⚙️ VRE: System details#
This page offers more details about the computational environment: what software is installed, how you can add new packages, and how you can replicate the software environment on other machines.
Hardware available
As this is a freely provided service, the per-user “hardware” available is limited. The limits are subject to change, but at time of writing they are:
1 CPU
3.5 GB RAM
10 GB persistent storage
If you try running some hardware and quota inspection commands that you are used to running on physical *nix machines, you may be confused by the outputs - this is a result of the virtualisation within a cloud environment
Software available: Python packages#
To see the full list:
Open a Terminal (File/New/Terminal) and enter: conda list (or equivalently, mamba list)
%conda list
Show code cell output
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
aacgmv2 2.7.0 pypi_0 pypi
affine 2.4.0 pyhd8ed1ab_0 conda-forge
alabaster 0.7.16 pypi_0 pypi
alembic 1.12.1 pyhd8ed1ab_0 conda-forge
altair 5.1.2 pyhd8ed1ab_0 conda-forge
anyio 4.1.0 pyhd8ed1ab_0 conda-forge
aom 3.7.1 h59595ed_0 conda-forge
apexpy 2.1.0 pypi_0 pypi
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
astropy-base 7.0.0 py311h2a3ca71_3 conda-forge
astropy-iers-data 0.2025.1.13.0.34.51 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
aws-c-auth 0.7.7 h4faf3ed_1 conda-forge
aws-c-cal 0.6.9 h3b91eb8_1 conda-forge
aws-c-common 0.9.8 hd590300_0 conda-forge
aws-c-compression 0.2.17 hfd9eb17_6 conda-forge
aws-c-event-stream 0.3.2 h1fff966_7 conda-forge
aws-c-http 0.7.14 hc86c171_2 conda-forge
aws-c-io 0.13.36 hc23c90e_0 conda-forge
aws-c-mqtt 0.9.10 hba57965_1 conda-forge
aws-c-s3 0.4.1 hfadff92_0 conda-forge
aws-c-sdkutils 0.1.12 hfd9eb17_5 conda-forge
aws-checksums 0.1.17 hfd9eb17_5 conda-forge
aws-crt-cpp 0.24.7 h97e63c7_6 conda-forge
aws-sdk-cpp 1.11.182 h8beafcf_7 conda-forge
babel 2.13.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
binutils 2.40 hdd6e379_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
binutils_linux-64 2.40 hbdbef99_2 conda-forge
blas 2.120 openblas conda-forge
blas-devel 3.9.0 20_linux64_openblas conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
bokeh 3.3.1 pyhd8ed1ab_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
bottleneck 1.3.7 py311h1f0f07a_1 conda-forge
branca 0.7.0 pyhd8ed1ab_1 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py311hb755f60_1 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.22.1 hd590300_0 conda-forge
c-blosc2 2.14.4 hb4ffafa_1 conda-forge
c-compiler 1.7.0 hd590300_0 conda-forge
ca-certificates 2024.12.14 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
cartopy 0.22.0 py311h320fe9a_1 conda-forge
cdf 3.9.1 h3218e01_0 local
cdflib 1.3.2 pyhd8ed1ab_1 conda-forge
certifi 2024.12.14 pyhd8ed1ab_0 conda-forge
certipy 0.1.3 py_0 conda-forge
cffi 1.16.0 py311hb3a22ac_0 conda-forge
cfitsio 4.3.1 hbdc6101_0 conda-forge
cftime 1.6.3 py311h1f0f07a_0 conda-forge
chaosmagpy 0.14 pypi_0 pypi
chardet 5.2.0 py311h38be061_2 conda-forge
charls 2.4.2 h59595ed_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.7.2 pyhd8ed1ab_1 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
coda 2.25.3 py311h1cc0e3f_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorcet 3.0.1 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
conda 23.10.0 py311h38be061_1 conda-forge
conda-index 0.5.0 pyhd8ed1ab_0 conda-forge
conda-libmamba-solver 23.11.1 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
configurable-http-proxy 4.6.0 he2f69ee_0 conda-forge
contextily 1.4.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py311h9547e67_0 conda-forge
coverage 7.3.3 py311h459d7ec_0 conda-forge
cramjam 2.7.0 py311h46250e7_1 conda-forge
cryptography 41.0.5 py311h63ff55d_0 conda-forge
cxx-compiler 1.7.0 h00ab1b0_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 3.0.6 py311hb755f60_0 conda-forge
cytoolz 0.12.2 py311h459d7ec_1 conda-forge
dask 2023.11.0 pyhd8ed1ab_0 conda-forge
dask-core 2023.11.0 pyhd8ed1ab_0 conda-forge
dask-glm 0.3.2 pyhd8ed1ab_0 conda-forge
dask-ml 2023.3.24 pyhd8ed1ab_1 conda-forge
datashader 0.16.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
debugpy 1.8.0 py311hb755f60_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.7 pyhd8ed1ab_0 conda-forge
distributed 2023.11.0 pyhd8ed1ab_0 conda-forge
docutils 0.17.1 pypi_0 pypi
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
eoxmagmod 0.14.0 pypi_0 pypi
et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fastparquet 2023.10.1 py311h1f0f07a_0 conda-forge
filelock 3.16.1 pyhd8ed1ab_1 conda-forge
fiona 1.9.5 py311hbac4ec9_0 conda-forge
fmt 10.1.1 h00ab1b0_0 conda-forge
folium 0.15.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.45.1 py311h459d7ec_0 conda-forge
fortran-compiler 1.7.0 heb67821_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freexl 2.0.0 h743c826_0 conda-forge
frozendict 2.4.6 py311h9ecbd09_0 conda-forge
fsspec 2023.10.0 pyhca7485f_0 conda-forge
future 1.0.0 pyhd8ed1ab_1 conda-forge
gcc 12.3.0 h8d2909c_2 conda-forge
gcc_impl_linux-64 12.3.0 he2b93b0_3 conda-forge
gcc_linux-64 12.3.0 h76fc315_2 conda-forge
gdal 3.7.3 py311h815a124_9 conda-forge
geographiclib 1.52 pyhd8ed1ab_0 conda-forge
geojson 3.1.0 pyhd8ed1ab_0 conda-forge
geopandas 0.14.1 pyhd8ed1ab_0 conda-forge
geopandas-base 0.14.1 pyha770c72_0 conda-forge
geoplot 0.5.1 pyhd8ed1ab_0 conda-forge
geopy 2.4.1 pyhd8ed1ab_0 conda-forge
geos 3.12.1 h59595ed_0 conda-forge
geotiff 1.7.1 hf074850_14 conda-forge
geoviews 1.11.0 pyhd8ed1ab_0 conda-forge
geoviews-core 1.11.0 pyha770c72_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
gfortran 12.3.0 h499e0f7_2 conda-forge
gfortran_impl_linux-64 12.3.0 hfcedea8_3 conda-forge
gfortran_linux-64 12.3.0 h7fe76b4_2 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.40 pyhd8ed1ab_0 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmdata-webinterface 1.0.8 pypi_0 pypi
gmp 6.3.0 h59595ed_0 conda-forge
gmpy2 2.1.2 py311h6a5fa03_1 conda-forge
greenlet 3.0.1 py311hb755f60_0 conda-forge
gxx 12.3.0 h8d2909c_2 conda-forge
gxx_impl_linux-64 12.3.0 he2b93b0_3 conda-forge
gxx_linux-64 12.3.0 h8a814eb_2 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h5py 3.12.1 nompi_py311hb639ac4_103 conda-forge
hapiclient 0.2.6 pypi_0 pypi
hapiplot 0.2.3b0 pypi_0 pypi
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
hdf5storage 0.1.19 pypi_0 pypi
holoviews 1.18.1 pyhd8ed1ab_0 conda-forge
hvplot 0.9.0 pyhd8ed1ab_0 conda-forge
ibpmodel 1.3.0 pypi_0 pypi
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
imagecodecs 2023.9.18 py311h089f87a_2 conda-forge
imageio 2.31.5 pyh8c1a49c_0 conda-forge
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
intake 0.7.0 pyhd8ed1ab_0 conda-forge
intake-xarray 0.7.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.26.0 pyhf8b6a83_0 conda-forge
ipyleaflet 0.18.1 pyhd8ed1ab_0 conda-forge
ipympl 0.9.3 pyhd8ed1ab_0 conda-forge
ipyparallel 8.6.1 pyhd8ed1ab_0 conda-forge
ipython 8.18.0 pyh0d859eb_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
isodate 0.7.2 pypi_0 pypi
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json-c 0.17 h7ab15ed_0 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h38be061_3 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.20.0 pyhd8ed1ab_0 conda-forge
jupyter 1.1.1 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter-server-mathjax 0.2.6 pyh5bfe37b_1 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.0 py311h38be061_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.10.1 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge
jupyterhub 4.0.2 pyh31011fe_0 conda-forge
jupyterhub-base 4.0.2 pyh31011fe_0 conda-forge
jupyterlab 4.0.9 pyhd8ed1ab_0 conda-forge
jupyterlab-git 0.50.0 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 h7f98852_2 conda-forge
kealib 1.5.2 hcd42e92_1 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py311h9547e67_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lazy_loader 0.3 pyhd8ed1ab_0 conda-forge
lcms2 2.15 hb7c19ff_3 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230802.1 cxx17_h59595ed_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarchive 3.7.2 h039dbb9_0 conda-forge
libarrow 14.0.1 h2b6da2a_4_cpu conda-forge
libarrow-acero 14.0.1 h59595ed_4_cpu conda-forge
libarrow-dataset 14.0.1 h59595ed_4_cpu conda-forge
libarrow-flight 14.0.1 h120cb0d_4_cpu conda-forge
libarrow-flight-sql 14.0.1 h61ff412_4_cpu conda-forge
libarrow-gandiva 14.0.1 hacb8726_4_cpu conda-forge
libarrow-substrait 14.0.1 h61ff412_4_cpu conda-forge
libavif16 1.0.2 hed45d22_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libboost-headers 1.84.0 ha770c72_0 conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.8.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgdal 3.7.3 hd74445f_9 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran-ng 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libgoogle-cloud 2.12.0 h5206363_4 conda-forge
libgrpc 1.59.3 hd6c4280_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
libkml 1.3.0 h01aab08_1018 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
liblapacke 3.9.0 20_linux64_openblas conda-forge
liblief 0.14.1 h5888daf_2 conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libllvm15 15.0.7 h5cf9203_3 conda-forge
libmamba 1.5.3 had39da4_2 conda-forge
libmambapy 1.5.3 py311hf2555c7_2 conda-forge
libnetcdf 4.9.2 nompi_h80fb2b6_112 conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libnuma 2.0.16 h0b41bf4_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libparquet 14.0.1 h352af49_4_cpu conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 16.1 h33b98f1_7 conda-forge
libprotobuf 4.24.4 hf27288f_0 conda-forge
libre2-11 2023.06.02 h7a70373_0 conda-forge
librttopo 1.1.0 h8917695_15 conda-forge
libsanitizer 12.3.0 h0f45ef3_3 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsolv 0.7.27 hfc55251_0 conda-forge
libspatialindex 1.9.3 h9c3ff4c_4 conda-forge
libspatialite 5.1.0 h7385560_2 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libthrift 0.19.0 hb90f79a_1 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.46.0 hd590300_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.11.6 h232c23b_0 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
linkify-it-py 2.0.0 pyhd8ed1ab_0 conda-forge
llvm-openmp 17.0.5 h4dfa4b3_0 conda-forge
llvmlite 0.41.1 py311ha6695c7_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lxml 6.1.3 pypi_0 pypi
lz4 4.3.2 py311h38e4bf4_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
magpysv 1.0 pypi_0 pypi
make 4.3 hd18ef5c_1 conda-forge
mako 1.3.0 pyhd8ed1ab_0 conda-forge
mamba 1.5.3 py311h3072747_2 conda-forge
mapclassify 2.6.1 pyhd8ed1ab_0 conda-forge
markdown 3.5.1 pyhd8ed1ab_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py311h459d7ec_1 conda-forge
matplotlib-base 3.8.2 py311h54ef318_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdit-py-plugins 0.4.0 pyhd8ed1ab_0 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
menuinst 2.2.0 py311h38be061_0 conda-forge
mercantile 1.2.1 pyhd8ed1ab_0 conda-forge
meson 1.6.1 pyhd8ed1ab_0 conda-forge
meson-python 0.17.1 pyh70fd9c4_1 conda-forge
metakernel 0.30.1 pyhd8ed1ab_0 conda-forge
minizip 4.0.3 h0ab5242_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
more-itertools 10.6.0 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.7 py311h9547e67_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 4.0.0 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.11.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.11.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.11.0 pyhd8ed1ab_0 conda-forge
nbdime 4.0.1 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
nbgitpuller 1.2.0 pyhd8ed1ab_0 conda-forge
nbval 0.10.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge
netcdf4 1.6.5 nompi_py311he8ad708_100 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
ninja 1.12.1 h297d8ca_0 conda-forge
nodejs 18.18.2 hb753e55_1 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.0.6 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.96 h1d7d5a4_0 conda-forge
numba 0.58.1 py311h96b013e_0 conda-forge
numcodecs 0.12.1 py311hb755f60_0 conda-forge
numexpr 2.8.7 py311h039bad6_104 conda-forge
numpy 1.26.0 pypi_0 pypi
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
octave_kernel 0.35.1 pyhd8ed1ab_0 conda-forge
openblas 0.3.25 pthreads_h7a3da1a_0 conda-forge
openjpeg 2.5.0 h488ebb8_3 conda-forge
openpyxl 3.1.2 py311h459d7ec_1 conda-forge
openssl 3.4.0 h7b32b05_1 conda-forge
orc 1.9.2 h4b38347_0 conda-forge
outcome 1.3.0.post0 pyhd8ed1ab_0 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pamela 1.1.0 pyh1a96a4e_0 conda-forge
pandas 2.1.3 py311h320fe9a_0 conda-forge
pandoc 3.1.3 h32600fe_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 1.3.4 pyhd8ed1ab_0 conda-forge
param 2.0.1 pyhca7485f_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
patch 2.7.6 h7f98852_1002 conda-forge
patchelf 0.17.2 h58526e2_0 conda-forge
patsy 0.5.3 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.1.0 py311ha6c5da5_0 conda-forge
pip 26.0.1 pypi_0 pypi
pixman 0.42.2 h59595ed_0 conda-forge
pkginfo 1.12.0 pyhd8ed1ab_1 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.0.0 pyhd8ed1ab_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_1 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
pooch 1.9.0 pypi_0 pypi
poppler 23.12.0 h590f24d_0 conda-forge
poppler-data 0.4.12 hd8ed1ab_0 conda-forge
portalocker 2.8.2 py311h38be061_1 conda-forge
postgresql 16.1 h8972f4a_7 conda-forge
ppigrf 2.0.0 pypi_0 pypi
proj 9.3.0 h1d62c97_2 conda-forge
prometheus_client 0.19.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.41 pyha770c72_0 conda-forge
prompt_toolkit 3.0.41 hd8ed1ab_0 conda-forge
protobuf 4.24.4 py311h46cbc50_0 conda-forge
psutil 5.9.5 py311h459d7ec_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge
py-lief 0.14.1 py311hfdbb021_2 conda-forge
pyamps 1.6 pypi_0 pypi
pyarrow 14.0.1 py311h39c9aba_4_cpu conda-forge
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py311h459d7ec_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyct 0.5.0 pyhd8ed1ab_0 conda-forge
pycurl 7.45.1 py311hae980a4_3 conda-forge
pyerfa 2.0.1.5 py311h9f3472d_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge
pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyproj 3.6.1 py311h1facc83_4 conda-forge
pyproject-metadata 0.9.0 pyhd8ed1ab_1 conda-forge
pyshp 2.3.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pyswipe 0.9.7 pypi_0 pypi
pytables 3.9.2 py311h3e8b7c9_2 conda-forge
pytest 7.4.3 pyhd8ed1ab_0 conda-forge
python 3.11.6 hab00c5b_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-libarchive-c 5.1 py311h38be061_1 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyviz_comms 3.0.0 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py311h1f0f07a_1 conda-forge
pyyaml 6.0.1 py311h459d7ec_1 conda-forge
pyzmq 25.1.1 py311h34ded2d_2 conda-forge
qdipole 0.6.0 h3218e01_0 local
rasterio 1.3.9 py311h40fbdff_0 conda-forge
rav1e 0.6.6 he8a937b_2 conda-forge
rdma-core 28.9 h59595ed_1 conda-forge
re2 2023.06.02 h2873b5e_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.31.0 pyhd8ed1ab_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
ripgrep 14.1.1 h8fae777_0 conda-forge
rpds-py 0.13.1 py311h46250e7_0 conda-forge
rtree 1.1.0 py311h3bb2b0f_0 conda-forge
ruamel.yaml 0.18.5 py311h459d7ec_0 conda-forge
ruamel.yaml.clib 0.2.7 py311h459d7ec_2 conda-forge
s2n 1.3.56 h06160fa_0 conda-forge
scikit-image 0.22.0 py311h320fe9a_2 conda-forge
scikit-learn 1.3.2 py311hc009520_1 conda-forge
scipy 1.11.4 py311h64a7726_0 conda-forge
seaborn 0.13.0 hd8ed1ab_0 conda-forge
seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge
selenium 4.16.0 pyhd8ed1ab_0 conda-forge
selenium-manager 4.16.0 he8a937b_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
shapely 2.0.2 py311h2032efe_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
snowballstemmer 2.2.0 pypi_0 pypi
snuggs 1.4.7 py_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
spacepy 0.7.0 pypi_0 pypi
sparse 0.14.0 pyhd8ed1ab_0 conda-forge
sphinx 1.8.6 pypi_0 pypi
sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi
sphinxcontrib-websupport 1.2.4 pypi_0 pypi
sqlalchemy 2.0.23 py311h459d7ec_0 conda-forge
sqlite 3.44.2 h2c6b66d_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.0 py311h1f0f07a_2 conda-forge
svt-av1 1.7.0 h59595ed_0 conda-forge
swarmface 0.3.0 pypi_0 pypi
swarmpal 0.1.0 pypi_0 pypi
swarmpyfac 0.2.2 pypi_0 pypi
sympy 1.12 pypyh9d50eac_103 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
tblib 2.0.0 pyhd8ed1ab_0 conda-forge
tenacity 9.0.0 pyhd8ed1ab_1 conda-forge
terminado 0.18.0 pyh0d859eb_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tifffile 2023.9.26 pyhd8ed1ab_0 conda-forge
tiledb 2.16.3 h8c794c1_3 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py311h459d7ec_1 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.13.0 pyhd8ed1ab_0 conda-forge
traittypes 0.2.1 pyh9f0ad1d_2 conda-forge
trio 0.23.2 py311h38be061_0 conda-forge
trio-websocket 0.11.1 pyhd8ed1ab_0 conda-forge
truststore 0.8.0 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge
typing-extensions 4.8.0 hd8ed1ab_0 conda-forge
typing_extensions 4.8.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzcode 2023c h0b41bf4_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uc-micro-py 1.0.1 pyhd8ed1ab_0 conda-forge
ucx 1.15.0 h64cca9d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
uriparser 0.9.7 hcb278e6_1 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
vires-extension 0.1.0 pypi_0 pypi
viresclient 0.15.2 pypi_0 pypi
watermark 2.4.3 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge
wsproto 1.2.0 pyhd8ed1ab_0 conda-forge
xarray 2023.12.0 pyhd8ed1ab_0 conda-forge
xarray-datatree 0.0.15 pypi_0 pypi
xerces-c 3.2.4 hac6953d_3 conda-forge
xlrd 2.0.1 pyhd8ed1ab_3 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xyzservices 2023.10.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zarr 2.16.1 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zfp 1.0.0 h59595ed_4 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstandard 0.23.0 py311hbc35293_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Note: you may need to restart the kernel to use updated packages.
VirES/EOX software#
- viresclient
Access to VirES server (download of Swarm products as pandas/xarray)
- eoxmagmod
Optimised forward evaluation of Swarm geomagnetic models
Swarm community software#
- chaosmagpy
CHAOS model forward code and geomag modelling utilities
- pyamps
AMPS model forward code
Wider geomagnetism and space physics community software#
- hapiclient
Fetching data from HAPI servers
- apexpy
Apex and quasi-dipole coordinate transformations
- spacepy
Tools for space physics
- magpysv
Generating secular variation time series from ground observatory data
General Python software (highlights)#
- pandas
Powerful analysis tool built around dataframes
- xarray
For labelled multi-dimensional arrays
- cartopy
Geospatial data processing and maps
- dask
Flexible library for parallel computing
- holoviz ecosystem
High level tools to simplify making complex visualisations
Note
We are seeking to evolve this list, which involves a wider effort to increase portability of software. Generally speaking, to add a package here, we require it to be available through pip or conda and that the software be designed for portability (no large data packages included, and manageable dependencies) and that it is actively maintained. See below to try adding a package yourself to test it.
Software lists and communities
Installing other packages#
The default environment comes from a Docker image which is based on the Jupyter Notebook Scientific Python Stack (jupyter/scipy-notebook) - with our own extra software and configuration layered on top. This image is loaded when your container starts (i.e. when you log in). It will spin down when you are not using it and restart when you access it again (in its original unmodified state). If you try to install other software, it may not survive the container restart, depending on how you do it. In any case, you will only be affecting your environment. Unless you fully understand what you are doing, you are likely to run into problems trying to install and use other software. In this case, please get in touch if you are interested in having access to some particular software.
If you install some packages with conda install ... or pip install ..., this will indeed install them and make them available to the default kernel immediately. However, they will disappear the next time your container shuts down. When you have not been active for some period of time (<~hours), the container within which your environment is running will shut down. When you log in again, the environment is created anew from the image that everybody shares, so your modifications will no longer be present. This means that installing packages (& extensions) in this way is only sensible for briefly trying them out.
Managing custom environments#
Tip
In the instructions below, you can replace conda with mamba for faster performance
If you need access to a different collection of packages (e.g. you need a certain unsupported package, or different versions of what is available), then the way to achieve this is through creating an additional kernel, which you can then optionally use to execute scripts or notebooks, in place of the default kernel (the default one will also remain available). This procedure is not covered in full here, but in short:
conda create --prefix <kernelpath> ipykernel <package1> <package2> ...
will create a new conda environment (see the existing ones with conda env list).
Note
See the conda documentation for more information on this. Note that to create the environment we must use --prefix rather than --name to specify the exact location (choosing the home directory), otherwise the environment location will default to /opt/conda/envs/ which is not permanent.
For example:
conda create --prefix ~/envs/my_env ipykernel numpy
will create an environment stored within ~/envs/ and called my_env, with the packages ipykernel (this is required in order to work with Jupyter notebooks), and numpy. This kernel then needs to be registered with Jupyter:
~/envs/my_env/bin/python -m ipykernel install --user --name my_env --display-name "my_env"
The kernel should now be available to use from within notebooks: when running a notebook, click the “Python 3” button near the top right to change the kernel, or from the top menu: Kernel / Change Kernel. You can also access the environment in a terminal with conda activate ~/envs/my_env. Since we have stored it in the home directory, it will not be lost when the container shuts down. You can see what kernels are installed and visible to Jupyter with jupyter kernelspec list.
A note on reproducability#
Execution environment:
An important scenario which is not fully supported by the VRE is ensuring reproducability of code in the future. The VRE is an evolving service which provides a single software environment which is updated over time. As newer versions of packages are installed, we can not guarantee that your code will run exactly the same in the future - this depends on the packages you use and how their behaviours and interfaces change over time. Managing your own custom conda environment as described above is one way to mitigate against this. The VRE as an easy-to-access environment where you can quickly experiment with things, share demonstrations of your code, run tutorials etc. For a detailed introduction to reproducability, please refer to The Turing Way. Another project which you may be interested in if you are working in geospace science is Resen which aims to tackle this issue of reproducability.
Data environment:
Aside from using a consistent software environment, input data must be identical between runs to ensure exact repeatability. VirES provides access to only the most recent available versions of data and models. This means that it is not possible to reproduce older results deterministically when using viresclient. The product version numbers are available within the data objects returned by viresclient, so you should record these when documenting and publishing your results. If you want to be able to repeat your analysis identically in the future (using the same product versions), we recommend you store the interim data returned by viresclient so that you are no longer relying on the VirES server.
Portability of the environment#
We would like to make it easier for you to run a compatible software stack on any machine (your laptop, workstation, or HPC etc.). While you can install viresclient within any Python environment and start accessing Swarm data, the exact combination of software and their versions means that a collaborator’s analysis code may not work the same within your environment. If both of you can share the same software stack, where one of you may work on the VRE for ease of use and the other may use an HPC system to run expensive computations, then it will make it easier to share analysis code. We are looking into solutions for how to do this reliably, given the differing requirements of institutional systems.