This repository has been archived by the owner on Aug 29, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
Software to add
Ashley Smith edited this page Feb 7, 2020
·
16 revisions
pytest
nbval https://github.com/computationalmodelling/nbval
watermark https://github.com/rasbt/watermark
nbgitpuller https://github.com/jupyterhub/nbgitpuller
chaosmagpy https://github.com/ancklo/ChaosMagPy
- to create nbgitpuller links, see https://jupyterhub.github.io/nbgitpuller/link.html
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)
-
Potentially various widgets https://jupyter.org/widgets
- need to review what options there are.. how to set up.. https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Basics.html
-
Investigate:
- nteract
- plot.ly
- jupyterlab-flake8 https://github.com/mlshapiro/jupyterlab-flake8
- jupytext https://github.com/mwouts/jupytext/
- nbdime https://github.com/jupyter/nbdime
- it's nice for viewing diffs, but clutters interface and potentially confusing
- jupyterlab-github https://github.com/jupyterlab/jupyterlab-github
- setting a github token to avoid rate-limiting is problematic
- not easy to copy nb's over to your own workspace
-
system cpu, ram usage:
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
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:
(standard scipy, jupyter stack +...)
ipywidgets
bokeh https://github.com/bokeh/bokeh
pandas
xarray
dask
cartopy
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
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
pyglow https://github.com/timduly4/pyglow
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
- Plan to review them and round up at https://magneticearth.github.io/pages/software.html
- make an "awesome list"?
- See also:
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
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