This page describes the build and installation of PyBaMM from the source code, available on GitHub. Note that this is not the recommended approach for most users and should be reserved to people wanting to participate in the development of PyBaMM, or people who really need to use bleeding-edge feature(s) not yet available in the latest released version. If you do not fall in the two previous categories, you would be better off installing PyBaMM using pip or conda.
Lastly, familiarity with the python ecosystem is recommended (pip, virtualenvs). Here is a gentle introduction/refresher: Python Virtual Environments: A Primer.
The following instructions are valid for both GNU/Linux distributions and MacOS. If you are running Windows, consider using the Windows Subsystem for Linux (WSL).
To obtain the PyBaMM source code, clone the GitHub repository
git clone https://github.com/pybamm-team/PyBaMM.git
or download the source archive on the repository’s homepage.
To install PyBaMM, you will need:
Python 3 (PyBaMM supports versions 3.8 and 3.9)
The python headers file for your current python version.
A BLAS library (for instance openblas).
A C compiler (ex: gcc).
A Fortran compiler (ex: gfortran).
On Ubuntu, you can install the above with
sudo apt install python3.X python3.X-dev libopenblas-dev gcc gfortran
Where X is the version sub-number.
On MacOS,
brew install python openblas gcc gfortran
Finally, we recommend using Tox. You can install it with
python3.X -m pip install --user tox
Depending on your operating system, you may or may not have pip installed along python.
If pip is not found, you probably want to install the python3-pip package.
PyBaMM comes with a DAE solver based on the IDA solver provided by the SUNDIALS library. To use this solver, you must make sure that you have the necessary SUNDIALS components installed on your system.
The IDA-based solver is currently unavailable on windows. If you are running windows, you can simply skip this section and jump to Installing PyBaMM.
# in the PyBaMM/ directory
tox -e pybamm-requires
This will download, compile and install the SuiteSparse and SUNDIALS libraries.
Both libraries are installed in ~/.local.
If you are using MacOS, an alternative to the above is to get the required SUNDIALS components from Homebrew:
brew install sundials
Next, clone the pybind11 and casadi-headers repositories:
# in the PyBaMM/ directory
git clone https://github.com/pybind/pybind11.git
That’s it.
If you’d rather do things yourself,
Make sure you have CMake installed
Compile and install SuiteSparse (PyBaMM only requires the KLU component).
Compile and install SUNDIALS.
Clone the pybind11 repository in the PyBaMM/ directory (make sure the directory is named pybind11).
PyBaMM ships with a python script that automates points 2. and 3. You can run it with
python scripts/install_KLU_Sundials.py
You should now have everything ready to build and install PyBaMM successfully.
# in the PyBaMM/ directory
tox -e dev # (GNU/Linux and MacOS)
#
python -m tox -e windows-dev # (Windows)
This creates a virtual environment .tox/dev (or windows-dev) inside the PyBaMM/ directory.
It comes ready with PyBaMM and some useful development tools like flake8 and black.
You can now activate the environment with
source .tox/dev/bin/activate # (GNU/Linux and MacOS)
#
.tox\windows-dev\Scripts\activate.bat # (Windows)
and run the tests to check your installation.
From the PyBaMM/ directory, you can install PyBaMM using python setup.py install or
pip install .
If you intend to contribute to the development of PyBaMM, it is convenient to install in “editable mode”, along with useful tools for development and documentation:
pip install -e .[dev,docs]
You can use Tox to run the unit tests and example notebooks in isolated virtual environments.
The default command
tox -e tests # (GNU/Linux and MacOS)
#
python -m tox -e windows-tests # (Windows)
will run the full test suite (integration and unit tests). This can take several minutes.
It is often sufficient to run the unit tests only. To do so, use
tox -e unit # (GNU/Linux and MacOS) # python -m tox -e windows-unit # (Windows)
You can run unit tests for PyBaMM using
# in the PyBaMM/ directory
python run-tests.py --unit
The above starts a sub-process using the current python interpreter (i.e. using your current python environment) and run the unit tests. This can take a few minutes.
You can also use the test runner to run the doctests:
python run-tests.py --doctest
There is more to the PyBaMM test runner. To see a list of all options, type
python run-tests.py --help
The documentation is built using
tox -e docs
This will build the documentation and serve it locally (thanks to sphinx-autobuild) for preview. The preview will be updated automatically following changes.
tox -e examples: Run the example scripts in examples/scripts.
tox -e flake8: Check for PEP8 compliance.
tox -e doctests: Run doctests.
tox -e coverage: Measure current test coverage.
If you are running Windows, the following tox commands must be prefixed by windows-:
tests
unit
examples
doctests
dev
For example, to run the full test suite on Windows you would type:
python -m tox -e windows-tests