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PySCeS changes (per GitHub release)

PySCeS release 1.2.1 (May 2024)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.2.1. This is a bugfix release.

Fixes

  • Fixed a bug in model evaluation where a model has events and assignment rules, and the assignment rule contains a variable name and a parameter with the variable a substring match of the parameter (e.g. E1 and E1tot). Previously, this led to garbage code during string replacements.
  • Cleaned up various error messages.

PySCeS release 1.2.0 (Feb 2024)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.2.0. This is the first release in the 1.2 series and contains some new features and various bug fixes.

New features

There have been major changes in the build system for PySCeS. This release implements meson-python, a PEP 517 compliant Python build backend that is suitable for building C and Fortran extension modules by implementing the meson build system. There is no more setup.py and project build options and metadata are now in pyproject.toml.

The main motivation for this has been support for Python 3.12, which deprecated the use of distutils, and consequently numpy dropped numpy.distutils. The previous build system had relied on numpy.distutils for building Fortran extension modules, which would no longer work on Python 3.12. In the mean time, scipy, numpy, as well as a number of other packages in the scientific Python ecosystem have moved their build systems to meson-python. This version thus brings PySCeS in line with the other packages.

In addition, binary wheels for macOS on Apple silicon (arm64) are provided for the first time (Python 3.11 and 3.12).

What has changed?

  • From a regular user perspective, not much. Installation is still via pip or conda.

  • From a developer perspective: there is no longer a setup.py. Metadata has been migrated to pyproject.toml. Build settings are spread between pyproject.toml and various meson.build files. The build is straightforward using one of:

    $ pip wheel -w dist .
$ python -m build .

    as long as the relevant compiler toolchain is installed (gcc and gfortran on Linux and macOS, RTools on Windows). Installation can be done with

    $ pip install .
         or
$ pip install --no-build-isolation -e .          (for an editable install)

    Refer to INSTALL.md.

  • Numpy version >=1.26 is required for the build, as older versions of f2py (which is distributed with numpy) are not compatible. At runtime, any numpy version > =1.23 is supported, older versions don't work due to ABI incompatibility.

  • Binaries (wheels) are distributed for Python versions 3.9-3.12. Python 3.8 support is dropped as the latest numpy and scipy versions also no longer support it.

  • Documentation has been updated to reflect these changes.

Bug fixes

  • Fixed a bug with assignment rule evaluation when one species was an exact substring of another species.
  • Use vectorised functions numpy.log, numpy.log10, numpy.exp instead of their math.* counterparts to support their application to arrays in e.g. assignment rules.
  • Removed a bunch of deprecated scipy.* functions that have moved to the numpy.* namespace.
  • Cleaned up unused imports.

PySCeS release 1.1.1 (Jul 2023)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.1.1. This is the first release in the 1.1 series and contains some new features and various bug fixes.

New features

  • When used in a notebook environment, the ipympl backend for matplotlib is now enabled if installed. This allows use in JupyterLab (as opposed to classic notebook). If ipympl is not installed, fallback is to the standard nbAgg, which is part of matplotlib.
  • Simulation results (mod.sim object) can now be returned as a pandas DataFrame if pandas is installed, otherwise a numpy recarray is returned as before. This option is configurable with custom_datatype = pandas in the user and system configuration files ( see https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#configuration), and can be enabled or disabled per session or per model: 
    pysces.enablePandas()
pysces.enablePandas(False)
mod.enableDataPandas()
mod.enableDataPandas(False)

Bug fixes

  • Fixed a bug in simulations with RateRules using Assimulo, where a wrong solver variable was being assigned internally.
  • Fixed SBML export when assignment rules were evaluating reaction rates.
  • Enabled assignment rules (forcing functions) to track parameter changes when using CVODE. This is needed in case events change parameters during the course of the simulation.

PySCeS release 1.1.0 (Apr 2023)

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.

PySCeS release 1.0.3 (Sep 2022)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.0.3. This is the third release in the 1.0 series.

What's new?

  • The build-system has been adapted to make use of scikit-build. This gets rid of the distutils and numpy.distutils dependencies, which are deprecated and will be removed with the release of Python 3.12.

Bug Fixes:

  • Fixed CVODE defaults and set default tolerances to more sane levels
  • Fixed string replacement in parsing and construction of PieceWise functions

PySCeS release 1.0.2 (May 2022)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.0.2. This is the second bug-fix release in the 1.0 series.

Fixes:

  • Fixed a number of bugs with RateRule execution with CVODE
  • Reintroduced the functionality to track additional items such as Assignment Rules during a simulation with CVODE
  • The Assimulo CVODE implementation has been updated, and legacy PySUNDIALS CVODE code removed
  • The RateRule and AssignmentRule implementations have been checked against the SBML Test Suite

PySCeS release 1.0.1 (Feb 2022)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.0.1. This is the first bug-fix release in the 1.0 series.

Fixes:

  • Fixed references to numpy/scipy
  • Fixed a bug in mod.Simulate(userinit=1) with CVODE
  • Fixed bug where the maximal number of steps in LSODA would not be honoured from the mod.__settings__["lsoda_mxstep"] dictionary entry
  • General cleanup of license files, version files, and the way requirements are handled

PySCeS release 1.0.0 (Sep 2021)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (https://pysces.github.io/) version 1.0.0.

What's new in this release:

  • Re-introduced support for CVODE as integrator under Python 3 (via Assimulo), which brings back support of events in models
  • Improved import and export of SBML
  • Automatic installation of optional dependencies with pip install "pysces [optional_dep]"
  • Extensive update of documentation
  • Numerous bug fixes

PySCeS release 0.9.8 (May 2020)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (http://pysces.sourceforge.net) version 0.9.8

What's new in this release:

  • The main change from a user perspective is that the default model directory and output directory on Windows have moved to %USERPROFILE%\Pysces and subfolders (e.g. C:\Users\<username>\Pysces). These folders are created by default on a fresh install. The previous default location was C:\Pysces. This change brings the Windows version in line with the Linux and macOS versions, and moreover allows multiple users to maintain their individual PySCeS configurations and model files on the same Windows machine.

  • If you are upgrading from a previous version: For backward compatibility, the original location is searched first, and used if found upon startup, so that existing installations should continue to function as previously.

  • Users wishing to migrate the PySCeS directory to the new location without losing any work should move the folder C:\Pysces to C:\Users\<username>\Pysces, and then edit the model_dir and output_dir keys in the configuration file C:\Users\<username>\Pysces\.pys_usercfg.ini to reflect the new paths.

  • Numerous bug fixes relating to Python 3 compatibility.

  • Other bug fixes.

PySCeS has its own project on the Anaconda cloud: https://anaconda.org/pysces

Install the latest version from the new site (Python 3.6 - 3.8) using:

conda install -c sbmlteam -c pysces pysces

If you are not using Anaconda, binary wheels are provided on PyPI for Windows, Linux and macOS (Python 3.6 - 3.8), which can be installed using:

pip install pysces

With Python 2 having reached its end of life, binaries for Python 2.7 are no longer provided. However, the PySCeS codebase continues to run under Python 2.7 and can be compiled from source if needed.

PySCeS release 0.9.7 (March 2019)

We are pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (http://pysces.sourceforge.net) version 0.9.7

PySCeS is now available for Python 3, many thanks to @jmrohwer and now has it's own project on the Anaconda cloud: https://anaconda.org/pysces

Install (0.9.7+) from the new site (Python 2.7, 3.6 and 3.7) using:

conda install -c sbmlteam -c pysces pysces

PySCeS release 0.9.6 (April 2018)

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (http://pysces.sourceforge.net) version 0.9.6.

This is mostly a bugfix release that enables SciPy 1.0 compatibility.

PySCeS has been updated to support the PyscesToolkit and is now available via the Anaconda cloud.

PySCeS release 0.9.5 (Aug 2017)

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (http://pysces.sourceforge.net) version 0.9.5.

PySCeS has been updated to support the PyscesToolkit and is now available via the Anaconda cloud.

PySCeS version 0.9.3 (March 2016)

I am pleased to announce the release of the Python Simulator for Cellular Systems: PySCeS (http://pysces.sourceforge.net) version 0.9.3.

This release contains new functionality (response coefficients of moiety conserved cycles), bugfixes (assignment rules) and updates (SED-ML and COMBINE archive export).

PySCeS releases 2004 - 2016

These releases are available for download from SourceForge

© Brett G. Olivier & Johann M. Rohwer, 2004-2024