Author: Jens Henrik Göbbert¶
List of included Python packages¶
This lists the python packages available and installed by the install script for Python, SciPy-Stack and Jupyter:
$EBROOTPYTHON/easybuild/*.eb$EBROOTSCIPYMINSTACK/easybuild/*.eb$EBROOTJUPYTER/easybuild/*.eb
In [ ]:
!ls $EBROOTJUPYTER/lib/python3.6/site-packages/ | grep .dist-info > ${PKG_DISTINFO}
In [1]:
pkg_list = [
# Python module
("setuptools", "41.6.0", ""),
("webencodings", "0.5.1", ""),
("six", "1.12.0", ""),
("decorator", "4.4.0", ""),
("MarkupSafe", "1.1.1", "markupsafe"),
("more-itertools", "7.2.0", "more_itertools"),
("pickleshare", "0.7.5", ""),
("jedi", "0.15.1", ""),
("wcwidth", "0.1.7", ""),
("attr", "19.3.0", ""),
("parso", "0.5.1", ""),
("jinja2", "2.10.1", ""),
("pytz", "2019.3", ""),
("pyparsing", "2.2.0", ""),
("packaging", "19.2", ""),
("urllib3", "1.25.6", ""),
("certifi", "2019.9.11", ""),
("requests", "2.22.0", ""),
("python-dateutil", "2.8.1", "dateutil"),
("Pillow", "6.2.1", "PIL"),
("ply", "3.11", ""),
("pyrsistent", "0.15.4", ""),
("lxml", "4.4.1", ""),
("idna", "2.8", ""),
("chardet", "3.0.4", ""),
("pycparser", "2.19", ""),
("cffi", "1.13.2", ""),
("psutil", "5.6.3", ""),
("SQLAlchemy", "1.3.10", "sqlalchemy"),
("certipy", "0.1.3", ""),
("python-editor", "1.0.4", "editor"),
("Mako", "1.1.0", "mako"),
("alembic", "1.2.1", ""),
("click", "7.0", ""),
("appdirs", "1.4.3", ""),
("cloudpickle", "1.2.2", ""),
("toolz", "0.10.0", ""),
("cryptography", "2.8", ""),
("prompt-toolkit", "2.0.10", "prompt_toolkit"),
("oauthlib", "3.1.0", ""),
("async-generator", "1.10", "async_generator"),
("smmap", "0.9.0", ""),
("typed-ast", "1.4.0", "typed_ast"),
# SciPy-Stack module
("cycler", "0.10.0", ""),
("numpy", "1.15.2", ""),
("scipy", "1.2.1", ""),
("sympy", "1.4", ""),
("pandas", "0.25.3", ""),
("mpmath", "1.1.0", ""),
("kiwisolver", "1.1.0", ""),
("backports.functools_lru_cache", "1.5", ""),
("matplotlib", "3.1.1", ""),
("xarray", "0.11.3", ""),
# Jupyter module
("pyOpenSSL", "19.0.0", "OpenSSL"),
("entrypoints", "0.3", ""),
("async_generator", "1.10", ""),
("absl-py", "0.8.1", "absl"),
("cryptography", "2.8", ""),
("tornado", "6.0.3", ""),
("bokeh", "1.3.4", ""),
("seaborn", "0.9.0", ""),
("nbformat", "4.4.0", ""),
("param", "1.9.2", ""),
("pyviz_comms", "0.7.2", ""),
("holoviews", "1.12.6", ""),
("alabaster", "0.7.12", ""),
("Babel", "2.7.0", "babel"),
("snowballstemmer", "2.0.0", ""),
("docutils", "0.15.2", ""),
("imagesize", "1.1.0", ""),
("sphinxcontrib-websupport", "1.1.2", "sphinxcontrib.websupport"),
("Sphinx", "1.8.5", "sphinx"),
("pexpect", "4.7.0", ""),
("ipython", "7.9.0", "IPython"),
("ipynb", "0.5.1", ""),
("jupyter_core", "4.6.1", ""),
("retrying", "1.3.3", ""),
("plotly", "4.2.1", ""),
("tikzplotlib", "0.8.4", ""),
("jupyter_client", "5.3.4", ""),
("traitlets", "4.3.3", ""),
("pyzmq", "18.1.0", "zmq"),
("singledispatch", "3.4.0.3", ""),
("ipyparallel", "6.2.4", ""),
("ipykernel", "5.1.3", ""),
("terminado", "0.8.2", ""),
("bleach", "3.1.0", ""),
("mistune", "0.8.4", ""),
("pandocfilters", "1.4.2", ""),
("Pygments", "2.4.2", "pygments"),
("testpath", "0.4.4", ""),
("nbconvert", "5.6.1", ""),
("ipython_genutils","0.2.0", ""),
("Send2Trash", "1.5.0", "send2trash"),
("notebook", "6.0.2", ""),
("version_information", "1.0.3", ""),
("lesscpy", "0.13.0", ""),
("prometheus-client", "0.7.1", "prometheus_client"),
("jupyterthemes", "0.20.0", ""),
("zipp", "0.6.0", ""),
("importlib_metadata", "0.23", ""),
("jsonschema", "3.1.1", ""),
("jupyterlab_launcher", "0.13.1",""),
("sphinx_rtd_theme","0.4.3", ""),
("future", "0.18.1", ""),
("commonmark", "0.9.1", ""),
("recommonmark", "0.6.0", ""),
("jupyterlab", "1.2.1", ""),
("json5", "0.8.5", ""),
("jupyterlab_server", "1.0.6", ""),
("ptyprocess", "0.6.0", ""),
("defusedxml", "0.6.0", ""),
("widgetsnbextension", "3.5.1", ""),
("ipywidgets", "7.5.1", ""),
("ipydatawidgets", "4.0.1", ""),
("traittypes", "0.2.1", ""),
("bqplot", "0.11.9", ""),
("jupyter_bokeh", "1.1.1", ""),
("pythreejs", "2.1.1", ""),
("PyWavelets", "1.1.1", "pywt"),
("imageio", "2.6.1", ""),
("networkx", "2.3", ""),
("scikit-image", "0.16.2", "skimage"),
("ipywebrtc", "0.5.0", ""),
("ipyvolume", "0.5.2", ""),
("branca", "0.3.1", ""),
("ipyleaflet", "0.11.4", ""),
("ipympl", "0.3.3", ""),
("PyYAML", "5.1.2", "yaml"),
("jupyter_nbextensions_configurator", "0.4.1", ""),
("jupyter_latex_envs", "1.4.6", "latex_envs"),
("jupyter_highlight_selected_word", "0.2.0", ""),
("jupyter_contrib_core", "0.3.3",""),
("jupyter_contrib_nbextensions", "0.5.1", ""),
("rise", "5.5.1", ""),
("typing-extensions", "3.7.4", "typing_extensions"),
("idna-ssl", "1.1.0", "idna_ssl"),
("multidict", "4.5.2", ""),
("yarl", "1.3.0", ""),
("async-timeout", "3.0.1", "async_timeout"),
("aiohttp", "3.6.2", ""),
("simpervisor", "0.3", ""),
("jupyter_server", "0.1.1", ""),
("jupyter-server-proxy", "1.1.0", "jupyter_server_proxy"),
("jupyterlab_github", "1.0.1", ""),
("jupyterlab-gitlab", "0.3.0", "jupyterlab_gitlab"),
("jupyterlab-quickopen", "0.3.0", "jupyterlab_quickopen"),
("zstandard", "0.12.0", ""),
("itk_core", "5.0.1", ""),
("itk_filtering", "5.0.1", ""),
("itk_segmentation","5.0.1", ""),
("itk_numerics", "5.0.1", ""),
("itk_registration","5.0.1", ""),
("itk_io", "5.0.1", ""),
("itk-meshtopolydata", "0.5.1", ""),
("pyct", "0.4.6", ""),
("colorcet", "2.0.2", ""),
("itkwidgets", "0.22.0", ""),
("ujson", "1.35", ""),
("jupyterlab_iframe", "0.2.1", ""),
("python-dotenv", "0.10.3", "dotenv"),
("jupyterlab_latex","1.0.0", ""),
("jupyterlab_slurm","1.0.5", ""),
("jupyterlmod", "1.7.5", ""),
("nbresuse", "0.3.2", ""),
("colorama", "0.4.1", ""),
("nbdime", "1.1.0", ""),
("smmap2", "2.0.5", "smmap"),
("gitdb2", "2.0.6", "gitdb"),
("GitPython", "3.0.4", "git"),
("jupyterlab-git", "0.8.1", "jupyterlab_git"),
("sidecar", "0.3.0", ""),
("pycodestyle", "2.5.0", ""),
("autopep8", "1.4.4", ""),
("yapf", "0.28.0", ""),
("toml", "0.10.0", ""),
("pathspec", "0.6.0", ""),
("typed_ast", "1.4.0", ""),
("regex", "2019.11.1",""),
("black", "19.3b0", ""),
("jupyterlab-code-formatter", "0.6.1", "jupyterlab_code_formatter"),
("pamela", "1.0.0", ""),
("certipy", "0.1.3", ""),
("oauthlib", "3.1.0", ""),
("jupyterhub", "1.0.0", ""),
("appmode", "0.6.0", ""),
("HeapDict", "1.0.1", "heapdict"),
("zict", "1.0.0", ""),
("tblib", "1.5.0", ""),
("sortedcontainers","2.1.0", ""),
("msgpack", "0.6.2", ""),
("dask", "2.6.0", ""),
("distributed", "2.6.0", ""),
("dask-jobqueue", "0.7.0", ""),
("dask_labextension", "1.0.3", ""),
("Automat", "0.8.0", "automat"),
("PyHamcrest", "1.9.0", "hamcrest"),
("Twisted", "19.7.0", "twisted"),
("autobahn", "19.10.1", ""),
("constantly", "15.1.0", ""),
("hyperlink", "19.0.0", ""),
("incremental", "17.5.0", ""),
("txaio", "18.8.1", ""),
("zope.interface", "4.6.0", ""),
("backcall", "0.1.0", ""),
("wslink", "0.1.11", ""),
("jupyterlab_pygments", "0.1.0",""),
("ipyvue", "1.0.0", ""),
("ipyvuetify", "1.1.1", ""),
("voila", "0.1.14", ""),
("voila-material", "0.2.5", "-"),
("voila-gridstack", "0.0.6", "-"),
("voila-vuetify", "0.1.1", "-"),
("dicom-upload", "v0.1.0", ""),
("fileupload", "master", ""),
("pvlink", "0.1.2", ""),
("julia", "0.5.0", ""),
("textwrap3", "0.9.2", ""),
("ansiwrap", "0.8.4", ""),
("backports.weakref","1.0.post1",""),
("backports.tempfile","1.0", ""),
("tqdm", "4.41.0", ""),
("tenacity", "6.0.0", ""),
("papermill", "1.2.1", ""),
# PythonPackages for Tutorials
("patsy", "0.5.1", ""),
("statsmodels", "0.10.2", ""),
("cftime", "1.0.4.2", ""),
("vega_datasets", "0.8.0", ""),
("arviz", "0.5.1", ""),
("Theano", "1.0.4", ""),
("altair", "3.3.0", ""),
("cssselect", "1.1.0", ""),
("smopy", "0.0.7", ""),
("joblib", "0.14.1", ""),
("scikit-learn", "0.22", ""),
("memory_profiler", "0.55.0", ""),
("h5py", "2.10.0", ""),
("line_profiler", "2.1.2", ""),
("pymc3", "3.8", ""),
("llvmlite", "0.30.0", ""),
("numba", "0.46.0", ""),
("numexpr", "2.7.0", ""),
("ipythonblocks", "1.9.0", ""),
("pydub", "0.23.1", ""),
("multipledispatch","0.6.0", ""),
("partd", "1.1.0", ""),
("locket", "0.2.0", ""),
("fsspec", "0.6.2", ""),
("datashape", "0.5.2", ""),
("datashader", "0.9.0", ""),
("selenium", "3.141.0", ""),
("graphviz", "0.13.2", ""),
("vincent", "0.4.4", ""),
("Shapely", "1.6.4.post2",""),
("pyshp", "2.1.0", ""),
("Cartopy", "0.17.0", ""),
("pandas-datareader","0.8.1", ""),
]
from pip._vendor import pkg_resources
def get_version(package):
package = package.lower()
return next((p.version for p in pkg_resources.working_set if p.project_name.lower() == package), f"{Fore.RED}NO MATCH{Style.RESET_ALL}")
Run a Sanity Check¶
A test of the Python packages follows here.
Attention:
- Slight changes in the version numbers are due to compatibility problems we encountered and therefore had to make adjustments.
- "NO MATCH" - Not all package versions can be automatically found by this script
- "IMPORT FAILED" - Import failures are possible if python packages are not ment to be importable by the developer.
In [1]:
import importlib
from colorama import Fore, Style
from timeit import default_timer as timer
print("PYPI NAME".ljust(20), ": ", "IMPORT NAME".ljust(20) + "REQ.VERS.|INST.VERS.".ljust(25) + "IMPORT TIME")
print("=================================================================================")
for pkg_name, pkg_version, pkg_importname in pkg_list:
if not pkg_importname:
pkg_importname = pkg_name
pkg = None
try:
# import package
start_time = timer()
if pkg_importname != "-":
pkg = importlib.import_module(pkg_importname)
import_time = timer() - start_time
# get version
try:
version = pkg.__version__
if not isinstance(pkg.__version__, str):
raise
except:
version = get_version(pkg_name)
if version != pkg_version:
version = pkg_version.ljust(10) + " != " + f"{Fore.RED}" + version.ljust(10) + f"{Style.RESET_ALL}"
print(pkg_name.ljust(20), ": ", pkg_importname.ljust(20), version.ljust(24), f"{import_time:.6f}"+"s")
except:
print(pkg_name.ljust(20), ": ", pkg_importname.ljust(20), f"{Fore.RED}IMPORT FAILED{Style.RESET_ALL}")
#try:
# print("".ljust(24), pkg.__file__)
#except:
# print("".ljust(24), f"{Fore.RED}UNKNOWN{Style.RESET_ALL}")
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