Difference between revisions of "Python"
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| − | + | [[Category:Software]][[Category:Language]][[Category:Programming]] | |
| − | [[Category:Software]][[Category: | ||
{| | {| | ||
<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|python}} |
|{{#vardefine:url|http://python.org}} | |{{#vardefine:url|http://python.org}} | ||
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
| Line 19: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version | + | Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version no longer supported after 2020-01-01. |
| − | == | + | |
| − | The <code> | + | ==Python vs Python-Core== |
| + | The <code>python</code> environment module provides a full-featured python installation with around 300 installed python modules for development and use of python applications for research. If you only need the core python build to provide a scripting interface for the application you are building see the <code>[[Python-core|python-core]]</code> environment module. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 35: | Line 33: | ||
<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | * After the appropriate environment module is loaded - type " | + | * After the appropriate environment module is loaded - type "python" at the command line to open an interactive session. |
| − | * To run a | + | * To run a python script type <code>python scriptname.py</code>. If the correct "shebang" line is used at the top of the script E.g. |
| − | #!/usr/bin/env | + | #!/usr/bin/env python |
| − | then the script can be run directly as <code>scriptname.py</code> if it's in the executable path or as <code>./scriptname.py</code> if it's in the current directory. The same rules apply to using a | + | then the script can be run directly as <code>scriptname.py</code> if it's in the executable path or as <code>./scriptname.py</code> if it's in the current directory. The same rules apply to using a python script in a batch job script. |
You can request installation of additional modules by {{Fileabug}}. | You can request installation of additional modules by {{Fileabug}}. | ||
| − | + | See also: [[Installing Personal Python Modules]] and [[Managing Python environments and Jupyter kernels]] | |
| + | |||
| + | ===Matplotlib backend=== | ||
If you are trying to use matplotlib and get an error similar to | If you are trying to use matplotlib and get an error similar to | ||
import _tkinter # If this fails your Python may not be configured for Tk | import _tkinter # If this fails your Python may not be configured for Tk | ||
ImportError: No module named _tkinter | ImportError: No module named _tkinter | ||
| + | or | ||
| + | This application failed to start because no Qt platform plugin could be initialized. | ||
then you should try the following: | then you should try the following: | ||
import matplotlib | import matplotlib | ||
matplotlib.use('Agg') | matplotlib.use('Agg') | ||
before importing pyplot from matplotlib. | before importing pyplot from matplotlib. | ||
| + | |||
| + | |||
| + | ===Output Buffering=== | ||
| + | If your job starts, but doesn't appear to produce output from 'print' statements in the job log for a long time, but you want to see that output immediately then turn off output buffering. You can either add a <code>flush=True</code> argument to the print calls you are interested in or run the script with | ||
| + | srun --unbuffered python SCRIPT.py | ||
}} | }} | ||
==Available modules== | ==Available modules== | ||
| − | To see all installed modules names load the environment module and run <code>pip3 list</code> or <code> | + | To see all installed modules names load the environment module and run <code>pip3 list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new module installation. Below is a list of modules and versions installed in the default python version. |
{{:Python_Modules}} | {{:Python_Modules}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 13:34, 4 October 2022
Description
Python is a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Python version 3 is the current implementation of Python while python2 is a legacy version no longer supported after 2020-01-01.
Python vs Python-Core
The python environment module provides a full-featured python installation with around 300 installed python modules for development and use of python applications for research. If you only need the core python build to provide a scripting interface for the application you are building see the python-core environment module.
Environment Modules
Run module spider python to find out what environment modules are available for this application.
System Variables
- HPC_PYTHON_DIR - installation directory
- HPC_PYTHON_BIN - executable directory
- HPC_PYTHON_LIB - library directory
and modifies PYTHONPATH and PYTHONHOME, so you could use them in your scripts.
Additional Information
- After the appropriate environment module is loaded - type "python" at the command line to open an interactive session.
- To run a python script type
python scriptname.py. If the correct "shebang" line is used at the top of the script E.g.
#!/usr/bin/env python
then the script can be run directly as scriptname.py if it's in the executable path or as ./scriptname.py if it's in the current directory. The same rules apply to using a python script in a batch job script.
You can request installation of additional modules by submitting a request ticket in the Support System. The support request tickets can be used for requesting software installation, finding a solution to a particular problem, or just asking a question.
See also: Installing Personal Python Modules and Managing Python environments and Jupyter kernels
Matplotlib backend
If you are trying to use matplotlib and get an error similar to
import _tkinter # If this fails your Python may not be configured for Tk ImportError: No module named _tkinter
or
This application failed to start because no Qt platform plugin could be initialized.
then you should try the following:
import matplotlib
matplotlib.use('Agg')
before importing pyplot from matplotlib.
Output Buffering
If your job starts, but doesn't appear to produce output from 'print' statements in the job log for a long time, but you want to see that output immediately then turn off output buffering. You can either add a flush=True argument to the print calls you are interested in or run the script with
srun --unbuffered python SCRIPT.py
Available modules
To see all installed modules names load the environment module and run pip3 list or python -c "help('modules')" command before submitting a request for a new module installation. Below is a list of modules and versions installed in the default python version.
Automatically generated list of python modules installed with the Python Package Manager (pip) under the default python version.
| Name | Version |
|---|---|
| absl-py | 0.9.0 |
| adjusttext | 0.7.3 |
| aenum | 2.2.3 |
| aesara-theano-fallback | 0.0.4 |
| affine | 2.3.0 |
| aiohttp | 3.6.2 |
| aiohttp-cors | 0.7.0 |
| aiohttp-session | 2.7.0 |
| aioredis | 1.3.1 |
| aiosignal | 1.2.0 |
| alabaster | 0.7.12 |
| amqp | 2.5.2 |
| anndata | 0.7.6 |
| annogesic | 1.0.15 |
| anyio | 3.5.0 |
| appdirs | 1.4.3 |
| argcomplete | 1.10.3 |
| argh | 0.26.2 |
| argon2-cffi | 21.3.0 |
| argon2-cffi-bindings | 21.2.0 |
| arrow | 0.15.5 |
| arrow-cpp | 4.0.1 |
| arviz | 0.11.2 |
| ase | 3.19.0 |
| asn1crypto | 1.3.0 |
| asteval | 0.9.18 |
| astor | 0.8.1 |
| astroid | 2.3.3 |
| astropy | 4.0 |
| astropy-healpix | 0.5 |
| astroquery | 0.4.3 |
| async-timeout | 3.0.1 |
| asyncinit | 0.2.4 |
| atomicwrites | 1.3.0 |
| atomman | 1.4.3 |
| attrs | 19.3.0 |
| audioread | 2.1.8 |
| auto-sklearn | 0.12.7 |
| autobahn | 22.3.2 |
| autogenes | 1.0.4 |
| autograd | 1.3 |
| autograd-gamma | 0.4.2 |
| avro | 1.10.2 |
| azure-core | 1.19.0 |
| azure-identity | 1.6.0 |
| azure-storage-blob | 12.8.1 |
| babel | 2.8.0 |
| backcall | 0.1.0 |
| backports | 1.0 |
| backports-csv | 1.0.7 |
| backports-zoneinfo | 0.2.1 |
| backports.functools_lru_cache | 1.6.4 |
| bagit | 1.7.0 |
| bamnostic | 1.1.4 |
| bash | 0.6 |
| bayesian-optimization | 1.1.0 |
| bcrypt | 3.1.7 |
| beast2-xml | 1.0.9 |
| beautifulsoup4 | 4.8.2 |
| bed-reader | 0.2.9 |
| bgen-reader | 4.0.8 |
| bibtexparser | 1.2.0 |
| bids-validator | 1.4.2 |
| billiard | 3.6.3.0 |
| bioblend | 0.13.0 |
| bioinfokit | 2.0.8 |
| biopython | 1.76 |
| bioservices | 1.7.1 |
| biothings-client | 0.2.1 |
| black | 19.10b0 |
| blackfynn | 3.5.0 |
| bleach | 3.1.1 |
| blessings | 1.7 |
| blinker-herald | 0.2.0 |
| bokeh | 1.4.0 |
| boltons | 20.0.0 |
| boto | 2.49.0 |
| boto3 | 1.18.64 |
| botocore | 1.15.9 |
| bottleneck | 1.3.4 |
| box2d-py | 2.3.8 |
| brotli | 1.0.9 |
| brotlipy | 0.7.0 |
| bx-python | 0.8.9 |
| bz2file | 0.98 |
| cachecontrol | 0.11.7 |
| cached_property | 1.5.2 |
| cachetools | 4.0.0 |
| cbgen | 1.0.1 |
| cdcs | 0.1.6 |
| cdsapi | 0.5.1 |
| celery | 4.4.0 |
| certifi | 2021.10.8 |
| cffi | 1.14.0 |
| cftime | 1.1.0 |
| cgen | 2020.1 |
| chardet | 3.0.4 |
| charset-normalizer | 2.0.0 |
| circos | 1.3.5 |
| cli-helpers | 1.2.1 |
| click | 7.0 |
| click-plugins | 1.1.1 |
| clickclick | 1.2.2 |
| cligj | 0.5.0 |
| cloudpickle | 1.3.0 |
| cnvkit | 0.9.6 |
| colorama | 0.4.3 |
| coloredlogs | 14.0 |
| colorful | 0.5.4 |
| colorlog | 4.1.0 |
| colormath | 3.0.0 |
| commonmark | 0.9.1 |
| compressed-rtf | 1.0.6 |
| configargparse | 1.0 |
| configobj | 5.0.6 |
| configparser | 4.0.2 |
| configspace | 0.4.19 |
| connexion | 2.6.0 |
| contractions | 0.0.25 |
| coverage | 5.0.3 |
| crcmod | 1.7 |
| crypto | 1.4.1 |
| cryptography | 2.8 |
| ctbbio | 0.47 |
| cucim | 0.19.0 |
| cvxopt | 1.2.4 |
| cvxpy | 1.2.0 |
| cvxpy-base | 1.2.0 |
| cwltool | 1.0.20191225192155 |
| cx_oracle | 8.3.0 |
| cycler | 0.10.0 |
| cymem | 2.0.3 |
| cython | 0.29.21 |
| cytoolz | 0.10.1 |
| dalex | 1.0.1 |
| dark-matter | 3.1.82 |
| dash | 1.19.0 |
| dash-core-components | 1.15.0 |
| dash-html-components | 1.1.2 |
| dash-renderer | 1.9.0 |
| dash-table | 4.11.2 |
| dask | 2.11.0 |
| dask-core | 2021.8.0 |
| dask-jobqueue | 0.7.0 |
| data | 0.4 |
| dataframe_image | 0.1.1 |
| datamodeldict | 0.9.8 |
| dbg | 1.5.2 |
| dcm2bids | 2.1.4 |
| deap | 1.3.1 |
| debugpy | 1.4.1 |
| decorator | 4.4.1 |
| deepdiff | 5.5.0 |
| defusedxml | 0.6.0 |
| demographics | 0.0.1 |
| dendropy | 4.4.0 |
| deprecated | 1.2.13 |
| deprecation | 2.1.0 |
| descartes | 1.1.0 |
| diff-cover | 3.0.1 |
| dill | 0.3.1.1 |
| dispy | 4.12.1 |
| distlib | 0.3.0 |
| distributed | 2.11.0 |
| docker-pycreds | 0.4.0 |
| docopt | 0.6.2 |
| docrep | 0.2.7 |
| docutils | 0.17.1 |
| docx2txt | 0.8 |
| drmaa | 0.7.9 |
| easydev | 0.9.38 |
| easyprocess | 1.1 |
| ebcdic | 1.1.1 |
| ecdsa | 0.15 |
| ecos | 2.0.10 |
| edgar | 5.1.14 |
| efficient-apriori | 1.1.0 |
| efficientnet | 1.1.0 |
| emcee | 3.1.0 |
| entrypoints | 0.3 |
| ephemeris | 0.10.4 |
| eralchemy | 1.2.10 |
| et-xmlfile | 1.0.1 |
| et_xmlfile | 1.0.1 |
| etelemetry | 0.1.2 |
| eukrep | 0.6.7 |
| exoplanet | 0.5.1 |
| extract-msg | 0.28.7 |
| fabric | 2.5.0 |
| fabric3 | 1.14.post1 |
| face-recognition-models | 0.3.0 |
| falconn | 1.3.1 |
| fastcluster | 1.1.26 |
| fastcsv | 0.1.3 |
| fastjsonschema | 2.15.3 |
| fastprogress | 1.0.0 |
| fbpca | 1.0 |
| filelock | 3.0.12 |
| filprofiler | 2022.01.1 |
| fiona | 1.8.13.post1 |
| fisher | 0.1.9 |
| flake8 | 3.7.9 |
| flask | 1.1.1 |
| flask-compress | 1.9.0 |
| flatbuffers | 1.11 |
| freetype-py | 2.2.0 |
| frozenlist | 1.3.0 |
| fsspec | 0.9.0 |
| ftfy | 5.7 |
| ftputil | 3.4 |
| funcsigs | 1.0.2 |
| future | 0.18.2 |
| galaxy-containers | 19.9.0 |
| galaxy-lib | 19.5.2 |
| galaxy-tool-util | 20.1.0.dev5 |
| galaxy-util | 20.1.0.dev0 |
| gast | 0.3.3 |
| gcsfs | 0.8.0 |
| gdown | 3.13.0 |
| gensim | 3.8.1 |
| geopandas | 0.7.0 |
| gevent | 1.4.0 |
| gffutils | 0.10.1 |
| gitdb | 4.0.2 |
| gitdb2 | 4.0.2 |
| gitpython | 3.1.0 |
| glmnet_py | 1.0.2 |
| glob2 | 0.7 |
| goatools | 1.1.6 |
| 3.0.0 | |
| google-api-core | 1.16.0 |
| google-auth | 1.27.0 |
| google-auth-oauthlib | 0.4.4 |
| google-cloud-bigquery | 1.24.0 |
| google-cloud-core | 1.3.0 |
| google-cloud-pubsub | 2.5.0 |
| google-cloud-storage | 1.25.0 |
| google-play-scraper | 0.1.1 |
| google-resumable-media | 0.5.0 |
| googleapis-common-protos | 1.51.0 |
| gpustat | 0.6.0 |
| gql | 2.0.0 |
| graphql-core | 2.3.2 |
| greenlet | 0.4.15 |
| grequests | 0.4.0 |
| grpc-google-iam-v1 | 0.12.3 |
| grpcio | 1.39.0 |
| grpcio-tools | 1.39.0 |
| gtts | 2.2.2 |
| gxformat2 | 0.11.1 |
| gym | 0.21.0 |
| gym-all | 0.21.0 |
| gym-box2d | 0.21.0 |
| gym-classic_control | 0.21.0 |
| gym-other | 0.21.0 |
| gym-toy_text | 0.21.0 |
| h5py | 2.10.0 |
| habanero | 1.0.0 |
| hail | 0.2.77 |
| hdbscan | 0.8.24 |
| heapdict | 1.0.1 |
| hep-benchmark-suite | 2.1 |
| hep-score | 1.0.0 |
| hiredis | 1.1.0 |
| html5lib | 1.0.1 |
| huggingface-hub | 0.1.2 |
| humanfriendly | 7.1.1 |
| humanize | 1.0.0 |
| hurry-filesize | 0.9 |
| hyperlink | 21.0.0 |
| hypothesis | 5.5.4 |
| idigbio | 0.8.5 |
| idna | 2.10 |
| igraph | 0.9.9 |
| imagecodecs | 2021.8.26 |
| imageio | 2.8.0 |
| imageio-ffmpeg | 0.4.5 |
| imapclient | 2.1.0 |
| importlib-metadata | 4.5.0 |
| inflect | 4.1.0 |
| inflection | 0.3.1 |
| iniconfig | 1.1.1 |
| insilicoseq | 1.4.6 |
| intervaltree | 3.0.2 |
| invoke | 1.4.1 |
| ipykernel | 5.1.4 |
| ipython | 7.12.0 |
| ipython-genutils | 0.2.0 |
| ipython_genutils | 0.2.0 |
| ipywidgets | 7.5.1 |
| irep | 1.1.14 |
| isodate | 0.6.0 |
| isort | 4.3.21 |
| itk | 5.1.2 |
| itk-core | 5.1.2 |
| itk-filtering | 5.1.2 |
| itk-io | 5.1.2 |
| itk-numerics | 5.1.2 |
| itk-registration | 5.1.2 |
| itk-segmentation | 5.1.2 |
| itsdangerous | 1.1.0 |
| janus | 0.6.1 |
| jax | 0.2.19 |
| jaxlib | 0.1.69 |
| jdcal | 1.4.1 |
| jedi | 0.16.0 |
| jeepney | 0.4.3 |
| jinja2 | 3.1.1 |
| jinja2-pluralize | 0.3.0 |
| jmespath | 0.9.5 |
| joblib | 0.14.1 |
| jsanimation | 0.1 |
| json5 | 0.9.6 |
| jsonnet | 0.16.0 |
| jsonpickle | 1.3 |
| jsonschema | 3.2.0 |
| jupyter | 1.0.0 |
| jupyter-client | 6.0.0 |
| jupyter-console | 6.1.0 |
| jupyter-packaging | 0.12.0 |
| jupyter-server | 1.16.0 |
| jupyter-server-proxy | 3.2.1 |
| jupyter_client | 6.1.12 |
| jupyter_core | 4.7.1 |
| jupyterlab | 3.3.2 |
| jupyterlab-pygments | 0.1.2 |
| jupyterlab-server | 2.12.0 |
| jupyterlab-vpython | 3.1.3 |
| jupyterlab_widgets | 1.0.0 |
| keras | 2.3.1 |
| keras-applications | 1.0.8 |
| keras-preprocessing | 1.1.0 |
| keyring | 21.4.0 |
| keyrings-alt | 3.1 |
| kiwisolver | 1.3.1 |
| kombu | 4.6.7 |
| kpal | 2.1.1 |
| langid | 1.1.6 |
| language-check | 1.1 |
| latex | 0.7.0 |
| lazy-object-proxy | 1.4.3 |
| lazy_import | 0.2.2 |
| ldap3 | 2.6.1 |
| ldpred | 1.0.11 |
| liac-arff | 2.5.0 |
| libcst | 0.3.20 |
| libopencv | 4.5.1 |
| librosa | 0.7.2 |
| libtiff | 0.4.2 |
| lifelines | 0.24.0 |
| lightkurve | 2.0.10 |
| line-profiler | 3.0.2 |
| llvmlite | 0.31.0 |
| lmdb | 0.98 |
| lmfit | 1.0.0 |
| locket | 0.2.0 |
| lockfile | 0.12.2 |
| logbook | 1.5.3 |
| loguru | 0.5.1 |
| loompy | 3.0.6 |
| lxml | 4.5.0 |
| lz4 | 3.1.10 |
| lzstring | 1.0.4 |
| mako | 1.1.1 |
| markdown | 3.2.1 |
| markupsafe | 2.0.1 |
| matplotlib-base | 3.3.0 |
| matplotlib-inline | 0.1.2 |
| matplotlib-venn | 0.11.5 |
| mccabe | 0.6.1 |
| memoization | 0.3.2 |
| misopy | 0.5.4 |
| mistune | 0.8.4 |
| mizani | 0.6.0 |
| mkl-service | 2.3.0 |
| modin | 0.13.2 |
| modin-core | 0.13.2 |
| modin-dask | 0.13.2 |
| modin-ray | 0.13.2 |
| more-itertools | 8.2.0 |
| moviepy | 1.0.1 |
| mpi4py | 3.0.3 |
| mpmath | 1.1.0 |
| msal | 1.15.0 |
| msal-extensions | 0.3.0 |
| msgpack | 1.0.0 |
| msgpack-numpy | 0.4.4.3 |
| msgpack-python | 0.5.6 |
| msrest | 0.6.21 |
| multidict | 4.7.6 |
| multiprocess | 0.70.9 |
| munch | 2.5.0 |
| murmurhash | 1.0.2 |
| mxnet | 1.7.0.post1 |
| mycli | 1.20.1 |
| mygene | 3.1.0 |
| mypy | 0.910 |
| mypy_extensions | 0.4.3 |
| mypylib | 0.1.15 |
| mysql-connector-python | 8.0.11 |
| naked | 0.1.31 |
| nanoget | 1.12.0 |
| nanomath | 0.23.1 |
| nanostat | 1.2.0 |
| natsort | 7.1.1 |
| nbclassic | 0.3.7 |
| nbclient | 0.5.13 |
| nbconvert | 6.4.5 |
| nbformat | 5.0.4 |
| ncbi-genome-download | 0.3.0 |
| nd2reader | 3.2.3 |
| neovim | 0.3.1 |
| nest-asyncio | 1.5.1 |
| netcdf4 | 1.5.3 |
| netcdftime | 1.0.0a2 |
| networkx | 2.4 |
| neurdflib | 5.0.1 |
| nglview | 2.7.8 |
| nglview-js-widgets | 2.7.7 |
| nibabel | 3.0.1 |
| nilearn | 0.6.2 |
| nipype | 1.4.2 |
| nltk | 3.4.5 |
| nose | 1.3.7 |
| notebook | 6.0.3 |
| notebook-shim | 0.1.0 |
| num2words | 0.5.10 |
| numba | 0.48.0 |
| numericalunits | 1.25 |
| numexpr | 2.7.1 |
| numpy | 1.22.3 |
| numpy-indexed | 0.3.5 |
| numpy-stl | 2.16.2 |
| numpy_groupies | 0.9.13 |
| nvidia-ml | 7.352.0 |
| nxviz | 0.6.2 |
| oauthlib | 3.1.0 |
| obspy | 1.2.1 |
| oktopus | 0.1.2 |
| olefile | 0.46 |
| openapi-spec-validator | 0.2.8 |
| openbabel | 3.0.0 |
| opencensus | 0.7.10 |
| opencensus-context | 0.1.1 |
| opencv | 4.5.1 |
| opencv-contrib-python | 4.5.5.62 |
| opencv-python | 4.5.5.62 |
| openpyxl | 3.0.5 |
| openslide-python | 1.1.2 |
| opt-einsum | 3.1.0 |
| opt_einsum | 3.3.0 |
| ordered-set | 3.1.1 |
| osqp | 0.6.2.post0 |
| ovito | 3.0.0.dev687 |
| oyaml | 0.9 |
| p4 | 0.1.5 |
| packaging | 20.1 |
| palettable | 3.3.0 |
| pandas | 1.0.1 |
| pandas-summary | 0.0.7 |
| pandocfilters | 1.4.2 |
| paramiko | 2.7.1 |
| parcels | 2.3.0 |
| parmap | 1.5.2 |
| parsimonious | 0.8.1 |
| parso | 0.6.2 |
| partd | 1.1.0 |
| paste | 3.4.1 |
| pathlib2 | 2.3.5 |
| pathos | 0.2.5 |
| pathspec | 0.7.0 |
| pathtools | 0.1.2 |
| patsy | 0.5.2 |
| pbr | 5.6.0 |
| pdfminer-six | 20191110 |
| pep8 | 1.7.1 |
| pepper | 0.0.3 |
| pexpect | 4.8.0 |
| pgcli | 2.2.0 |
| pgspecial | 1.11.9 |
| photutils | 0.7.2 |
| phyde | 0.4.3 |
| pickleshare | 0.7.5 |
| pika | 1.1.0 |
| pillow | 7.0.0 |
| pims | 0.5 |
| pip | 21.1.1 |
| pipenv | 2018.11.26 |
| pkginfo | 1.5.0.1 |
| plac | 1.1.3 |
| planemo | 0.70.0 |
| plantcv | 3.13.4 |
| platypus-opt | 1.0.4 |
| plinkio | 0.9.7 |
| plotly | 4.10.0 |
| plotly-express | 0.4.1 |
| plotnine | 0.6.0 |
| pluggy | 0.13.1 |
| plumbum | 1.6.8 |
| ply | 3.11 |
| pomegranate | 0.12.0 |
| pooch | 1.6.0 |
| popcorn | 0.9.9 |
| portalocker | 1.7.1 |
| potentials | 0.3.2 |
| pox | 0.2.7 |
| ppft | 1.6.6.1 |
| precession | 1.0.3 |
| preshed | 3.0.2 |
| prettytable | 0.7.2 |
| primer3-py | 0.6.0 |
| prody | 2.0 |
| proglog | 0.1.9 |
| progressbar2 | 3.55.0 |
| progressbar33 | 2.4 |
| proj | 0.1.0 |
| prometheus-client | 0.7.1 |
| prometheus_client | 0.11.0 |
| promise | 2.3 |
| prompt-toolkit | 3.0.3 |
| proto-plus | 1.19.0 |
| protobuf | 3.11.3 |
| prov | 1.5.3 |
| psutil | 5.7.2 |
| psycopg2 | 2.8.4 |
| ptyprocess | 0.7.0 |
| pudb | 2019.2 |
| pure-sasl | 0.6.2 |
| py | 1.11.0 |
| py-opencv | 4.5.1 |
| py-spy | 0.3.3 |
| py2casefold | 1.0.1 |
| py4j | 0.10.9 |
| pyahocorasick | 1.4.0 |
| pyaml | 19.12.0 |
| pyarrow | 4.0.1 |
| pyasn1 | 0.4.8 |
| pyasn1-modules | 0.2.8 |
| pybedtools | 0.8.1 |
| pybids | 0.10.2 |
| pycodestyle | 2.5.0 |
| pycontractions | 2.0.1 |
| pycos | 4.8.15 |
| pycparser | 2.19 |
| pycrypto | 2.6.1 |
| pycryptodome | 3.14.1 |
| pydot | 1.4.1 |
| pydotplus | 2.0.2 |
| pyemd | 0.5.1 |
| pyerfa | 2.0.0 |
| pyfaidx | 0.5.8 |
| pyflakes | 2.1.1 |
| pyglet | 1.5.16 |
| pygments | 2.5.2 |
| pygpu | 0.7.6 |
| pygraphviz | 1.5 |
| pyjwt | 1.7.1 |
| pymbolic | 2021.1 |
| pymc3 | 3.11.2 |
| pymc3-ext | 0.1.0 |
| pymysql | 0.9.3 |
| pynacl | 1.3.0 |
| pynisher | 0.6.4 |
| pynndescent | 0.5.4 |
| pynvim | 0.4.1 |
| pyopenssl | 20.0.1 |
| pyparsing | 2.4.7 |
| pyproj | 2.5.0 |
| pyqt | 5.12.3 |
| pyqt-impl | 5.12.3 |
| pyqt5-sip | 4.19.18 |
| pyqtchart | 5.12 |
| pyqtwebengine | 5.12.1 |
| pyrfr | 0.8.2 |
| pyroms | 0.0.0 |
| pyroms-toolbox | 0.2.0 |
| pyrsistent | 0.15.7 |
| pysam | 0.15.4 |
| pyside2 | 5.13.2 |
| pysnptools | 0.5.3 |
| pysocks | 1.7.1 |
| pyspark | 3.1.2 |
| pytest | 5.3.5 |
| pytest-cov | 2.10.0 |
| python | 3.8.5 |
| python-dateutil | 2.8.2 |
| python-flatbuffers | 2.0 |
| python-graphviz | 0.8.4 |
| python-json-logger | 0.1.11 |
| python-levenshtein | 0.12.2 |
| python-libsbml | 5.18.0 |
| python-lzo | 1.14 |
| python-magic | 0.4.25 |
| python-mimeparse | 1.6.0 |
| python-pptx | 0.6.21 |
| python-utils | 2.5.6 |
| python-wget | 3.2 |
| python_abi | 3.8 |
| pytools | 2020.1 |
| pytorch-ignite | 0.4.4 |
| pytz | 2019.3 |
| pytz-deprecation-shim | 0.1.0.post0 |
| pyu2f | 0.1.5 |
| pyvcf | 0.6.8 |
| pyvirtualdisplay | 2.2 |
| pyvo | 1.1 |
| pywavelets | 1.1.1 |
| pyyaml | 5.3 |
| pyzbar | 0.1.8 |
| pyzmq | 19.0.0 |
| qdldl-python | 0.1.5 |
| qtconsole | 4.6.0 |
| qumulo-api | 4.2.0 |
| radio-beam | 0.3.2 |
| ray | 1.0.0 |
| ray-core | 1.9.2 |
| ray-default | 1.9.2 |
| rdflib | 4.2.2 |
| rdflib-jsonld | 0.4.0 |
| reademption | 1.0.0 |
| readme-renderer | 26.0 |
| redis-py | 4.1.4 |
| reframed | 1.1.0 |
| regex | 2020.2.20 |
| reportlab | 3.5.34 |
| repoze-lru | 0.7 |
| reproject | 0.7.1 |
| requests | 2.25.1 |
| requests-cache | 0.5.2 |
| requests-oauthlib | 1.3.0 |
| requests-toolbelt | 0.9.1 |
| resampy | 0.2.2 |
| retrying | 1.3.3 |
| rfc3986 | 1.4.0 |
| routes | 2.4.1 |
| rsa | 4.0 |
| rtree | 0.9.4 |
| ruamel-yaml | 0.16.0 |
| ruamel-yaml-clib | 0.2.0 |
| rx | 1.6.1 |
| s3transfer | 0.5.0 |
| sacremoses | 0.0.46 |
| salib | 1.3.11 |
| scandir | 1.10.0 |
| schema-salad | 4.5.20191229160203 |
| schwimmbad | 0.3.2 |
| scikit-image | 0.16.2 |
| scikit-learn | 0.22.1 |
| scikit-optimize | 0.8.1 |
| scipy | 1.5.1 |
| scs | 3.2.0 |
| seaborn | 0.10.0 |
| seaborn-base | 0.11.2 |
| secretstorage | 2.3.1 |
| selenium | 3.141.0 |
| semantic-version | 2.8.5 |
| semver | 2.9.1 |
| send2trash | 1.8.0 |
| sentry-sdk | 1.4.3 |
| setproctitle | 1.1.10 |
| setuptools | 57.5.0 |
| sh | 1.14.2 |
| shap | 0.39.0 |
| shapely | 1.7.0 |
| shellescape | 3.4.1 |
| shiboken2 | 5.14.1 |
| shortuuid | 1.0.1 |
| shutilwhich | 1.1.0 |
| simpervisor | 0.4 |
| simplejson | 3.17.0 |
| six | 1.12.0 |
| sklearn | 0.0 |
| slicer | 0.0.7 |
| slicerator | 1.0.0 |
| smac | 0.13.1 |
| smart-open | 1.10.0 |
| smart_open | 5.2.1 |
| smmap | 3.0.1 |
| snakeviz | 2.1.1 |
| snappy | 1.1.8 |
| sniffio | 1.2.0 |
| snowballstemmer | 2.0.0 |
| sortedcontainers | 2.1.0 |
| soundfile | 0.10.3.post1 |
| soupsieve | 2.0 |
| spectral-cube | 0.4.5 |
| speechrecognition | 3.8.1 |
| sphinx | 3.1.1 |
| sphinxcontrib-fulltoc | 1.2.0 |
| sphinxcontrib-htmlhelp | 1.0.3 |
| sphinxcontrib-serializinghtml | 1.1.4 |
| spyder-kernels | 2.1.3 |
| spython | 0.2.1 |
| sqlacodegen | 2.3.0 |
| sqlalchemy | 1.3.13 |
| sqlparse | 0.3.0 |
| statsmodels | 0.13.2 |
| stomp-py | 7.0.0 |
| subprocess32 | 3.5.4 |
| suds-jurko | 0.6 |
| sympy | 1.6.1 |
| synapseclient | 2.4.0 |
| tabulate | 0.8.3 |
| tblib | 1.6.0 |
| tedana | 0.0.9a1 |
| tempdir | 0.7.1 |
| tenacity | 8.0.1 |
| tensorboard | 2.5.0 |
| tensorboard-data-server | 0.6.1 |
| tensorboard-plugin-wit | 1.8.0 |
| tensorboardx | 2.1 |
| terminado | 0.8.3 |
| terminaltables | 3.1.0 |
| testpath | 0.5.0 |
| textract | 1.6.5 |
| textsearch | 0.0.17 |
| texttable | 1.6.4 |
| textwrap3 | 0.9.2 |
| theano-pymc | 1.1.2 |
| threadpoolctl | 2.2.0 |
| tifffile | 2021.3.17 |
| tokenizers | 0.10.3 |
| toml | 0.10.0 |
| tomli | 2.0.1 |
| tomlkit | 0.10.1 |
| toolshed | 0.4.6 |
| toolz | 0.10.0 |
| torch | 1.9.0 |
| torchvision | 0.10.0 |
| tornado | 6.0.3 |
| tox | 3.15.2 |
| tqdm | 4.46.0 |
| trackpy | 0.4.2 |
| traitlets | 4.3.3 |
| traits | 6.0.0 |
| transformers | 4.12.5 |
| twine | 3.2.0 |
| twython | 3.7.0 |
| txaio | 22.2.1 |
| typed-ast | 1.4.1 |
| typing-extensions | 3.7.4.1 |
| typing_extensions | 3.10.0.0 |
| typing_inspect | 0.7.1 |
| tzdata | 2022.1 |
| tzlocal | 4.2 |
| ujson | 4.2.0 |
| umap-learn | 0.5.1 |
| uncertainties | 3.1.2 |
| unidecode | 1.1.1 |
| urllib3 | 1.25.10 |
| urwid | 2.1.0 |
| versioneer | 0.18 |
| vine | 1.3.0 |
| virtualenv | 20.0.25 |
| virtualenv-clone | 0.5.3 |
| visidata | 2.5 |
| vispy | 0.6.6 |
| vpython | 7.6.3 |
| wandb | 0.12.1 |
| watchdog | 0.10.4 |
| wcwidth | 0.1.8 |
| webencodings | 0.5.1 |
| websocket-client | 0.57.0 |
| werkzeug | 1.0.0 |
| wheel | 0.37.0 |
| widgetsnbextension | 3.5.1 |
| wrapt | 1.12.0 |
| wurlitzer | 2.1.1 |
| xarray | 0.15.1 |
| xlrd | 1.2.0 |
| xlsx2csv | 0.7.8 |
| xlsxwriter | 3.0.1 |
| xmltodict | 0.12.0 |
| yarl | 1.6.0 |
| yt | 3.6.0 |
| zict | 2.0.0 |
| zipp | 3.4.1 |