Pyntacle

A python command line tool for network analysis based on non canonical metrics and HPC computing.

• Compatibility: Python 3.5+
• Contributions: [email protected]
• Website: http://pyntacle.css-mendel.it
• Bug report: https://github.com/mazzalab/pyntacle/issues

Installation

The easiest way to install Pyntacle is to download it from Anaconda , a cross-platform distribution for data analysis and scientific computing. This is the recommended installation method for most users.

Instructions for installing from source on various Linux distributions and MacOS X are also provided.

Installing Pyntacle using Anaconda or Miniconda

Installing Pyntacle and all its dependencies can be challenging for inexperienced users. There are several advantages in using Anaconda to install not only Pyntacle, but also Python and other packages: it is cross platform (Linux, MacOS X, Windows), you do not require administrative rights to install it (it goes in the user home directory), it allows you to work in virtual environments, which can be used as safe sandbox-like sub-systems that can be created, used, exported or deleted at your will.

You can choose between the full Anaconda and its lite version, Miniconda . The difference between the two is that Anaconda comes with hundreds of packages and can be a bit heavier to install, while Miniconda allows you to create a minimal, self-contained Python installation, and then use the Conda command to install additional packages of your choice.

In any case, Conda is the package manager that the Anaconda and Miniconda distributions are built upon. It is both cross-platform and language agnostic (it can play a similar role to a pip and virtualenv combination), and you need to set it up by running either the Anaconda installer or the Miniconda installer , choosing the ++Python 3.X++ version.

The next step is to create a new Conda environment (if you are familiar with virtual environments, these are analogous to a virtualenv but they also allow you to specify precisely which Python version to install).

Linux and MacOS X

Run the following commands from a terminal window:

conda create -n name_of_my_env python=3.6

This will create a minimal environment with only Python v.3.6 installed in it. To put your self inside this environment run:

source activate name_of_my_env

And finally, install the latest version of Pyntacle:

conda install -y -c bfxcss -c conda-forge pyntacle

Windows

Warning: Windows users could experience some issues when installing Conda or Miniconda in folders that whose name contains whitespaces (e.g. "%userprofile%\John Doe\Miniconda"). This is a known bug, as reported here and here. If this occurs, we recommend to create a new directory with no whitespaces (e.g. "%userprofile%\John_Doe\) and install Conda in there.

Open a windows prompt or (even better) an Anaconda prompt , and type:

conda create -y -n name_of_my_env python=3.6

Then, activate the newly created environment:

activate name_of_my_env

Finally, install the latest version of Pyntacle:

conda install -y -c bfxcss -c conda-forge pyntacle

Installing Pyntacle from source

Installing from source is advised for advanced users only. The following instructions were written for Mac OS v.11+ and a few major Linux distros. System requirements can vary for other distros/versions.

The source code can be downloaded from our GitHub releases page as a .tar.gz file. Before trying to install Pyntacle, there are system requirements that need to be satisfied on each platform.

Debian, Ubuntu

As a user with admin rights, run:

apt-get install -y build-essential linux-headers-$(uname -r) libgl1-mesa-glx libigraph0v5 libigraph0-dev libcairo2-dev libffi-dev libjpeg-dev libgif-dev libblas-dev liblapack-dev git python3-pip python3-tk

Ubuntu/Debian version <= 16.04

For Ubuntu/Debian 16.04 and older, you also have to install two dependencies from the PyPi repository, by running:

pip3 install numpy
pip3 install llvmlite

Then, the numba package needs to be installed manually by cloning the developer's Git repository:

git clone git://github.com/numba/numba.git ; cd numba; python3 setup.py install; cd ..; rm -rf numba

Finally, extract the pyntacle source tar.gz file navigate into it and run as an administrator (or add --user if you do not have admin rights and prefer to install the pyntacle binary in ~/.local/bin):

python3 setup.py install

CentOS7

As an admin, you need to run:

yum groupinstall -y development kernel-headers-`uname -r` kernel-devel-`uname -r` gcc gcc-c++ yum-utils; yum install -y https://centos7.iuscommunity.org/ius-release.rpm; yum install -y wget python36u-devel.x86_64 igraph-devel.x86_64 cairo-devel.x86_64 atlas-devel.x86_64 libffi-devel.x86_64 python36u-pip python36u-tkinter.x86_64
wget https://github.com/pygobject/pycairo/releases/download/v1.14.1/pycairo-1.14.1.tar.gz ; tar -xf pycairo-1.14.1.tar.gz; cd pycairo-1.14.1; python3.6 setup.py build ; sudo python3.6 setup.py install; cd ..; rm -rf pycairo-1.14.1*

Finally, extract the Pyntacle source tar.gz file, navigate into the extracted folder and run as an administrator (or add --user if you do not have admin rights and prefer to install the Pyntacle binary in ~/.local/bin):

python3.6 setup.py install

MacOS X

In order to compile from source, you need some of the tools that are conveniently packed in XCode, which has to be downloaded and installed from the Mac App Store. Once you have XCode - and you have opened at least once -, you will need to install the XCode Command Line Tools, by opening a terminal, typing:

xcode-select --install

and following the prompt on screen.

Additionally, you need other dependencies to compile Pyntacle. You can easily fetch them using the package manager Mac Ports .

Once Mac Ports is installed, getting the dependencies is easy:

port install py36-cairo py36-setuptools py36-pandas py36-seaborn py36-colorama py36-xlsxwriter py36-igraph py36-numba py36-psutil

Finally, extract the Pyntacle source tar.gz file, navigate into it and run:

python3.6 setup.py install --user

For your convenience, you can make the newly installed binary available system-wide (requires administrative rights):

ln -s /Users/$USER/Library/Python/3.6/bin/pyntacle /opt/local/bin

CUDA support

Independently of the OS in use, if you need CUDA support, you must also install the CUDA toolkit by downloading and installing the Toolkit from the NVIDIA website.

Release history

Changelog for current and past releases:

1.0:

Major update of Pyntacle, including:

• New major feature: Group centralities. A redesign of single-node centralities that accounts for the centrality of groups have been added to Pyntacle and a new command, groupcentrality has now been added to the Pyntacle command line. Its behavior is similar to the keyplayer command. Users can compute group centrality indices for predetermined sets of nodes or perform group centrality-based searches for sets of nodes that optimize predetermined group centrality scores
• Octopus redesign
• All graphs imported from either the command line or through the io_stream methods now have the same id-->node name pairing, with the exceptions of pickled igraphs (binary)
• Node isolates are now removed from graphs when imported through any Pyntacle import istance
• GPU-based computation of the shortest paths using the Floyd-Warshall algorithm is now an experimental feature and is disabvled in the Pyntacle command line. Users can choose to override this behavior in the Pyntacle library by using the correct Cmode enumerator
• Added exceptions and specific behaviors to unusual group-based search calculations that caused exceptions before
• Minor bugfixes

0.2:

• Added the --input-separator option to all commands.
• Added the --repeat option to pyntacle generate, so that the user can decide how many random graphs need to be created in one run.
• Bugfix in the edgelist importer, when a header is present.
• Bugfix for edgelist when node names are numbers, and now whitelines are skipped.
• Communities gracefully exits when no get_modules are found or all get_modules are filtered out by the user's custom filters.
• Major editing of the main inline help to match the documentation on the website.
• Added warnings in documentation for Windows users that have whitespaces in the Conda installation folder.
• Minor bugfixes

0.1.3:

• Bugfixes

0.1.2:

• Bugfixes

0.1.1:

• The first release of Pyntacle.

License

This work is licensed under a GNU General Public License v3.0.