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Software to add

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Ashley Smith edited this page Feb 4, 2020 · 16 revisions

Packages to add (now?)

nbval          https://github.com/computationalmodelling/nbval
watermark      https://github.com/rasbt/watermark
nbgitpuller    https://github.com/jupyterhub/nbgitpuller
chaosmagpy     https://github.com/ancklo/ChaosMagPy

Set up a similar local test environment:

conda create --name py37_new -c conda-forge python=3.7 pip scipy jupyter jupyterlab xarray dask intake cartopy nodejs ipywidgets bokeh holoviews geoviews hvplot datashader panel param pyct[cmd] netcdf4 fastparquet selenium heliopy spiceypy rise tqdm numexpr Cython h5py hdf5storage jupyter joblib scikit-learn imagesize alabaster snowballstemmer babel docutils sphinxcontrib-websupport sphinx future soupsieve beautifulsoup4 lxml pyqtgraph logbook

pip install viresclient chaosmagpy magpysv pyamps spacepy pysat pytplot ocbpy aacgmv2 nbgitpuller nbresuse

jupyter labextension install jupyterlab-topbar-extension jupyterlab-system-monitor @pyviz/jupyterlab_pyviz

(no eoxmagmod)

Jupyter Extensions

Available through conda-forge
rise                           https://github.com/damianavila/RISE
Available through pip
nbgitpuller                    https://github.com/jupyterhub/nbgitpuller
                                - to create links, see https://jupyterhub.github.io/nbgitpuller/link.html

Install with jupyter labextension install ...

https://github.com/jtpio/jupyterlab-topbar#installation

# container extension
jupyter labextension install jupyterlab-topbar-extension

# system metrics
jupyter labextension install jupyterlab-system-monitor
pip install nbresuse

General packages

Available through conda-forge
nodejs
intake            https://github.com/intake/intake
geopandas         https://github.com/geopandas/geopandas

holoviz provides a metapackage that is meant to help install the wide array of associated packages. Available on pyviz channel but could be an issue due to dependency max version requirements.

holoviz         https://holoviz.org/installation.html
                https://github.com/holoviz/holoviz/blob/master/setup.cfg#L33

holoviz components can be installed individually from conda-forge:

holoviews
geoviews
hvplot
datashader
panel
param
pyct[cmd]      https://github.com/pyviz-dev/pyct
netdf4
fastparquet
selenium

See also:

Already included (see list at bottom of page)

(standard scipy, jupyter stack +...)

ipywidgets
bokeh         https://github.com/bokeh/bokeh
pandas
xarray
dask
cartopy

Python packages (research domain specific)

Available through pip
chaosmagpy    https://github.com/ancklo/ChaosMagPy
pysat         https://github.com/pysat/pysat
              (need to check that NASA CDF is set up right)
pytplot       https://github.com/MAVENSDC/pytplot
              (requires nodejs & bokeh - these are covered in previous section)
ocbpy         https://github.com/aburrell/ocbpy
aacgmv2       https://github.com/aburrell/aacgmv2

Warning: pysat requires pandas<0.25

Available through conda-forge or pip
heliopy       https://github.com/heliopython/heliopy
              (This includes astropy)
               but need to check what additional optional dependencies to include: http://docs.heliopy.org/en/stable/guide/installing.html
spiceypy      https://github.com/AndrewAnnex/SpiceyPy

Potential additions?

pyglow   https://github.com/timduly4/pyglow
Already included
apexpy        https://github.com/aburrell/apexpy
magpysv       https://github.com/gracecox/MagPySV
pyamps        https://github.com/klaundal/pyAMPS
spacepy       https://github.com/spacepy/spacepy
viresclient

From Ask

good - not installed:

  • basemap
  • ggplot (or ggplot2, may actually be called plotnine)
  • pygal
  • Plotly (or Plot.ly)
  • geoplotlib
  • Gleam
  • missingno
  • Leather
  • folium
  • PyROOT (might be require also instaling the ROOT framework)
  • PyGSL (might require also getting the tool gsl)
  • GMPY2 (might require also getting the tool gmp)
  • PyAMG
  • PyTrilinos
  • paramnormal
  • MetroloPy
  • Chaco
  • PyQwt
  • HippoDraw
  • Binggles
  • gnuplot.py (assumes the tool gnuplot is also installed)
  • OpenCV
  • Veusz
  • PyX
  • Dot2Tex
  • VPython
  • Pandas3D
  • SpaceFuncs
  • pyqtgraph
  • autograd
  • AstroPy
  • BOTEC
  • APLpy
  • Healpy
  • Pysolar
  • pywcgrid
  • pyregion
  • monte
  • PyMC2
  • PyBayes
  • NIFTY
  • SimPy
  • EMPy
  • scikit-rf
  • OSGeo
  • SimPEG
  • Colour

less important - not installed:

  • pytest
  • hypothesis
  • twine
  • wheel
  • networkx
  • nose
  • numpydoc
  • Bottleneck
  • KryPy
  • IDL
  • SMOP
  • pygame (some use for its visualization libraries)
  • Yellowbrick
  • graceplot (assumes the tool Grace is also installed)
  • pyreport
  • CMA
  • CVXOPT
  • CVXPY
  • DEAP
  • ECsPy
  • Mystic
  • PuLP
  • PyEvolve
  • scikits.optimization
  • FUncDesigner
  • PyMPI
  • Pypar
  • Joblib
  • jug
  • Pyslice
  • PyOpenCL
  • PyCUDA
  • PyCSP
  • pyem
  • hcluster
  • PyPR
  • Theano
  • Mousai
  • CDAT
  • seawater
  • atmqty
  • NZMATH
  • mdp
  • FiPy
  • SfePy
  • FEval
  • peak-o-mat

Packages currently installed

Package                  Version
------------------------ -----------
alabaster                0.7.12
alembic                  1.0.8
apexpy                   1.0.3
asn1crypto               0.24.0
async-generator          1.10
attrs                    19.1.0
Babel                    2.7.0
backcall                 0.1.0
beautifulsoup4           4.7.1
bleach                   3.1.0
blinker                  1.4
bokeh                    1.0.4
Cartopy                  0.17.0
cdflib                   0.3.16
certifi                  2019.6.16
certipy                  0.1.3
cffi                     1.12.3
chardet                  3.0.4
Click                    7.0
cloudpickle              0.8.1
conda                    4.6.14
conda-package-handling   1.4.1
cryptography             2.7
cycler                   0.10.0
Cython                   0.29.7
cytoolz                  0.9.0.1
dask                     1.1.5
decorator                4.4.0
defusedxml               0.5.0
dill                     0.2.9
distributed              1.28.0
docutils                 0.15.2
entrypoints              0.3
eoxmagmod                0.9.5
fastcache                1.1.0
ffnet                    0.8.4
filelock                 3.0.10
future                   0.17.1
glob2                    0.7
gmdata-webinterface      1.0.8
gmpy2                    2.0.8
h5py                     2.9.0
heapdict                 1.0.0
ibp                      0.6.0
idna                     2.8
imageio                  2.5.0
imagesize                1.1.0
ipykernel                5.1.2
ipympl                   0.3.3
ipyparallel              6.2.4
ipython                  7.8.0
ipython-genutils         0.2.0
ipywidgets               7.5.1
jedi                     0.15.1
Jinja2                   2.10.1
jsonschema               3.0.2
jupyter                  1.0.0
jupyter-client           5.3.1
jupyter-console          6.0.0
jupyter-core             4.4.0
jupyterhub               1.0.0
jupyterlab               0.35.5
jupyterlab-server        0.2.0
kiwisolver               1.1.0
libarchive-c             2.8
lief                     0.9.0
llvmlite                 0.27.1
locket                   0.2.0
magpysv                  1.0
Mako                     1.0.7
MarkupSafe               1.1.1
matplotlib               3.1.1
metakernel               0.24.2
mistune                  0.8.4
mock                     3.0.5
mpmath                   1.1.0
msgpack                  0.6.1
nbconvert                5.6.0
nbformat                 4.4.0
networkx                 2.3
notebook                 6.0.1
numba                    0.42.1
numexpr                  2.6.9
numpy                    1.17.1
oauthlib                 3.0.1
octave-kernel            0.31.0
olefile                  0.46
OWSLib                   0.18.0
packaging                19.0
pamela                   1.0.0
pandas                   0.24.2
pandocfilters            1.4.2
parso                    0.5.1
partd                    0.3.9
patsy                    0.5.1
pexpect                  4.7.0
pickleshare              0.7.5
Pillow                   6.1.0
pip                      19.2.3
pkginfo                  1.5.0.1
prometheus-client        0.7.1
prompt-toolkit           2.0.9
protobuf                 3.7.1
psutil                   5.6.2
ptyprocess               0.6.0
pyamps                   1.3.1
pycosat                  0.6.3
pycparser                2.19
pycryptodome             3.9.0
pycurl                   7.43.0.2
pyepsg                   0.4.0
Pygments                 2.4.2
PyJWT                    1.7.1
pykdtree                 1.3.1
pyOpenSSL                19.0.0
pyparsing                2.4.2
pyproj                   2.3.1
pyrsistent               0.15.4
pyshp                    2.1.0
PySocks                  1.7.0
python-dateutil          2.8.0
python-editor            1.0.4
pytz                     2019.2
PyWavelets               1.0.3
PyYAML                   5.1
pyzmq                    18.0.2
qtconsole                4.5.5
requests                 2.22.0
ruamel-yaml              0.15.71
scikit-image             0.14.2
scikit-learn             0.20.3
scipy                    1.3.1
seaborn                  0.9.0
Send2Trash               1.5.0
setuptools               41.2.0
Shapely                  1.6.4.post2
six                      1.12.0
snowballstemmer          1.9.1
sortedcontainers         2.1.0
soupsieve                1.9.1
spacepy                  0.2.0
Sphinx                   1.8.5
sphinxcontrib-websupport 1.1.2
SQLAlchemy               1.3.3
statsmodels              0.9.0
swarmpyfac               0.1.2
sympy                    1.3
tables                   3.5.2
tblib                    1.3.2
terminado                0.8.2
testpath                 0.4.2
toolz                    0.9.0
tornado                  6.0.3
tqdm                     4.35.0
traitlets                4.3.2
urllib3                  1.25.3
vincent                  0.4.4
viresclient              0.4.3
wcwidth                  0.1.7
webencodings             0.5.1
wheel                    0.33.6
widgetsnbextension       3.5.1
xarray                   0.12.3
xlrd                     1.2.0
zict                     0.1.4
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