Obtaining and installing PyRETIS¶
PyRETIS and its requirements can be installed using pip or using conda as described below. We also describe how PyRETIS can be installed in a virtual environment and how it can be installed directly from the source code using git.
Prerequisites¶
PyRETIS requires Python 3.9 or higher. Please make sure that you have an updated version of Python installed on your system. PyRETIS depends on several other Python packages, however, these should be installed automatically as part of the installation of PyRETIS. A list of the dependencies can be found below.
Installing via pip
¶
The latest version of PyRETIS can be installed using pip with the following command:
python -m pip install git+https://gitlab.com/pyretis/pyretis.git
A direct installation of PyRETIS 2:
python -m pip install pyretis
PyRETIS offers an analysis tool, named PyVisA. Its GUI requires PyQt5 to be executed. To install PyQt5 via pip:
python -m pip install pyqt5
PyVisA also requires mdtraj and this has to be installed after installing PyRETIS:
python -m pip install git+https://github.com/mdtraj/mdtraj.git
Note: Please make sure that you are using a Python environment
of version 3.7 or newer. On some systems, Python 2 may still be the default
version and pip
might actually try to install for Python 2.
In this case, use pip3
in the command above.
Installing via conda
¶
PyRETIS can be installed using conda with the following commands:
conda create --name pyretis
conda activate pyretis
conda install pyretis -c conda-forge (working only with pyretis 2)
PyRETIS offers an analysis tool, named PyVisA. Its GUI requires PyQt5 and mdtraj to be executed. To install PyQt5 and mdtraj via conda:
conda install pyqt -c conda-forge
conda install mdtraj -c conda-forge
Note: Since PyRETIS will only work with Python 3.7 or newer, please make sure that you are using an environment with a recent version of Python.
Optional: Setting up a virtual environment for pip¶
You can also install PyRETIS in a virtual environment. Using a virtual environment makes it easier to maintain different versions of PyRETIS and it’s dependencies. The following steps are needed to set up a virtual environment:
Install the virtualenv package. This can be done using
pip
:[sudo] python -m pip install virtualenv
or using a package manager for your operative system, for instance
apt
if you are using a Debian-like Linux:[sudo] apt-get install virtualenv
Create a folder dedicated to your virtual environments, for instance in your home directory:
mkdir ~/name-of-environment-folder cd ~/name-of-environment-folder
Install the new environment with the desired Python3 interpreter, using the path to the desired Python executable (usually found in
/usr/bin/
), and a name for the virtual environment folder (pyretis-env
):virtualenv -p /usr/bin/python3 ~/name-of-environment-folder/pyretis-env
Note, if you want more control over which version of Python to use, you can use the
-p
option in the command above to specify this. For instance, for version 3.8:virtualenv -p /usr/bin/python3.8 ~/name-of-environment-folder/pyretis-env
Activate the environment:
source ~/name-of-environment-folder/pyretis-env/bin/activate
Install PyRETIS:
python -m pip install git+https://gitlab.com/pyretis/pyretis.git
(Optional) PyVisA’s GUI requisite:
python -m pip install pyqt5
(Optional) PyVisA’s also requisite mdtraj:
python -m pip install git+https://github.com/mdtraj/mdtraj.git
The folder ~/name-of-environment-folder/pyretis-env
now contains a new Python environment
where PyRETIS has been installed. Since you have sourced the
virtual environment, python -m pip
will now refer to the version of pip
installed in the environment and when you install packages, they will be
installed inside the folder ~/name-of-environment-folder/pyretis-env
.
Note: that you will have to source the environment each time you want to make use of it
using the source
command given above.
Optional: Installing from the PyRETIS git repository¶
Previous versions and the latest (possibly unstable) sources can be
obtained using git
:
git clone git@gitlab.com:pyretis/pyretis.git
or,
git clone https://gitlab.com/pyretis/pyretis.git
After cloning the repository, PyRETIS can be
installed via pip
(after navigating to the main source directory):
python -m pip install .
or, alternatively:
python setup.py install
and, to be able to run PyVisA’s GUI, add pyqt5
:
python -m pip install pyqt5
Then, install mdtraj
:
python -m pip install git+https://github.com/mdtraj/mdtraj.git
Optional: Installing a development version from the PyRETIS git repository¶
After cloning the repository as described above, check out the development branch you are interested in, e.g.:
git checkout develop
Then install the development requirements (these are defined in the file
requirements-dev.txt
, note that they include pyqt5, which is not
supported in some environments):
python -m pip install -r requirements-dev.txt
Finally, install PyRETIS using:
python -m pip install -e .
Testing your installation¶
After installing from the PyRETIS source, your installation can be tested by running the tests from the main directory:
python -m unittest discover -v -s test
Requirements for PyRETIS¶
In order to run PyRETIS, several Python libraries are needed, for instance
SciPy, NumPy, and matplotlib
(see also the information on installing the SciPy Stack).
A list of the requirements can be found in the file
requirements.txt
in the source
code directory. These packages can be installed by:
python -m pip install -r requirements.txt
after downloading the requirements.txt
file.
This should be automatically done if you
are installing PyRETIS using pip
/conda
.
Notes: (1) the analysis package PyVisA requires PyQt5 and mdtraj, which has to be installed separately as described above.