Installation steps

silx supports most operating systems and different versions of the Python programming language.

This table summarizes the support matrix of silx:

System Python vers. Qt and its bindings
Windows 3.5-3.8 PyQt5.6+, PySide2
MacOS 3.5-3.8 PyQt5.6+, PySide2
Linux 3.5-3.8 PyQt5.3+, PySide2

For the description of silx dependencies, see the Dependencies section.

For all platforms, you can install silx with pip, see Installing with pip.

To install silx in a Virtual Environment, there is short version here-after and a longer description: Installing silx in a virtualenv.

You can also install silx from the source, see Installing from source.

Installing with pip

To install silx (and all its dependencies), run:

pip install silx[full]

To install silx with a minimal set of dependencies, run:

pip install silx

Note

Use pip’s --user option to install locally for the current user.

Note

  • If numpy is not yet installed, you might need to install it first.
  • Replace the pip command with pip3 to install silx or any other library for Python 3.

Dependencies

The mandatory dependencies are:

The GUI widgets depend on the following extra packages:

Tools for reading and writing files depend on the following packages:

  • h5py for HDF5 files
  • fabio for multiple image formats

silx.opencl further depends on OpenCL and the following packages too :

The complete list of dependencies with the minimal version is described in the requirement.txt at the top level of the source package.

Build dependencies

In addition to run-time dependencies, building silx requires a C/C++ compiler, numpy and cython (optional).

On Windows it is recommended to use Python 3.5, because with previous versions of Python, it might be difficult to compile extensions (i.e. binary modules).

This project uses Cython (version > 0.21) to generate C files. Cython is mandatory to build silx from the development branch.

The complete list of dependencies for building the package, including its documentation, is described in the requirement-dev.txt at the top level of the source package.

Linux

Packages are available for a few distributions:

You can also follow one of those installation procedures:

Installing a Debian package

Debian 9 (Stretch) packages are available on http://www.silx.org/pub/debian/ for amd64 computers. To install it, you need to download this file :

http://www.silx.org/pub/debian/silx.list

and copy it into the /etc/apt/sources.list.d folder. Then run apt-get update and apt-get install python-silx

wget http://www.silx.org/pub/debian/silx.list
sudo cp silx.list /etc/apt/sources.list.d
sudo apt-get update
sudo apt-get install python-silx python3-silx silx

The python-silx and python3-silx packages provide the library, while the silx package provides the executable (silx view, silx convert ...).

Note

The packages are built automatically, hence not signed. You have to accept the installation of non-signed packages.

If the packages are not installed, it might be due to the priority list. You can display the priority list using apt-cache policy python-silx. If the Pin-number of silx.org is too low compared to other sources: download http://www.silx.org/pub/debian/silx.pref into /etc/apt/preferences.d and start the update/install procedure again.

Windows

The simplest way of installing silx on Windows is to install it with pip, see Installing with pip:

pip install silx[full]

This assumes you have Python and pip installed and configured. If you don’t, read the following sections.

Alternatively, you can check:

Installing Python

Download and install Python from python.org.

We recommend that you install the 64bit version of Python, which is not the default version suggested on the Python website. The 32bit version has limited memory, and also we don’t provide a binary wheel for it. This means that you would have to install silx from its sources, which requires you to install a C compiler first.

We also encourage you to use Python 3.5 or newer as former versions are no longer officially supported.

Configure Python as explained on docs.python.org to add the python installation directory to your PATH environment variable.

Alternative Scientific Python stacks exists such as WinPython or Anaconda. They all offer most of the scientific packages already installed which makes the installation of dependencies much easier.

Using pip

Configure your PATH environment variable to include the pip installation directory, the same way as described for Python.

The pip installation directory will likely be C:\Python35\Scripts\.

Then you will be able to use all the pip commands listed below in a command prompt.

MacOS

Apple ships Python 2.7 by default on their operating systems. You must install Python 3.5 or newer to install silx.

Then, install silx with pip, see Installing with pip:

pip install silx[full]

This should work without issues, as binary wheels of silx are provided on PyPi.

Virtual Environment

Virtual environments are self-contained directory trees that contain a Python installation for a particular version of Python, plus a number of additional packages. They do not require administrator privileges, nor root access.

To create a virtual environment, decide upon a directory where you want to place it (for example myenv), and run the venv module as a script with the directory path:

python3 -m venv  myenv

This will create the myenv directory if it doesn’t exist, and also create directories inside it containing a copy of the Python interpreter, the standard library, and various supporting files.

Once you’ve created a virtual environment, you may activate it.

On Windows, run:

myenv\\Scripts\\activate.bat

On Unix or MacOS, run:

source myenv/bin/activate

You can install, upgrade, and remove packages using a program called pip within your virtual environment (see Installing with pip).

pip install silx[full]

Installing from source

Building silx from the source requires some Build dependencies which may be installed using:

pip install -r https://github.com/silx-kit/silx/raw/0.8/requirements-dev.txt

Building from source

Source package of silx releases can be downloaded from the pypi project page.

After downloading the silx-x.y.z.tar.gz archive, extract its content:

tar xzvf silx-x.y.z.tar.gz

Alternatively, you can get the latest source code from the master branch of the git repository: https://github.com/silx-kit/silx

You can now build and install silx from its sources:

cd silx-x.y.z
pip uninstall -y silx
pip install . [--user]

Known issues

There are specific issues related to MacOSX. If you get this error:

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1335: ordinal not in range(128)

This is related to the two environment variables LC_ALL and LANG not being defined (or wrongly defined to UTF-8). To set the environment variables, type on the command line:

export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8

Advanced build options

In case you want more control over the build procedure, the build command is:

python setup.py build

There are few advanced options to setup.py build:

  • --no-cython: Prevent Cython (even if installed) from re-generating the C source code. Use the one provided by the development team.
  • --no-openmp: Recompiles the Cython code without OpenMP support (default for MacOSX).
  • --openmp: Recompiles the Cython code with OpenMP support (default for Windows and Linux).

Package the build into a wheel and install it:

python setup.py bdist_wheel
pip install dist/silx*.whl

To build the documentation, using Sphinx:

python setup.py build build_doc

Testing

To run the tests of an installed version of silx, run the following on the python interpreter:

import silx.test
silx.test.run_tests()

To run the test suite of a development version, use the run_tests.py script at the root of the source project.

python ./run_tests.py