v1.14.2

v1.14.2 - Minor bug fixes

Minor changes

• Fixed a segmentation fault resulting from having a species start with zero concentration. Two simple models were added to the validation process to catch this error.
• Changes to the validation process were made. Previously, 15 trajectories would be generated for each model before testing the differences of NFsim and SSA versus NFsim and ODE. Now only one trajectory would be tested and more would generate upon faliure until a model failed 15 times in a row.

v1.14.1

v1.14.1 - Minor bug fix

Minor changes

• Added a missing "[" when no operations are present

v1.14.0

v1.14.0 - New event output file format

Previous version was incorrectly labeled as 1.2.x where it should have been labeled 1.13.x. To avoid breaking other pipelines that rely on these releases, we avoided re-naming those versions but we are correcting the release numbering for this release and future releases.

Major changes

• We have added a new file format that documents every reaction firing in a JSON file. This new JSON file format can be used with the command line argument -rxnlog and replaces the file format released in the last version. Please see enhancement issue #35 and pull request #36 for more details on the file format. A JSON schema is also in the main folder of the repo here.

Minor changes

• The -connect option added in the previous version had a bug where any model with a Delete BNG operation in it wouldn't function with this option. This is now fixed and -connect should be usable with any BNG model.

While none of these changes should have any backwards compatibility issues, please see this release if you are trying to replicate work done before 2021.

v1.2.2

v1.2.2 from April 2022 - Minor bug fixes

• Removed a debug statement for tagged reactions.
• Trying to run a compartmental model now fails with an appropriate error message
• Hardcoded upper CPU time limit was removed, -maxcputime option is temporarily removed.

v1.2.1

v1.2.1 from Feb 2022 - Minor fix

An accidentally leftover debug statement was removed.

v1.2.0

v1.2.0 from Jan 2022 - Connectivity and time dependent parameter features

• We have added a new built-in function called TFUN that can pull values from a file given a counter observable in a model. See this pull request for more information.
• A new option is added to infer connectivity between reaction rules. This option allows the user to infer "connected" rules before a model is ran and each time a rule fires, only connected rules are checked for updates, instead of every possible rule in the system. This speeds up certain model, see this pull request for more information.

While none of these changes should have any backwards compatibility issues, please see this release if you are trying to replicate work done before 2021.

v1.12.1

v1.12.1 from Aug, 2016 - Final release before new features, release date: 1/12/2022

This is the first GitHub release of NFSim and the final one before major changes.

We will be adding new features next version which might not be compatible with earlier versions. This release will only contain the binaries for each OS and not the source code. The code these binaries correspond to can be found in 058df06.