Installation and advice

See our general advice on using Python and and on installing a good scientific Python environment.

The simplest method (with conda)

The simplest method to install FluidImage is to use conda (installed with miniconda) and the conda-forge channel (activated with the command conda config --add channels conda-forge).

To just install FluidImage, you can run:

conda install fluidimage

Alternativally, you can install FluidImage in a dedicated conda environment with:

conda create -n env_fluidimage fluidimage

If you use an environment, you will need to activate it with conda activate env_fluidimage.

Slightly more complicated: with pip, from the package on PyPI or the repository

FluidImage depends on Python >= 3.6 and on Python packages that are today very simple to install with pip or conda, namely numpy, scipy, matplotlib, h5py, scikit-image, pyfftw and IPython. You should not care about these dependencies because they are going to be installed automatically for you.

PyQt5 is used only for some graphical user interfaces, so you need to install it manually if needed. This can be done with pip install pyqt5 or conda install pyqt.

I would also advice to install Jupyterlab, which interacts nicely with FluidImage.

To compile, or not to compile?

We choose to use the static Python compiler Pythran for some numerical functions. Our microbenchmarks show that the performances are as good as what we are able to get with Fortran or C++!

We don’t upload “wheels” (package with already compiled binaries) on PyPI, so installing with pip can involve local compilation. Some code in FluidImage will be compiled only if Pythran is available during installation. Therefore, to install FluidImage with compilation, you need to install Pythran before FluidImage, which can be done with:

pip install pythran colorlog

Moreover, you need a C++ compiler (we recommend clang). With conda, it’s very easy to install clang with conda install clangdev.

Finally, for better performance, Pythran needs a configuration file with something like (see the Pythran documentation):

complex_hook = True

CXX = clang++
CC = clang

Ready? Let’s install with pip

To install the last version of FluidImage uploaded to the Python Package Index:

pip install fluidimage -U

However, the project is in an active phase of development so it can be better to use the last version (from the mercurial repository hosted on Heptapod). Moreover, like that, you get all examples and tutorials! For FluidImage, we use the revision control software Mercurial and the main repository is hosted in, so you can get the source with the command:

hg clone

If you are new with Mercurial and Heptapod, you can also read this short tutorial.

If you really can’t use Mercurial, you can also just manually download the package from the Heptapod page or from the PyPI page.

To install in development mode (with a virtualenv or with conda):

cd fluidimage
pip install -e .

or (without virtualenv):

pip install -e . --user

After the installation, it is a good practice to run the unit tests by running pytest from the root directory.