MacOS installation guide
Myokit needs a C compiler, Python, and the Sundials ODE solvers to run. Each step of the installation is discussed separately below.
Installing the dependencies
The following components are required to run Myokit:
The compiler
First, if you haven't already, install Xcode and the Xcode Command Line Tools to obtain a compiler (called Clang). These can be obtained at developer.apple.com (you may need to create an account).
Sundials
Next, you need to install Sundials. This can be done easily via homebrew, but a manual install is also possible.
To use homebrew, first follow the instructions on the website to install it. Next, open a terminal and install Sundials by typing
$ brew install sundials
or, in some versions of homebrew,
$ brew install homebrew-science/sundials
Python
Myokit requires Python 3.8 or newer, including the packages NumPy, lxml, Matplotlib and PyQT (either PyQt6, PySide6, PyQt5, or PySide2).
Most of these packages will automatically be installed when you install Myokit (see below), but the PyQt package may require an additional step.
Python is installed on macs by default, but many users prefer to re-install via some alternative route. If you installed Sundials via homebrew, we recommend you use the homebrew version of Python too.
Help I've got multile Python versions!
If you end up with multiple Python versions on your
machine, spend some time familiarising yourself with the
different ways of loading Python (and its package manager
"pip"). In particular, make sure you know which Python
version is called when you type python
or pip on the command line.
Virtual environments
Myokit has a small set of dependencies, and tries to be
compatible with all recent versions of them. So in general
it is not necessary to run it from within a virtual
environment.
If you do want to use virtual environments, some mac users
have reported problems mixing conda with brew-installed
Sundials, so we recommend using virtualenv
instead (which can also be installed using brew).
Installing Myokit
To install Myokit, run
$ pip install myokit
Or use the longer form of the same command:
$ python -m pip install myokit
To also install a GUI component, use either
$ pip install myokit[pyqt]
or
$ pip install myokit[pyside]
Note: If you get a "zsh: no matches found" error at this point, you may need to escape the brackets, e.g.
$ pip install myokit\[pyqt\]
Once installed, try running a simulation using
$ python -m myokit run example
To run Myokit's IDE, type:
$ python -m myokit ide
To upgrade an existing Myokit installation, use
$ pip install --upgrade myokit
Adding OpenCL support
If you want to use the OpenCL based libraries, look here for instructions.
Uninstall
To uninstall Myokit, use
pip uninstall myokit
Python, Sundials, etc. will need to be uninstalled separately.
Licensing
Please note: GCC, Xcode, Sundials, Python etc. are not part of Myokit, and come with their own user licenses.
Further questions
If you have any questions, please email Michael Clerx (michael@myokit.org) or check out the issues page.