Cytoscape Web 1.0.7

This release expands Cytoscape Web’s app integration capabilities with the new App API, runtime app registration, improved App Manager behavior, and richer service-app data exchange. The release also polishes core workflows with a more capable NDEx browser, clearer table/search feedback, better visual style and annotation handling, safer table imports, and UI stability fixes for menus, panels, context menus, and node creation.

Cytoscape Web 1.0.6

This release improves NDEx loading safeguards, layout numeric editing, color palette reversal, network deletion navigation, merged/network-updated summaries, and error reporting behavior. It also includes version/documentation updates and groundwork for the upcoming App API.

Cytoscape Web v1.0.5

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Cytoscape Web v1.0.5 Release Notes

Highlights

This release brings a major rework of the subnetwork (hierarchy) viewer, numerous bug fixes for data integrity and UI interactions, bundle size
optimizations, and significant internal codebase improvements.

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New Features & Enhancements

• Subnetwork Viewer Rework: Replaced the show/hide mode with a new visibility toggle approach. The hierarchy viewer and circle packing panel
  now support multi-selection of leaf nodes and search within the subnetwork viewer. Clicking a subnetwork node in circle packing view now zooms
  into that specific subnetwork.
• URL-based Subnetwork Navigation: Subnetwork node selection and active network view tabs are now reflected in the URL, enabling deep linking
  and shareable views.
• Database Snapshot Import/Export: Added workspace loading functionality with database snapshot import/export capabilities, including automatic
  cleanup of existing workspaces before import.
• Flexible Table Data Import: Enhanced the TableDataLoader to support configurable file delimiters.
• Improved Error Messages: More descriptive error messages in the subnetwork panel when query/network fetch fails.
• Cell Mapping Service App: Added the cell mapping service app to the service-apps fixtures.

Bug Fixes

• Fixed subnetwork state not being exported when clicking the root network share button
• Fixed network views being corrupted by double serialization when stored in IndexedDB
• Fixed floating toolbar click events not firing in the network panel
• Fixed circle packing layout not rendering properly after switching networks
• Fixed opaque aspects not being exported properly (including when empty)
• Fixed merged networks not having layout applied properly
• Fixed saving a local network to NDEx not replacing properly in the workspace
• Fixed race condition between processing import query parameters and UI parameters
• Fixed valid URLs being incorrectly classified as invalid
• Fixed table import form crashing on list-of-boolean parsing
• Fixed FilterConfig objects potentially storing Maps in IndexedDB (Safari compatibility)
• Fixed background taps in the network panel not removing selections in HCX networks
• Fixed subnetwork tables not being displayed
• Fixed subnetwork filter being applied when visual styles do not exist yet
• Fixed network panel tabs not activating the network panel when clicked
• Partial fix for the delete network bug (prevent re-loading deleted networks)

Performance

• Bundle size optimizations: Lazy loading for PDF export, image generation, rich text editor, and table import form components
• Tree-shaken lodash imports to reduce bundle size
• Removed render-blocking delay in the loading screen
• Removed cx2js dependency

Dependency Updates

• Upgraded Cytoscape.js to v3.33.1

Developer Notes

• Major codebase reorganization: consolidated external API, database, stores, and hooks modules under a unified data folder
• Refactored CX2 model handling, NDEx client, and network creation methods
• Added extensive unit test coverage for stores (VisualStyleStore, ViewModelStore, UiStateStore, WorkspaceStore), models, hooks, and CX
  converters
• Introduced Playwright skeleton and test infrastructure
• Added data-testid attributes across components for improved testability
• Refactored state management to use functional/immutable patterns (Immer-based)
• Standardized file naming conventions (camelCase for non-type/non-component files)
• Added input validation schemas and external input validation policies
• Improved Immer proxy serialization and error handling in database operations

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v1.0.4

What's Changed

• Fix styling issue in network property editor (CW-583). by @jingjingbic in #457
• Splash Screen by @keiono in #459
• Fixes for Browser Back / Forward Button issues by @keiono in #462
• Cx2 validator checkpoint by @d2fong in #461
• Fixed crash problem when user clicks Data menu by @keiono in #465
• implement ring chart by @yihangx in #464
• New store for viewport state by @keiono in #468
• Fix CW-603 by @yihangx in #471
• Misc table features by @d2fong in #467
• Sif file import by @d2fong in #469
• Decimal delimiters by @d2fong in #470
• Update default visual style to be similar to Cytoscape Desktop by @d2fong in #475
• Set node size locked and arrow color matches edge to false when impor… by @d2fong in #476
• Fix search by @d2fong in #474
• Sif orphan nodes by @d2fong in #477
• fix CW-600 by @yihangx in #473
• 1.0.4 fit rework by @d2fong in #485
• Remove console.log statements polluting dev/prod. Instead centralize logging in a debug toggle/filterable system
• Rework routing architecture
• Simplify bootstrap code for loading workspaces on app initialization
• Fix issues related to serializing cytoscape web models to IndexedDB in Safari
• Fix issues related to fitting networks to screen on initial load
• Fix issues where HCX networks would not display edges when all filters were toggled off
• Fix issues where HCX networks would not save positions
• Fix issue where the circle packing layout would crash

Full Changelog: v1.0.3...v1.0.4

v1.0.3

What's Changed

• Fix for Hiview's UI Blocking Problem by @keiono in #434
• New URL parameter for the selected network view by @keiono in #435
• Hotfix for issue where the table browser would block the UI by @d2fong in #436
• Undo by @d2fong in #433
• Hiview selection and sharing bugs by @keiono in #437
• Fixed missing selection issue when copy & paste URL by @keiono in #439
• Improved network file drag & drop and bug fixes by @keiono in #443
• add the latest citation and make it clickable by @yihangx in #446
• Import export graphics by @d2fong in #444
• Fix issue where multiple files could be uploaded in the file upload modal by @d2fong in #445
• custom graphics bugs by @d2fong in #447
• reverse pie order by @yihangx in #448
• Fix issue where special properties like name, description etc were displayed twice when importing cx2 files by @d2fong in #449
• fix pie chart default start angle set it to 0 by @yihangx in #450
• Fix CW-573. Updates the URL of developer tutorial. by @jingjingbic in #453
• Reorganized right-panel to correctly expand contents for wide displays by @keiono in #454
• Fix CW-571. Updated citation text and refactor the code of citation window. by @jingjingbic in #456
• Adjust the style of network property editor to always show the confirm/cancel button (CW-583) by @jingjingbic in #458

Full Changelog: v1.0.2...v1.0.3

v1.0.2

This is a bug fix release for the NAR paper.

What's Changed

• Fix issue where annotations may not be rendered by @d2fong in #426
• Anchor 'cancel' and 'confirm' in Export Network Dialog by @GAOChengzhan in #429
• Fix issue where users could input floats into integer columns by @d2fong in #428
• Import network description/properties from URL-fetched CX2 by @chrtannus in #430
• Layout rename by @keiono in #432

New Contributors

• @chrtannus made their first contribution in #430

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

This release includes the following fixes:

• Minor improvements on 'Saving Workspace' by @GAOChengzhan in #414
• Add Visibility 'LOCAL' and 'Imported Time' for local networks by @GAOChengzhan in #415
• Clear messages if the url is redirected to another workspace by @GAOChengzhan in #416
• Partial fix for CW-513 by @d2fong in #417
• CW-516 Fixed timing issue after loading workspace. by @keiono in #420
• Fix CW-515 by @yihangx in #419
• Show last commit time and build time by @GAOChengzhan in #424
• Debug save local networks to workspace by @GAOChengzhan in #421
• Clear urlNetIdRef after use by @GAOChengzhan in #423
• UI tweak on Merge Network Dialog by @GAOChengzhan in #425
• Tooltip for duplicated App Menu Items by @GAOChengzhan in #427

Full Changelog: v1.0.0...v1.0.1

v1.0.0

Release Note

This is the first release of Cytoscape Web. Reference build can be accessed from: https://web.cytoscape.org/