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 11:35:20 (+0100) on 10 Oct 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 |
3.7.7.1 | 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 |
1.7.1.1 | 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 |
1.8.3.1 | 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 |