niamoto product mocks (demo-video)
• Add Niamoto marketing site plan with partner assets
• Improve index generator configuration workflow
• Build Remotion product demo
• Wire Intro/Outro scenes and add TransitionLabels (demo-video)
• Add Acts 4-6 — Collections, Site Builder, Publish (demo-video)
• Add UI components, cursor system, and Acts 1-3 (demo-video)
• Bootstrap Remotion demo video project (media)

Bug Fixes

• Resolve site builder lint warning
• Polish demo video interactions
• Refine demo video transitions
• Bind geospatial extractor to runtime config
• Stabilize previews and GitHub Pages deployment

Refactoring

• Replace screencast architecture with motion graphics foundation (demo-video)

Documentation

• Move DESIGN_SYSTEM.md to docs/ for project-wide visibility
• Add DESIGN_SYSTEM.md documenting the visual system (demo-video)
• Add motion graphics brainstorm and implementation plan
• Mark Phase 0+1 checkboxes as complete in demo video plan

Other

• Apply rounded corners for Windows/Linux and macOS HIG padding (icons)
• Update lock files for v0.14.7

Bug Fixes

• Prevent desktop preview request storms

Bug Fixes

• Harden desktop connectivity and updates
• Disable in-app windows updates
• Reduce collections preview load on low-power devices

Bug Fixes

• Preserve collection tab navigation
• Tighten publish readiness flow
• Improve UI rendering smoothness
• Smooth import query refresh states

Bug Fixes

• Improve Linux updater install flow
• Prevent duplicate update toasts
• Repair packaged desktop widgets and feedback

Bug Fixes

• Enable Tauri devtools feature for desktop debug mode

Other

• Update uv.lock

Refactoring

• Compact desktop UI density

Other

• Update Tauri lockfile version

Features

• Unify desktop and app startup loaders
• Add desktop debug mode and feedback fallback

Bug Fixes

• Clarify collection batch progress
• Clear stale widget suggestion caches after import
• Hide sidebar branding in desktop builds

Refactoring

• Overhaul theme system — consolidate to 6 themes, unique fonts, offline fonts, font selector
• Unify collection transform state

Other

• Desaturate herbier accent color — subtler stone tone

Bug Fixes

• Force bash shell for Tauri build on Windows (restores Windows desktop binaries)

Features

• Add multi-source enrichment workflow
• Redesign enrichment workspace
• Expand enrichment provider integrations
• Add Catalogue of Life rich enrichment
• Add shared name verifier for rich enrichers
• Add BHL references enrichment
• Add iNaturalist rich enrichment
• Add spatial enrichment v1
• Add logos for BHL and spatial providers
• Restore collection selector in CollectionPanel toolbar
• Replace collection select with custom dropdown
• Improve collections computation feedback

Performance

• Lazy load collection previews

Bug Fixes

• Resolve TypeScript errors across forms and views
• Ensure site configs include a home page
• Auto fit map previews to data
• Stabilize Tauri dev startup
• Reduce redundant frontend polling
• Harden widget previews and config inference
• Harden Tauri desktop runtime
• Resolve frontend context split regressions
• Harden desktop update and packaging flows
• Improve Windows desktop compatibility
• Disable Windows sidecar console for desktop builds
• Limit entity list to 15 items with max-height cap
• Polish enrichment workspace and preview

Refactoring

• Reorganize sidebar navigation and header
• Stabilize frontend lint architecture
• Enforce frontend architecture boundaries
• Split site config hooks
• Lazy load Monaco editors
• Standardize frontend data queries
• Consolidate frontend theme state
• Consolidate enrichment configuration workflow
• Add ARIA region labels to enrichment panel columns
• Replace enrichment config tabs with accordion sections
• Replace enrichment 2-col grid with 3-col ResizablePanelGroup
• Extract enrichment render helpers to separate file
• Extract useEnrichmentState hook from EnrichmentTab

Documentation

• Add enrichment tab UX consolidation design
• Add spatial enrichment v1 design
• Add iNaturalist rich enrichment design
• Add BHL references enrichment design
• Add GN verifier shared design
• Add Catalogue of Life rich enrichment design
• Add demo video production plan
• Add GN-assisted TAXREF rich design
• Add Tropicos rich enrichment design
• Add GBIF rich enrichment implementation plan
• Add GBIF rich enrichment design

Other

• Fix desktop project reload fixture
• Compact enrichment workspace layout
• Update lockfiles for 0.13.2

Bug Fixes

• Use native Linux titlebar chrome

Features

• Surface enrichment progress on dashboard cards
• Add desktop update test harness

Documentation

• Add desktop update harness design

Other

• Drop macOS Intel matrix (macos-13 runner retired)
• Add macOS Intel and Linux arm64 to release builds
• Refresh uv.lock

Features

• Improve publish workspace and desktop window state
• Refine panel navigation and transitions

Bug Fixes

• Streamline widget detail preview and forms
• Correct language switcher paths in exports
• Harden desktop update relaunch flow

Refactoring

• Polish publish preview copy and layout

Documentation

• Add publish layout redesign spec

Other

• Update Tauri lockfile for 0.12.4

Bug Fixes

• Simplify theme picker cards
• Open preview in browser from desktop
• Stabilize GUI import and publishing workflows

Other

• Bump Node to 22 for publish and binaries workflows

Bug Fixes

• Harden GUI runtime diagnostics

Bug Fixes

• Improve widget and transformer form handling
• Tighten desktop settings behavior
• Recover offline indicator on reconnect
• Align widget previews and layout config
• Hide legends in layout overview miniatures via Plotly relayout
• Improve preview engine resilience and health endpoint
• Improve Tauri startup, updater UX, and collections UI

Refactoring

• Improve collection layout overview
• Compact source cards with consistent icon-only actions

Style

• Compact widget list items in collection panel

Other

• Refresh safe dependencies

Bug Fixes

• Disable automatic RUSTSEC issue creation in dependency audit workflow
• Fix NIAMOTO_PYINSTALLER_MODE env var passing in Tauri CI build
• Allow desktop startup without pre-selected project (welcome mode)
• Add --reset-user-config flag to dev_desktop.sh
• Fix WelcomeScreen button text color

Features

• Add in-app feedback system with Cloudflare Worker proxy
• Add html2canvas-pro screenshot and enriched debug context for feedback
• Add page transition and card entrance animations
• Add 8 new theme presets with extended style categories and fallback logic
• Add Tauri desktop release readiness
• Add collapsible widget list panel
• Merge Sources tab into Blocs as dialog overlay
• Add enriched collections overview with status cards
• Simplify API export UX for non-technical users

Bug Fixes

• Address feedback form reset, cooldown enforcement, screenshot capture, and error sanitization
• Refine macOS desktop header alignment
• Restore dev hot reload workflow
• Wire theme polish review fixes
• Isolate scroll zones and harmonize tab headers
• Move collapse toggle to right, fix scrollbar and scroll issues
• Use i18n for relative time in collections overview
• Resolve tab mismatch, API settings access, and stale i18n keys

Refactoring

• Migrate shell components to theme-aware utilities
• Redesign sources dashboard workflow
• Site module UX revamp with unified view and first-launch experience
• Merge header and tabs into single compact toolbar
• Move pipeline status from banner to breadcrumb
• Flatten collections sidebar with status dots
• Rename Groups module to Collections in GUI

Style

• Darken sidebar across all 10 themes

Features

• Extend pre-import impact checks with data compatibility analysis
• Add iOS and Android icon sets
• Replace logo with new N lettermark design

Performance

• Speed up reference field suggestions

Bug Fixes

• Enforce canonical home page export
• Improve desktop startup recovery
• Add unittest to PyInstaller hidden imports
• Polish publish workflow panels
• Stabilize publish previews and history
• Harden import and widget flows
• Harden import summary navigation
• Stabilize GUI startup context
• Preserve enrichment tab state in onboarding UI
• Make PyInstaller install portable in CI
• Restore binary build packaging

Refactoring

• Redesign sources workspace
• Simplify publish workflow

Documentation

• Add sources mission control design
• Add publish UI simplification design

Features

• Add release automation infrastructure (CI workflows, Trusted Publishers, skill)
• Show live import progress events
• Stream auto-config analysis events
• Classify auxiliary stats sources separately
• Improve semantic relationship detection

Performance

• Streamline transform and export pipelines (parallel execution)
• Add pytest-xdist parallel execution and mark slow benchmarks

Bug Fixes

• Fix auto-configure job polling timeout for CI with xdist
• Fix CI uv venv cached virtualenv handling
• Use correct codecov-action v5 parameter name
• Skip benchmark tests when subset instance is unavailable
• Translate api enrichment UI
• Support reference-only spatial widgets
• Restore map suggestions for coordinate fields

Refactoring

• Migrate geospatial I/O to pyogrio
• Close UI architecture review findings
• Finalize frontend feature architecture cleanup
• Simplify import flow and configuration review UX
• Streamline reference enrichment flow
• Extract smart auto-config decision layer
• Harden and centralize auto-config rules
• Move plotly-bundles to scripts/build/
• Clean up scripts directory, archive obsolete utilities
• Remove publish.sh, move scripts to dev/, update docs for CI-based PyPI publish

Documentation

• Rewrite GUI documentation in English
• Refine repository guidance for coding agents
• Add ML model regeneration design

Other

• Realign dependencies and raise minimum Python to 3.12
• Regenerate ML models for sklearn 1.8
• Pin pyinstaller and update desktop packaging
• Replace battle test phases with focused import suites

Features

• Integrate ML acquisition wave and retraining results
• Replace synthetic anonymous holdout with diversified real columns
• Retrained models on enriched gold set (2525 cols)
• Add niamoto-nc to gold set, fix basal_area merge
• Expand alias registry — 13 new concepts, 76.6% concept (+5.3)
• Multi-dataset eval suite — 418 cols, 7 datasets, 71% concept
• Full instance evaluation with annotations — 57 cols, alias 25% → ML 46% concept
• Retrain all models with cross-rank reciprocity features — ProductScore 79.25 → 80.04 (+0.79)
• Add fusion surrogate autoresearch runner
• Add product-oriented evaluation and surrogate fusion loop
• Complete Phase 3 — profiles, affordances, patterns, anomalies
• Concept taxonomy, enriched data, coarsened training (2231 cols)
• Add gold set builder, training scripts, and CLI metric
• Add alias registry, ml_mode API, and evaluation harness

Bug Fixes

• Correct silver.yml ground-truth annotations for afrique dataset
• Broaden pre-commit large-file exclusion to cover ml/models/*.joblib
• Raise ML confidence threshold to 0.6 to prevent false positives
• Clean up stale paths and packaging after ml/ centralization
• Restore ml autoresearch and packaging entrypoints
• Skip pre-commit hooks in autoresearch runner commits
• Replace codex with claude cli in surrogate runner
• Defer stack validation in surrogate runner, add scope filter
• Harden surrogate autoresearch prompt
• Defer stack baseline in surrogate runner
• Address gpt-5.4 review — ship models, fix hierarchy ID, anonymous inference, coordinates
• Address codex review — align identifier namespace, geometry affordances, drop rapidfuzz
• Address P1 review findings — remove dead code and unsafe deserialization

Refactoring

• Centralize offline ML workspace under ml
• Simplify FK heuristic, delegate specific id types to alias registry
• Address P3 review findings
• Address P2 review findings
• Replace old pattern matching with alias registry, remove old MLColumnDetector

Performance

• Batch fusion features in evaluate.py — ProductScore 14h → 42min
• Batch fusion feature extraction — training 5h → 15min, identical results

Documentation

• Update CHANGELOG for v0.9.0 release
• Fix CodeRabbit review findings — paths and changelog accuracy
• Reorganize ml detection knowledge base
• Add pertinence audit plan and update autoresearch programmes
• Add standards-based dataset acquisition plan
• Rename NiamotoOfflineScore → GlobalScore, remove CSV mention
• Add info tooltips to dashboard hero stat cards
• Update error patterns with fix status after session improvements
• Add workflow schema and improvement timeline to dashboard
• Add training & evaluation guide — complete workflow documentation
• Update dashboard and experiment doc with V5 results (77.5% concept)
• Rewrite ML detection dashboard with current data and new sections
• Remove archived obsolete documentation
• Translate all ML detection docs to English, rewrite index, fix cross-references
• Archive obsolete files and reorganize documentation structure
• Log retraining, ProductScore 80.04, batch optimization 20x, instance eval
• Log session 2026-03-19 — runner fixes, cross-rank gain, plateau
• Add integration status report, fix restore_paths for untracked files
• Rewrite overview for botanist audience
• Update roadmap with enriched dataset results

Chores

• Add ablation runner and tune header convergence
• Update uv.lock for 0.8.1

Other Changes

• Autoresearch(values): macro-F1 0.3522 → 0.3527 (+0.05 pts)
• Autoresearch(values): macro-F1 0.3433 → 0.3522 (+0.89 pts)
• Autoresearch(values): macro-F1 0.3403 → 0.3433 (+0.30 pts)
• Autoresearch(values): macro-F1 0.3370 → 0.3403 (+0.33 pts)
• Autoresearch(values): macro-F1 0.2877 → 0.3068 (+1.91 pts)
• Autoresearch(values): macro-F1 0.3063 → 0.3257 (+1.9 pts)
• Autoresearch(values): macro-F1 0.3005 → 0.3063 (+0.6 pts)
• Autoresearch(values): macro-F1 0.2877 → 0.3005 (+1.3 pts)
• Autoresearch(header): macro-F1 0.5640 → 0.5641 (+0.01 pts)
• Autoresearch(header): macro-F1 0.5591 → 0.5640 (+0.49 pts)
• Autoresearch(header): macro-F1 0.5529 → 0.5591 (+0.62 pts)
• Autoresearch(header): macro-F1 0.5497 → 0.5529 (+0.32 pts)
• Autoresearch(header): macro-F1 0.5470 → 0.5497 (+0.27 pts)
• Autoresearch(header): macro-F1 0.5383 → 0.5470 (+0.87 pts)
• Autoresearch(header): macro-F1 0.5375 → 0.5383 (+0.08 pts)
• Autoresearch(header): macro-F1 0.5370 → 0.5375 (+0.05 pts)
• Autoresearch(header): macro-F1 0.5283 → 0.5370 (+0.87 pts)
• Autoresearch(header): macro-F1 0.4937 → 0.5283 (+3.46 pts)
• Autoresearch(header): macro-F1 0.4931 → 0.4937 (+0.06 pts)
• Autoresearch(header): macro-F1 0.4864 → 0.4931 (+0.67 pts)
• Autoresearch(header): macro-F1 0.4763 → 0.4864 (+1.01 pts)
• Autoresearch(header): macro-F1 0.4455 → 0.4763 (+3.08 pts)
• Autoresearch(header): macro-F1 0.3658 → 0.4455 (+7.97 pts)

Bug Fixes

• Add monaco-editor types as dev dependency

Refactoring

• Declarative registries, POST inline, smart entity selection (#55)

Features

• Add multi-platform deployment from GUI
• Add sidebar layout to Data, Groups and Publish modules
• Add pipeline status hooks, home page and staleness banner
• Simplify navigation, fix multi-lang export and map rendering
• Refactor footer as category-based sections with internal/external links
• Create niamoto-subset instance from niamoto-nc for fast testing
• Centre de notifications connecté aux jobs du pipeline
• Bouton transform dans GroupPanel + checkbox composite dans Build
• Ajouter group_by, endpoints active/last-run et job composite transform→export
• Ajouter JobFileStore + fix os.chdir() thread-unsafe
• Add shimmer loading skeleton with widget-type icons
• Add Plotly bundle splitting (core 1.3MB, maps 2.2MB)
• Migrate all preview components to unified engine and delete legacy queue
• Wire preview engine invalidation and migrate recipes (Phase 4)
• Add usePreviewFrame hook and shared preview components (Phase 3)
• Add unified preview engine (Phase 1)
• Add combined widget analysis previews
• Centralize table resolver and transform config models
• Full offline support for desktop application
• Enrich raster_stats and land_use with layer-select UI hints
• Add geographic layers API and LayerSelectField widget
• Add Phase 2.1 form widgets for transform configuration
• Add KeyValuePairsField and TagsField widgets with auto-detection
• Enrich Pydantic models with UI hints and fix Select.Item bug
• Use native macOS titlebar overlay instead of custom traffic lights
• Add multilingual support and i18n infrastructure
• Add MapRenderer service and fix layout preview issues
• Refactor index config with side panel editor and reusable preview
• Improve site preview navigation and widget suggestions
• Complete i18n migration for all UI components
• Enhance site builder with improved navigation and group preview
• Add x_label and y_label quick edit fields for axis customization
• Implement Option A hybrid layout with improved widget modal
• Add multi-field pattern detection for combined widgets
• Add drag-and-drop widget reordering and layout.order support
• Add specialized parameter editors and preview service
• Add unified widget recipe editor with wizard interface
• Enhance relation detection and support for class_object_field_aggregator
• Add index generator configuration and widget management
• Enhance desktop app with welcome screen, site config UI and layout editor
• Add advanced theme system with typography, shapes, and effects
• Replace bootstrap with intelligent widget suggestion system
• Integrate Tauri for desktop application support

Bug Fixes

• Remove obsolete deploy CLI tests and fix SyntaxWarning
• Comprehensive i18n audit — replace all French fallbacks with English, fix namespace issues and add missing translation keys
• Add fixed seed to ML detector tests for cross-version reproducibility
• Remove duplicate legacy preview route that shadowed templates router
• Address PR #54 review comments (CI, build scripts, docs)
• Datetime serialization in job store and obsolete preview mount test
• Prevent duplicate toasts and wrong group name on transform completion
• Supprimer read_only=True des connexions DuckDB API
• Codex review #3 — conditional polling, strict types, i18n timeAgo
• Corrections revue Codex #2 — sécurité, i18n, robustesse
• Extraire les chaînes FR hardcodées vers i18n (sources + publish)
• Corrections revue Codex — filtrage job_type, progression monotone, polling reprise
• Résoudre le montage preview et les chemins relatifs export
• Resolve full export pipeline for taxons, plots, and shapes
• Ajouter skipif pour les tests dépendant des instances locales
• Corriger la génération de config des suggestions et les tests cassés
• Add html.escape() to all widget error messages and data interpolations
• Add padding to info_grid widget container
• Refresh button now bypasses browser cache and shows shimmer
• Categorical_distribution type coercion for YAML string categories
• Rewrite _render_entity_map and pass is_map=True to Plotly
• Series_extractor bar_plot field name mismatch and missing param forwarding
• Stabilize widget previews and shape scalar gauges
• Correct widget previews for entity and class_object sources
• Add minimal Tailwind classes and CSS chevron for navigation preview
• Remove CDN dependencies (Tailwind, Font Awesome) from previews
• Force iframe preview refresh after widget reorder
• Fix drag & drop snap-back and refresh layout after reorder
• Make request optional in preview_template for direct call from layout.py
• Exclude FastAPI-injected request parameter from signature test
• Fix TypeScript errors and preview refresh
• Finalize analysis transformer output and formatting
• Stabilize config scaffolding and import config access
• Formatting and remaining test updates for v1 config contract
• Handle inline content_markdown in static pages
• Update test assertions and mocks for recent changes
• Ensure gauge widget is proposed for all numeric columns
• Improve relation reference_key detection
• Handle identical values in distribution preview and fix binary counter
• Improve widget suggestions and fix geometry serialization errors
• Use working directory context for Config in GUI API
• Update tests for absolute database path and refine numeric/categorical detection

Updates

• Ci: upgrade GitHub Actions to Node.js 24 compatible versions

Refactoring

• Migrate deployers from services to plugins, add GUI deploy API with health check and unpublish
• Flatten sidebar navigation and remove Labs/Tools sections
• Delegate to TransformerService with shared code path
• Intégrer JobFileStore dans les routers transform et export
• Finalize preview engine — dead code removal, security hardening, ETag optimization
• Consolidate HTML wrappers, remove dead Plotly bundle, fix review findings
• Extract preview_utils and decouple engine from PreviewService
• Migrate hooks to React Query + debounce
• Optimize widget preview system performance
• Migrate npm to pnpm and update build scripts
• Update EntityKind types, config generator and components
• Harden routers, normalize YAML None values, migrate to table resolver
• Rename Index tab to Liste for better UX
• Reorganize components directory structure
• Reorganize routes and consolidate API structure
• Cleanup legacy code and reorganize components
• Separate data loading from transformation logic

Documentation

• Alléger le plan transform trigger + corrections revue Codex
• Ajouter les plans shapes config et transform trigger + jobs robustes
• Add preview architecture, API reference, and widget thumbnail guide
• Mark all acceptance criteria as validated
• Add architecture docs, v1 release plan and config contract
• Rewrite plugin dev guide with modern Pydantic patterns + update plan
• Add Phase 3.3 user documentation for transform widgets
• Add Phase 3.2 config simplification analysis (6 axes identified)
• Update plan - mark Phase 2.5 layers as completed

Tests

• Add preview engine tests and update layout tests
• Add e2e, data explorer, stats and service tests
• Add Phase 3.1 end-to-end tests for GUI config generation (30 tests)
• Add Phase 1.3 transform config validation tests (56 tests)

Style

• Replace Rocket icon with Send and Menu with PanelLeft
• Redesign command palette with grouped layout and descriptions

Chores

• Sync tauri version to 0.7.5 and add it to bumpversion config
• Update npm dependencies to fix security vulnerabilities

Features

• Add PyInstaller support and resource cascade system

Bug Fixes

• Correct PyInstaller settings to prevent numpy and DLL corruption
• Replace Unicode arrows and bullets with ASCII, fix run command description
• Replace all Unicode emojis with cross-platform emoji() function
• Replace Unicode characters with ASCII-only for Windows compatibility
• Replace Unicode characters with ASCII in spec file
• Commit package-lock.json for reproducible builds
• Actually check directory emptiness before blocking init
• Improve init command path handling and error messages
• Restore working directory after init command
• Handle Windows paths in project name extraction
• Correct project path derivation in plugins command
• Remove hard dependency on uv tool
• Flatten Windows zip structure for easier extraction

Performance

• Reduce binary size by 43% through dependency optimization

Documentation

• Add comprehensive git tag management commands

Other Changes

• Ci: remove macOS Intel build to save GitHub Actions quota

Bug Fixes

• Correction de 13 bugs dans les plugins transformers et l'API smart_config
• Preserve large integer ID precision and load group_by dynamically

Updates

• Build: upgrade minimum Python version from 3.10 to 3.11

Tests

• Amélioration de la couverture de tests de 60% à 68%
• Fix test assertions and add auxiliary file cleanup

Chores

• Move Claude Code config files to gitignore

Features

• Remove hardcoded table references in showcase metrics
• Remove hardcoded entity references in data explorer and showcase
• Complete EntityRegistry v2 migration for stats and entities
• Add development tooling with instance context management
• Add intelligent onboarding wizard with auto-configuration
• Add transform-source-select widget with group context
• Migrate 11 transformers to entity-select widget
• Add dynamic entity-select widget and update config templates
• Migrate aggregation transformers to EntityRegistry
• Migrate 3 distribution transformers to EntityRegistry
• Migrate remaining 3 class_objects transformers to EntityRegistry
• Migrate categories_extractor and series_extractor class_objects transformers to EntityRegistry
• Migrate loaders to EntityRegistry and create refactoring tracking system
• Add environment variable substitution and plugin config validation
• Add partners section to TeamSection component with logos and descriptions
• Add PerspectivesSection component and integrate into showcase page fix: update Rich version in StackTechSection fix: include 'perspectives' in showcase store sections
• Implement pipeline management with tabs and shared state
• Add Cloudflare deployment functionality and integrate into the GUI
• Add API demo component and integrate into showcase page
• Add exports structure API endpoint and update UI components for directory visualization
• Add YAML configuration editor and backup functionality
• Update API documentation page and navigation structure
• Add Plotly.js and react-plotly.js for data visualization
• Update GUI documentation and improve language switcher component
• Implement enrichment preview functionality in Data Explorer
• Add package.json to repo for Docker builds
• Enhance showcase components with improved YAML configuration display and updated use case statistics
• Implement interactive showcase pages with real data pipeline integration
• Expose plugin param schemas for dynamic gui config
• Implement unified pipeline editor with ReactFlow
• Improve Transform interface and add pipeline specifications
• Implement hierarchical navigation and transform pipeline interface
• Add SQLite performance optimizations
• Update CLAUDE.md for development guidelines and commands; update permissions in settings.local.json; refine error handling in bar_plot and donut_chart widgets

Bug Fixes

• Preserve large integer IDs precision in index generation
• Fix pytest collection and test database artifacts
• Update instance initialization to EntityRegistry v2 format
• Improve fallback logic for displaying configuration path or file in ImportDemo component
• Update file count logic to handle edge cases and reorder sections in showcase store
• Resolve CI/CD build issues with GUI dist directory
• Restore .gitkeep file for CI/CD builds

Improvements

• Refactor code structure for improved readability and maintainability

Refactoring

• Prepare EntityRegistry v2 migration

Documentation

• Reorganize and fix Sphinx documentation structure
• Reorganize documentation structure and add ML detection system

Chores

• Upgrade all dependencies to latest versions
• Remove old pipeline editor and dead import code

Features

• Enhance ShapeProcessor to support group_id configuration
• Update documentation and configuration for multiple data sources
• Enhance StatsLoader to support dynamic key field lookup

Bug Fixes

• Update Tropicos API name in enrichment configuration
• Improve API enrichment field translations
• Simplify publish script to handle GUI packaging properly
• Ensure GUI dist directory exists for CI/CD builds
• Resolve CI/CD build issue with GUI dist directory
• Correct caching logic in api_taxonomy_enricher

Features

• Enhance API enrichment with chained requests and improve GUI packaging

Features

• Add support for binomial naming in TaxonomyImporter
• Enhance taxonomy name generation logic in TaxonomyImporter

Bug Fixes

• Refine entity existence check in PlotImporter

Chores

• Update CHANGELOG for version 0.7.0 release

Features

• Introduce Tropicos enricher plugin for enhanced taxonomy data enrichment
• Enhance ShapeImporter and StatsLoader for improved feature handling and ID generation
• Introduce comprehensive GUI enhancements and CLI improvements
• Update CLI help message and initialization options
• Enhance interactive map functionality with Mapbox support
• Implement hierarchical shape support and enhancements
• Implement new Shape ID generation format in documentation and code
• Enhance geospatial extraction and interactive map functionality
• Enhance FieldAggregator to support JSON field access
• Add project initialization and metadata enhancements
• Integrate i18n support across components and add language switcher
• Enhance shape import functionality and configuration management
• Introduce faceted spinner and enhance circular progress component
• Enhance import process with progress tracking and new UI components
• Add table fields retrieval and enhance import field handling
• Enhance PlotImporter and import functionality
• Enhance ShapeProcessor to support group_id configuration
• Update documentation and configuration for multiple data sources
• Enhance import functionality with progress tracking and hierarchy configuration
• Implement new import-v2 interface with enhanced functionality
• Introduce taxonomy hierarchy configuration and streamline import process
• Integrate httpx for enhanced API interactions and improve import functionality
• Enhance import wizard and API integration for improved data handling
• Add React-based GUI configuration interface for Niamoto

Bug Fixes

• Update API URL and enhance drag-and-drop functionality in import wizard
• Prevent rendering of empty widgets in WidgetPlugin and RadialGaugeWidget
• Improve zoom level calculation in InteractiveMapWidget
• Update parent linking logic in TaxonomyImporter
• Update drag-and-drop cursor styles and hierarchy level descriptions
• Correct hierarchy level description in PlotHierarchyConfig component
• Standardize field naming in advanced options for import functionality

Refactoring

• Improve geospatial data handling in GeospatialExtractor
• Unify source configuration structure across documentation and code
• Remove taxon estimation logic from OccurrencesStep and SummaryStep
• Streamline import wizard and remove deprecated components

Features

• Enhance ShapeProcessor to support group_id configuration
• Update documentation and configuration for multiple data sources
• Enhance StatsLoader to support dynamic key field lookup

Updates

• Update uv.lock to include upload times for package distributions and bump revision to 2

Features

• Add support for multiple data sources in transformations
• Enhance export command output and improve plot importer functionality
• Enhance console output utilities

Refactoring

• Standardize success and error indicators in console output
• Clean up imports and enhance progress tracking

Chores

• Update shape import configuration and enhance testing

Features

• Implement JSON API exporter and enhance data access utilities

Features

• Update version to 0.5.6, enhance installation and quickstart documentation, and refine configuration handling in tests. Added templates directory to documentation and improved export configuration assertions in tests.

Refactoring

• Simplify value formatting logic in RadialGaugeWidget

Features

• Enhance configuration file handling and directory setup

Features

• Add screenshots to README and enhance data availability checks in widgets

Bug Fixes

• Update bar plot widget to handle cases with no meaningful y-axis data

Updates

• Update CHANGELOG.md

Chores

• Update pyproject.toml for wheel packaging and modify README for asset links

Features

• Enhance Tailwind CSS configuration and implement image gallery features
• Major documentation overhaul and database aggregator plugin

Refactoring

• Remove deprecated template compatibility test from IndexGenerator

Features

• Enhance template handling and CLI options in Niamoto
• Add run and stats commands to Niamoto CLI
• Integrate Tailwind CSS for enhanced styling and remove legacy assets

Refactoring

• Update asset paths and enhance static page layout

Features

• Add bump2version to development dependencies
• Update dependencies and enhance project configuration
• Enhance widget tooltips and JSON parsing capabilities
• Refactor Plotly widgets to utilize shared utility functions for layout and rendering
• Enhance widget styling and structure for modern design
• Enhance InteractiveMapWidget with loading indicator and improved error handling
• Adjust positioning and rotation in ConcentricRingsWidget for improved label visibility
• Update ConcentricRingsWidget to use annotations for segment labels and percentages
• Add stacked area normalized transformation and concentric rings widget
• Enhance data transformation and radial gauge widget functionality
• Add gradient color generation to BarPlotWidget
• Enhance data transformation and bar plot widget functionality
• Enhance InteractiveMapWidget with TopoJSON support and optimize GeoJSON handling
• Enhance HtmlPageExporter with field selection and navigation data extraction

Bug Fixes

• Add ORDER BY clause to SQL queries in HtmlPageExporter for consistent result ordering

Refactoring

• Modernize export system with configurable IndexGeneratorPlugin and reorganize templates │ │ │ │ - Add new IndexGeneratorPlugin for configurable index page generation with filtering, custom display fields, and multiple views │ │ - Update HtmlPageExporter to integrate new plugin with fallback to traditional generation │ │ - Add comprehensive configuration models for index generation (IndexGeneratorConfig, IndexGeneratorDisplayField, etc.) │ │ - Reorganize template structure: move legacy templates to niamoto-legacy/ folder for backward compatibility │ │ - Modernize base templates with Tailwind CSS v4, improved responsive design, and configurable theming │ │ - Update template references to use simplified paths (group_detail.html instead of _layouts/group_detail_with_sidebar.html)

Features

• Add auto-zoom capability and improve empty state handling in map and info grid widgets
• • improve test isolation and prevent config file creation during tests - simplify nested field handling by using existing _get_field_from_table method -improve JSON field handling and use temporary directories for tests
• Enhance taxonomy import to handle family and genus level entries with taxon IDs
• Add PyPI token authentication support and release documentation

Bug Fixes

• Correct quotation marks in LICENSE and update Plotly version in pyproject.toml for Scattermap support; enhance README with instructions for managing multiple Niamoto installations

Refactoring

• Improve plugin test reliability by reloading modules and fixing imports
• Consolidate plugin system mocking with contextmanager in tests

Chores

• Bump niamoto version from 0.4.2 to 0.5.0

Features

• Add plugins command to list and inspect available plugins
• Add auto-color feature to bar plots and enhance hierarchical navigation tests
• Add auto-color generation for bar plots and simplify widget layout template
• Add map attribution toggle and improve progress tracking in HTML export
• Add hierarchical configuration support for plot imports
• Implement configurable top ranking plugin with direct, hierarchical and join modes
• Add hierarchical plot structure with nested set model support
• Improve hierarchical navigation with auto-scroll and enhanced styling
• Implement hierarchical navigation widget with Tailwind CSS styling
• Add PyPI token authentication support and release documentation
• Implement HTML page exporter with configurable widgets
• Remove config files and add config folder to gitignore

Bug Fixes

• Fix interactive map widget for all groups

Refactoring

• Improve plugin test structure with mock registry helper and better error handling
• Migrate from mapbox to standard plotly map types and remove token requirement
• Optimize hierarchical navigation by loading data from external JS files
• Centralize config models and restructure tests
• Improve error handling, validation, and tests

Features

• Major core refactoring, taxonomy implementation, and testing overhaul
• Add support for creating named fields from labels in MultiColumnExtractor
• Add 'nb_species' to plot information and improve value handling in templates and data extraction, redising the shape_index page
• Update links in forests, plots, and trees templates to point to index pages
• Refactor data import process to use ImporterService and improve error handling
• Enhance GitHub deployment with configurable user identity and improved branch handling
• Update page generator and template for improved data handling and localization
• Add index page generation for taxons, plots, and shapes; update navigation links
• Add Endemia logo to footer and index templates
• Enhance node opening functionality with smooth scrolling effect
• Add API taxonomy enricher and enhance plugin documentation

Bug Fixes

• Enhance info panel rendering by adding support for external data sources and improving value checks
• Improve error handling in page generation and refactor UICN translation function in taxon index template

Documentation

• Reorganize documentation structure and improve formatting
• Add API documentation for plugin system

Tests

• Enhance GitHub deployment tests with branch existence checks

Features

• Enhance plugin architecture and add direct reference loader

Bug Fixes

• Fix commited mock files

Refactoring

• Improve plugin architecture with enhanced registry and tests
• Optimize test suite performance and fix environment test

Features

• Add ecological transformer plugins for biodiversity analysis
• Update shape processor and add forest cover layer
• Ci: configure Codecov upload with token and add HTML coverage artifact

Bug Fixes

• Fix test suite to handle exceptions properly in test environment
• Improve third-party plugin loading and configuration handling
• Use unique artifact name to avoid conflict in GitHub Actions
• Remove unused variable simplified_utm
• Create uv-managed virtual environment before installing dependencies

Improvements

• Refactor!: introduce plugin-based architecture

Refactoring

• Reorganize transformer plugins architecture and improve geospatial processing
• Reorganize plugin architecture and improve error handling
• Move source and field into params for consistency
• Improve code organization and naming consistency

Style

• Fix formatting issues and pre-commit config

Chores

• Simplify pre-commit config using hooks file
• Add pre-commit-hooks.yaml for local hooks

Other Changes

• Ci: specify Codecov slug to resolve repository not found error
• Build(ci): run Ruff, Mypy, and Pytest within uv-managed environment

Bug Fixes

• Update generate-requirements hook stage to pre-commit

Refactoring

• Restructure project architecture and testing framework

Features

• Add deployment tools

Bug Fixes

• Add UTF-8 encoding for file operations
• Force UTF-8 encoding for API JSON files
• Force UTF-8 encoding for JavaScript files

Updates

• Update conf.py

Bug Fixes

• Force UTF-8 encoding for config files

Bug Fixes

• Fix niamoto configuration overview

Refactoring

• Update project metadata and version detection

Features

• Ci(docs): add Read the Docs configuration
• Ci(docs): add Read the Docs configuration
• Ci(docs): add Read the Docs configuration

Bug Fixes

• Resolve theme and static directory issues
• Switch to pip for RTD installation
• Correct poetry configuration in RTD yaml
• Update RTD configuration for poetry and Python 3.11

Other Changes

• Remove old files

Performance

• Optimize geometry storage with TopoJSON conversion

Documentation

• Update README with new Niamoto CLI commands

Improvements

• feat(cli): overhaul commands, integrate configs, and improve help output

Bug Fixes

• Resolve Windows encoding issues in CLI output

Updates

• Update python versio requirements

Documentation

• Update CLI documentation with new command structure

Features

• Move all js dependencies locally for offline static pages

Refactoring

• Adopt multi-file config, update templates, reorganize CLI, and switch from DuckDB to SQLite

Bug Fixes

• Improve resources page layout and code readability
• Update resources.html -- fix description

Updates

• Update forests.html -- typos
• Update plots.html -- typos
• Update index.html -- Upcase acronyms
• Update methodology.html -- typos
• Update index.html -- Typos

Chores

• Resolve merge conflicts

Features

• Standardize widgets across all view types
• Updated navigation links in _nav.html and index.html, faq in methodology.html.html
• Update shape statistics calculations and template
• Add legacy forest statistics support

Bug Fixes

• Improve navigation and data handling
• Fix _nav.html and resources.html

Improvements

• Refactor transform_geometry method to guarantee output is in MultiPolygon format regardless of input geometry type. The method now: - Wraps Polygon geometries within a MultiPolygon to ensure consistency. - Iterates over individual geometries in MultiPolygon inputs, transforming each polygon separately. - Raises a ValueError for unsupported geometry types.

Updates

• Update resources.html
• Update resources.html
• Update resources.html

Refactoring

• Migrate from specific to configuration-based widget system

Bug Fixes

• Improve navigation and data display

Refactoring

• Improve shape rendering and update static pages

Bug Fixes

• Increase HTTP buffer size for large commits

Improvements

• Refactor spatial coordinate extraction and indexing methods to handle WKB, WKT, and POINT string formats

Bug Fixes

• Ensure button container becomes fixed on scroll
• Make "access data" button always visible, reduce menu banner height, enable click on logos on the first page

Features

• Improve chart configurations for Holdridge, Strates and phenology data
• Add unit tests for Config and ImporterService classes

Bug Fixes

• Ensure correct sorting order for horizontal bar charts
• Improve chart displays for top species and substrate distribution
• Change subtitle of static site. Fixes #9

Updates

• • Update dependencies - Applied ruff formatting corrections

Features

• Enhance taxonomy tree with search and instant scroll
• Add extra_data to TaxonRef in API generator
• Add validation and handling for standard fields and ranks in taxonomy import
• Add static pages for tree, plot, and forest presentations

Updates

• Update templates and structure in _base.html, index.html, and methodology.html

Features

• Add functionality for dynamic plot ID extraction and handling
• Enhance map and chart display for shape pages, improve UI/UX
• Optimize ShapeStatsCalculator
• Implement global exception handling and logging
• Calculate elevation distribution and refactor layer processing for shape statistics calculation
• Update configuration and refactor shape import process
• Enhance PlotStatsCalculator to support optional source filtering
• Add dynamic link adjustments and depth variable for static page navigation; Refactor API generation
• Add presentation pages to Niamoto static site, redesign menu and footer
• Revamped configuration system, added plot and shape calculations, static plot page generation, and updated taxon pages.
• Add tests datas to gitignore

Bug Fixes

• Fix deploy-static-content command Update version
• Fix command.py

Improvements

• Enhance CLI with dynamic link adjustments, depth variable, and main command segregation
• Refactored database reset and import commands
• Refactor: Updated all code comments to Google Docstring style for improved readability and consistency. Documentation : Enhanced Sphinx documentation generation for better project understanding.
• Refactor: Overhaul code architecture for dynamic data handling and enhanced modularity

Updates

• Update database system from SQLite to DuckDB
• Update version number in pyproject.toml
• Update readme import_data command signature

Other Changes

• Remove unnecessary JSON parsing in static/js/index.js
• Initial commit
• Initial commit