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Installing PySCeS

Binary install packages for all three OSs and recent Python versions are provided. Anaconda packages are available for 64-bit Windows and Linux, as well as macOS x86_64 and Apple Silicon (arm64) architectures. Anaconda users can conveniently install PySCeS with:

$ conda install -c conda-forge -c pysces pysces

Any dependencies will be installed automatically, including the optional dependencies Assimulo, ipyparallel and libSBML.

NOTE: Anaconda packages are only provided for Python versions 3.9-3.11. The reason is that Assimulo has not been ported to Python 3.12 and still depends on numpy.distutils. As soon as this has happened, PySCeS Anaconda packages for 3.12 will be built.

Alternatively, you can use pip to install PySCeS from PyPI. Core dependencies will be installed automatically. Wheels are available for 64-bit Windows and Linux, as well as macOS architectures x86_64 and arm64 (starting from PySCeS version 1.2.0, supporting Python 3.11 and 3.12).

$ pip install pysces

To install the optional dependences:

  • pip install "pysces[parscan]" - for ipyparallel
  • pip install "pysces[sbml]" - for libSBML
  • pip install "pysces[cvode]" - for Assimulo
  • pip install "pysces[all]" - for all of the above

NOTE: Installation of Assimulo via pip may well require C and Fortran compilers to be properly set up on your system, as binary packages are only provided for a very limited number of Python versions and operating systems on PyPI. This is not guaranteed to work! If you require Assimulo, the conda install is by far the easier option as up-to-date binaries are supplied for all OSs and recent Python versions.

For more information on installing and configuring PySCeS please see the PySCeS User Guide

Compilation from source

As an alternative to a binary installation, you can also build your own PySCeS installation from source. This requires Fortran and C compilers.

Windows build

The fastest way to build your own copy of PySCeS is to use Anaconda for installing Python and the required libraries. In addition, the RTools compiler toolchain is required.

  • Download and install Anaconda for Python 3
  • Obtain Git for Windows
  • Obtain the RTools compiler toolchain (version 4.0.0.20220206), either using Chocolatey (choco install rtools -y --version=4.0.0.20220206) or by direct download
    • Install in C:\rtools40 (Chocolatey automatically installs to this path)
    • Add c:\rtools40\ucrt64\bin and c:\rtools40\usr\bin to the system PATH
  • Create a PySCeS environment using conda and activate it:
$ conda create -n pyscesdev -c conda-forge python=3.11 numpy=1.26 scipy \ 
  matplotlib sympy packaging pip wheel ipython python-libsbml \
  assimulo meson meson-python ninja
$ conda activate pyscesdev
  • Clone and enter the PySCeS code repository using git
(pyscesdev)$ git clone https://github.com/PySCeS/pysces.git pysces-src
(pyscesdev)$ cd pysces-src
  • Now you can build and install PySCeS into the pyscesdev environment
(pyscesdev)$ pip install --no-deps --no-build-isolation .

Linux build

All modern Linux distributions ship with gcc and gfortran. In addition, the Python development headers (python-dev or python-devel, depending on your distro) need to be installed.

Clone the source from Github as described above, change into the source directory and run:

$ pip install .

macOS build

The Anaconda build method, described above for Windows, should also work on macOS.

Alternatively, Python 3 may be obtained via Homebrew and the compilers may be installed via Xcode. Clone the source from Github as described above, change into the source directory and run:

$ pip install .

© Johann M. Rohwer & Brett G. Olivier, January 2024