Python-Libs

Introduction

A collection of Python packages, including NumPy and SciPy, useful for numerical work are installed.

We try to provide an up-to-date library of some of the most common Python libraries. Users can, however, make use of virtualenv and pip to install their own libraries and create dedicated Python environments.

Usage

Setting the module environment

When you log in, load the appropriate module for the version of Python you wish to use e.g. python/native (for version supplied by the opearting system, 2.6.6 on arc2 and polaris), python/2.6.5 , python/3.1.2 , then load the python-lib module.

e.g.

This will add the packages appropriate for that version of Python.

Python programs/scripts

We recommend that python programs begin with the following line:

This will cause it to be automatically run under the first version of python found in your PATH . e.g. the loaded python module.

This is particularly important if using any MPI features in python-libs

Compilers

Those who wish to build their own Python libraries on top of this module may want to use the same compiler for compatibility and so avoid build issues.

The python module now sets environment variable PYTHON_BUILD_MODULES . The modules used to build a particular python version can be shown by loading the appropriate module and executing echo $PYTHON_BUILD_MODULES

Please note that, although we previously used the version of GCC bundled with the operating system, this is no longer the case for more recent pythons.

Installing own versions of python packages

Although additional packages can be added to python-libs on request, virtualenv is installed as part of python-libs/2.1.0 or later. This provides an easy way to install python packages under your own account.

However, in order to allow virtualenv and pip to work seamlessly with python-libs, an additional export PYTHONPATH command is required on top of the normal use of environments:

e.g.

It is also possible to manage your own python packages completely independently of python-libs. To do this, you will need to install the pip tool and then the virtualenv tool. For almost all situations, python-libs will remain the most appropriate way of using Python packages.

Step 1: Load your preferred version of Python (note that the Python 2 pip tool is different to the Python 3 pip tool), eg:
module load python/2.7.6

Step 2: Download the pip installer:

Step 3: Run the script to install pip in the user home directory:

Step 4: Set the user $PATH so that pip will run (you will also need to put this line in your ~/.bashrc or ~/.bashprofile ):

Step 5: Install virtualenv:

You will now be able to use pip and virtualenv for your preferred version of Python without needing to load python-libs.

For the most up=to-date instructions on how to install (and uninstall) pip and virtualenv installed this way:

pip instructions
virtualenv instructions

MPI

Some of the Python packages contained in this module are built against a version of MPI (see contents list for details). When launching a Python MPI script within a job, please use the following command:

For mpi4py:

For vtk in versions of python-libs prior to 2.0.0:

Contents

python-libs/3.1.0

Changes since python-libs/3.0.1:

  • Minor upgrade of numpy from 1.12.0 to 1.12.1
  • ffmpeg prereq upgraded from 3.2.1 to 3.4
  • numba GPU-offload functionality enabled

Additional major packages (note – some packages require a GPU and are not installed on clusters without GPUs – pycuda, pyopencl, cv2, tensorflow, keras, caffe):

Package Version Python Versions Supported Modules Built Against
boost 1_65_1
pycuda 2017.1.1 cuda/8.0.61
pyopencl 2017.2 cuda/8.0.61
skimage 0.13.1
line_profiler 2.0
snakeviz 0.4.2
memory_profiler 0.47
cv2 3.3.1 cuda/9.0.176 ffmpeg/3.4 mkl/2017.1.132
tensorflow 1.4.0 cuda/9.0.176 intelmpi/2017.1.132 mkl/2017.1.132
keras 2.0.9
caffe c430690 cuda/9.0.176 mkl/2017.1 hdf5/1.8.17

python-libs/3.0.1

Due to an oversight, python-libs/3.0.0 was installed without the copy of scipy advertised below. The only difference in this release is that it adds it back in.

python-libs/3.0.0

Note: due to the Python community moving on from older versions, this release will not work with versions of python below 2.7.

Changes from python-libs/2.x.x :

  • General upgrade of package versions
  • A reduction in the packages offered, as many in previous versions of python-libs can be installed by the user into a virtualenv using pip

Documentation can be found by searching for the package on the Python Package Index

Package Version Python Versions Supported Modules Built Against
backports.shutil_get_terminal_size 1.0.0
bottleneck 1.2.0
Cython 0.25.2
decorator 4.0.11
docutils 0.13.1
enum34 1.1.6
h5py 2.6.0 intelmpi/2017.1.132 hdf5/1.8.17
ipython 5.2.2
ipython_genutils 0.1.0
llvmlite 0.16.0 llvm/3.9.1
matplotlib 2.0.0
mpi4py 2.0.0 intelmpi/2017.1.132
netCDF4 1.2.7 hdf5/1.8.17 netcdf/4.4.1
nose 1.3.7
numba 0.31.0
numexpr 2.6.2 mkl/2017.1
numpy 1.12.0 mkl/2017.1 fftw/3.3.6-pl1 suitesparse/4.5.4
pandas 0.19.2
pexpect 4.2.1
pickleshare 0.7.4
pip 9.0.1
prompt_toolkit 1.0.13
ptyprocess 0.5.1
pygments 2.2.0
pytest 3.0.6
pytest-cov 2.4.0
scipy 0.18.1 mkl/2017.1 fftw/3.3.6-pl1 suitesparse/4.5.4
setuptools 33.1.1
simplegeneric 0.8.1
six 1.10.0
sphinx 1.5.2
sympy 1.0
tables 3.3.0 hdf5/1.8.17
traitlets 4.3.2
virtualenv 15.1.0

python-libs/2.4.0

Note: not all packages are available for all the different versions of Python. Details of the range of python versions can be found in the table below.

Changes from python-libs/2.3.0 :

  • Added tau (profiling for serial and parallel Python 2.x codes)
  • symbol indicates there is a link to external resources
Package Version Python Versions Supported Description Modules Built Against
basemap* 1.0.7 >=2.4.0 Transform map projections
biggus* 0.7.0 Virtual large arrays and lazy evaluation
bottleneck* 0.8.0 Fast numpy array functions
cairo* 1.8.6 >3.0.0 Gnome graphics library
cdo* 1.2.3 >3.0.0 Python bindings to CDO
cartopy* 0.11.0 >=2.7.0 Cartographic library with matplotlib support proj/4.8.0
coverage* 3.7 >=2.3.0 Coverage measurement
curl* 7.19.0.1 >=2.4.0 <3.0.0 Fetch URLs
cv* 2.4.6.1 <3.0.0 OpenCV openmpi/1.6.5 ffmpeg/2.0.2
Cython* 0.19.2 >=2.4.0 C Extensions for Python
dateutil* 1.5 >=2.3.0 <3.0.0 Extensions to datatime module
dateutil* 2.0 >=3.0.0 Extensions to datatime module
docutils* 0.11 >=2.4.0 Text processing system
gdal* 1.11.0.0 >=2.7.0 <3.0.0 GDAL python bindings gdal/1.11.0
gobject* 2.20.0 3.0.0 Gnome object library
gtk* 2.16.0 <3.0.0 Gnome Toolkit library
h5py* 2.2.0 HDF5 file format (including MPI parallel I/O) hdf5/1.8.12 openmpi/1.6.5
HTSeq 0.5.4p5 <3.0.0 High-throughput sequencing data analysis
ipython* 1.1.0 Interactive Python interpreter
iris* 1.7.1 >=2.7.0 <3.0.0 Meteorology and Climatology library udunits/2.2.17
matplotlib* 1.3.1 2D plotting library
mpi4py* 1.3.1 Bindings for the Message Passing Interface openmpi/1.6.5
nco* Language bindings for NCO nco/4.3.7 (need any nco module loaded to work)
netCDF4* 1.0.7 >=2.4.0 NetCDF file format hdf5/1.8.12 netcdf/4.3.0
nltk* 3.0.0 >=2.6.0 Natural Language Toolkit
nose* 1.3.0 unit testing
numexpr* 2.2.2 Numerical array expression evaluator mkl/11.0u5
numpy* 1.8.0 Scientific computing atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
ordereddict* 1.1 >=2.4.0 <2.7.0 Substitute for python2.7’s collections.OrderedDict
pandas* 0.14.1 High performance data structures and data analysis
paramiko* 1.15.1 =2.6.0 SSHv2 client/server
pep* 1.5.7 Python style guide checker
petsc4py* 3.4.3 <3.0.0 PETSc mkl/11.0u5 openmpi/1.6.5 hdf5/1.8.12 hypre/2.9.0b fftw/3.3.3 netcdf/4.3.0
pip* 1.5.4 >=2.6.0 Python package install tool
plumbum* 1.4.2 Shell combinators library
pycrypto* 2.6.1 Python cryptography toolkit
pyke/pyke3* 1.1.1 >=2.5.0 Python Knowledge Engine
pypar* 2.1.5_108 <3.0.0 Parallel library (MPI) openmpi/1.6.5
pyproj* 1.9.3 Python interface to PROJ.4 library
pyresample* 1.1.0 >=2.5.0 <3.0.0 Geospatial image resampling
pysam* 0.7.5 SAM/BAM sequence alignment and mapping format
pyshp* 1.2.1 Python read/write support for ESRI Shapefile
pysvn* 1.7.8 >=2.6.0 SVN
pytest* 2.4.2 >=2.4.0 Python testing tool
pytest-cov* 1.6 >=2.4.0 Coverage reporting
pytz* 2013.8 >=2.4.0 Timezone database
rpy2* 2.4.3 >=2.7.0 Python interface to the R language R/3.0.2 (need this module loaded to work)
scipy* 0.13.2 not 3.3.2 Scientific tools atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
setuptools* 1.3.2 Package installation tool
shapely* 1.4.3 >=2.6.0 Geometric objects, predicates, and operations geos/3.4.2
six* 1.8.0 Python 2 and 3 compatibility utilities
sklearn* 0.15.2 not 3.3.2 Machine learning
sphinx* 1.2.3 Python documentation generator
sumatra* 0.5.2 >=2.6.0 <0 Manage numerical simulation projects
sympy* 0.7.4.1 Symbolic mathematics
tables* 3.0.0 Hierarchical datasets (HDF5) hdf5/1.8.12
tau 2.24 >3.0.0 Tuning and Analysis Utilities – profiler openmpi/1.6.5 papi/5.4.0 otf2/1.2.1 scorep/1.3
virtualenv* 1.11.6 Create isolated python environments
vtk* 6.0.0 >3.0.0 Visualization Toolkit (VTK)

python-libs/2.3.0

Note: not all packages are available for all the different versions of Python. Details of the range of python versions can be found in the table below.

Changes from python-libs/2.2.0 :

  • Added support for python/3.3.6
  • scipy now available for all python versions other than python/3.3.2
  • mpi4py now available for all python versions other than python/3.3.2
  • Added sklean (Machine Learning)
  • symbol indicates there is a link to external resources
Package Version Python versions supported Description Modules built against
basemap* 1.0.7 >=2.4.0 Transform map projections
biggus* 0.7.0 Virtual large arrays and lazy evaluation
bottleneck* 0.8.0 Fast numpy array functions
cairo* 1.8.6 >3.0.0 Gnome graphics library
cdo* 1.2.3 >3.0.0 Python bindings to CDO
Cartopy* 0.11.0 >=2.7.0 Cartographic library with matplotlib support proj/4.8.0
coverage* 3.7 >=2.3.0 Coverage measurement
curl* 7.19.0.1 >=2.4.0 <3.0.0 Fetch URLs
cv* 2.4.6.1 <3.0.0 OpenCV openmpi/1.6.5 ffmpeg/2.0.2
Cython* 0.19.2 >=2.4.0 C Extensions for Python
dateutil* 1.5 >=2.3.0 <0 Extensions to datatime module
dateutil* 2.0 >=3.0.0 Extensions to datatime module
docutils* 0.11 >=2.4.0 Text processing system
gdal* 1.11.0.0 >=2.7.0 <0 GDAL python bindings gdal/1.11.0
gobject* 2.20.0 >3.0.0 Gnome object library
gtk* 2.16.0 <0 Gnome Toolkit library
h5py* 2.2.0 HDF5 file format (including MPI parallel I/O) hdf5/1.8.12 openmpi/1.6.5
HTSeq 0.5.4p5 <3.0.0 High-throughput sequencing data analysis
ipython* 1.1.0 Interactive Python interpreter
iris* 1.7.1 >=2.7.0 <3.0.0 Meteorology and Climatology library udunits/2.2.17
matplotlib* 1.3.1 2D plotting library
mpi4py* 1.3.1 Bindings for the Message Passing Interface openmpi/1.6.5
nco* Language bindings for NCO nco/4.3.7 (need any nco module loaded to work)
netCDF4* 1.0.7 >=2.4.0 NetCDF file format hdf5/1.8.12 netcdf/4.3.0
nltk* 3.0.0 >=2.6.0 Natural Language Toolkit
nose* 1.3.0 unit testing
numexpr* 2.2.2 Numerical array expression evaluator
numpy* 1.8.0 Scientific computing atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
ordereddict* 1.1 >=2.4.0 <2.7.0 Substitute for python2.7’s collections.OrderedDict
pandas* 0.14.1 High performance data structures and data analysis
paramiko* 1.15.1 >=2.6.0 SSHv2 client/server
pep* 1.5.7 Python style guide checker
petsc4py* 3.4.3 <3.0.0 PETSc mkl/11.0u5 openmpi/1.6.5 hdf5/1.8.12 hypre/2.9.0b fftw/3.3.3 netcdf/4.3.0
pip* 1.5.4 >=2.6.0 Python package install tool
plumbum* 1.4.2 Shell combinators library
pycrypto* 2.6.1 Python cryptography toolkit
pyke/pyke3* 1.1.1 >=2.5.0 Python Knowledge Engine
pypar* 2.1.5_108 <3.0.0 Parallel library (MPI) openmpi/1.6.5
pyproj* 1.9.3 Python interface to PROJ.4 library
pyresample* 1.1.0 >=2.5.0 <3.0.0 Geospatial image resampling
pysam* 0.7.5 SAM/BAM sequence alignment and mapping format
pyshp* 1.2.1 Python read/write support for ESRI Shapefile
pysvn* 1.7.8 >=2.6.0 SVN
pytest* 2.4.2 >=2.4.0 Python testing tool
pytest-cov* 1.6 >=2.4.0 Coverage reporting
pytz* 2013.8 >=2.4.0 Timezone database
rpy2* 2.4.3 >=2.7.0 Python interface to the R language R/3.0.2 (need this module loaded to work)
scipy* 0.13.2 not 3.3.2 Scientific tools atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
setuptools* 1.3.2 Package installation tool
shapely* 1.4.3 >=2.6.0 Geometric objects, predicates, and operations geos/3.4.2
six* 1.8.0 Python 2 and 3 compatibility utilities
sklearn* 0.15.2 not 3.3.2 Machine learning
sphinx* 1.2.3 Python documentation generator
sumatra* 0.5.2 >=2.6.0 <3.0.0 Manage numerical simulation projects
sympy* 0.7.4.1 Symbolic mathematics
tables* 3.0.0 Hierarchical datasets (HDF5) hdf5/1.8.12
virtualenv* 1.11.6 Create isolated python environments
vtk* 6.0.0 >3.0.0 Visualization Toolkit (VTK)


python-libs/2.2.0

Note: not all packages are available for all the different versions of Python. Details of the range of python versions can be found in the table below.

Changes from python-libs/2.1.0 :

  • Added pep8
  • Added pyke/pyke3
  • Added six
  • Added Sphinx
  • Added pycrypto
  • Added paramiko
  • Added plumbum
  • Added biggus
  • Added rpy2
  • Added pyproj
  • Added pyresample
  • Added Shapely
  • Added pyshp
  • Added Cartopy
  • Added gdal
  • Added iris
  • Added nco
  • Added cdo
  • Added nltk
  • symbol indicates there is a link to external resources
Package Version Python versions supported Description Modules built against
basemap* 1.0.7 >=2.4.0 Transform map projections
biggus* 0.7.0 Virtual large arrays and lazy evaluation
bottleneck* 0.8.0 Fast numpy array functions
cairo* 1.8.6 <3.0.0 Gnome graphics library
cdo* 1.2.3 <3.0.0 Python bindings to CDO
Cartopy* 0.11.0 >=2.7.0 Cartographic library with matplotlib support proj/4.8.0
coverage* 3.7 >=2.3.0 Coverage measurement
curl* 7.19.0.1 >=2.4.0 <3.0.0 Fetch URLs
cv* 2.4.6.1 >3.0.0 OpenCV openmpi/1.6.5 ffmpeg/2.0.2
Cython* 0.19.2 >=2.4.0 C Extensions for Python
dateutil* 1.5 >=2.3.0 <3.0.0 Extensions to datatime module
dateutil* 2.0 >=3.0.0 Extensions to datatime module
docutils* 0.11 >=2.4.0 Text processing system
gdal* 1.11.0.0 >=2.7.0 <3.0.0 GDAL python bindings gdal/1.11.0
gobject* 2.20.0 >3.0.0 Gnome object library
gtk* 2.16.0 <3.0.0 Gnome Toolkit library
h5py* 2.2.0 HDF5 file format (including MPI parallel I/O) hdf5/1.8.12 openmpi/1.6.5
HTSeq* 0.5.4p5 <3.0.0 High-throughput sequencing data analysis
ipython* 1.1.0 Interactive Python interpreter
iris* 1.7.1 >=2.7.0 <3.0.0 Meteorology and Climatology library udunits/2.2.17
matplotlib* 1.3.1 2D plotting library
mpi4py* 1.3.1 <3.0.0 Bindings for the Message Passing Interface openmpi/1.6.5
nco* Language bindings for NCO nco/4.3.7 (need any nco module loaded to work)
netCDF4* 1.0.7 >=2.4.0 NetCDF file format hdf5/1.8.12 netcdf/4.3.0
nltk* 3.0.0 >=2.6.0 Natural Language Toolkit
nose* 1.3.0 unit testing
numexpr* 2.2.2 Numerical array expression evaluator mkl/11.0u5
numpy* 1.8.0 Scientific computing atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
ordereddict* 1.1 >=2.4.0 <2.7.0 Substitute for python2.7’s collections.OrderedDict
pandas* 0.14.1 High performance data structures and data analysis
paramiko* 1.15.1 >=2.6.0 SSHv2 client/server
pep* 1.5.7 Python style guide checker
petsc4py* 3.4.3 <3.0.0 PETSc mkl/11.0u5 openmpi/1.6.5 hdf5/1.8.12 hypre/2.9.0b fftw/3.3.3 netcdf/4.3.0
pip* 1.5.4 >=2.6.0 Python package install tool
plumbum* 1.4.2 Shell combinators library
pycrypto* 2.6.1 Python cryptography toolkit
pyke/pyke3* 1.1.1 >=2.5.0 Python Knowledge Engine
pypar* 2.1.5_108 <3.0.0 Parallel library (MPI) openmpi/1.6.5
pyproj* 1.9.3 Python interface to PROJ.4 library
pyresample* 1.1.0 >=2.5.0 <<3.0.0 Geospatial image resampling
pysam* 0.7.5 SAM/BAM sequence alignment and mapping format
pyshp* 1.2.1 Python read/write support for ESRI Shapefile
pysvn* 1.7.8 >=2.6.0 SVN
pytest* 2.4.2 >=2.4.0 Python testing tool
pytest-cov* 1.6 >=2.4.0 Coverage reporting
pytz* 2013.8 >=2.4.0 Timezone database
rpy2* 2.4.3 >=2.7.0 Python interface to the R language R/3.0.2 (need this module loaded to work)
scipy* 0.13.2 <3.0.0 Scientific tools atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
setuptools* 1.3.2 Package installation tool
Shapely* 1.4.3 >=2.6.0 Geometric objects, predicates, and operations geos/3.4.2
six* 1.8.0 Python 2 and 3 compatibility utilities
Sphinx* 1.2.3 Python documentation generator
Sumatra* 0.5.2 >=2.6.0 <3.0.0 Manage numerical simulation projects
sympy* 0.7.4.1 Symbolic mathematics
tables* 3.0.0 Hierarchical datasets (HDF5) hdf5/1.8.12
virtualenv* 1.11.6 Create isolated python environments
vtk* 6.0.0 <3.0.0 Visualization Toolkit (VTK)


python-libs/2.1.0

Note: not all packages are available for all the different versions of Python. Details of the range of python versions can be found in the table below.

Changes from python-libs/2.0.0 :

  • Added pip
  • Added virtualenv
  • Added gobject
  • Added cairo
  • Added gtk
  • Added pypar
  • Added bottleneck
  • Added pandas
  • symbol indicates there is a link to external resources
Package Version Python versions supported Description Modules built against
basemap* 1.0.7 >=2.4.0 Transform map projections
bottleneck* 0.8.0 Fast numpy array functions
cairo* 1.8.6 <3.0.0 Gnome graphics library
coverage* 3.7 >=2.3.0 Coverage measurement
curl* 7.19.0.1 >=2.4.0 <3.0.0 Fetch URLs
cv* 2.4.6.1 <3.0.0 OpenCV openmpi/1.6.5 ffmpeg/2.0.2
Cython* 0.19.2 >=2.4. C Extensions for Python
dateutil* 1.5 >=2.3.0 <3.0.0 Extensions to datatime module
dateutil* 2.0 >=3.0.0 Extensions to datatime module
docutils* 0.11 >=2.4.0 Text processing system
gobject* 2.20.0 <3.0.0 Gnome object library
gtk* 2.16.0 <3.0.0 Gnome Toolkit library
h5py* 2.2.0 HDF5 file format (including MPI parallel I/O) hdf5/1.8.12 openmpi/1.6.5
HTSeq* 0.5.4p5 <3.0.0 High-throughput sequencing data analysis
ipython* 1.1.0 Interactive Python interpreter
matplotlib* 1.3.1 2D plotting library
mpi4py* 1.3.1 <3.0.0 Bindings for the Message Passing Interface openmpi/1.6.5
netCDF4* 1.0.7 >=2.4.0 NetCDF file format hdf5/1.8.12 netcdf/4.3.0
nose* 1.3.0 unit testing
numexpr* 2.2.2 Numerical array expression evaluator mkl/11.0u5
numpy* 1.8.0 Scientific computing atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
ordereddict* 1.1 >=2.4.0 <2.7.0 Substitute for python2.7’s collections.OrderedDict
pandas* 0.14.1 High performance data structures and data analysis
petsc4py* 3.4.3 <3.0.0 PETSc mkl/11.0u5 openmpi/1.6.5 hdf5/1.8.12 hypre/2.9.0b fftw/3.3.3 netcdf/4.3.0
pip* 1.5.4 >=2.6.0 Python package install tool
pypar* 2.1.5_108 <3.0.0 Parallel library (MPI) openmpi/1.6.5
pysam* 0.7.5 SAM/BAM sequence alignment and mapping format
pysvn* 1.7.8 >=2.6.0 SVN
pytest* 2.4.2 >=2.4.0 Python testing tool
pytest-cov* 1.6 >=2.4.0 Coverage reporting
pytz* 2013.8 >=2.4.0 Timezone database
scipy* 0.13.2 <3.0.0 Scientific tools atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
setuptools* 1.3.2 Package installation tool
Sumatra* 0.5.2 >=2.6.0 <3.0.0 Manage numerical simulation projects
sympy* 0.7.4.1 Symbolic mathematics
tables* 3.0.0 Hierarchical datasets (HDF5) hdf5/1.8.12
virtualenv* 1.11.6 Create isolated python environments
vtk* 6.0.0 <3.0.0 Visualization Toolkit (VTK)

python-libs/2.0.0

Note: not all packages are available for all the different versions of Python. Details of the range of python versions can be found in the table below.

Note: changes from python-libs/1.x.x : many. An uplift in package and underlying support library version numbers. Initial support for python/3.x.x

  • symbol indicates there is a link to external resources
Package Version Python versions supported Description Modules built against
basemap* 1.0.7 >=2.4.0 Transform map projections
coverage* 3.7 >=2.3.0 Coverage measurement
curl* 7.19.0.1 >=2.4.0 Fetch URLs
cv* 2.4.6.1 >3.0.0 OpenCV openmpi/1.6.5 ffmpeg/2.0.2
Cython* 0.19.2 >=2.4.0 C Extensions for Python
dateutil* 1.5 >=2.3.0 <3.0.0 Extensions to datatime module
dateutil* 2.0 >=3.0.0 Extensions to datatime module
docutils* 0.11 >=2.4.0 Text processing system
h5py* 2.2.0 HDF5 file format (including MPI parallel I/O) hdf5/1.8.12 openmpi/1.6.5
HTSeq* 0.5.4p5 >3.0.0 High-throughput sequencing data analysis
ipython* 1.1.0 Interactive Python interpreter
matplotlib* 1.3.1 2D plotting library
mpi4py* 1.3.1 >3.0.0 Bindings for the Message Passing Interface openmpi/1.6.5
netCDF4* 1.0.7 >=2.4.0 NetCDF file format hdf5/1.8.12 netcdf/4.3.0
nose* 1.3.0 unit testing
numexpr* 2.2.2 Numerical array expression evaluator mkl/11.0u5
numpy* 1.8.0 Scientific computing atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
ordereddict* 1.1 >=2.4.0 <2.7.0 Substitute for python2.7’s collections.OrderedDict
petsc4py* 3.4.3 >3.0.0 PETSc mkl/11.0u5 openmpi/1.6.5 hdf5/1.8.12 hypre/2.9.0b fftw/3.3.3 netcdf/4.3.0
pysam* 0.7.5 SAM/BAM sequence alignment and mapping format
pysvn* 1.7.8 >=2.6.0 SVN
pytest* 2.4.2 >=2.4.0 Python testing tool
pytest-cov* 1.6 >=2.4.0 Coverage reporting
pytz* 2013.8 >=2.4.0 Timezone database
scipy* 0.13.2 >3.0.0 Scientific tools atlas/3.10.1 suitesparse/4.2.1 fftw/3.3.3
setuptools* 1.3.2 Package installation tool
Sumatra* 0.5.2 >=2.6.0 <3.0.0 Manage numerical simulation projects
sympy* 0.7.4.1 Symbolic mathematics
tables* 3.0.0 Hierarchical datasets (HDF5) hdf5/1.8.12
vtk* 6.0.0 >3.0.0 Visualization Toolkit (VTK)