Releases: StochSS/stochss
Releases · StochSS/stochss
v.2.3.1
Changes
- Incorporated new GillesPy2 C++ solvers (ODE and Tau-Leaping) for jobs and notebooks
- Zip archives can now be unzipped from user file system
- Added mass-action message when there are no parameters
Bug Fixes
- Fixed issue where spatial models were not directing to correct page in projects
- Fixed issue with job results storage - now only errors when all writes fail
v2.3
Changes
- New domain property static domain allows user to indicate whether the domain is static or dynamic
- Type description files can now be imported with imported mesh files
- Users can now set metadata for their projects.
- Archive section in the project manager allows workflows to be archived by moving the model to the trash.
- Parameter sweep workflows have a new time series results visualizer.
- Users can now set the timespan settings for workflows when using the new layout.
- New loading page provides some useful info while waiting for files to upload or workflow or projects to update.
- Auto navigation is now setup for workflows and domains when using open links.
- Users are taken back to the home page when notebooks have finished uploading.
- Users are taken back to the previous page after selecting a notebook workflow from the workflow selection page.
- Updated the spatial notebook template.
- The add existing model modal has been re-designed.
- The project manager page has been re-designed.
- The workflow manager page has been re-designed.
- Converting a workflow or job to a notebook can now only be done in the workflow managers results section.
- Save plot to project view function has been removed.
- Parameters are now added manually by a user for parameter sweep workflows.
- Updated the naming for the Standard Deviation + Mean plot type.
- Users can view status logs for StochSS functions
- Updated parameter sweep workflow allows users to sweep through more than 2 parameters and view time series plots.
- Updated the Example SIR Epidemic project
Bug Fixes
- Fixed bug with adding notes to workflows.
- Fixed bug with loading spatial model domains in older models.
- Fixed bug with duplicating workflows when the model couldn't be found
- Fixed bug with event assignments
- Fixed bug with visualization plots when an error was previously displayed.
v2.2.1
Changes
- Added Julia plots
- Spatial Model Enhancements
- Domain Editor Enhancements
- Added spatial notebooks to list of workflows
- Updated NPM
Bug Fixes
- Note button text now reflects the correct status of the container
- The type select list in the advanced section of the domain editor now updates when a type is re-named
- Model preview errors are now shown whenever errors are sent in the response dictionary
- Fixed model preview show/hide bug
- Volume and Advanced sections of the model editor are only displayed for Models
- Models are now uploaded with the proper extension (.mdl)
- 2D parameter sweep heat maps now show the correct axes labels
- Changes to spatial models now update the models section of the Project Manager
- Type ID's are now properly set when loading types from a file
v2.2.0
v2.1.6
Changes
- Added automatic redirection for models opened using open.stochss.org. User will now be redirected to the Model editor with the model when uploading .mdl files, or the jupyter notebook interface when uploading .ipynb files.
- Updated GillesPy2 to version 1.5.7
Bug Fixes
- Fixed issue with running workflows using older .mdl files
- Fixed upload issue with Safari 14
v2.1.5
Changes
- Added Pre-Simulation validation for new drop-down simulations. Page will now scroll to errors when trying to run simulations.
- Removed "Add Existing Workflow"
- Changed all remaining references to "Species" to "Variables"
- Ensemble workflows now default to 100 trajectories
- Parameter Sweep workflows now default to 20 trajectories
- Set Plotly control bar to always visible
- Update tutorial images to match current version
Bug Fixes
- Fixed bug causing notebook downloads to fail
- Fixed bug causing notebook workflow creation to fail
- Fixed grammatical error in default mode modal
v2.1.4
Changes
- Moved Show/Hide Preview button to left side of fixed bottom bar
- Can now view annotations in View Mode for model components
- Changed "Model Settings" to "Timespan"
- Moved "System Volume" to "Advanced"
- Added validation for System Volume and Timespan entries
- Changed bottom bar buttons, now "Preview" along with workflows can be selected from "Simulate"
- Improved layout for varying screen sizes
- Simplified "Events" and "Rules" subheaders
- Redesigned "View Mode" for "Events"
- Added check for pre-existing model names
- Added Preview Options button for model previews
Bug Fixes
- Fixed bug with Hide/Show Preview not switching correctly
- Fixed workflow group bug when adding an existing workflow to a project.
v2.1.3
Changes
- Updated GillesPy2 version to 1.5.6.
- Made it easier to import existing models into a project.
- Added axis titles to the preview plots on the Model Editor.
- Moved Events, Rules, SBML Components sections in the Model Editor to a separate "Advanced" section.
- Retooled the nomenclature of model components to be more accessible to various audiences.
- Added descriptions for each section of the Model Editor.
- Added a fixed menu bar to the Model Editor section.
- Fixed the preview plot in the Model Editor to the bottom of the page.
- Added descriptions for Reaction Types in the Model Editor.
- Added a "View" mode for Model Editor sections.
Bug Fixes
- Model names containing a period now display correctly in the Project Manager.
- Project name properly displays in breadcrumb links in the Model Editor.
v2.1.2
Changes
- Updated the Readme.
- Added a contributing guide.
- Added a code of conduct.
Bug Fixes
- Fixed a bug that was preventing StochSS models from being converted correctly to SBML.
- Fixed bugs related to uploading files.
- Fixed bugs with the file browser.
v2.1.1
Bug Fix
- Fixed bug with redirect to project for uploading using external link