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‎CHANGES.md‎

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# PySCeS changes (per GitHub release)
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## PySCeS release 1.1.0 (Apr 2023)
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We are pleased to announce a new minor release (version 1.1.0) of the Python
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Simulator for Cellular Systems: PySCeS (https://pysces.github.io/). This is the
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first release in the 1.1 series.
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### What's new?
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The most significant new feature in Version 1.1 is a major upgrade in the way
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**PySCeS handles events in simulations**. The definition of events follows the
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framework described in the SBML Level 3 Version 2 specification, thus making the
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event handling SBML-compliant. Specifically, event **persistence** (for events with
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a delay) is now handled correctly, and simultaneous events can be executed
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according to their assigned **priorities**.
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The new **event specification** in the PySCeS input file reads:
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```
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Event: <name>, <trigger>, <optional_kwargs> { <assignments> }
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```
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To achieve this, three new optional keyword arguments have been added as a
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comma-separated list to the event specification. The general syntax for these
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arguments is `<attribute>=<value>`. The keywords are:
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- *delay* (float): specifies a delay between when the trigger is fired (and the
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assignments are evaluated) and the eventual assignment to the model. If this
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keyword is not specified, a value of `0.0` is assumed.
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- *priority* (integer or None): specifies a priority for events that trigger at the
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same simulation time. Events with a higher priority are executed before those
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with a lower priority, while events without a priority (`None`) are executed in
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random positions in the sequence. If this keyword is not specified, a value of
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`None` is assumed.
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- *persistent* (boolean): is only relevant to events with a delay, where the
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situation may occur that the trigger condition no longer holds by the time the
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delay in the simulation has passed. The persistent attribute specifies how to
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deal with this situation: if `True`, the event executes nevertheless; if `False`,
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the event does not execute if the trigger condition is no longer valid. If the
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keyword is not specified, a default of `True` is assumed.
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The following event illustrates the use of a delay of ten time units with a
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non-persistent trigger and a priority of 3:
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```
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Event: event2, geq(_TIME_, 15.0), delay=10.0, persistent=False, priority=3 {
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V3 = V3*vfact2
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}
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```
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The legacy event syntax is still supported.
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### Other changes
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- A new setting has been added to the settings dictionary of the `PysMod` class
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with the following default:
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`mod.__settings__["cvode_access_solver"] = True`
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This specifies if the Assimulo solver object is available from within the
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`PysMod` instance to make low-level changes to the integration algorithm. The
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current default emulates previous behaviour, but the setting can be changed to
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`False`, which facilitates serialization of the `PysMod` class in e.g. parallel
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computations. Previously, the attached Assimulo solver object would prevent
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serialization. Thanks @c-barry
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- Documentation has been updated to reflect the changes to the event syntax.
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- Various bug fixes, including dealing with deprecations for Numpy 1.24.x
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compatibility.
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README: https://github.com/PySCeS/pysces/blob/master/README.md
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DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
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© Brett Olivier and Johann Rohwer, April 2023.
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## PySCeS release 1.0.3 (Sep 2022)
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We are pleased to announce the release of the Python Simulator for Cellular
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Systems: PySCeS (https://pysces.github.io/) version 1.0.3. This is the third
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release in the 1.0 series.
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### What's new?
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- The build-system has been adapted to make use of `scikit-build`. This gets rid of
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the `distutils` and `numpy.distutils` dependencies, which are deprecated and will
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be removed with the release of Python 3.12.
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### Bug Fixes:
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- Fixed CVODE defaults and set default tolerances to more sane levels
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- Fixed string replacement in parsing and construction of `PieceWise` functions
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README: https://github.com/PySCeS/pysces/blob/master/README.md
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DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
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&copy; Brett Olivier and Johann Rohwer, September 2022.
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## PySCeS release 1.0.2 (May 2022)
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We are pleased to announce the release of the Python Simulator for Cellular Systems:
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PySCeS (https://pysces.github.io/) version 1.0.2.
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This is the second bug-fix release in the 1.0 series.
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### Fixes:
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- Fixed a number of bugs with `RateRule` execution with CVODE
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- Reintroduced the functionality to track additional items such as Assignment Rules
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during a simulation with CVODE
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- The Assimulo `CVODE` implementation has been updated, and legacy PySUNDIALS CVODE
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code removed
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- The `RateRule` and `AssignmentRule` implementations have been checked against the
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SBML Test Suite
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README: https://github.com/PySCeS/pysces/blob/master/README.md
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DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
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&copy; Brett Olivier and Johann Rohwer, May 2022.
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## PySCeS release 1.0.1 (Feb 2022)
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We are pleased to announce the release of the Python Simulator for Cellular Systems:
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PySCeS (https://pysces.github.io/) version 1.0.1. This is the first bug-fix release
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in the 1.0 series.
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### Fixes:
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- Fixed references to numpy/scipy
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- Fixed a bug in `mod.Simulate(userinit=1)` with CVODE
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- Fixed bug where the maximal number of steps in LSODA would not be honoured from the
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`mod.__settings__["lsoda_mxstep"]` dictionary entry
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- General cleanup of license files, version files, and the way requirements are handled
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README: https://github.com/PySCeS/pysces/blob/master/README.md
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DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
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&copy; Brett Olivier and Johann Rohwer, February 2022.
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## PySCeS release 1.0.0 (Sep 2021)
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We are pleased to announce the release of the Python Simulator for Cellular
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Systems: PySCeS (https://pysces.github.io/) version 1.0.0.
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**What's new in this release:**
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- Re-introduced support for CVODE as integrator under Python 3 (via Assimulo),
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which brings back support of events in models
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- Improved import and export of SBML
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- Automatic installation of optional dependencies with `pip install "pysces
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[optional_dep]"`
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- Extensive update of documentation
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- Numerous bug fixes
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**README:** https://github.com/PySCeS/pysces/blob/master/README.md
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**DOCUMENTATION:** https://pyscesdocs.readthedocs.io/en/latest/
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&copy; Brett Olivier and Johann Rohwer, September 2021.
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## PySCeS release 0.9.8 (May 2020)
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We are pleased to announce the release of the Python Simulator for Cellular Systems:

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