PySCeS release 1.1.0

We are pleased to announce a new minor release (version 1.1.0) of the Python
Simulator for Cellular Systems: PySCeS (https://pysces.github.io/). This is the
first release in the 1.1 series.

What's new?

The most significant new feature in Version 1.1 is a major upgrade in the way
PySCeS handles events in simulations. The definition of events follows the
framework described in the SBML Level 3 Version 2 specification, thus making the
event handling SBML-compliant. Specifically, event persistence (for events with
a delay) is now handled correctly, and simultaneous events can be executed
according to their assigned priorities.

The new event specification in the PySCeS input file reads:

Event: <name>, <trigger>, <optional_kwargs> { <assignments> }

To achieve this, three new optional keyword arguments have been added as a
comma-separated list to the event specification. The general syntax for these
arguments is <attribute>=<value>. The keywords are:

• delay (float): specifies a delay between when the trigger is fired (and the
  assignments are evaluated) and the eventual assignment to the model. If this
  keyword is not specified, a value of 0.0 is assumed.
• priority (integer or None): specifies a priority for events that trigger at the
  same simulation time. Events with a higher priority are executed before those
  with a lower priority, while events without a priority (None) are executed in
  random positions in the sequence. If this keyword is not specified, a value of
  None is assumed.
• persistent (boolean): is only relevant to events with a delay, where the
  situation may occur that the trigger condition no longer holds by the time the
  delay in the simulation has passed. The persistent attribute specifies how to
  deal with this situation: if True, the event executes nevertheless; if False,
  the event does not execute if the trigger condition is no longer valid. If the
  keyword is not specified, a default of True is assumed.

The following event illustrates the use of a delay of ten time units with a
non-persistent trigger and a priority of 3:

Event: event2, geq(_TIME_, 15.0), delay=10.0, persistent=False, priority=3 {
V3 = V3*vfact2
}

The legacy event syntax is still supported.

Other changes

• A new setting has been added to the settings dictionary of the PysMod class
  with the following default:
  mod.__settings__["cvode_access_solver"] = True
  This specifies if the Assimulo solver object is available from within the
  PysMod instance to make low-level changes to the integration algorithm. The
  current default emulates previous behaviour, but the setting can be changed to
  False, which facilitates serialization of the PysMod class in e.g. parallel
  computations. Previously, the attached Assimulo solver object would prevent
  serialization. Thanks @c-barry
• Documentation has been updated to reflect the changes to the event syntax.
• Various bug fixes, including dealing with deprecations for Numpy 1.24.x
  compatibility.

README: https://github.com/PySCeS/pysces/blob/main/README.md

DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/

© Brett Olivier and Johann Rohwer, April 2023.