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Python Packagesยง

We provide a collection of installed Python packages for each minor version of Python, as a bundle module. This page lists the packages for the current recommended Python 3 bundle.

This can be loaded using:

module load python3/recommended

The version of Python 3 provided with this bundle is currently Python 3.8.6.

Note that some packages we do not provide this way, because they have complicated non-Python dependencies. These are usually provided using the normal application modules system. This includes TensorFlow.

The following list was last updated at 15:31:31 (+0000) on 02 Feb 2021.

Module Version Description
acora 2.2 Fast multi-keyword search engine for text strings
appdirs 1.4.4 A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
args 0.1.0 Command Arguments for Humans.
ase 3.20.1 Atomic Simulation Environment
astor 0.8.1 Read/rewrite/write Python ASTs
astropy 4.2 Astronomy and astrophysics core library
attrs 20.3.0 Classes Without Boilerplate
backcall 0.2.0 Specifications for callback functions passed in to an API
biopython 1.78 Freely available tools for computational molecular biology.
bitarray 1.6.1 efficient arrays of booleans -- C extension
BoltzTraP2 20.7.1 band-structure interpolator and transport coefficient calculator
certifi 2020.11.8 Python package for providing Mozilla's CA Bundle.
cffi 1.14.4 Foreign Function Interface for Python calling C code.
cftime 1.3.0 Time-handling functionality from netcdf4-python
chardet 3.0.4 Universal encoding detector for Python 2 and 3
click 7.1.2 Composable command line interface toolkit
clint 0.5.1 Python Command Line Interface Tools
colorama 0.4.4 Cross-platform colored terminal text.
coloredlogs 14.0 Colored terminal output for Python's logging module
colormath 3.0.0 Color math and conversion library.
cryptography 3.2.1 cryptography is a package which provides cryptographic recipes and primitives to Python developers.
cutadapt 3.0 trim adapters from high-throughput sequencing reads
cvxopt 1.2.5 Convex optimization package
cycler 0.10.0 Composable style cycles
Cython 0.29.21 The Cython compiler for writing C extensions for the Python language.
cyvcf2 0.20.9 fast vcf parsing with cython + htslib
deap 1.3.1 Distributed Evolutionary Algorithms in Python
decorator 4.4.2 Decorators for Humans
distlib 0.3.1 Distribution utilities
dnaio 0.4.4 Read FASTA and FASTQ files efficiently
ecdsa 0.16.1 ECDSA cryptographic signature library (pure python)
emcee 3.0.2 The Python ensemble sampling toolkit for MCMC
ephem Compute positions of the planets and stars
filelock 3.0.12 A platform independent file lock.
funcparserlib 0.3.6 Recursive descent parsing library based on functional combinators
future 0.18.2 Clean single-source support for Python 3 and 2
hankel 1.1.0 Hankel Transformations using method of Ogata 2005
humanfriendly 9.0 Human friendly output for text interfaces using Python
hy 0.19.0 Lisp and Python love each other.
idna 2.10 Internationalized Domain Names in Applications (IDNA)
imageio 2.9.0 Library for reading and writing a wide range of image, video, scientific, and volumetric data formats.
iniconfig 1.1.1 iniconfig: brain-dead simple config-ini parsing
ipython 7.19.0 IPython: Productive Interactive Computing
ipython-genutils 0.2.0 Vestigial utilities from IPython
jedi 0.17.2 An autocompletion tool for Python that can be used for text editors.
Jinja2 2.11.2 A very fast and expressive template engine.
joblib 0.17.0 Lightweight pipelining: using Python functions as pipeline jobs.
kiwisolver 1.3.1 A fast implementation of the Cassowary constraint solver
ldap3 2.8.1 A strictly RFC 4510 conforming LDAP V3 pure Python client library
llvmlite 0.34.0 lightweight wrapper around basic LLVM functionality
lxml 4.6.2 Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
lzstring 1.0.4 lz-string for python
Mako 1.1.3 A super-fast templating language that borrows the best ideas from the existing templating languages.
Markdown 3.3.3 Python implementation of Markdown.
MarkupSafe 1.1.1 Safely add untrusted strings to HTML/XML markup.
matplotlib 3.3.3 Python plotting package
mpmath 1.1.0 Python library for arbitrary-precision floating-point arithmetic
multiqc 1.9 Create aggregate bioinformatics analysis reports across many samples and tools
netCDF4 1.5.4 Provides an object-oriented python interface to the netCDF version 4 library.
networkx 2.5 Python package for creating and manipulating graphs and networks
nibabel 3.2.1 Access a multitude of neuroimaging data formats
ninja 1.10.0.post2 Ninja is a small build system with a focus on speed
nose 1.3.7 nose extends unittest to make testing easier
numba 0.51.2 compiling Python code using LLVM
numpy 1.19.4 NumPy is the fundamental package for array computing with Python.
obspy 1.2.2 ObsPy - a Python framework for seismological observatories.
packaging 20.7 Core utilities for Python packages
pandas 1.1.4 Powerful data structures for data analysis, time series, and statistics
parso 0.7.1 A Python Parser
pexpect 4.8.0 Pexpect allows easy control of interactive console applications.
pickleshare 0.7.5 Tiny 'shelve'-like database with concurrency support
Pillow 8.0.1 Python Imaging Library (Fork)
pip 20.3 The PyPA recommended tool for installing Python packages.
pluggy 0.13.1 plugin and hook calling mechanisms for python
Pmw 2.0.1 Python Mega Widgets
prompt-toolkit 3.0.8 Library for building powerful interactive command lines in Python
ptyprocess 0.6.0 Run a subprocess in a pseudo terminal
py 1.9.0 library with cross-python path, ini-parsing, io, code, log facilities
pyasn1 0.4.8 ASN.1 types and codecs
pycparser 2.20 C parser in Python
pyerfa Python bindings for ERFA
pyfastaq 3.17.0 Script to manipulate FASTA and FASTQ files, plus API for developers
Pygments 2.7.2 Pygments is a syntax highlighting package written in Python.
pyparsing 2.4.7 Python parsing module
pysam 0.15.4 pysam
pysamstats 1.1.2 A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file.
pyspglib This is the pyspglib module.
pytest 6.1.2 pytest: simple powerful testing with Python
python-dateutil 2.8.1 Extensions to the standard Python datetime module
python-Levenshtein 0.12.0 Python extension for computing string edit distances and similarities.
pytz 2020.4 World timezone definitions, modern and historical
PyWavelets 1.1.1 PyWavelets, wavelet transform module
PyYAML 5.3.1 YAML parser and emitter for Python
qutip 4.5.2 QuTiP: The Quantum Toolbox in Python
regex 2020.11.13 Alternative regular expression module, to replace re.
requests 2.25.0 Python HTTP for Humans.
rply 0.7.7 A pure Python Lex/Yacc that works with RPython
scikit-image 0.17.2 Image processing in Python
scikit-learn 0.23.2 A set of python modules for machine learning and data mining
scipy 1.5.4 SciPy: Scientific Library for Python
seaborn 0.11.0 seaborn: statistical data visualization
setuptools 50.3.2 Easily download, build, install, upgrade, and uninstall Python packages
simplejson 3.17.2 Simple, fast, extensible JSON encoder/decoder for Python
six 1.15.0 Python 2 and 3 compatibility utilities
spectra 0.0.11 Color scales and color conversion made easy for Python.
spglib 1.16.0 This is the spglib module.
SQLAlchemy 1.3.20 Database Abstraction Library
sshpubkeys 3.1.0 SSH public key parser
tabulate 0.8.7 Pretty-print tabular data
threadpoolctl 2.1.0 threadpoolctl
tifffile 2020.11.26 Read and write TIFF(r) files
toml 0.10.2 Python Library for Tom's Obvious, Minimal Language
traitlets 5.0.5 Traitlets Python configuration system
urllib3 1.26.2 HTTP library with thread-safe connection pooling, file post, and more.
virtualenv 20.2.1 Virtual Python Environment builder
wcwidth 0.2.5 Measures the displayed width of unicode strings in a terminal
weblogo 3.7.5 WebLogo3 : Sequence Logos Redrawn
wheel 0.35.1 A built-package format for Python
xlrd 1.2.0 Library for developers to extract data from Microsoft Excel (tm) spreadsheet files
XlsxWriter 1.3.7 A Python module for creating Excel XLSX files.
xlutils 2.0.0 Utilities for working with Excel files that require both xlrd and xlwt
xlwt 1.3.0 Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+
xopen 1.0.1 Open compressed files transparently