v2.1.0

Changes

• New feature: added the ability to organize models and workflows within a 'project.'
• New feature: experimental support for exporting a StochSS project to a COMBINE archive.
• New feature: local file persistence is available when building StochSS from source (see the README for more info).
• Updated the GillesPy2 version to 1.5.5.
• New home page for user containers.
• Relicensed StochSS 2 under the GNU General Public License version 3.
• Renamed the 'master' branch to 'main.'
• Workflow result plots now load automatically.
• Redesigned the workflow selection page.
• Models are now saved when creating a new workflow from the model editor.
• Added breadcrumb links to various pages to allow easier navigation when using projects.
• Model attributes and simulation settings can now be viewed while a workflow is in the 'running' state.
• Added more checks for invalid characters when naming and uploading files.
• Added a google form to gather feedback from users.
• Added a link to the StochSS Gitter community.

Bug Fixes

• Fixed a bug that prevented parameter sweep bugs from being duplicated correctly.
• Fixed a bug that was preventing model inference notebooks for being created when the referenced model was in the root directory of the user's files.
• Fixed a bug that was causing model rules to generate incorrectly when creating a jupyter notebook workflow from a model.
• Fixed a bug that was preventing proper error propagation from GillesPy2.
• Fixed a bug where parameters could be deleted even if they were in use by a model event.
• Fixed a bug that was causing annotations to not load correctly for parameters and events.
• Fixed a bug where downloading the standard deviation plot for an ensemble simulation workflow would return the wrong plot.

v2.0.1

Changes

• New feature: model exploration notebook using the sciope library
• Implemented unit tests and continuous integration with GitHub Actions.
• Updated parameter sweep workflows to use the more efficient Variable SSA C Solver in GillesPy2.
• Updated documentation pages, including the Quickstart.
• Added a new example model: Lotkavolterra Oscillator.

Bug Fixes

• Assignment rules, rate rules, and function definitions are now constructed correctly in generated jupyter notebooks.
• Errors are now correctly propogated to StochSS when converting an SBML model to a StochSS model.
• Workflow settings and Model settings are now stored separately on the user's filesystem.
• JupyterHub implementation now imposes resource limits on normal users (4G memory, 2 logical CPUs per user), with the ability to add exceptions for power users.
• Reaction details now updates correctly when zero parameters are present in a model.
• Actions button on the File Browser page now updates correctly when new files are automatically selected.
• Copies of files without file extensions are now duplicated correctly.

v2.0

Release of StochSS 2.0 (next-gen) @ https://app.stochss.org