v0.7.1

What's Changed

• Bump eventsource from 1.1.0 to 1.1.1 by @dependabot in #349
• Bump terser from 4.8.0 to 4.8.1 by @dependabot in #353
• Bump moment from 2.29.3 to 2.29.4 by @dependabot in #354
• Feature/shorten names by @meganrm in #363

Full Changelog: v0.7.0...v0.7.1

v0.7.0

What's Changed

• Load binary .simularium files
• Bump minimist from 1.2.5 to 1.2.6 by @dependabot in #333
• Bump moment from 2.29.1 to 2.29.2 by @dependabot in #337
• Feature/update drag n drop by @toloudis in #339
• won't show time controls if there is no time range by @meganrm in #343
• fix loading from url, was still assuming pure json format by @toloudis in #345

Full Changelog: v0.6.2...v0.7.0

v0.6.2

✨ New Features

• Added Nature Methods citation 🎉

🐛 Bug Fixes

• Fixed landing page layout

Pull requests included in this release

• fix horizontal scroll by @meganrm in #332
• added citation by @meganrm in #334
• fix issue after merge main by @meganrm in #336

Full Changelog: v0.6.1...v0.6.2

v0.6.1

🐛 Bug Fixes and Improvements

• Fixed a bug that prevented some server error messages from displaying
• Fixed a bug that caused menus from the top nav to go off screen sometimes
• Fixed a bug that kept left and right arrow keys from working inside the input box of the Upload by URL modal
• Left-aligned the current time display so it doesn't move back and forth during trajectory playback
• Updated the visual glossary to reflect updates to the viewer UI and made its layout more user-friendly
• Updated the Simularium overview image on the landing page

🔧 Behind the Scenes

• Updated many dependencies
• Added return types to React components

Pull requests included in this release

• Fix/server error messages not displaying by @schoinh in #303
• Bump follow-redirects from 1.5.10 to 1.14.7 by @dependabot in #301
• Bump node-fetch from 2.6.5 to 2.6.7 by @dependabot in #305
• Update eslint from v5.14.1 to v8.7.0 by @schoinh in #306
• Add return type to React components by @schoinh in #307
• Feature/update visual glossary and landing page image by @schoinh in #313
• Fix/menus go off screen sometimes by @schoinh in #312
• Feature/place visual glossary key next to image on wider screens by @schoinh in #314
• Bump follow-redirects from 1.14.7 to 1.14.8 by @dependabot in #316
• Fix/current time is hard to read when number of decimal places keeps changing by @schoinh in #317
• Bump url-parse from 1.5.3 to 1.5.10 by @dependabot in #325
• Fix/can't use arrow keys in input box of Upload by URL modal by @schoinh in #323
• Feature/update overview figure on landing page by @schoinh in #330

Full Changelog: v0.6.0...v0.6.1

v0.6.0

✨ New Features

Warning messages - Unexpected things can happen when loading a trajectory, but often they are not fatal (does not affect successful loading and playback of a trajectory file). Now, only fatal errors are shown as errors, and all other messages are shown as warnings (example below).

🐛 Bug Fixes and Improvements

• Updated simularium-viewer to from v3.1.0 to v3.3.1 (details)
• Fixed bugs related to old trajectory data or old error messages sticking around when they shouldn't
• Fixed a bug that prevented proper playback of trajectories that do not start time 0 (e.g., Actin in Clathrin-mediated Endocytosis)
• Fixed a bug that prevented stepping back to the first frame of some trajectories (e.g., Membrane Wrapping a Nanoparticle)
• Contents no longer overflow out of the nav bar when a trajectory title is very long

🔧 Behind the Scenes

We have moved Simularium repositories to a new GitHub organization called Simularium. GitHub links in this repo were updated to reflect this change.

Pull requests included in this release

• Update viewer from v3.1.0 to v3.2.2 by @schoinh in #278
• Feature/treat warning messages as warnings by @schoinh in #284
• Fix/old error message comes back after going to landing page by @schoinh in #285
• Fix/previous trajectory persists when new trajectory fails to load by @schoinh in #287
• Fix/can't step back to first frame of some trajectories by @schoinh in #291
• Update GitHub URLs to reflect new Simularium org by @schoinh in #293
• Update viewer to v3.3.1 by @schoinh in #299
• Fix/nav bar overflowing when title is long by @schoinh in #290

Full Changelog: v0.5.1...v0.6.0

v0.5.1

What's Changed

🐛 Bug Fixes and Improvements

• Fixed a bug that prevented the agent list from being displayed in the left panel for some trajectories loaded by drag-and-drop

Pull requests included in this release

• Fix/agent list sometimes not loading for drag-and-drop by @schoinh in #275

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

✨ New Features

• Load custom geometry files - Now you can drag-and-drop geometry files along with a Simularium trajectory file into the Simularium viewer. Alternatively, you can specify geometry files hosted on the web as URLs, or PDBs as IDs or URLs, in the trajectory file.
• User-specified colors for agents - The Simularium viewer now supports user-specified colors for agents and their states.

🐛 Bug Fixes and Improvements

• Updated simularium-viewer from v3.0.0 to v3.1.0, which includes improved performance for PDB rendering in addition to support for the new features above
• Updated the landing page and "Quick start" to reflect recent improvements

Pull requests included in this release

• Feature/list visualization options on landing page by @schoinh in #256
• Feature/load local geometry files by @schoinh in #253
• Fix/spelling for Omar Quintero in acknowledgments by @schoinh in #258
• Feature/update loading and sharing instructions in Quick Start by @schoinh in #257
• Fix/broken styling in agent list by @schoinh in #260
• Fix/file load error handling by @schoinh in #259
• Feature/update viewer by @meganrm in #262
• remove unmodified state by @meganrm in #265
• update viewer by @meganrm in #271
• Feature/auto-expand agent groups with no parent color by @schoinh in #272

Full Changelog: v0.4.0...v0.5.0

v0.4.0

✨ New Features

• A new way to load trajectories by URL - In addition to manually navigating to a URL like https://simularium.allencell.org/viewer?trajUrl=[link to your file], you can now go to "Load model" -> "From a URL" on the top nav and just paste in the URL to your trajectory file. Click "Load" and your simulation will load in the viewer.

  

• Landing page updates - An updated project summary and a new Acknowledgments section

🐛 Bug Fixes and Improvements

• Updated simularium-viewer to from v2.9.7 to v3.0.0, which allows v3 .simularium trajectory files from simulariumio to be loaded into and viewed in the Simularium Viewer without error. Full support for v3 trajectory files is coming in a future release.
• Fixed a bug that caused the time input box in the playback area to be too narrow sometimes

🔧 Behind the Scenes

• Achieved 100% unit test coverage for all Redux selectors
• Finished reorganizing of Redux state

v0.3.0

✨ New Features

New SpringSaLaD and MEDYAN example models - 5 of them!

🐛 Bug Fixes and Improvements

• Fixed a bug that caused the time input (current time) box to be excessively wide for some trajectories
• Fixed bugs that affected the "All" checkbox at the top of the agent list

🔧 Behind the Scenes

We did a lot of overdue cleanup and maintenance for this release:

• Renamed the master branch to main
• Removed old config files and npm dependencies that are no longer used
• Unit test improvements - We migrated all tests from Mocha/Chai to Jest and added many new unit tests, with the goal of 100% unit test coverage for all util functions and Redux selectors.
• Reorganized the Redux state tree to better accommodate new types of state data we have now
• Started using auto-changelog to automatically generate a list of commits every time we release a new version. You can see our changelog at CHANGELOG.md.

v0.2.2

✨ New Features

• Check out our new example models:

  • Membrane Wrapping a Nanoparticle
  • Spatiotemporal oscillations in the E. coli Min system
  • Sequestration of CaMKII in dendritic spines

• New camera controls - Toggle between rotate and pan modes, and toggle the focus mode off and on

  

• Interactive time display - Until now, the time display at the bottom of the Simularium viewer has been read-only. Now, you can click on the current time display to edit it. Hit Enter or Tab, and the simulation will skip to the time you entered.

  

• Now you can use Google Drive links to a trajectory file for a shareable Simularium link, in addition to Dropbox and Amazon S3!

• The Quick Start page is updated with instructions for:

  • Converting trajectory outputs from four additional simulation engines (MCell, Smoldyn, SpringSaLaD, and MEDYAN) to the .simularium format
  • Creating a shareable Simularium link for your trajectory file

🐛 Bug Fixes and Improvements

Updated simularium-viewer to from v2.9.3 to v2.9.7, which includes:

• Fixes for numerous playback and file loading bugs
• Rendering optimizations