Difference between revisions of "Osgeolive-jupyter"

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=== opendatacube ===
 
=== opendatacube ===
 +
 +
 +
<pre>
 +
Package                      Version
 +
----------------------------- ----------------------------
 +
adal                          1.2.7
 +
adlfs                        2022.4.0
 +
affine                        2.3.1
 +
aiobotocore                  2.2.0
 +
aiohttp                      3.8.1
 +
aioitertools                  0.10.0
 +
aiosignal                    1.2.0
 +
alembic                      1.7.7
 +
ansiwrap                      0.8.4
 +
anyio                        3.5.0
 +
appdirs                      1.4.4
 +
argon2-cffi                  21.3.0
 +
argon2-cffi-bindings          21.2.0
 +
asciitree                    0.3.3
 +
asgiref                      3.5.0
 +
asn1crypto                    1.5.1
 +
astropy                      5.0.4
 +
asttokens                    2.0.5
 +
async-generator              1.10
 +
async-timeout                4.0.2
 +
attrs                        21.4.0
 +
av                            9.2.0
 +
awscli                        1.22.76
 +
azure-core                    1.23.1
 +
azure-data-tables            12.4.0
 +
azure-datalake-store          0.0.51
 +
azure-identity                1.9.0
 +
azure-storage-blob            12.11.0
 +
Babel                        2.9.1
 +
backcall                      0.2.0
 +
backports.functools-lru-cache 1.6.4
 +
beautifulsoup4                4.11.1
 +
black                        22.3.0
 +
bleach                        5.0.0
 +
blinker                      1.4
 +
blosc                        1.10.2
 +
bokeh                        2.4.2
 +
boltons                      21.0.0
 +
boto3                        1.21.21
 +
botocore                      1.24.21
 +
Bottleneck                    1.3.4
 +
bqplot                        0.12.33
 +
branca                        0.4.2
 +
brotlipy                      0.7.0
 +
cached-property              1.5.2
 +
cachetools                    5.0.0
 +
cachey                        0.2.1
 +
Cartopy                      0.20.2
 +
cchardet                      2.1.7
 +
certifi                      2021.10.8
 +
certipy                      0.1.3
 +
cf-xarray                    0.7.2
 +
cffi                          1.15.0
 +
cfgrib                        0.9.10.1
 +
cftime                        1.6.0
 +
cgen                          2020.1
 +
charset-normalizer            2.0.12
 +
ciso                          0.1.0
 +
click                        8.0.4
 +
click-plugins                1.1.1
 +
cligj                        0.7.2
 +
cloudpickle                  2.0.0
 +
cmip6-preprocessing          0.0.0
 +
cmocean                      2.0
 +
colorama                      0.4.3
 +
colorcet                      3.0.0
 +
colorspacious                1.1.2
 +
colour                        0.1.5
 +
commonmark                    0.9.1
 +
configobj                    5.0.6
 +
contextily                    1.2.0
 +
croniter                      0.3.36
 +
cryptography                  36.0.2
 +
cycler                        0.11.0
 +
cytoolz                      0.11.2
 +
dask                          2022.2.1
 +
dask-gateway                  0.9.0
 +
dask-geopandas                0.1.0
 +
dask-glm                      0.2.0
 +
dask-image                    2021.12.0
 +
dask-kubernetes              2022.1.0
 +
dask-labextension            5.2.0
 +
dask-ml                      2022.1.22
 +
dataclasses                  0.8
 +
datacube                      1.8.6
 +
datashader                    0.14.0
 +
datashape                    0.5.4
 +
debugpy                      1.6.0
 +
decorator                    5.1.1
 +
defusedxml                    0.7.1
 +
descartes                    1.1.0
 +
distributed                  2022.2.1
 +
docker                        5.0.3
 +
docker-pycreds                0.4.0
 +
docopt                        0.6.2
 +
docrep                        0.3.2
 +
docutils                      0.15.2
 +
donfig                        0.7.0
 +
eccodes                      1.4.0
 +
elementpath                  2.5.1
 +
entrypoints                  0.4
 +
eofs                          1.4.0
 +
erddapy                      1.2.1
 +
ESMPy                        8.2.0
 +
executing                    0.8.3
 +
fastapi                      0.75.2
 +
fasteners                    0.17.3
 +
fastjmd95                    0.2.1
 +
fastjsonschema                2.15.3
 +
fastprogress                  1.0.2
 +
filelock                      3.6.0
 +
findlibs                      0.0.2
 +
Fiona                        1.8.21
 +
flit-core                    3.7.1
 +
flox                          0.4.1
 +
folium                        0.12.1.post1
 +
fonttools                    4.33.3
 +
frozenlist                    1.3.0
 +
fsspec                        2022.3.0
 +
future                        0.18.2
 +
gcsfs                        2022.3.0
 +
GDAL                          3.4.2
 +
gdown                        4.4.0
 +
geocube                      0.2.0
 +
geogif                        0.1.3
 +
geographiclib                1.52
 +
geojson                      2.5.0
 +
geopandas                    0.10.2
 +
geopy                        2.2.0
 +
geoviews                      1.9.5
 +
google-api-core              2.5.0
 +
google-auth                  2.6.6
 +
google-auth-oauthlib          0.5.1
 +
google-cloud-core            2.2.2
 +
google-cloud-storage          2.1.0
 +
google-crc32c                1.1.2
 +
google-resumable-media        2.1.0
 +
googleapis-common-protos      1.56.0
 +
graphviz                      0.20
 +
greenlet                      1.1.2
 +
grpcio                        1.45.0
 +
gsw                          3.4.0
 +
h11                          0.13.0
 +
h5netcdf                      0.0.0
 +
h5py                          3.6.0
 +
HeapDict                      1.0.1
 +
holoviews                    1.14.8
 +
hvplot                        0.7.3
 +
idna                          3.3
 +
imagecodecs                  2022.2.22
 +
imageio                      2.18.0
 +
importlib-metadata            4.11.3
 +
importlib-resources          5.7.1
 +
iniconfig                    1.1.1
 +
intake                        0.6.5
 +
intake-esm                    2021.8.17
 +
intake-geopandas              0.4.0
 +
intake-xarray                0.6.0
 +
ipyevents                    2.0.1
 +
ipyfilechooser                0.6.0
 +
ipykernel                    6.13.0
 +
ipyleaflet                    0.16.0
 +
ipysheet                      0.5.0
 +
ipython                      8.3.0
 +
ipython-genutils              0.2.0
 +
ipytree                      0.2.1
 +
ipywidgets                    7.6.5
 +
isodate                      0.6.1
 +
jdcal                        1.4.1
 +
jedi                          0.18.1
 +
Jinja2                        3.1.1
 +
jmespath                      1.0.0
 +
joblib                        1.1.0
 +
json5                        0.9.5
 +
jsonpickle                    2.1.0
 +
jsonschema                    4.4.0
 +
jupyter-client                7.3.0
 +
jupyter-core                  4.9.2
 +
jupyter-panel-proxy          0.1.0
 +
jupyter-resource-usage        0.6.1
 +
jupyter-server                1.17.0
 +
jupyter-server-proxy          3.2.1
 +
jupyter-telemetry            0.1.0
 +
jupyterhub                    2.2.1
 +
jupyterlab                    3.3.1
 +
jupyterlab-geojson            3.2.0
 +
jupyterlab-pygments          0.2.2
 +
jupyterlab-server            2.13.0
 +
jupyterlab-widgets            1.1.0
 +
kiwisolver                    1.4.2
 +
kubernetes                    23.3.0
 +
kubernetes-asyncio            22.6.4
 +
lark-parser                  0.12.0
 +
leafmap                      0.9.2
 +
llvmlite                      0.36.0
 +
locket                        1.0.0
 +
lz4                          4.0.0
 +
Mako                          1.2.0
 +
mapclassify                  2.4.3
 +
Markdown                      3.3.6
 +
MarkupSafe                    2.1.1
 +
marshmallow                  3.15.0
 +
marshmallow-oneofschema      3.0.1
 +
matplotlib                    3.5.1
 +
matplotlib-inline            0.1.3
 +
mercantile                    1.2.1
 +
MetPy                        1.3.0
 +
mistune                      0.8.4
 +
morecantile                  3.1.2
 +
mpi4py                        3.1.3
 +
msal                          1.17.0
 +
msal-extensions              0.3.1
 +
msgpack                      1.0.3
 +
msrest                        0.6.21
 +
multidict                    6.0.2
 +
multipledispatch              0.6.0
 +
munch                        2.5.0
 +
munkres                      1.1.4
 +
mypy-extensions              0.4.3
 +
natsort                      8.1.0
 +
nb-conda-kernels              2.3.1
 +
nbclassic                    0.3.7
 +
nbclient                      0.5.13
 +
nbconvert                    6.5.0
 +
nbformat                      5.3.0
 +
nbgitpuller                  1.0.2
 +
nbstripout                    0.5.0
 +
nc-time-axis                  1.4.1
 +
nest-asyncio                  1.5.5
 +
netCDF4                      1.5.8
 +
networkx                      2.8
 +
noise                        1.2.2
 +
notebook                      6.4.11
 +
notebook-shim                0.1.0
 +
numba                        0.53.1
 +
numcodecs                    0.9.1
 +
numexpr                      2.8.0
 +
numpy                        1.22.3
 +
numpy-groupies                0.9.15
 +
oauthlib                      3.2.0
 +
odc-algo                      0.2.2
 +
odc-geo                      0.2.0
 +
odc-stac                      0.3.0
 +
packaging                    21.3
 +
pamela                        1.0.0
 +
pandas                        1.4.2
 +
pandocfilters                1.5.0
 +
panel                        0.13.0
 +
papermill                    2.3.4
 +
param                        1.12.1
 +
parcels                      2.3.0
 +
parso                        0.8.3
 +
partd                        1.2.0
 +
pathspec                      0.9.0
 +
patsy                        0.5.2
 +
pdal                          3.1.2
 +
pdal-plugins                  1.2.0
 +
pendulum                      2.1.2
 +
pexpect                      4.8.0
 +
pickleshare                  0.7.5
 +
Pillow                        9.1.0
 +
PIMS                          0.5
 +
Pint                          0.19.2
 +
pip                          20.3.4
 +
planetary-computer            0.4.6
 +
platformdirs                  2.5.1
 +
pluggy                        1.0.0
 +
pooch                        1.6.0
 +
portalocker                  2.4.0
 +
prefect                      1.2.1
 +
progressbar2                  4.0.0
 +
prometheus-client            0.14.1
 +
prompt-toolkit                3.0.29
 +
protobuf                      3.19.4
 +
pscript                      0.7.5
 +
psutil                        5.9.0
 +
psycopg2                      2.9.3
 +
ptyprocess                    0.7.0
 +
pure-eval                    0.2.2
 +
py                            1.11.0
 +
pyarrow                      7.0.0
 +
pyasn1                        0.4.8
 +
pyasn1-modules                0.2.7
 +
pycamhd                      0.7.0
 +
pycparser                    2.21
 +
PyCRS                        1.0.2
 +
pyct                          0.4.6
 +
pycurl                        7.45.1
 +
pydantic                      1.9.0
 +
pydap                        3.3.0
 +
pyepsg                        0.4.0
 +
pyerfa                        2.0.0.1
 +
pygeos                        0.12.0
 +
Pygments                      2.12.0
 +
PyJWT                        2.3.0
 +
pykdtree                      1.3.4
 +
pymbolic                      2021.1
 +
pyOpenSSL                    22.0.0
 +
pyorbital                    1.7.1
 +
pyparsing                    3.0.8
 +
pyproj                        3.3.1
 +
PyQt5                        5.12.3
 +
PyQt5-sip                    4.19.18
 +
PyQtChart                    5.12
 +
PyQtWebEngine                5.12.1
 +
pyresample                    1.23.0
 +
pyrsistent                    0.18.1
 +
pyshp                        2.2.0
 +
PySocks                      1.7.1
 +
pyspectral                    0.11.0
 +
pystac                        1.2.0
 +
pystac-client                0.3.2
 +
pytest                        7.1.2
 +
python-box                    6.0.2
 +
python-dateutil              2.8.2
 +
python-geotiepoints          1.4.0
 +
python-gist                  0.10.6
 +
python-gnupg                  0.4.8
 +
python-json-logger            2.0.1
 +
python-slugify                6.1.2
 +
python-utils                  3.1.0
 +
pytools                      2022.1.6
 +
pytz                          2022.1
 +
pytzdata                      2020.1
 +
pyu2f                        0.1.5
 +
pyviz-comms                  2.2.0
 +
PyWavelets                    1.3.0
 +
PyYAML                        5.4.1
 +
pyzmq                        22.3.0
 +
rasterio                      1.2.10
 +
rechunker                    0.4.2
 +
requests                      2.27.1
 +
requests-oauthlib            1.3.1
 +
rfc3339-validator            0.1.4
 +
rich                          12.3.0
 +
rio-cogeo                    3.2.0
 +
rio-mucho                    1.0.0
 +
rio-tiler                    1.4.0
 +
rio-toa                      0.3.0
 +
rioxarray                    0.11.1
 +
rsa                          4.7.2
 +
Rtree                        1.0.0
 +
ruamel.yaml                  0.17.21
 +
ruamel.yaml.clib              0.2.6
 +
s3fs                          2022.3.0
 +
s3transfer                    0.5.2
 +
sarsen                        0.9.0
 +
satpy                        0.36.0
 +
scikit-image                  0.19.2
 +
scikit-learn                  1.0.2
 +
scipy                        1.8.0
 +
seaborn                      0.11.2
 +
Send2Trash                    1.8.0
 +
setuptools                    59.8.0
 +
Shapely                      1.8.0
 +
shellingham                  1.4.0
 +
simpervisor                  0.4
 +
six                          1.16.0
 +
slicerator                    1.1.0
 +
sniffio                      1.2.0
 +
snuggs                        1.4.7
 +
sortedcontainers              2.4.0
 +
soupsieve                    2.3.1
 +
sparse                        0.13.0
 +
SQLAlchemy                    1.4.36
 +
stac-vrt                      1.0.3
 +
stack-data                    0.2.0
 +
stackstac                    0.4.1
 +
starlette                    0.17.1
 +
statsmodels                  0.13.2
 +
strict-rfc3339                0.7
 +
tabulate                      0.8.9
 +
tblib                        1.7.0
 +
tenacity                      8.0.1
 +
terminado                    0.13.3
 +
text-unidecode                1.3
 +
textwrap3                    0.9.2
 +
threadpoolctl                3.1.0
 +
tifffile                      2022.4.28
 +
tiledb                        0.14.2
 +
tinycss2                      1.1.1
 +
toml                          0.10.2
 +
tomli                        2.0.1
 +
toolz                        0.11.2
 +
tornado                      6.1
 +
tqdm                          4.64.0
 +
traitlets                    5.1.1
 +
traittypes                    0.2.1
 +
trollimage                    1.18.3
 +
trollsift                    0.4.0
 +
typed-ast                    1.5.3
 +
typer                        0.4.1
 +
typing-extensions            4.2.0
 +
unicodedata2                  14.0.0
 +
Unidecode                    1.3.4
 +
urllib3                      1.26.9
 +
uvicorn                      0.17.6
 +
voila                        0.3.5
 +
wcwidth                      0.2.5
 +
webencodings                  0.5.1
 +
WebOb                        1.8.7
 +
websocket-client              1.3.2
 +
websockets                    10.3
 +
wheel                        0.37.1
 +
whitebox                      2.1.2
 +
whiteboxgui                  0.7.0
 +
widgetsnbextension            3.5.2
 +
wrapt                        1.14.0
 +
xarray                        2022.3.0
 +
xarray-sentinel              0.9.1
 +
xarray-spatial                0.3.3
 +
xarrayutils                  1.1.1
 +
xcape                        0+untagged.33.g4d4ab9d.dirty
 +
xclim                        0.36.0
 +
xcube                        0.9.1
 +
xesmf                        0.6.2
 +
xgcm                          0.7.0
 +
xhistogram                    0.3.1
 +
xlayers                      0.2.2
 +
xmitgcm                      0.5.2
 +
xmlschema                    1.10.0
 +
xpublish                      0.1.0
 +
xrft                          0.0.0
 +
xyzservices                  2022.4.0
 +
yarl                          1.7.2
 +
zarr                          2.11.3
 +
zict                          2.2.0
 +
zipp                          3.8.0
 +
</pre>
  
 
<pre>
 
<pre>

Revision as of 22:05, 16 June 2022

Python Libraries Strategy

Some priority python for the Jupyter Notebooks of 2022

  • GeoPandas (and pySAL) : gpd 0.10.2direct link to GEOS 3.10, popular extension to Pandas data science; please recall that pySAL is merging into the GeoPandas project overall; GeoPandas+pySAL use matplotlib graphics base, prefers Folium for web maps (?)
  • Numpy & Pandas : np '1.21.5',pd 1.3.5 fundamental packages
  • PostGIS writing done with pyscopg2 (low-level) or geoalchemy2 (ORM based on sqlalchemy)
  • rasterio : modern geoTIFF handling; sophisticated library design; not easy to build from source 1.2.10
  • Shapely & Fiona : direct link to libGEOS/ogr from python; example Notebooks in place Shapely-1.8.0 Fiona-1.8.21
  • opendatacube core and Notebook client examples v1.8.6 -LINK- odc-geo a minimal Opendatacube setup (see below)
  • pySTAC spatial-temporal analysis standard; opendatacube collaborators v1.4 -LINK-
  • stactools is a collection of interfaces and utilities, TBD from odc soon -LINK-
  • Scikit-Learn : original machine-learning library by international research team led by French math; stands the tests of time; integrated with SciPy for Fortran, BLAS, LAPACK libs; numpy for data allocation; important primitives like PCA, SVM, and KNN are optimized in practical ways, and then benchmarked against pure Fortran or C++ for comparison 0.23.2
  • boto for AWS S3, other data store transfer; can use AWS credentials (or Hetzner, or..) modern version using pip installed locally
  • osmium libosmium2-dev, libosmium2-doc, python3-pyosmium, osmium-tool : a C++ framework for working with OSM data files; osmium library bindings for Python 3 ## osmium version 1.14.0; libosmium version 2.18.0; Supported PBF compression types: none zlib lz4; Copyright (C) 2013-2022 Jochen Topf <jochen@topf.org>
  • mapnik libmapnik3.1, python3-mapnik : mapnik rendering engine for OSM maps and others libmapnik.so.3.1.0
  • mapclassify : part of pySAL, versions must match with geopandas setup
  • lightgbm : MSFT python, tricky to install, might have to wait until other versions are sorted here
  • inline maps vs slippy maps : cartopy, other matplotlib variants are inline static; notebook web maps need js libs e.g. ipyleaflet
  • EOmaps TODO evaluate here -LINK-
  • georasters TODO evaluate -LINK
  • Canada Met - Meteorological Service of Canada Open Data User Documentation -LINK-
  • LiDAR : this is slightly painful since modern commercial GIS is flooded with this tech, delivered by advanced Western companies seeking something novel to sell. Changes to the LASzip licensing have enabled inclusion, but as of today, no Debian maintainer in place, and bas wants PDAL out at this time. -EMAIL- -EMAIL2- *update* PDAL via dot-deb is included in ol15
  • DeepLearning "no" : deep learning has taken over in the modern AI/ML research, for funding and hype, but not on this disk. Please note that the ML libraries on osgeolive are completely useful, accurate and performant today.. no need for a constant and fast Internet connection, nor a compute infrastructure the size of a large naval ship, or special impenetrable models that can only be built by those machines. -LINK- Serious and in-demand applications like "facial recognition" are not included here. Many real applications to remote sensing are built using DeepLearning, but those are not available on this disk. Some benefits of not including DeepLearning : no dependencies on tricky GPU libs; not suffering from fast-updates of important ML core libraries; avoid black-box training models, and their disk space; avoid software patent problems in Western Nations.

"I feel that a common and well-known distro like this is an opportunity to build engineering cooperation, between teams that may not interact otherwise.. like the physical code sprints" -darkblueb in California

Example Notebooks in previous OSGeoLive -LINK-

Other Resources: Pangeo PYTHIA -LINK-

opendatacube "Cube in a Box" -LINK-

--

Jammy Notes

Using PPA ubuntugis-unstable & Ubuntu Universe dot-deb packages, the installation results look roughly like this: 

mjam@x10jam:~$ cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04 LTS"

#--
 libgeos3.10.2   (libgeos3.10.2) 
 libgdal-dev     (3.4.3+dfsg-1~jammy0)
 postgresql-14-postgis-3     (3.2.0+dfsg-1~focal0)
 PGSQL="140" POSTGIS="3.2.0 c3e3cc0" GEOS="3.10.2-CAPI-1.16.0" PROJ="8.2.1" LIBJSON="0.15" 
#--

System:
    python: 3.10.4 (main, Apr  2 2022, 09:04:19) [GCC 11.2.0]
executable: /usr/bin/python3
   machine: Linux-5.15.0-25-generic-x86_64-with-glibc2.35

Python dependencies:
          pip: 22.0.2
   setuptools: 59.6.0
      sklearn: 0.23.2
        numpy: 1.21.5
        scipy: 1.8.0
       Cython: None
       pandas: 1.3.5
   matplotlib: 3.5.1
       joblib: 0.17.0
threadpoolctl: 3.1.0

Built with OpenMP: True

Jupyter jammy Version

dbb@x10jam:~$ jupyter --version
Selected Jupyter core packages...
IPython          : 7.31.1
ipykernel        : 6.7.0
ipywidgets       : 6.0.0
jupyter_client   : 7.1.2
jupyter_core     : 4.9.1
jupyter_server   : not installed
jupyterlab       : not installed
nbclient         : 0.5.6
nbconvert        : 6.4.0
nbformat         : 5.1.3
notebook         : 6.4.8
qtconsole        : not installed
traitlets        : 5.1.1
dbb@x10jam:~$ jupyter --paths
config:
    /home/dbb/.jupyter
    /home/dbb/.local/etc/jupyter
    /usr/etc/jupyter
    /usr/local/etc/jupyter
    /etc/jupyter
data:
    /home/dbb/.local/share/jupyter
    /usr/local/share/jupyter
    /usr/share/jupyter
runtime:
    /home/dbb/.local/share/jupyter/runtime

Jupyter jammy Install

dbb@x10jam:~$ sudo apt install jupyter 
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done


The following additional packages will be installed:
  fonts-glyphicons-halflings jupyter-client jupyter-console jupyter-core jupyter-nbconvert
  jupyter-nbextension-jupyter-js-widgets jupyter-nbformat jupyter-notebook libjs-backbone libjs-bootstrap libjs-bootstrap-tour
  libjs-codemirror libjs-es6-promise libjs-jed libjs-jquery-typeahead libjs-marked libjs-moment libjs-requirejs
  libjs-requirejs-text libjs-text-encoding libjs-xterm node-jed python3-argon2 python3-ipywidgets python3-jupyter-console
  python3-notebook python3-prometheus-client python3-send2trash python3-terminado python3-widgetsnbextension
Suggested packages:
  jupyter-qtconsole libjs-jquery-lazyload libjs-json
The following NEW packages will be installed:
  fonts-glyphicons-halflings jupyter jupyter-client jupyter-console jupyter-core jupyter-nbconvert
  jupyter-nbextension-jupyter-js-widgets jupyter-nbformat jupyter-notebook libjs-backbone libjs-bootstrap libjs-bootstrap-tour
  libjs-codemirror libjs-es6-promise libjs-jed libjs-jquery-typeahead libjs-marked libjs-moment libjs-requirejs
  libjs-requirejs-text libjs-text-encoding libjs-xterm node-jed python3-argon2 python3-ipywidgets python3-jupyter-console
  python3-notebook python3-prometheus-client python3-send2trash python3-terminado python3-widgetsnbextension
0 upgraded, 31 newly installed, 0 to remove and 15 not upgraded.
Need to get 3,969 kB of archives.
After this operation, 33.5 MB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://mirrors.wikimedia.org/ubuntu jammy/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-2 [117 kB]

...                  
Fetched 3,969 kB in 13s (301 kB/s)                                                                                              
Extracting templates from packages: 100%
Selecting previously unselected package fonts-glyphicons-halflings.
(Reading database ... 436812 files and directories currently installed.)


Jupyter R Install

dbb@x10jam:~$ sudo apt install r-cran-sf
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done


The following additional packages will be installed:
  bzip2-doc gfortran gfortran-11 libblas-dev libbz2-dev libc-ares2 libgfortran-11-dev libjs-d3 libjs-es5-shim
  libjs-highlight.js libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-json
  libjs-microplugin.js libjs-modernizr libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack-dev
  libnlopt0 libnode72 libreadline-dev libudunits2-0 libudunits2-data littler node-highlight.js node-html5shiv
  node-normalize.css nodejs nodejs-doc r-base-core r-base-dev r-cran-abind r-cran-acepack r-cran-askpass r-cran-assertthat
  r-cran-backports r-cran-base64enc r-cran-bench r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-boot
  r-cran-brio r-cran-broom r-cran-cachem r-cran-callr r-cran-caret r-cran-catools r-cran-cba r-cran-checkmate r-cran-chron
  r-cran-class r-cran-classint r-cran-cli r-cran-cliapp r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-commonmark
  r-cran-conquer r-cran-covr r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-cvst r-cran-data.table r-cran-dbi
  r-cran-dbitest r-cran-dbplyr r-cran-ddalpha r-cran-decor r-cran-deldir r-cran-deoptimr r-cran-desc r-cran-diffobj
  r-cran-digest r-cran-dimred r-cran-domc r-cran-dplyr r-cran-drr r-cran-dt r-cran-dygraphs r-cran-e1071 r-cran-earth
  r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastica r-cran-fastmap r-cran-fastmatch r-cran-filehash
  r-cran-fnn r-cran-fontbitstreamvera r-cran-fontliberation r-cran-fontquiver r-cran-foreach r-cran-foreign r-cran-formula
  r-cran-fs r-cran-fts r-cran-furrr r-cran-future r-cran-future.apply r-cran-gdata r-cran-generics r-cran-geometry
  r-cran-geosphere r-cran-ggplot2 r-cran-gh r-cran-gitcreds r-cran-globals r-cran-glue r-cran-goftest r-cran-gower
  r-cran-gplots r-cran-gridextra r-cran-gtable r-cran-gtools r-cran-hexbin r-cran-highr r-cran-hmisc r-cran-hms
  r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-igraph r-cran-ini r-cran-interp
  r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jpeg r-cran-jsonlite r-cran-kernlab r-cran-kernsmooth r-cran-knitr
  r-cran-ks r-cran-labeling r-cran-later r-cran-lattice r-cran-latticeextra r-cran-lava r-cran-lazyeval r-cran-lifecycle
  r-cran-linprog r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lobstr r-cran-logcondens r-cran-lpsolve r-cran-lubridate
  r-cran-lwgeom r-cran-magic r-cran-magrittr r-cran-mapproj r-cran-maps r-cran-maptools r-cran-markdown r-cran-mass
  r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-mclust r-cran-mda r-cran-memoise r-cran-mets r-cran-mgcv
  r-cran-mime r-cran-minqa r-cran-misc3d r-cran-mlbench r-cran-mlmetrics r-cran-mockery r-cran-mockr r-cran-modeldata
  r-cran-modelmetrics r-cran-multcomp r-cran-multicool r-cran-munsell r-cran-mvtnorm r-cran-nlme r-cran-nloptr r-cran-nnet
  r-cran-numderiv r-cran-openssl r-cran-palmerpenguins r-cran-parallelly r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig
  r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-plot3d r-cran-plotmo r-cran-plotrix r-cran-pls r-cran-plyr r-cran-png
  r-cran-polyclip r-cran-pracma r-cran-praise r-cran-prettycode r-cran-prettyunits r-cran-proc r-cran-processx r-cran-prodlim
  r-cran-profmem r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-ps r-cran-purrr r-cran-quadprog
  r-cran-quantmod r-cran-quantreg r-cran-r6 r-cran-ragg r-cran-rann r-cran-rappdirs r-cran-raster r-cran-rcolorbrewer
  r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcppprogress r-cran-rcpproll r-cran-recipes r-cran-rematch2
  r-cran-reshape2 r-cran-rex r-cran-rgdal r-cran-rgl r-cran-rlang r-cran-rmarkdown r-cran-rmysql r-cran-robustbase r-cran-rocr
  r-cran-rpart r-cran-rpostgresql r-cran-rprojroot r-cran-rsample r-cran-rspectra r-cran-rsqlite r-cran-rstudioapi r-cran-runit
  r-cran-s2 r-cran-sandwich r-cran-sass r-cran-scales r-cran-selectr r-cran-setrng r-cran-sfsmisc r-cran-shiny r-cran-slider
  r-cran-sodium r-cran-sourcetools r-cran-sp r-cran-sparsem r-cran-spatial r-cran-spatstat r-cran-spatstat.core
  r-cran-spatstat.data r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-squarem
  r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-svglite r-cran-sys r-cran-systemfonts
  r-cran-teachingdemos r-cran-tensor r-cran-terra r-cran-testit r-cran-testthat r-cran-textshaping r-cran-th.data r-cran-tibble
  r-cran-tidyr r-cran-tidyselect r-cran-tikzdevice r-cran-timedate r-cran-timereg r-cran-timeseries r-cran-tinytex
  r-cran-tseries r-cran-ttr r-cran-units r-cran-utf8 r-cran-vctrs r-cran-vdiffr r-cran-viridis r-cran-viridislite r-cran-waldo
  r-cran-warp r-cran-webutils r-cran-withr r-cran-wk r-cran-wkutils r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-xts
  r-cran-yaml r-cran-zoo r-doc-html r-recommended ttf-bitstream-vera

Suggested packages:
  gfortran-multilib gfortran-doc gfortran-11-multilib gfortran-11-doc libcoarrays-dev liblapack-doc readline-doc npm elpa-ess
  r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-fonts-extra texlive-extra-utils texinfo r-cran-forcats r-cran-ggbeeswarm
  r-cran-ggridges r-cran-roxygen2 r-cran-aer r-cran-bbmle r-cran-car r-cran-cmprsk r-cran-coda r-cran-emmeans r-cran-epir
  r-cran-gam r-cran-gee r-cran-geepack r-cran-glmnet r-cran-gmm r-cran-irlba r-cran-lavaan r-cran-leaps r-cran-lmtest
  r-cran-lsmeans r-cran-metafor r-cran-network r-cran-ordinal r-cran-plm r-cran-psych r-cran-robust r-cran-spdep
  r-cran-spatialreg r-cran-spelling r-cran-survey r-cran-systemfit r-cran-bradleyterry2 r-cran-ellipse r-cran-party
  r-cran-randomforest r-cran-gclus r-cran-devtools r-cran-tinytest r-cran-spdata r-cran-whoami r-cran-vcd r-cran-shinyjs
  r-cran-r.utils r-cran-nanotime r-cran-clipr r-cran-nmf r-cran-rtsne r-cran-energy r-cran-optimx r-cran-pcapp
  r-cran-reticulate r-cran-scatterplot3d r-cran-vegan r-cran-unitizer r-cran-r.rsp r-bioc-affy r-bioc-biobase r-bioc-limma
  r-cran-cairo r-cran-readr r-cran-ape r-bioc-graph r-cran-magick r-cran-formatr r-cran-webshot r-cran-fields r-cran-bookdown
  r-cran-lavasearch2 r-cran-polycor r-cran-tidyverse r-cran-getopt r-cran-mapdata r-cran-rcurl r-cran-ucminf r-cran-cowplot
  r-cran-tkrplot r-cran-formattable r-cran-gbm r-cran-mlr r-cran-partykit r-cran-rmpi r-cran-doparallel r-cran-itertools
  r-cran-pbmcapply r-cran-pingr r-cran-ncdf4 r-cran-gstat r-cran-inline r-cran-rvest r-cran-usethis r-cran-tufte
  r-cran-rsconnect r-cran-gert r-cran-dichromat r-cran-stars r-cran-sm r-cran-gsl r-cran-locfit r-cran-randomfields
  r-cran-randomfieldsutils r-cran-nleqslv r-cran-tcltk2 r-cran-logspline r-cran-zeallot r-cran-remotes

The following NEW packages will be installed:
  bzip2-doc gfortran gfortran-11 libblas-dev libbz2-dev libc-ares2 libgfortran-11-dev libjs-d3 libjs-es5-shim
  libjs-highlight.js libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-json
  libjs-microplugin.js libjs-modernizr libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack-dev
  libnlopt0 libnode72 libreadline-dev libudunits2-0 libudunits2-data littler node-highlight.js node-html5shiv
  node-normalize.css nodejs nodejs-doc r-base-core r-base-dev r-cran-abind r-cran-acepack r-cran-askpass r-cran-assertthat
  r-cran-backports r-cran-base64enc r-cran-bench r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-boot
  r-cran-brio r-cran-broom r-cran-cachem r-cran-callr r-cran-caret r-cran-catools r-cran-cba r-cran-checkmate r-cran-chron
  r-cran-class r-cran-classint r-cran-cli r-cran-cliapp r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-commonmark
  r-cran-conquer r-cran-covr r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-cvst r-cran-data.table r-cran-dbi
  r-cran-dbitest r-cran-dbplyr r-cran-ddalpha r-cran-decor r-cran-deldir r-cran-deoptimr r-cran-desc r-cran-diffobj
  r-cran-digest r-cran-dimred r-cran-domc r-cran-dplyr r-cran-drr r-cran-dt r-cran-dygraphs r-cran-e1071 r-cran-earth
  r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastica r-cran-fastmap r-cran-fastmatch r-cran-filehash
  r-cran-fnn r-cran-fontbitstreamvera r-cran-fontliberation r-cran-fontquiver r-cran-foreach r-cran-foreign r-cran-formula
  r-cran-fs r-cran-fts r-cran-furrr r-cran-future r-cran-future.apply r-cran-gdata r-cran-generics r-cran-geometry
  r-cran-geosphere r-cran-ggplot2 r-cran-gh r-cran-gitcreds r-cran-globals r-cran-glue r-cran-goftest r-cran-gower
  r-cran-gplots r-cran-gridextra r-cran-gtable r-cran-gtools r-cran-hexbin r-cran-highr r-cran-hmisc r-cran-hms
  r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-igraph r-cran-ini r-cran-interp
  r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jpeg r-cran-jsonlite r-cran-kernlab r-cran-kernsmooth r-cran-knitr
  r-cran-ks r-cran-labeling r-cran-later r-cran-lattice r-cran-latticeextra r-cran-lava r-cran-lazyeval r-cran-lifecycle
  r-cran-linprog r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lobstr r-cran-logcondens r-cran-lpsolve r-cran-lubridate
  r-cran-lwgeom r-cran-magic r-cran-magrittr r-cran-mapproj r-cran-maps r-cran-maptools r-cran-markdown r-cran-mass
  r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-mclust r-cran-mda r-cran-memoise r-cran-mets r-cran-mgcv
  r-cran-mime r-cran-minqa r-cran-misc3d r-cran-mlbench r-cran-mlmetrics r-cran-mockery r-cran-mockr r-cran-modeldata
  r-cran-modelmetrics r-cran-multcomp r-cran-multicool r-cran-munsell r-cran-mvtnorm r-cran-nlme r-cran-nloptr r-cran-nnet
  r-cran-numderiv r-cran-openssl r-cran-palmerpenguins r-cran-parallelly r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig
  r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-plot3d r-cran-plotmo r-cran-plotrix r-cran-pls r-cran-plyr r-cran-png
  r-cran-polyclip r-cran-pracma r-cran-praise r-cran-prettycode r-cran-prettyunits r-cran-proc r-cran-processx r-cran-prodlim
  r-cran-profmem r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-ps r-cran-purrr r-cran-quadprog
  r-cran-quantmod r-cran-quantreg r-cran-r6 r-cran-ragg r-cran-rann r-cran-rappdirs r-cran-raster r-cran-rcolorbrewer
  r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcppprogress r-cran-rcpproll r-cran-recipes r-cran-rematch2
  r-cran-reshape2 r-cran-rex r-cran-rgdal r-cran-rgl r-cran-rlang r-cran-rmarkdown r-cran-rmysql r-cran-robustbase r-cran-rocr
  r-cran-rpart r-cran-rpostgresql r-cran-rprojroot r-cran-rsample r-cran-rspectra r-cran-rsqlite r-cran-rstudioapi r-cran-runit
  r-cran-s2 r-cran-sandwich r-cran-sass r-cran-scales r-cran-selectr r-cran-setrng r-cran-sf r-cran-sfsmisc r-cran-shiny
  r-cran-slider r-cran-sodium r-cran-sourcetools r-cran-sp r-cran-sparsem r-cran-spatial r-cran-spatstat r-cran-spatstat.core
  r-cran-spatstat.data r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-squarem
  r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-svglite r-cran-sys r-cran-systemfonts
  r-cran-teachingdemos r-cran-tensor r-cran-terra r-cran-testit r-cran-testthat r-cran-textshaping r-cran-th.data r-cran-tibble
  r-cran-tidyr r-cran-tidyselect r-cran-tikzdevice r-cran-timedate r-cran-timereg r-cran-timeseries r-cran-tinytex
  r-cran-tseries r-cran-ttr r-cran-units r-cran-utf8 r-cran-vctrs r-cran-vdiffr r-cran-viridis r-cran-viridislite r-cran-waldo
  r-cran-warp r-cran-webutils r-cran-withr r-cran-wk r-cran-wkutils r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-xts
  r-cran-yaml r-cran-zoo r-doc-html r-recommended ttf-bitstream-vera
0 upgraded, 325 newly installed, 0 to remove and 15 not upgraded.
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Get:1 http://mirrors.wikimedia.org/ubuntu jammy/main amd64 bzip2-doc all 1.0.8-5build1 [500 kB]

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Get:325 http://mirrors.wikimedia.org/ubuntu jammy/universe amd64 r-recommended all 4.1.2-1ubuntu2 [2,624 B]   
                  
Fetched 299 MB in 12min 45s (391 kB/s)                                                                                          
Extracting templates from packages: 100%
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(Reading database ... 438665 files and directories currently installed.)


Setting up libjs-json (0~20210531+~1.0.8-1) ...
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Setting up bzip2-doc (1.0.8-5build1) ...
Setting up ttf-bitstream-vera (1.10-8.2) ...
Setting up r-doc-html (4.1.2-1ubuntu2) ...
Setting up libgfortran-11-dev:amd64 (11.2.0-19ubuntu1) ...
Setting up libjs-sifter.js (0.6.0+dfsg-2) ...
Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
Setting up node-html5shiv (3.7.3+dfsg-4) ...
Setting up libnlopt0:amd64 (2.7.1-3build1) ...
Setting up libjs-microplugin.js (0.0.3+dfsg-1.1) ...
Setting up libc-ares2:amd64 (1.18.1-1build1) ...
Setting up libreadline-dev:amd64 (8.1.2-1) ...
Setting up libjs-modernizr (2.6.2+ds1-4) ...
Setting up libnode72:amd64 (12.22.9~dfsg-1ubuntu3) ...
Setting up libjs-jquery-datatables (1.11.4+dfsg-1) ...
Setting up libjs-es5-shim (4.6.4-1) ...
Setting up r-base-core (4.1.2-1ubuntu2) ...

Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.5.0-1) ...
Setting up r-cran-squarem (2021.1-1) ...
Setting up libjs-d3 (3.5.17-4) ...
Setting up liblapack-dev:amd64 (3.10.0-2ubuntu1) ...
Setting up r-cran-fastmatch (1.1-3-1) ...
Setting up r-cran-gtable (0.3.0+dfsg-2build1) ...
Setting up r-cran-labeling (0.4.2-1) ...
Setting up r-cran-rcppprogress (0.4.2-2build1) ...
Setting up r-cran-sourcetools (0.1.7-3) ...
Setting up r-cran-lattice (0.20-45-1) ...
Setting up r-cran-ps (1.6.0-1) ...
Setting up r-cran-nlme (3.1.155-1) ...
Setting up r-cran-farver (2.1.0-1) ...
Setting up gfortran-11 (11.2.0-19ubuntu1) ...
Setting up r-cran-pls (2.8-0-1) ...
Setting up r-cran-formula (1.2-4-1) ...
Setting up r-cran-hexbin (1.28.2-1) ...
Setting up r-cran-xml (3.99-0.9-1) ...
Setting up r-cran-spatstat.utils (2.3-0-1) ...
Setting up libudunits2-data (2.2.28-3) ...
Setting up libjs-highlight.js (9.18.5+dfsg1-1) ...
Setting up r-cran-viridislite (0.4.0-2) ...
Setting up r-cran-cluster (2.1.2-2) ...
Setting up r-cran-fontbitstreamvera (0.1.1+dfsg-4build1) ...
Setting up r-cran-sparsem (1.81-1) ...
Setting up r-cran-statmod (1.4.36-1) ...
Setting up r-cran-nnet (7.3-17-1) ...
Setting up libjs-prettify (2015.12.04+dfsg-1.1) ...
Setting up r-cran-tensor (1.5-4) ...
Setting up r-cran-lazyeval (0.2.2-1build1) ...
Setting up r-cran-lpsolve (5.6.15-1build1) ...
Setting up r-cran-wk (0.6.0-1) ...
Setting up r-cran-commonmark (1.7-2) ...
Setting up r-cran-proxy (0.4-26-1) ...
Setting up r-cran-r6 (2.5.1-1) ...
Setting up r-cran-pkgkitten (0.2.2-2) ...
Setting up r-cran-jpeg (0.1-9-1) ...
Setting up r-cran-chron (2.3-56-1) ...
Setting up r-cran-numderiv (2016.8-1.1-3) ...
Setting up node-normalize.css (8.0.1-5) ...
Setting up r-cran-magrittr (2.0.2-1) ...
Setting up r-cran-testit (0.13-1) ...
Setting up r-cran-rappdirs (0.3.3-1) ...
Setting up libblas-dev:amd64 (3.10.0-2ubuntu1) ...
Setting up r-cran-quadprog (1.5-8-1build1) ...
Setting up libbz2-dev:amd64 (1.0.8-5build1) ...
Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
Setting up libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ...
Setting up r-cran-littler (0.3.15-1) ...
Setting up r-cran-prettycode (1.1.0-2build1) ...
Setting up r-cran-fs (1.5.2+dfsg-1) ...
Setting up r-cran-filehash (2.4-2-3) ...
Setting up r-cran-rcpp (1.0.8-1) ...
Setting up r-cran-palmerpenguins (0.1.0-2) ...
Setting up r-cran-curl (4.3.2+dfsg-1) ...
Setting up r-cran-profmem (0.6.0+dfsg-1) ...
Setting up r-cran-codetools (0.2-18-1) ...
Setting up r-cran-brio (1.1.3-1) ...
Setting up r-cran-boot (1.3-28-2) ...
Setting up r-cran-diffobj (0.3.5-1) ...
Setting up r-cran-maps (3.4.0-1) ...
Setting up r-cran-rlang (1.0.1-1) ...
Setting up r-cran-matrixstats (0.61.0-1) ...
Setting up r-cran-listenv (0.8.0+dfsg-1build1) ...
Setting up r-cran-assertthat (0.2.1-2build1) ...
Setting up littler (0.3.15-1) ...
Setting up r-cran-multicool (0.1-12-1) ...
Setting up r-cran-pracma (2.3.6-1) ...
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Setting up r-cran-processx (3.5.2-2) ...
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Setting up r-cran-fansi (1.0.2-1) ...
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Setting up r-cran-mclust (5.4.9-1) ...
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update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
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Setting up r-cran-future (1.24.0+dfsg-1) ...
Setting up r-cran-geometry (0.4.5-1build2) ...
Setting up r-cran-htmlwidgets (1.5.4+dfsg-1) ...
Setting up r-cran-reshape2 (1.4.4-2build1) ...
Setting up r-cran-interp (1.0-33-1build2) ...
Setting up r-cran-future.apply (1.8.1-1) ...
Setting up r-cran-raster (3.5-15-1) ...
Setting up r-cran-fts (0.9.9.2-2) ...
Setting up r-cran-rgdal (1.5-28+dfsg-1) ...
Setting up r-cran-systemfonts (1.0.4-1) ...
Setting up r-cran-th.data (1.1-0-1) ...
Setting up r-cran-httr (1.4.2-1) ...
Setting up r-cran-scales (1.1.1-1build1) ...
Setting up r-cran-memoise (2.0.1-1) ...
Setting up r-cran-lava (1.6.10+dfsg-1) ...
Setting up r-cran-covr (3.5.1+dfsg-2) ...
Setting up r-cran-promises (1.2.0.1+dfsg-1) ...
Setting up r-cran-e1071 (1.7-9-1) ...
Setting up r-cran-spatstat.data (2.1-2-1) ...
Setting up r-cran-multcomp (1.4-18-1) ...
Setting up r-cran-svglite (2.1.0-1) ...
Setting up r-cran-spatstat.geom (2.3-2-1) ...
Setting up r-cran-knitr (1.37+dfsg-1) ...
Setting up r-cran-earth (5.3.1-1) ...
Setting up r-cran-pkgbuild (1.3.1-1) ...
Setting up r-cran-rspectra (0.16-0-1build2) ...
Setting up r-cran-drr (0.0.4-2build1) ...
Setting up r-cran-gplots (3.1.1-2) ...
Setting up r-cran-gh (1.3.0-1) ...
Setting up r-cran-ttr (0.24.3-1) ...
Setting up r-cran-vctrs (0.3.8-2) ...
Setting up r-cran-pillar (1.7.0+dfsg-1) ...
Setting up r-cran-timereg (2.0.1-1) ...
Setting up r-cran-pkgload (1.2.4-1) ...
Setting up r-cran-rocr (1.0-11-2build1) ...
Setting up r-cran-prodlim (2019.11.13-1build1) ...
Setting up r-cran-mlmetrics (1.1.1-3build1) ...
Setting up r-cran-ddalpha (1.3.11-1build2) ...
Setting up r-cran-dimred (0.2.4-1) ...
Setting up r-cran-httpuv (1.6.5+dfsg-1) ...
Setting up r-cran-rpart (4.1.16-1) ...
Setting up r-cran-tibble (3.1.6+dfsg-1) ...
Setting up r-cran-dygraphs (1.1.1.6+dfsg-2build1) ...
Setting up r-cran-shiny (1.5.0+dfsg-2) ...
Setting up r-cran-textshaping (0.3.6-1) ...
Setting up r-cran-ipred (0.9-12-1) ...
Setting up r-cran-bench (1.1.2-1) ...
Setting up r-cran-furrr (0.2.3-1) ...
Setting up r-cran-tidyselect (1.1.2+dfsg-1) ...
Setting up r-cran-wkutils (0.1.1-1) ...
Setting up r-cran-slider (0.2.2-1) ...
Setting up r-cran-classint (0.4-3-1build1) ...
Setting up r-cran-ragg (1.2.1-1) ...
Setting up r-cran-hms (1.1.1-1) ...
Setting up r-cran-rmarkdown (2.6+dfsg-1) ...
Setting up r-cran-mets (1.2.9+dfsg-1) ...
Setting up r-cran-blob (1.2.2-1) ...
Setting up r-cran-dplyr (1.0.8-2) ...
Setting up r-cran-spatstat.core (2.3-2-1) ...
Setting up r-cran-dbplyr (2.1.1-1) ...
Setting up r-cran-rsqlite (2.2.9-1) ...
Setting up r-cran-decor (1.0.1-1) ...
Setting up r-cran-progress (1.2.2-2build1) ...
Setting up r-cran-quantmod (0.4.18-1) ...
Setting up r-recommended (4.1.2-1ubuntu2) ...
Setting up r-cran-crosstalk (1.2.0+dfsg-1) ...
Setting up r-cran-dt (0.17+dfsg-3) ...
Setting up r-cran-ggplot2 (3.3.5+dfsg-2) ...
Setting up r-cran-rematch2 (2.1.2-2build1) ...
Setting up r-cran-tseries (0.10-49-1) ...
Setting up r-cran-viridis (0.6.2-1) ...
Setting up r-cran-rgl (0.108.3-1) ...
Setting up r-cran-waldo (0.3.1-1) ...
Setting up r-cran-tidyr (1.2.0-1) ...
Setting up r-cran-recipes (0.1.17+dfsg-1) ...
Setting up r-cran-rsample (0.1.1-1) ...
Setting up r-cran-spatstat.linnet (2.3-1-1) ...
Setting up r-cran-cliapp (0.1.1-1) ...
Setting up r-cran-spatstat (2.3-0-1) ...
Setting up r-cran-htmltable (2.4.0-1) ...
Setting up r-cran-caret (6.0-90+dfsg-1) ...
Setting up r-cran-testthat (3.1.2-1) ...
Setting up r-cran-mockery (0.4.3+dfsg-1) ...
Setting up r-cran-broom (0.7.12+dfsg-1) ...
Setting up r-cran-misc3d (0.9-1-1) ...
Setting up r-cran-conquer (1.2.2-1) ...
Setting up r-cran-vdiffr (1.0.2-1) ...
Setting up r-cran-dbitest (1.7.2-1) ...
Setting up r-cran-nloptr (2.0.0-1) ...
Setting up r-cran-hmisc (4.6-0-1) ...
Setting up r-cran-quantreg (5.88-1) ...
Setting up r-cran-lme4 (1.1-28-1) ...
Setting up r-cran-plot3d (1.4-2) ...
Setting up r-cran-ks (1.13.3-1) ...
Setting up r-cran-logcondens (2.1.6-1) ...
Processing triggers for sgml-base (1.30) ...
Processing triggers for install-info (6.8-4build1) ...
Processing triggers for mailcap (3.70+nmu1ubuntu1) ...
Processing triggers for fontconfig (2.13.1-4.2ubuntu5) ...
Setting up libudunits2-0 (2.2.28-3) ...
Processing triggers for desktop-file-utils (0.26-1ubuntu3) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for libc-bin (2.35-0ubuntu3) ...
Processing triggers for man-db (2.10.2-1) ...
Processing triggers for tex-common (6.17) ...
Running mktexlsr. This may take some time... done.
Setting up r-cran-units (0.8-0+dfsg-1) ...
Setting up r-cran-sf (1.0-6+dfsg-1) ...
Setting up r-cran-lwgeom (0.2-8-1build1) ...


opendatacube

Package                       Version
----------------------------- ----------------------------
adal                          1.2.7
adlfs                         2022.4.0
affine                        2.3.1
aiobotocore                   2.2.0
aiohttp                       3.8.1
aioitertools                  0.10.0
aiosignal                     1.2.0
alembic                       1.7.7
ansiwrap                      0.8.4
anyio                         3.5.0
appdirs                       1.4.4
argon2-cffi                   21.3.0
argon2-cffi-bindings          21.2.0
asciitree                     0.3.3
asgiref                       3.5.0
asn1crypto                    1.5.1
astropy                       5.0.4
asttokens                     2.0.5
async-generator               1.10
async-timeout                 4.0.2
attrs                         21.4.0
av                            9.2.0
awscli                        1.22.76
azure-core                    1.23.1
azure-data-tables             12.4.0
azure-datalake-store          0.0.51
azure-identity                1.9.0
azure-storage-blob            12.11.0
Babel                         2.9.1
backcall                      0.2.0
backports.functools-lru-cache 1.6.4
beautifulsoup4                4.11.1
black                         22.3.0
bleach                        5.0.0
blinker                       1.4
blosc                         1.10.2
bokeh                         2.4.2
boltons                       21.0.0
boto3                         1.21.21
botocore                      1.24.21
Bottleneck                    1.3.4
bqplot                        0.12.33
branca                        0.4.2
brotlipy                      0.7.0
cached-property               1.5.2
cachetools                    5.0.0
cachey                        0.2.1
Cartopy                       0.20.2
cchardet                      2.1.7
certifi                       2021.10.8
certipy                       0.1.3
cf-xarray                     0.7.2
cffi                          1.15.0
cfgrib                        0.9.10.1
cftime                        1.6.0
cgen                          2020.1
charset-normalizer            2.0.12
ciso                          0.1.0
click                         8.0.4
click-plugins                 1.1.1
cligj                         0.7.2
cloudpickle                   2.0.0
cmip6-preprocessing           0.0.0
cmocean                       2.0
colorama                      0.4.3
colorcet                      3.0.0
colorspacious                 1.1.2
colour                        0.1.5
commonmark                    0.9.1
configobj                     5.0.6
contextily                    1.2.0
croniter                      0.3.36
cryptography                  36.0.2
cycler                        0.11.0
cytoolz                       0.11.2
dask                          2022.2.1
dask-gateway                  0.9.0
dask-geopandas                0.1.0
dask-glm                      0.2.0
dask-image                    2021.12.0
dask-kubernetes               2022.1.0
dask-labextension             5.2.0
dask-ml                       2022.1.22
dataclasses                   0.8
datacube                      1.8.6
datashader                    0.14.0
datashape                     0.5.4
debugpy                       1.6.0
decorator                     5.1.1
defusedxml                    0.7.1
descartes                     1.1.0
distributed                   2022.2.1
docker                        5.0.3
docker-pycreds                0.4.0
docopt                        0.6.2
docrep                        0.3.2
docutils                      0.15.2
donfig                        0.7.0
eccodes                       1.4.0
elementpath                   2.5.1
entrypoints                   0.4
eofs                          1.4.0
erddapy                       1.2.1
ESMPy                         8.2.0
executing                     0.8.3
fastapi                       0.75.2
fasteners                     0.17.3
fastjmd95                     0.2.1
fastjsonschema                2.15.3
fastprogress                  1.0.2
filelock                      3.6.0
findlibs                      0.0.2
Fiona                         1.8.21
flit-core                     3.7.1
flox                          0.4.1
folium                        0.12.1.post1
fonttools                     4.33.3
frozenlist                    1.3.0
fsspec                        2022.3.0
future                        0.18.2
gcsfs                         2022.3.0
GDAL                          3.4.2
gdown                         4.4.0
geocube                       0.2.0
geogif                        0.1.3
geographiclib                 1.52
geojson                       2.5.0
geopandas                     0.10.2
geopy                         2.2.0
geoviews                      1.9.5
google-api-core               2.5.0
google-auth                   2.6.6
google-auth-oauthlib          0.5.1
google-cloud-core             2.2.2
google-cloud-storage          2.1.0
google-crc32c                 1.1.2
google-resumable-media        2.1.0
googleapis-common-protos      1.56.0
graphviz                      0.20
greenlet                      1.1.2
grpcio                        1.45.0
gsw                           3.4.0
h11                           0.13.0
h5netcdf                      0.0.0
h5py                          3.6.0
HeapDict                      1.0.1
holoviews                     1.14.8
hvplot                        0.7.3
idna                          3.3
imagecodecs                   2022.2.22
imageio                       2.18.0
importlib-metadata            4.11.3
importlib-resources           5.7.1
iniconfig                     1.1.1
intake                        0.6.5
intake-esm                    2021.8.17
intake-geopandas              0.4.0
intake-xarray                 0.6.0
ipyevents                     2.0.1
ipyfilechooser                0.6.0
ipykernel                     6.13.0
ipyleaflet                    0.16.0
ipysheet                      0.5.0
ipython                       8.3.0
ipython-genutils              0.2.0
ipytree                       0.2.1
ipywidgets                    7.6.5
isodate                       0.6.1
jdcal                         1.4.1
jedi                          0.18.1
Jinja2                        3.1.1
jmespath                      1.0.0
joblib                        1.1.0
json5                         0.9.5
jsonpickle                    2.1.0
jsonschema                    4.4.0
jupyter-client                7.3.0
jupyter-core                  4.9.2
jupyter-panel-proxy           0.1.0
jupyter-resource-usage        0.6.1
jupyter-server                1.17.0
jupyter-server-proxy          3.2.1
jupyter-telemetry             0.1.0
jupyterhub                    2.2.1
jupyterlab                    3.3.1
jupyterlab-geojson            3.2.0
jupyterlab-pygments           0.2.2
jupyterlab-server             2.13.0
jupyterlab-widgets            1.1.0
kiwisolver                    1.4.2
kubernetes                    23.3.0
kubernetes-asyncio            22.6.4
lark-parser                   0.12.0
leafmap                       0.9.2
llvmlite                      0.36.0
locket                        1.0.0
lz4                           4.0.0
Mako                          1.2.0
mapclassify                   2.4.3
Markdown                      3.3.6
MarkupSafe                    2.1.1
marshmallow                   3.15.0
marshmallow-oneofschema       3.0.1
matplotlib                    3.5.1
matplotlib-inline             0.1.3
mercantile                    1.2.1
MetPy                         1.3.0
mistune                       0.8.4
morecantile                   3.1.2
mpi4py                        3.1.3
msal                          1.17.0
msal-extensions               0.3.1
msgpack                       1.0.3
msrest                        0.6.21
multidict                     6.0.2
multipledispatch              0.6.0
munch                         2.5.0
munkres                       1.1.4
mypy-extensions               0.4.3
natsort                       8.1.0
nb-conda-kernels              2.3.1
nbclassic                     0.3.7
nbclient                      0.5.13
nbconvert                     6.5.0
nbformat                      5.3.0
nbgitpuller                   1.0.2
nbstripout                    0.5.0
nc-time-axis                  1.4.1
nest-asyncio                  1.5.5
netCDF4                       1.5.8
networkx                      2.8
noise                         1.2.2
notebook                      6.4.11
notebook-shim                 0.1.0
numba                         0.53.1
numcodecs                     0.9.1
numexpr                       2.8.0
numpy                         1.22.3
numpy-groupies                0.9.15
oauthlib                      3.2.0
odc-algo                      0.2.2
odc-geo                       0.2.0
odc-stac                      0.3.0
packaging                     21.3
pamela                        1.0.0
pandas                        1.4.2
pandocfilters                 1.5.0
panel                         0.13.0
papermill                     2.3.4
param                         1.12.1
parcels                       2.3.0
parso                         0.8.3
partd                         1.2.0
pathspec                      0.9.0
patsy                         0.5.2
pdal                          3.1.2
pdal-plugins                  1.2.0
pendulum                      2.1.2
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        9.1.0
PIMS                          0.5
Pint                          0.19.2
pip                           20.3.4
planetary-computer            0.4.6
platformdirs                  2.5.1
pluggy                        1.0.0
pooch                         1.6.0
portalocker                   2.4.0
prefect                       1.2.1
progressbar2                  4.0.0
prometheus-client             0.14.1
prompt-toolkit                3.0.29
protobuf                      3.19.4
pscript                       0.7.5
psutil                        5.9.0
psycopg2                      2.9.3
ptyprocess                    0.7.0
pure-eval                     0.2.2
py                            1.11.0
pyarrow                       7.0.0
pyasn1                        0.4.8
pyasn1-modules                0.2.7
pycamhd                       0.7.0
pycparser                     2.21
PyCRS                         1.0.2
pyct                          0.4.6
pycurl                        7.45.1
pydantic                      1.9.0
pydap                         3.3.0
pyepsg                        0.4.0
pyerfa                        2.0.0.1
pygeos                        0.12.0
Pygments                      2.12.0
PyJWT                         2.3.0
pykdtree                      1.3.4
pymbolic                      2021.1
pyOpenSSL                     22.0.0
pyorbital                     1.7.1
pyparsing                     3.0.8
pyproj                        3.3.1
PyQt5                         5.12.3
PyQt5-sip                     4.19.18
PyQtChart                     5.12
PyQtWebEngine                 5.12.1
pyresample                    1.23.0
pyrsistent                    0.18.1
pyshp                         2.2.0
PySocks                       1.7.1
pyspectral                    0.11.0
pystac                        1.2.0
pystac-client                 0.3.2
pytest                        7.1.2
python-box                    6.0.2
python-dateutil               2.8.2
python-geotiepoints           1.4.0
python-gist                   0.10.6
python-gnupg                  0.4.8
python-json-logger            2.0.1
python-slugify                6.1.2
python-utils                  3.1.0
pytools                       2022.1.6
pytz                          2022.1
pytzdata                      2020.1
pyu2f                         0.1.5
pyviz-comms                   2.2.0
PyWavelets                    1.3.0
PyYAML                        5.4.1
pyzmq                         22.3.0
rasterio                      1.2.10
rechunker                     0.4.2
requests                      2.27.1
requests-oauthlib             1.3.1
rfc3339-validator             0.1.4
rich                          12.3.0
rio-cogeo                     3.2.0
rio-mucho                     1.0.0
rio-tiler                     1.4.0
rio-toa                       0.3.0
rioxarray                     0.11.1
rsa                           4.7.2
Rtree                         1.0.0
ruamel.yaml                   0.17.21
ruamel.yaml.clib              0.2.6
s3fs                          2022.3.0
s3transfer                    0.5.2
sarsen                        0.9.0
satpy                         0.36.0
scikit-image                  0.19.2
scikit-learn                  1.0.2
scipy                         1.8.0
seaborn                       0.11.2
Send2Trash                    1.8.0
setuptools                    59.8.0
Shapely                       1.8.0
shellingham                   1.4.0
simpervisor                   0.4
six                           1.16.0
slicerator                    1.1.0
sniffio                       1.2.0
snuggs                        1.4.7
sortedcontainers              2.4.0
soupsieve                     2.3.1
sparse                        0.13.0
SQLAlchemy                    1.4.36
stac-vrt                      1.0.3
stack-data                    0.2.0
stackstac                     0.4.1
starlette                     0.17.1
statsmodels                   0.13.2
strict-rfc3339                0.7
tabulate                      0.8.9
tblib                         1.7.0
tenacity                      8.0.1
terminado                     0.13.3
text-unidecode                1.3
textwrap3                     0.9.2
threadpoolctl                 3.1.0
tifffile                      2022.4.28
tiledb                        0.14.2
tinycss2                      1.1.1
toml                          0.10.2
tomli                         2.0.1
toolz                         0.11.2
tornado                       6.1
tqdm                          4.64.0
traitlets                     5.1.1
traittypes                    0.2.1
trollimage                    1.18.3
trollsift                     0.4.0
typed-ast                     1.5.3
typer                         0.4.1
typing-extensions             4.2.0
unicodedata2                  14.0.0
Unidecode                     1.3.4
urllib3                       1.26.9
uvicorn                       0.17.6
voila                         0.3.5
wcwidth                       0.2.5
webencodings                  0.5.1
WebOb                         1.8.7
websocket-client              1.3.2
websockets                    10.3
wheel                         0.37.1
whitebox                      2.1.2
whiteboxgui                   0.7.0
widgetsnbextension            3.5.2
wrapt                         1.14.0
xarray                        2022.3.0
xarray-sentinel               0.9.1
xarray-spatial                0.3.3
xarrayutils                   1.1.1
xcape                         0+untagged.33.g4d4ab9d.dirty
xclim                         0.36.0
xcube                         0.9.1
xesmf                         0.6.2
xgcm                          0.7.0
xhistogram                    0.3.1
xlayers                       0.2.2
xmitgcm                       0.5.2
xmlschema                     1.10.0
xpublish                      0.1.0
xrft                          0.0.0
xyzservices                   2022.4.0
yarl                          1.7.2
zarr                          2.11.3
zict                          2.2.0
zipp                          3.8.0

http://ci.terria.io/main/
https://datacube-core.readthedocs.io/en/latest/installation/database/setup.html
https://docs.xarray.dev/en/stable/user-guide/plotting.html#robust
https://github.com/opendatacube/datacube-core/releases/tag/1.8.7
https://github.com/opendatacube/odc-geo/issues
https://github.com/opendatacube/odc-geo/releases/tag/v0.2.0
https://github.com/opendatacube/odc-stac/releases/tag/v0.3.0
https://github.com/opendatacube/odc-stac/wiki/Generating-Rotated-Images-to-Save-Space
https://github.com/opendatacube/odc-tools/blob/develop/apps/dc_tools/odc/apps/dc_tools/fs_to_dc.py
https://maps.digitalearth.africa/
https://odc-geo.readthedocs.io/en/latest/_api/odc.geo.xr.ODCExtensionDs.html
https://odc-geo.readthedocs.io/en/latest/_api/odc.geo.xr.ODCExtension.html
https://odc-geo.readthedocs.io/en/latest/raster-tools.html#plotting-on-a-map
https://odc-stac-demo.netlify.app/
https://sandbox.digitalearth.africa/hub/login?next=%2Fhub%2F
https://www.usgs.gov/landsat-missions/landsat-collection-2-level-2-science-products

Alternately, you can configure the ODC connection to Postgres using environment variables:
DB_HOSTNAME
DB_USERNAME
DB_PASSWORD
DB_DATABASE


via Paul Haesler on Slack #open-data-cube 

# install numpy, pyproj and rasterio from Ubuntu distro via apt
sudo apt-get install python3-numpy python3-rasterio python3-pyproj

# Create virtualenv inheriting numpy and rasterio from system site-packages.
cd ~/venvs
virtualenv -p `which python3` --system-site-packages odc

# Activate new virtualenv
source odc/bin/activate

# Compile and install cf-units from source:
cd ~/src
git clone git@github.com:SciTools/cf-units.git cf-units
cd cf-units
pip install -e .

# install datacube-core from source (from pypi should be fine after next release)
cd ~/src/datacube/core
pip install -e .[all]

odc-geo

$ pip install --user --upgrade-strategy only-if-needed odc-geo
Collecting odc-geo
  Downloading odc_geo-0.1.1-py3-none-any.whl (81 kB)
     |                              | 81 kB 254 kB/s 
Requirement already satisfied: affine in ./.local/lib/python3.8/site-packages (from odc-geo) (2.3.0)
Collecting cachetools
  Downloading cachetools-5.0.0-py3-none-any.whl (9.1 kB)
Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (from odc-geo) (1.21.5)
Requirement already satisfied: pyproj in /usr/lib/python3/dist-packages (from odc-geo) (3.2.1)
Requirement already satisfied: shapely in /usr/lib/python3/dist-packages (from odc-geo) (1.8.0)
Installing collected packages: cachetools, odc-geo
Successfully installed cachetools-5.0.0 odc-geo-0.1.1

odc-stac

$ pip install --user --upgrade-strategy only-if-needed odc-stac
Collecting odc-stac
  Downloading odc_stac-0.2.4-py3-none-any.whl (32 kB)
Requirement already satisfied: affine in ./.local/lib/python3.8/site-packages (from odc-stac) (2.3.0)
Collecting datacube>=1.8.5
  Downloading datacube-1.8.6-py2.py3-none-any.whl (272 kB)
     |                               | 272 kB 307 kB/s 
Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (from odc-stac) (1.21.5)
Requirement already satisfied: pandas in ./.local/lib/python3.8/site-packages (from odc-stac) (1.4.1)
Requirement already satisfied: xarray>=0.19 in ./.local/lib/python3.8/site-packages (from odc-stac) (0.21.1)
Collecting toolz
  Downloading toolz-0.11.2-py3-none-any.whl (55 kB)
     |                               | 55 kB 324 kB/s 
Collecting pystac<2,>=1.0.0
  Downloading pystac-1.4.0-py3-none-any.whl (137 kB)
     |                               | 137 kB 252 kB/s 
Requirement already satisfied: jinja2 in /usr/lib/python3/dist-packages (from odc-stac) (2.10.1)
Requirement already satisfied: rasterio>=1.0.2 in ./.local/lib/python3.8/site-packages (from datacube>=1.8.5->odc-stac) (1.2.10)
Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (5.3.1)
Requirement already satisfied: sqlalchemy in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (1.3.12)
Requirement already satisfied: shapely>=1.6.4 in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (1.8.0)
Requirement already satisfied: psycopg2 in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (2.8.4)
Collecting distributed
  Downloading distributed-2022.4.0-py3-none-any.whl (853 kB)
     |                                | 853 kB 297 kB/s 
Requirement already satisfied: jsonschema in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (3.2.0)
Collecting dask[array]
  Downloading dask-2022.4.0-py3-none-any.whl (1.1 MB)
     |                                | 1.1 MB 300 kB/s 
Collecting lark-parser>=0.6.7
  Downloading lark_parser-0.12.0-py2.py3-none-any.whl (103 kB)
     |                                | 103 kB 339 kB/s 
Collecting cloudpickle>=0.4
  Downloading cloudpickle-2.0.0-py3-none-any.whl (25 kB)
Collecting netcdf4
  Downloading netCDF4-1.5.8-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
     |                                | 4.7 MB 221 kB/s 
Requirement already satisfied: python-dateutil in ./.local/lib/python3.8/site-packages (from datacube>=1.8.5->odc-stac) (2.8.2)
Requirement already satisfied: cachetools in ./.local/lib/python3.8/site-packages (from datacube>=1.8.5->odc-stac) (5.0.0)
Requirement already satisfied: click>=5.0 in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (7.0)
Requirement already satisfied: pyproj>=2.5 in /usr/lib/python3/dist-packages (from datacube>=1.8.5->odc-stac) (3.2.1)
Requirement already satisfied: pytz>=2020.1 in ./.local/lib/python3.8/site-packages (from pandas->odc-stac) (2021.3)
Requirement already satisfied: packaging>=20.0 in /usr/lib/python3/dist-packages (from xarray>=0.19->odc-stac) (20.3)
Requirement already satisfied: cligj>=0.5 in /usr/lib/python3/dist-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (0.5.0)
Requirement already satisfied: attrs in /usr/lib/python3/dist-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (19.3.0)
Requirement already satisfied: certifi in /usr/lib/python3/dist-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (2019.11.28)
Requirement already satisfied: snuggs>=1.4.1 in ./.local/lib/python3.8/site-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (1.4.7)
Requirement already satisfied: setuptools in /usr/lib/python3/dist-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (45.2.0)
Requirement already satisfied: click-plugins in /usr/lib/python3/dist-packages (from rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (1.1.1)
Requirement already satisfied: psutil>=5.0 in /usr/lib/python3/dist-packages (from distributed->datacube>=1.8.5->odc-stac) (5.5.1)
Collecting zict>=0.1.3
  Downloading zict-2.1.0-py3-none-any.whl (11 kB)
Collecting tornado>=6.0.3
  Downloading tornado-6.1-cp38-cp38-manylinux2010_x86_64.whl (427 kB)
     |                               | 427 kB 184 kB/s 
Requirement already satisfied: urllib3 in /usr/lib/python3/dist-packages (from distributed->datacube>=1.8.5->odc-stac) (1.25.8)
Collecting tblib>=1.6.0
  Downloading tblib-1.7.0-py2.py3-none-any.whl (12 kB)
Collecting msgpack>=0.6.0
  Downloading msgpack-1.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (322 kB)
     |                               | 322 kB 191 kB/s 
Collecting sortedcontainers!=2.0.0,!=2.0.1
  Downloading sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting fsspec>=0.6.0
  Downloading fsspec-2022.3.0-py3-none-any.whl (136 kB)
     |                             | 136 kB 255 kB/s 
Collecting partd>=0.3.10
  Downloading partd-1.2.0-py3-none-any.whl (19 kB)
Collecting cftime
  Downloading cftime-1.6.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (238 kB)
     |                               | 238 kB 305 kB/s 
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil->datacube>=1.8.5->odc-stac) (1.14.0)
Requirement already satisfied: pyparsing>=2.1.6 in /usr/lib/python3/dist-packages (from snuggs>=1.4.1->rasterio>=1.0.2->datacube>=1.8.5->odc-stac) (2.4.6)
Collecting heapdict
  Downloading HeapDict-1.0.1-py3-none-any.whl (3.9 kB)
Collecting locket
  Downloading locket-0.2.1-py2.py3-none-any.whl (4.1 kB)
Installing collected packages: toolz, fsspec, locket, partd, cloudpickle, dask, heapdict, zict, tornado, tblib, msgpack, sortedcontainers, distributed, lark-parser, cftime, netcdf4, datacube, pystac, odc-stac
Successfully installed cftime-1.6.0 cloudpickle-2.0.0 dask-2022.4.0 datacube-1.8.6 distributed-2022.4.0 fsspec-2022.3.0 heapdict-1.0.1 lark-parser-0.12.0 locket-0.2.1 msgpack-1.0.3 netcdf4-1.5.8 odc-stac-0.2.4 partd-1.2.0 pystac-1.4.0 sortedcontainers-2.4.0 tblib-1.7.0 toolz-0.11.2 tornado-6.1 zict-2.1.0

Focal Notes

Focal Setup Steps

APT install into the system OS python, major, stable parts first.. as a set .. ; 

  ## note gdal & postgis are installed at an earlier step via package dot-deb
  ## -------------------------------------------------------------------------
  591  sudo apt install python3-dev python3-pip
  405  sudo apt install ipython3 python3-scipy
            apt install python3-pandas  ## <== stale version currently
  408  sudo apt install r-cran-sf       ## match libgeos w/R language bindings
  429  sudo apt install python3-shapely python3-fiona
  614  sudo apt install --yes python3-geoalchemy2
  ##-- show the parts explicitly for Jupyter on Ubuntu via dot-deb ---------------
  670  sudo apt install --yes jupyter-core jupyter-client jupyter-console jupyter-nbformat jupyter-nbconvert  \
                              jupyter-notebook python3-ipykernel
  673  sudo apt install python-notebook-doc jupyter
  ##--
       sudo apt install python3-sklearn-lib  python3-pyosmium

next 

pip install --user  --upgrade-strategy=only-if-needed  py3-pkg
  # installs to `~/.local/lib/python3.8/` 
# 
  605  pip install --user   wheel
  835  pip install --user --upgrade  --upgrade-strategy=only-if-needed pandas 
  836  pip install --user --upgrade  --upgrade-strategy=only-if-needed scikit-image
  837  pip install --user --upgrade  --upgrade-strategy=only-if-needed imageio
  838  pip install --user --upgrade  --upgrade-strategy=only-if-needed numba
  630  pip install --user   folium
  839  pip install --user --upgrade  --upgrade-strategy=only-if-needed sentinelhub
  867  pip install --user --upgrade  --upgrade-strategy=only-if-needed openeo
  841  pip install --user --upgrade  --upgrade-strategy=only-if-needed eo-learn
  853  pip install --user --upgrade  --upgrade-strategy=only-if-needed ipyleaflet

  606  pip install --user   lightgbm  ## libs also have an R interface, optional engines

all [ rasterio, networkx, sklearn, boto, more...  ] into   ~/.local/lib/python3.8/  (below)

    note: https://pip.pypa.io/en/stable/cli/pip_install/#hash-checking-mode

next 

   $ mkdir -p ~/.jupyter/notebooks/ ;# default Jupyter notebooks & assets ; TODO will change.

this opinionated install will update/amend/evolve as installer code and more dot-debs are crafted later this year. 

$ ./do_start_jupyter.sh
#---------------------------
#!/bin/bash

jupyter notebook --no-browser --ip=192.168.1.131 --notebook-dir=.jupyter/notebooks


~/.bashrc

##-
PATH=$PATH:~/.local/bin




dbb@focalk:/etc$ cat lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04.3 LTS"
#--
 libgeos3.10.1   (3.10.1-1~focal0) 
 libgdal-dev     (3.4.0+dfsg-1~focal0)
 postgresql-12-postgis-3     (3.2.0+dfsg-1~focal0)
 PGSQL="120" GEOS="3.10.1-CAPI-1.16.0" PROJ="8.2.0" LIBXML="2.9.10" LIBJSON="0.13.1"
#--


geoxarray

$ pip install --user rioxarray
Collecting rioxarray
  Downloading rioxarray-0.10.3.tar.gz (47 kB)
     |                              | 47 kB 272 kB/s 
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: packaging in /usr/lib/python3/dist-packages (from rioxarray) (20.3)
Requirement already satisfied: xarray>=0.17 in ./.local/lib/python3.8/site-packages (from rioxarray) (0.21.1)
Requirement already satisfied: rasterio>=1.1.1 in ./.local/lib/python3.8/site-packages (from rioxarray) (1.2.10)
Requirement already satisfied: pyproj>=2.2 in /usr/lib/python3/dist-packages (from rioxarray) (3.2.1)
Requirement already satisfied: pandas>=1.1 in ./.local/lib/python3.8/site-packages (from xarray>=0.17->rioxarray) (1.4.1)
Requirement already satisfied: numpy>=1.18 in ./.local/lib/python3.8/site-packages (from xarray>=0.17->rioxarray) (1.21.5)
Requirement already satisfied: click-plugins in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (1.1.1)
Requirement already satisfied: cligj>=0.5 in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (0.5.0)
Requirement already satisfied: attrs in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (19.3.0)
Requirement already satisfied: certifi in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (2019.11.28)
Requirement already satisfied: click>=4.0 in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (7.0)
Requirement already satisfied: affine in ./.local/lib/python3.8/site-packages (from rasterio>=1.1.1->rioxarray) (2.3.0)
Requirement already satisfied: snuggs>=1.4.1 in ./.local/lib/python3.8/site-packages (from rasterio>=1.1.1->rioxarray) (1.4.7)
Requirement already satisfied: setuptools in /usr/lib/python3/dist-packages (from rasterio>=1.1.1->rioxarray) (45.2.0)
Requirement already satisfied: python-dateutil>=2.8.1 in ./.local/lib/python3.8/site-packages (from pandas>=1.1->xarray>=0.17->rioxarray) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in ./.local/lib/python3.8/site-packages (from pandas>=1.1->xarray>=0.17->rioxarray) (2021.3)
Requirement already satisfied: pyparsing>=2.1.6 in /usr/lib/python3/dist-packages (from snuggs>=1.4.1->rasterio>=1.1.1->rioxarray) (2.4.6)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.1->pandas>=1.1->xarray>=0.17->rioxarray) (1.14.0)
Building wheels for collected packages: rioxarray
  Building wheel for rioxarray (PEP 517) ... done
  Created wheel for rioxarray: filename=rioxarray-0.10.3-py3-none-any.whl size=55624 sha256=925199c830a54ca5e9b02e89060e822e27014db5cbe601fd6b513d106fe66687
  Stored in directory: /home/dbb/.cache/pip/wheels/42/71/40/298b7df47153454b8eb3ef8e5441dafa413e5a2d7ac1832b17
Successfully built rioxarray
Installing collected packages: rioxarray
Successfully installed rioxarray-0.10.3


OSM software stack

osm2pgsql and libosmium 


# jammy universe

    Thu May 26 07:55:03 PM PDT 2022

osm2pgsql   1.6.0+ds-1
libosmium2-dev  Version: 2.18.0-1

Sat 26 Feb 2022 07:10:31 PM PST

# ubuntugis-unstable  focal
osm2pgsql  1.3.0+ds-1~focal2

# git repo
osm2pgsql  1.6    lonvia committed on Jan 24 2022
osm2pgsql  1.5.1  Thu Jul 29 09:49:35 2021 +0200

# osm2pgsql cmake variables set
PROJ6_INCLUDE_DIR  /usr/include
PROJ_LIBRARY  /usr/lib/x86_64-linux-gnu/libproj.so
WITH_LUA  ON
EXTERNAL_LIBOSMIUM  FALSE
# from osm2pgsql/contrib/libosmium/
LIBOSMIUM_VERSION_STRING "2.17.0"

$ apt show libosmium2-dev  =>   2.17.2-1~focal0

## the result of apt installing Universe  python3-pyosmium  2.15.3-1build2
$ osmium --version  => osmium version 1.11.1, libosmium version 2.15.4

so, that is behind slightly from 2.17.x osmium headers

## rebuild osm2pgsql 1.6.0,   better !
$  osm2pgsql --version
2022-02-26 20:14:19  osm2pgsql version 1.6.0
Build: Debug
Compiled using the following library versions:
Libosmium 2.17.3
Proj [API 6] 8.2.0
Lua 5.3.3

$ sudo make install
  ...
[ 95%] Built target osm2pgsql_lib
[100%] Built target osm2pgsql
Install the project...
-- Install configuration: "Debug"
-- Installing: /usr/local/bin/osm2pgsql
-- Installing: /usr/local/bin/osm2pgsql-replication
-- Installing: /usr/local/share/man/man1/osm2pgsql-replication.1
-- Installing: /usr/local/share/osm2pgsql/default.style
-- Installing: /usr/local/share/osm2pgsql/empty.style
-- Installing: /usr/local/share/man/man1/osm2pgsql.1

    OSMnx  
      in tutorial   https://pygis.io/docs/d_access_osm.html
      code  https://pypi.org/project/osmnx/#files



## osm2pgsql FLEX layout post-processing via LUA

./flex-config/
  route-relations.lua   unitable.lua   geometries.lua
  data-types.lua   attributes.lua   compatible.lua
  simple.lua   places.lua   generic.lua   with-schema.lua

./tests/data/
  test_output_flex_multigeom_polygon.lua
  test_output_flex_way.lua
  test_output_flex_area_3857.lua
  test_output_flex_attr.lua
  test_output_flex_stage2.lua
  test_output_flex_nocluster.lua
  test_output_flex_multigeom_multipolygon_split.lua
  test_output_flex_multigeom.lua
  test_output_flex_multigeom_multipolygon.lua
  test_output_flex_nodes.lua
  test_output_flex_area_4326.lua
  test_output_flex_relation_combinations.lua
  test_output_flex_nogeom.lua
  test_output_flex_area.lua
  test_output_flex_lua_fail.lua
  test_output_flex_bbox.lua
  test_output_flex_types.lua
  test_output_flex_area_mix.lua
  test_output_flex_relation_changes.lua
  test_output_flex_schema.lua
  test_output_flex_multigeom_geometry_split.lua
  test_output_flex_stage2_alt.lua
  test_output_flex_uni.lua
  test_output_flex.lua
  test_output_flex_validgeom.lua
  test_output_flex_line.lua
  test_output_flex_invalid_geom.lua
  test_output_flex_multigeom_geometry.lua
  test_output_flex_relations.lua

## a full list of osmium verbs
osmium-add-locations-to-ways   osmium-export                  osmium-merge-changes
osmium-apply-changes           osmium-extract                 osmium-query-locations-index
osmium-cat                     osmium-file-formats            osmium-renumber
osmium-changeset-filter        osmium-fileinfo                osmium-show
osmium-check-refs              osmium-getid                   osmium-sort
osmium-create-locations-index  osmium-getparents              osmium-tags-filter
osmium-derive-changes          osmium-index-types             osmium-time-filter
osmium-diff                    osmium-merge

Focal Jupyter Overview

                                    Sat 19 Feb 2022 07:18:48 PM PST
$ jupyter --version
jupyter core     : 4.6.3
jupyter-notebook : 6.0.3
qtconsole        : not installed
ipython          : 7.13.0
ipykernel        : 5.2.0
jupyter client   : 6.1.2
jupyter lab      : not installed
nbconvert        : 5.6.1
ipywidgets       : 6.0.0
nbformat         : 5.0.4
traitlets        : 4.3.3

##-------------------------------
Python version: 3.8.10 (default, Nov 26 2021, 20:14:08) [GCC 9.3.0]
pandas version: 0.25.3   <== a weak spot in this setup
matplotlib version: 3.1.2
NumPy version: 1.17.4
SciPy version: 1.3.3
IPython version: 7.13.0
scikit-learn version: 1.0.2
##-----------------------------------------
dbb@focalk:~$ ipython3
Python 3.8.10 (default, Nov 26 2021, 20:14:08) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.13.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import sklearn                                                                                               
In [2]: from sklearn import show_versions                                                                            
In [3]: show_versions()                                                                                              

System:
    python: 3.8.10 (default, Nov 26 2021, 20:14:08)  [GCC 9.3.0]
executable: /usr/bin/python3
   machine: Linux-5.13.0-30-generic-x86_64-with-glibc2.29

Python dependencies:
          pip: 20.0.2
   setuptools: 45.2.0
      sklearn: 1.0.2
        numpy: 1.17.4
        scipy: 1.3.3
       Cython: 0.29.14
       pandas: 0.25.3      <== a weak spot in this setup
   matplotlib: 3.1.2
       joblib: 1.1.0
threadpoolctl: 3.1.0

Built with OpenMP: True
--
dbb@focalk:~$ jupyter --paths
config:
    /home/dbb/.jupyter
    /usr/local/etc/jupyter
    /etc/jupyter
data:
    /home/dbb/.local/share/jupyter
    /usr/local/share/jupyter
    /usr/share/jupyter
runtime:
    /home/dbb/.local/share/jupyter/runtime

Focal APT Repos

dbb@focalk:/etc/apt$ cat sources.list
# Automatically generated by Calamares on 2022-01-02.
# Lines starting with "deb" are mandatory, while lines starting with "deb-src"
# are for more detailed package information.
...
-------------------------

dbb@focalk:/etc/apt$ cat sources.list.d/ubuntugis-ubuntu-ubuntugis-unstable-focal.list

deb http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu focal main
deb-src http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu focal main

eo-learn pip Fix-It Session

eolearn -- aprox. of python3 dependancies 

import 
:  pandas as pd
:  geopandas as gpd
:  shapely.  geometry, ops, wkt
:  rasterio. features, transform, warp
:  skimage.  feature, filters.rank, morphology, segmentation
:  boto3, cv2
:  fiona
:  graphviz
:  ------------------------------------------
:  abc, attr, base64
:  collections, concurrent.futures
:  dataclasses, datetime as dt
:  dateutil, dateutil.parser
:  fs, functools, gzip
:  importlib, inspect, itertools as it
:  json, logging, multiprocessing, os
:  pickle, ray, re, registration
:  tempfile, threading, time, traceback
:  unittest.mock as mock, uuid, warnings
: --------------------------

##-----------------------------------------------------------------
$ pip install --user --upgrade  --upgrade-strategy=only-if-needed    pandas
Collecting pandas
  Downloading pandas-1.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     |                                | 11.7 MB 79 kB/s 
Collecting pytz>=2020.1
  Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
     |                                | 503 kB 260 kB/s 
Collecting python-dateutil>=2.8.1
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     |                                | 247 kB 210 kB/s 
Collecting numpy>=1.18.5; platform_machine != "aarch64" and platform_machine != "arm64" and python_version < "3.10"
  Downloading numpy-1.22.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
     |                                | 16.8 MB 11 kB/s 
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.1->pandas) (1.14.0)
ERROR: sentinelhub 3.4.4 has requirement pillow<=8.4.0,>=8.3.2, but you'll have pillow 7.0.0 which is incompatible.
ERROR: scikit-image 0.19.2 has requirement scipy>=1.4.1, but you'll have scipy 1.3.3 which is incompatible.
ERROR: numba 0.55.1 has requirement numpy<1.22,>=1.18, but you'll have numpy 1.22.2 which is incompatible.
ERROR: imageio 2.16.0 has requirement pillow>=8.3.2, but you'll have pillow 7.0.0 which is incompatible.
Installing collected packages: pytz, python-dateutil, numpy, pandas
Successfully installed numpy-1.22.2 pandas-1.4.1 python-dateutil-2.8.2 pytz-2021.3

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed     scikit-image
Requirement already up-to-date: scikit-image in ./.local/lib/python3.8/site-packages (0.19.2)
Requirement already satisfied, skipping upgrade: imageio>=2.4.1 in ./.local/lib/python3.8/site-packages (from scikit-image) (2.16.0)
Requirement already satisfied, skipping upgrade: packaging>=20.0 in /usr/lib/python3/dist-packages (from scikit-image) (20.3)
Collecting scipy>=1.4.1
  Downloading scipy-1.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (41.6 MB)
     |                                | 41.6 MB 20 kB/s 
Requirement already satisfied, skipping upgrade: pillow!=7.1.0,!=7.1.1,!=8.3.0,>=6.1.0 in /usr/lib/python3/dist-packages (from scikit-image) (7.0.0)
Requirement already satisfied, skipping upgrade: numpy>=1.17.0 in ./.local/lib/python3.8/site-packages (from scikit-image) (1.22.2)
Requirement already satisfied, skipping upgrade: PyWavelets>=1.1.1 in ./.local/lib/python3.8/site-packages (from scikit-image) (1.2.0)
Requirement already satisfied, skipping upgrade: networkx>=2.2 in ./.local/lib/python3.8/site-packages (from scikit-image) (2.6.3)
Requirement already satisfied, skipping upgrade: tifffile>=2019.7.26 in ./.local/lib/python3.8/site-packages (from scikit-image) (2022.2.9)
Installing collected packages: scipy
Successfully installed scipy-1.8.0

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed      imageio
Requirement already up-to-date: imageio in ./.local/lib/python3.8/site-packages (2.16.0)
Requirement already satisfied, skipping upgrade: numpy>=1.20.0 in ./.local/lib/python3.8/site-packages (from imageio) (1.22.2)
Collecting pillow>=8.3.2
  Downloading Pillow-9.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB)
     |                                | 4.3 MB 99 kB/s 
ERROR: sentinelhub 3.4.4 has requirement pillow<=8.4.0,>=8.3.2, but you'll have pillow 9.0.1 which is incompatible.
Installing collected packages: pillow
Successfully installed pillow-9.0.1

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed      numba
Requirement already up-to-date: numba in ./.local/lib/python3.8/site-packages (0.55.1)
Collecting numpy<1.22,>=1.18
  Downloading numpy-1.21.5-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     |                                | 15.7 MB 361 kB/s 
Requirement already satisfied, skipping upgrade: setuptools in /usr/lib/python3/dist-packages (from numba) (45.2.0)
Requirement already satisfied, skipping upgrade: llvmlite<0.39,>=0.38.0rc1 in ./.local/lib/python3.8/site-packages (from numba) (0.38.0)
ERROR: sentinelhub 3.4.4 has requirement pillow<=8.4.0,>=8.3.2, but you'll have pillow 9.0.1 which is incompatible.
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.22.2
    Uninstalling numpy-1.22.2:
      Successfully uninstalled numpy-1.22.2
Successfully installed numpy-1.21.5

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed       sentinelhub
Requirement already up-to-date: sentinelhub in ./.local/lib/python3.8/site-packages (3.4.4)
Requirement already satisfied, skipping upgrade: oauthlib in /usr/lib/python3/dist-packages (from sentinelhub) (3.1.0)
Requirement already satisfied, skipping upgrade: requests-oauthlib in ./.local/lib/python3.8/site-packages (from sentinelhub) (1.3.1)
Requirement already satisfied, skipping upgrade: dataclasses-json in ./.local/lib/python3.8/site-packages (from sentinelhub) (0.5.6)
Requirement already satisfied, skipping upgrade: numpy in ./.local/lib/python3.8/site-packages (from sentinelhub) (1.21.5)
Requirement already satisfied, skipping upgrade: pyproj>=2.2.0 in /usr/lib/python3/dist-packages (from sentinelhub) (3.2.1)
Requirement already satisfied, skipping upgrade: python-dateutil in ./.local/lib/python3.8/site-packages (from sentinelhub) (2.8.2)
Requirement already satisfied, skipping upgrade: requests>=2.5.0 in /usr/lib/python3/dist-packages (from sentinelhub) (2.22.0)
Requirement already satisfied, skipping upgrade: tifffile in ./.local/lib/python3.8/site-packages (from sentinelhub) (2022.2.9)
Requirement already satisfied, skipping upgrade: utm in ./.local/lib/python3.8/site-packages (from sentinelhub) (0.7.0)
Collecting pillow<=8.4.0,>=8.3.2
  Downloading Pillow-8.4.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
     |                                | 3.1 MB 43 kB/s 
Requirement already satisfied, skipping upgrade: click in /usr/lib/python3/dist-packages (from sentinelhub) (7.0)
Requirement already satisfied, skipping upgrade: aenum>=2.1.4 in ./.local/lib/python3.8/site-packages (from sentinelhub) (3.1.8)
Requirement already satisfied, skipping upgrade: boto3 in ./.local/lib/python3.8/site-packages (from sentinelhub) (1.21.2)
Requirement already satisfied, skipping upgrade: shapely in /usr/lib/python3/dist-packages (from sentinelhub) (1.8.0)
Requirement already satisfied, skipping upgrade: botocore in ./.local/lib/python3.8/site-packages (from sentinelhub) (1.24.2)
Requirement already satisfied, skipping upgrade: tqdm in ./.local/lib/python3.8/site-packages (from sentinelhub) (4.62.3)
Requirement already satisfied, skipping upgrade: typing-inspect>=0.4.0 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub) (0.7.1)
Requirement already satisfied, skipping upgrade: marshmallow-enum<2.0.0,>=1.5.1 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub) (1.5.1)
Requirement already satisfied, skipping upgrade: marshmallow<4.0.0,>=3.3.0 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub) (3.14.1)
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil->sentinelhub) (1.14.0)
Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in ./.local/lib/python3.8/site-packages (from boto3->sentinelhub) (0.10.0)
Requirement already satisfied, skipping upgrade: s3transfer<0.6.0,>=0.5.0 in ./.local/lib/python3.8/site-packages (from boto3->sentinelhub) (0.5.1)
Requirement already satisfied, skipping upgrade: urllib3<1.27,>=1.25.4 in /usr/lib/python3/dist-packages (from botocore->sentinelhub) (1.25.8)
Requirement already satisfied, skipping upgrade: typing-extensions>=3.7.4 in ./.local/lib/python3.8/site-packages (from typing-inspect>=0.4.0->dataclasses-json->sentinelhub) (4.1.1)
Requirement already satisfied, skipping upgrade: mypy-extensions>=0.3.0 in ./.local/lib/python3.8/site-packages (from typing-inspect>=0.4.0->dataclasses-json->sentinelhub) (0.4.3)
Installing collected packages: pillow
  Attempting uninstall: pillow
    Found existing installation: Pillow 9.0.1
    Uninstalling Pillow-9.0.1:
      Successfully uninstalled Pillow-9.0.1
Successfully installed pillow-8.4.0

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed      eo-learn
Requirement already up-to-date: eo-learn in ./.local/lib/python3.8/site-packages (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-io>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-coregistration>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-features>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-mask>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-ml-tools>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-core>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-visualization>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: eo-learn-geometry>=1.0.0 in ./.local/lib/python3.8/site-packages (from eo-learn) (1.0.0)
Requirement already satisfied, skipping upgrade: rasterio>=1.2.7 in ./.local/lib/python3.8/site-packages (from eo-learn-io>=1.0.0->eo-learn) (1.2.10)
Requirement already satisfied, skipping upgrade: sentinelhub>=3.4.0 in ./.local/lib/python3.8/site-packages (from eo-learn-io>=1.0.0->eo-learn) (3.4.4)
Requirement already satisfied, skipping upgrade: fiona>=1.8.18 in /usr/lib/python3/dist-packages (from eo-learn-io>=1.0.0->eo-learn) (1.8.20)
Requirement already satisfied, skipping upgrade: rtree in /usr/lib/python3/dist-packages (from eo-learn-io>=1.0.0->eo-learn) (0.9.4)
Requirement already satisfied, skipping upgrade: geopandas>=0.8.1 in /usr/lib/python3/dist-packages (from eo-learn-io>=1.0.0->eo-learn) (0.10.2)
Requirement already satisfied, skipping upgrade: boto3 in ./.local/lib/python3.8/site-packages (from eo-learn-io>=1.0.0->eo-learn) (1.21.2)
Requirement already satisfied, skipping upgrade: opencv-contrib-python-headless>=4.1 in ./.local/lib/python3.8/site-packages (from eo-learn-coregistration>=1.0.0->eo-learn) (4.5.5.62)
Requirement already satisfied, skipping upgrade: thunder-registration in ./.local/lib/python3.8/site-packages (from eo-learn-coregistration>=1.0.0->eo-learn) (1.0.1)
Requirement already satisfied, skipping upgrade: python-dateutil in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (2.8.2)
Requirement already satisfied, skipping upgrade: scipy in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (1.8.0)
Requirement already satisfied, skipping upgrade: numba>=0.53.0 in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (0.55.1)
Requirement already satisfied, skipping upgrade: numpy in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (1.21.5)
Requirement already satisfied, skipping upgrade: scikit-learn in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (1.0.2)
Requirement already satisfied, skipping upgrade: scikit-image>=0.19.0 in ./.local/lib/python3.8/site-packages (from eo-learn-features>=1.0.0->eo-learn) (0.19.2)
Requirement already satisfied, skipping upgrade: lightgbm>=2.0.11 in ./.local/lib/python3.8/site-packages (from eo-learn-mask>=1.0.0->eo-learn) (3.3.2)
Requirement already satisfied, skipping upgrade: shapely in /usr/lib/python3/dist-packages (from eo-learn-ml-tools>=1.0.0->eo-learn) (1.8.0)
Requirement already satisfied, skipping upgrade: attrs>=19.2.0 in /usr/lib/python3/dist-packages (from eo-learn-core>=1.0.0->eo-learn) (19.3.0)
Requirement already satisfied, skipping upgrade: tqdm>=4.27 in ./.local/lib/python3.8/site-packages (from eo-learn-core>=1.0.0->eo-learn) (4.62.3)
Requirement already satisfied, skipping upgrade: fs in ./.local/lib/python3.8/site-packages (from eo-learn-core>=1.0.0->eo-learn) (2.4.15)
Requirement already satisfied, skipping upgrade: fs-s3fs in ./.local/lib/python3.8/site-packages (from eo-learn-core>=1.0.0->eo-learn) (1.1.1)
Requirement already satisfied, skipping upgrade: pydot in /usr/lib/python3/dist-packages (from eo-learn-visualization>=1.0.0->eo-learn) (1.4.1)
Requirement already satisfied, skipping upgrade: jinja2 in /usr/lib/python3/dist-packages (from eo-learn-visualization>=1.0.0->eo-learn) (2.10.1)
Requirement already satisfied, skipping upgrade: matplotlib in /usr/lib/python3/dist-packages (from eo-learn-visualization>=1.0.0->eo-learn) (3.1.2)
Requirement already satisfied, skipping upgrade: graphviz>=0.10.1 in ./.local/lib/python3.8/site-packages (from eo-learn-visualization>=1.0.0->eo-learn) (0.19.1)
Requirement already satisfied, skipping upgrade: pygments in /usr/lib/python3/dist-packages (from eo-learn-visualization>=1.0.0->eo-learn) (2.3.1)
Requirement already satisfied, skipping upgrade: descartes in /usr/lib/python3/dist-packages (from eo-learn-geometry>=1.0.0->eo-learn) (1.1.0)
Requirement already satisfied, skipping upgrade: certifi in /usr/lib/python3/dist-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (2019.11.28)
Requirement already satisfied, skipping upgrade: setuptools in /usr/lib/python3/dist-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (45.2.0)
Requirement already satisfied, skipping upgrade: click-plugins in /usr/lib/python3/dist-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (1.1.1)
Requirement already satisfied, skipping upgrade: cligj>=0.5 in /usr/lib/python3/dist-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (0.5.0)
Requirement already satisfied, skipping upgrade: affine in ./.local/lib/python3.8/site-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (2.3.0)
Requirement already satisfied, skipping upgrade: snuggs>=1.4.1 in ./.local/lib/python3.8/site-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (1.4.7)
Requirement already satisfied, skipping upgrade: click>=4.0 in /usr/lib/python3/dist-packages (from rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (7.0)
Requirement already satisfied, skipping upgrade: pyproj>=2.2.0 in /usr/lib/python3/dist-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (3.2.1)
Requirement already satisfied, skipping upgrade: oauthlib in /usr/lib/python3/dist-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (3.1.0)
Requirement already satisfied, skipping upgrade: aenum>=2.1.4 in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (3.1.8)
Requirement already satisfied, skipping upgrade: dataclasses-json in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (0.5.6)
Requirement already satisfied, skipping upgrade: requests>=2.5.0 in /usr/lib/python3/dist-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (2.22.0)
Requirement already satisfied, skipping upgrade: tifffile in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (2022.2.9)
Requirement already satisfied, skipping upgrade: utm in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (0.7.0)
Requirement already satisfied, skipping upgrade: requests-oauthlib in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (1.3.1)
Requirement already satisfied, skipping upgrade: pillow<=8.4.0,>=8.3.2 in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (8.4.0)
Requirement already satisfied, skipping upgrade: botocore in ./.local/lib/python3.8/site-packages (from sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (1.24.2)
Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in ./.local/lib/python3.8/site-packages (from boto3->eo-learn-io>=1.0.0->eo-learn) (0.10.0)
Requirement already satisfied, skipping upgrade: s3transfer<0.6.0,>=0.5.0 in ./.local/lib/python3.8/site-packages (from boto3->eo-learn-io>=1.0.0->eo-learn) (0.5.1)
Requirement already satisfied, skipping upgrade: thunder-python>=1.2.0 in ./.local/lib/python3.8/site-packages (from thunder-registration->eo-learn-coregistration>=1.0.0->eo-learn) (1.4.2)
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil->eo-learn-features>=1.0.0->eo-learn) (1.14.0)
Requirement already satisfied, skipping upgrade: llvmlite<0.39,>=0.38.0rc1 in ./.local/lib/python3.8/site-packages (from numba>=0.53.0->eo-learn-features>=1.0.0->eo-learn) (0.38.0)
Requirement already satisfied, skipping upgrade: threadpoolctl>=2.0.0 in ./.local/lib/python3.8/site-packages (from scikit-learn->eo-learn-features>=1.0.0->eo-learn) (3.1.0)
Requirement already satisfied, skipping upgrade: joblib>=0.11 in ./.local/lib/python3.8/site-packages (from scikit-learn->eo-learn-features>=1.0.0->eo-learn) (1.1.0)
Requirement already satisfied, skipping upgrade: PyWavelets>=1.1.1 in ./.local/lib/python3.8/site-packages (from scikit-image>=0.19.0->eo-learn-features>=1.0.0->eo-learn) (1.2.0)
Requirement already satisfied, skipping upgrade: imageio>=2.4.1 in ./.local/lib/python3.8/site-packages (from scikit-image>=0.19.0->eo-learn-features>=1.0.0->eo-learn) (2.16.0)
Requirement already satisfied, skipping upgrade: networkx>=2.2 in ./.local/lib/python3.8/site-packages (from scikit-image>=0.19.0->eo-learn-features>=1.0.0->eo-learn) (2.6.3)
Requirement already satisfied, skipping upgrade: packaging>=20.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.19.0->eo-learn-features>=1.0.0->eo-learn) (20.3)
Requirement already satisfied, skipping upgrade: wheel in /usr/lib/python3/dist-packages (from lightgbm>=2.0.11->eo-learn-mask>=1.0.0->eo-learn) (0.34.2)
Requirement already satisfied, skipping upgrade: pytz in ./.local/lib/python3.8/site-packages (from fs->eo-learn-core>=1.0.0->eo-learn) (2021.3)
Requirement already satisfied, skipping upgrade: appdirs~=1.4.3 in ./.local/lib/python3.8/site-packages (from fs->eo-learn-core>=1.0.0->eo-learn) (1.4.4)
Requirement already satisfied, skipping upgrade: pyparsing>=2.1.6 in /usr/lib/python3/dist-packages (from snuggs>=1.4.1->rasterio>=1.2.7->eo-learn-io>=1.0.0->eo-learn) (2.4.6)
Requirement already satisfied, skipping upgrade: typing-inspect>=0.4.0 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (0.7.1)
Requirement already satisfied, skipping upgrade: marshmallow<4.0.0,>=3.3.0 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (3.14.1)
Requirement already satisfied, skipping upgrade: marshmallow-enum<2.0.0,>=1.5.1 in ./.local/lib/python3.8/site-packages (from dataclasses-json->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (1.5.1)
Requirement already satisfied, skipping upgrade: urllib3<1.27,>=1.25.4 in /usr/lib/python3/dist-packages (from botocore->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (1.25.8)
Requirement already satisfied, skipping upgrade: boto>=2.36.0 in ./.local/lib/python3.8/site-packages (from thunder-python>=1.2.0->thunder-registration->eo-learn-coregistration>=1.0.0->eo-learn) (2.49.0)
Requirement already satisfied, skipping upgrade: bolt-python>=0.7.0 in ./.local/lib/python3.8/site-packages (from thunder-python>=1.2.0->thunder-registration->eo-learn-coregistration>=1.0.0->eo-learn) (0.7.1)
Requirement already satisfied, skipping upgrade: mypy-extensions>=0.3.0 in ./.local/lib/python3.8/site-packages (from typing-inspect>=0.4.0->dataclasses-json->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (0.4.3)
Requirement already satisfied, skipping upgrade: typing-extensions>=3.7.4 in ./.local/lib/python3.8/site-packages (from typing-inspect>=0.4.0->dataclasses-json->sentinelhub>=3.4.0->eo-learn-io>=1.0.0->eo-learn) (4.1.1)

$ pip install --user --upgrade  --upgrade-strategy=only-if-needed      ipyleaflet
Collecting ipyleaflet
  Downloading ipyleaflet-0.15.0-py2.py3-none-any.whl (3.3 MB)
     |                                | 3.3 MB 364 kB/s 
Collecting traittypes<3,>=0.2.1
  Downloading traittypes-0.2.1-py2.py3-none-any.whl (8.6 kB)
Collecting xyzservices>=2021.8.1
  Downloading xyzservices-2022.2.0-py3-none-any.whl (35 kB)
Collecting ipywidgets<8,>=7.6.0
  Downloading ipywidgets-7.6.5-py2.py3-none-any.whl (121 kB)
     |                                | 121 kB 338 kB/s 
Requirement already satisfied, skipping upgrade: traitlets>=4.2.2 in /usr/lib/python3/dist-packages (from traittypes<3,>=0.2.1->ipyleaflet) (4.3.3)
Requirement already satisfied, skipping upgrade: ipykernel>=4.5.1 in /usr/lib/python3/dist-packages (from ipywidgets<8,>=7.6.0->ipyleaflet) (5.2.0)
Requirement already satisfied, skipping upgrade: ipython>=4.0.0; python_version >= "3.3" in /usr/lib/python3/dist-packages (from ipywidgets<8,>=7.6.0->ipyleaflet) (7.13.0)
Requirement already satisfied, skipping upgrade: ipython-genutils~=0.2.0 in /usr/lib/python3/dist-packages (from ipywidgets<8,>=7.6.0->ipyleaflet) (0.2.0)
Collecting jupyterlab-widgets>=1.0.0; python_version >= "3.6"
  Downloading jupyterlab_widgets-1.0.2-py3-none-any.whl (243 kB)
     |                                | 243 kB 376 kB/s 
Collecting widgetsnbextension~=3.5.0
  Downloading widgetsnbextension-3.5.2-py2.py3-none-any.whl (1.6 MB)
     |                                | 1.6 MB 359 kB/s 
Requirement already satisfied, skipping upgrade: nbformat>=4.2.0 in /usr/lib/python3/dist-packages (from ipywidgets<8,>=7.6.0->ipyleaflet) (5.0.4)
Requirement already satisfied, skipping upgrade: pexpect in /usr/lib/python3/dist-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets<8,>=7.6.0->ipyleaflet) (4.6.0)
Requirement already satisfied, skipping upgrade: notebook>=4.4.1 in /usr/lib/python3/dist-packages (from widgetsnbextension~=3.5.0->ipywidgets<8,>=7.6.0->ipyleaflet) (6.0.3)
Installing collected packages: traittypes, xyzservices, jupyterlab-widgets, widgetsnbextension, ipywidgets, ipyleaflet
Successfully installed ipyleaflet-0.15.0 ipywidgets-7.6.5 jupyterlab-widgets-1.0.2 traittypes-0.2.1 widgetsnbextension-3.5.2 xyzservices-2022.2.0

##jupyter nbextension enable --py --sys-prefix{?} ipyleaflet  # can be skipped for notebook 5.3 and above


R setup


--
R language example 

''Explainable Machine Learning for Land Cover Classification'' by Courage K.  2021

<pre>
# Load the libraries example code from aigeolabs.com
rm(list=ls())
library(sf)    # represents simple features as native R objects
library(rgdal) # interface to the “Geospatial Data Abstraction Library (GDAL)
library(raster) # provides important functions for importing and handling raster data
library(rasterVis) # provides functions to display raster objects
library(dplyr) # provides basic data transformation functions
library(ggplot2) # provides extension for visualizations
library(mapview) # provides functions to visualize geospatial data
library(randomForest) # implements Breiman’s random forest (RF) algorithm
library(kernlab) # implements support vector machine (SVM) algorithm
library(corrplot) # provides graphical display of a correlation matrix
library(iml)   # Keras-base tools for analyzing machine learning models
library(caret) #  machine learning helper

##--------------



OSGeoLive install_R.sh ver14

apt-get --assume-yes install r-base-core r-cran-sp r-cran-rpostgresql r-cran-udunits2 \
  r-cran-ggplot2 r-cran-sf r-cran-lwgeom r-cran-spdata r-cran-rgdal r-cran-maptools


osgeolive 10 patch

in 2016, after being alerted -LINK- , I used pip to upgrade ipywidgets on the OSGeo-Live 10.0 base system.

The following is a modified patch file showing the changes in Python 2.7: 


## Major components, version changed
-ipykernel==4.2.2
+ipykernel==4.5.2
...
-ipython==4.0.2
+ipython==5.1.0
-ipywidgets==5.1.5
+ipywidgets==5.2.2
-jupyter-client==4.1.1
+jupyter-client==4.4.0
 jupyter-console==4.1.0
-jupyter-core==4.0.6
+jupyter-core==4.2.1
-notebook==4.2.1
+notebook==4.3.0
-nbconvert==4.1.0
-nbformat==4.0.1
+nbconvert==5.0.0
+nbformat==4.2.0
+html5lib==0.9999999
-ptyprocess==0.5
+ptyprocess==0.5.1
-pexpect==4.0.1
-pickleshare==0.5
+pexpect==4.2.1
+pickleshare==0.7.4

-decorator==4.0.6
+decorator==4.0.10

##-- misc other additions --
+backports-abc==0.5
+backports.shutil-get-terminal-size==1.0.0
+bleach==1.5.0
+certifi==2016.9.26
+configparser==3.5.0
-enum34==1.1.2
+entrypoints==0.2.2
+enum34==1.1.6
-mistune==0.7.1
+mistune==0.7.3
+pandocfilters==1.4.1
+pathlib2==2.1.0
+prompt-toolkit==1.0.9
-Pygments==2.1
+Pygments==2.1.3
-pyzmq==15.2.0
+pyzmq==16.0.2
+testpath==0.3
-tornado==4.2.1
-traitlets==4.1.0
+tornado==4.4.2
+traitlets==4.3.1
+wcwidth==0.1.7
-widgetsnbextension==1.2.3
+widgetsnbextension==1.2.6

##-- misc other python libs (unchanged)
 anyjson==0.3.3
 Biggus==0.13.0
 Cartopy==0.14.2
 celery==3.1.20
 cf-units==1.0.0
 colorama==0.3.7
 cycler==0.9.0
 defer==1.0.6
 descartes==1.0.1
 filemagic==1.6
 Fiona==1.6.3
 Iris==1.9.2
 imposm==2.6.0
 imposm.parser==1.0.7
 ipyleaflet==0.2.0
 jsonschema==2.5.1
 meld==3.14.2
 ModestMaps==1.4.6
 netCDF4==1.2.4
 Nik4==1.6.0
 numpy==1.11.0
 osmapi==0.6.2
 OWSLib==0.10.3
 pandas==0.17.1
 psutil==3.4.2
 psycopg2==2.6.1
 pykml==0.1.1
 pywps==3.2.5
 rasterio==0.31.0
 TileStache==1.49.8

Python Packages All

jammy Snapshot python install

                       Thu May 26 07:55:03 PM PDT 2022

$ ls /usr/lib/python3/dist-packages/| grep info | sed -e 's/\.dist-info//'
affine-2.3.0.egg-info
alabaster-0.7.12.egg-info
appdirs-1.4.4.egg-info
apt_xapian_index-0.49.egg-info
argon2_cffi-21.1.0.egg-info
asciitree-0.3.3.egg-info
attrs-21.2.0.egg-info
Babel-2.8.0.egg-info
backcall-0.2.0.egg-info
bcrypt-3.2.0.egg-info
beautifulsoup4-4.10.0.egg-info
beniget-0.4.1.egg-info
bleach-4.1.0.egg-info
blinker-1.4.egg-info
blosc-1.9.2.egg-info
Bottleneck-1.3.2.egg-info
branca-0.4.2.egg-info
Brotli-1.0.9.egg-info
certifi-2020.6.20.egg-info
cftime-1.5.2.egg-info
chardet-4.0.0.egg-info
click-8.0.3.egg-info
click_plugins-1.1.1.egg-info
cligj-0.7.2.egg-info
cloudpickle-2.0.0.egg-info
colorama-0.4.4.egg-info
command_not_found-0.3.egg-info
cryptography-3.4.8.egg-info
cupshelpers-1.0-py3.10.egg-info
cycler-0.11.0.egg-info
dask-2022.1.0+dfsg.egg-info
dbus_python-1.2.18.egg-info
decorator-4.4.2.egg-info
defer-1.0.6.egg-info
defusedxml-0.7.1.egg-info
descartes-1.1.0.egg-info
distributed-2022.1.0+ds.1.egg-info
distro-1.7.0.egg-info
distro_info-1.1build1.egg-info
distro_info.py
docutils-0.17.1.egg-info
dropbox-11.26.0.egg-info
entrypoints-0.4
et_xmlfile-1.0.1.egg-info
fasteners-0.14.1.egg-info
Fiona-1.8.21.egg-info
folium-0.0.0.egg-info
fonttools-4.29.1.egg-info
fs-2.4.12.egg-info
fsspec-2022.1.0
fusepy-3.0.1.egg-info
future-0.18.2.egg-info
galternatives-1.0.8.egg-info
gast-0.5.2.egg-info
GDAL-3.4.1.egg-info
GeoAlchemy2-0.10.2.egg-info
geographiclib-1.52.egg-info
geopandas-0.10.2.egg-info
geopy-2.2.0.egg-info
greenlet-1.1.2.egg-info
h5netcdf-0.12.0.egg-info
h5py-3.6.0.egg-info
h5py._debian_h5py_serial-3.6.0.egg-info
HeapDict-1.0.1.egg-info
html5lib-1.1.egg-info
httplib2-0.20.2.egg-info
idna-3.3.egg-info
imagesize-1.3.0.egg-info
importlib_metadata-4.6.4.egg-info
iniconfig-1.1.1.egg-info
ipykernel-6.7.0.egg-info
ipython-7.31.1.egg-info
ipython_genutils-0.2.0.egg-info
ipywidgets-6.0.0.egg-info
jdcal-1.0.egg-info
jedi-0.18.0.egg-info
jeepney-0.7.1
Jinja2-3.0.3.egg-info
joblib-0.17.0.egg-info
jsonschema-3.2.0.egg-info
jupyter_client-7.1.2.egg-info
jupyter_console-6.4.0.egg-info
jupyter_core-4.9.1.egg-info
jupyterlab_pygments-0.1.2.egg-info
keyring-23.5.0.egg-info
kiwisolver-1.3.2.egg-info
language_selector-0.1.egg-info
latexcodec-2.0.1.egg-info
launchpadlib-1.10.16.egg-info
lazr.restfulclient-0.14.4.egg-info
lazr.uri-1.0.6.egg-info
libarchive_c-2.9.egg-info
libvirt_python-8.0.0.egg-info
llvmlite-0.38.0.egg-info
locket-0.2.1.egg-info
lubuntu_update_notifier-0.4.dev0.egg-info
lxml-4.8.0.egg-info
lz4-3.1.3+dfsg.egg-info
Markdown-3.3.6.egg-info
markdown_it_py-1.1.0.egg-info
MarkupSafe-2.0.1.egg-info
matplotlib-3.5.1.egg-info
matplotlib_inline-0.1.3.egg-info
mdit_py_plugins-0.3.0
monotonic-1.6.egg-info
more_itertools-8.10.0.egg-info
mpmath-0.0.0.egg-info
msgpack-1.0.3.egg-info
munch-2.5.0.egg-info
myst_parser-0.16.1
nbclient-0.5.6.egg-info
nbconvert-6.4.0.egg-info
nbformat-5.1.3.egg-info
nbsphinx-0.8.7.egg-info
nest_asyncio-1.5.4.egg-info
netCDF4-1.5.8.egg-info
netifaces-0.11.0.egg-info
nose-1.3.7.egg-info
notebook-6.4.8.egg-info
numba-0.55.1.egg-info
numcodecs-0.9.1+ds.egg-info
numexpr-2.8.1.egg-info
numpy-1.21.5.egg-info
numpydoc-1.2.egg-info
oauthlib-3.2.0.egg-info
odfpy-1.4.2.egg-info
olefile-0.46.egg-info
openpyxl-3.0.9.egg-info
osmium-3.2.0.egg-info
OWSLib-0.25.0.egg-info
packaging-21.3.egg-info
pandas-1.3.5.egg-info
pandocfilters-1.5.0.egg-info
paramiko-2.9.3.egg-info
parso-0.8.1.egg-info
partd-1.2.0.egg-info
pbr-5.8.0.egg-info
pexpect-4.8.0.egg-info
pickleshare-0.7.5.egg-info
Pillow-9.0.1.egg-info
pip-22.0.2
plotly-5.4.0.egg-info
pluggy-0.13.0.egg-info
ply-3.11.egg-info
prometheus_client-0.9.0.egg-info
prompt_toolkit-3.0.28.egg-info
psutil-5.9.0.egg-info
psycopg2-2.9.2.egg-info
ptyprocess-0.7.0
py-1.10.0.egg-info
pybtex-0.23.0.egg-info
pybtex_docutils-1.0.1.egg-info
pycairo-1.20.1.egg-info
pycups-2.0.1.egg-info
pydata_sphinx_theme-0.7.2.egg-info
pygit2-1.6.1.egg-info
Pygments-2.11.2.egg-info
PyGObject-3.42.0.egg-info
PyJWT-2.3.0.egg-info
PyNaCl-1.5.0
pyparsing-2.4.7.egg-info
pyproj-3.3.0.egg-info
PyQt5-5.15.6
PyQt5_sip-12.9.1.egg-info
pyrsistent-0.18.1.egg-info
pytest-6.2.5.egg-info
python_apt-2.3.0+ubuntu2.egg-info
python_dateutil-2.8.1.egg-info
python_debian-0.1.43ubuntu1.egg-info
python_markdown_math-0.8.egg-info
pythran-0.10.0.egg-info
pytz-2022.1.egg-info
pyxdg-0.27.egg-info
PyYAML-5.4.1.egg-info
pyzmq-22.3.0.egg-info
QScintilla-2.11.6
rasterio-1.2.10.egg-info
reportlab-3.6.8.egg-info
requests-2.25.1.egg-info
roman-3.3.egg-info
Rtree-0.9.7.egg-info
scikit_learn-0.23.2.egg-info
scipy-1.8.0.egg-info
SecretStorage-3.3.1.egg-info
Send2Trash-1.8.1b0
setuptools-59.6.0.egg-info
Shapely-1.8.0.egg-info
simplejson-3.17.6.egg-info
six-1.16.0.egg-info
sklearn_pandas-2.0.3.egg-info
snowballstemmer-2.2.0.egg-info
snuggs-1.4.7.egg-info
sortedcontainers-2.1.0.egg-info
soupsieve-2.3.1.egg-info
Sphinx-4.3.2.egg-info
sphinxcontrib_bibtex-2.4.1.egg-info
SQLAlchemy-1.4.31.egg-info
ssh_import_id-5.11.egg-info
stone-3.3.1
sympy-1.9.egg-info
systemd_python-234.egg-info
tables-3.7.0.egg-info
tblib-1.7.0.egg-info
tenacity-6.3.1.egg-info
terminado-0.13.1.egg-info
testpath-0.5.0.egg-info
threadpoolctl-3.1.0
toml-0.10.2.egg-info
toolz-0.11.2.egg-info
tornado-6.1.egg-info
traitlets-5.1.1.egg-info
ubuntu_advantage_tools-27.8.egg-info
ubuntu_drivers_common-0.0.0.egg-info
ufoLib2-0.13.1
ufw-0.36.1.egg-info
unattended_upgrades-0.1.egg-info
unicodedata2-14.0.0.egg-info
urllib3-1.26.5.egg-info
usb_creator-0.3.7.egg-info
wadllib-1.3.6.egg-info
wcwidth-0.2.5.egg-info
webencodings-0.5.1.egg-info
wheel-0.37.1.egg-info
widgetsnbextension-2.0.0.egg-info
xarray-0.16.1.egg-info
xdg-5.egg-info
xkit-0.0.0.egg-info
xlwt-1.3.0.egg-info
zarr-0.0.0.egg-info
zict-2.0.0.egg-info
zipp-1.0.0.egg-info

Focal Snapshot local

                Sat 26 Feb 2022 07:10:31 PM PST

$ ls .local/lib/python3.8/site-packages/ | grep info | sed -e 's/\.dist-info//'
aenum-3.1.8
affine-2.3.0
appdirs-1.4.4
bolt_python-0.7.1
boto-2.49.0
boto3-1.21.2
botocore-1.24.2
branca-0.4.2
charset_normalizer-2.0.12
dataclasses_json-0.5.6
Deprecated-1.2.13
eo_learn-1.0.0
eo_learn_core-1.0.0
eo_learn_coregistration-1.0.0
eo_learn_features-1.0.0
eo_learn_geometry-1.0.0
eo_learn_io-1.0.0
eo_learn_mask-1.0.0
eo_learn_ml_tools-1.0.0
eo_learn_visualization-1.0.0
folium-0.12.1.post1
fs-2.4.15
fs_s3fs-1.1.1
graphviz-0.19.1
imageio-2.16.0
ipyleaflet-0.15.0
ipywidgets-7.6.5
jmespath-0.10.0
joblib-1.1.0
jupyterlab_widgets-1.0.2
lightgbm-3.3.2
llvmlite-0.38.0
marshmallow-3.14.1
marshmallow_enum-1.5.1
mypy_extensions-0.4.3
networkx-2.6.3
numba-0.55.1
numpy-1.21.5
opencv_contrib_python_headless-4.5.5.62
openeo-0.9.2
pandas-1.4.1
Pillow-8.4.0
python_dateutil-2.8.2
pytz-2021.3
PyWavelets-1.2.0
rasterio-1.2.10
requests-2.27.1
requests_oauthlib-1.3.1
s3transfer-0.5.1
scikit_image-0.19.2
scikit_learn-1.0.2
scipy-1.8.0
sentinelhub-3.4.4
snuggs-1.4.7
threadpoolctl-3.1.0
thunder_python-1.4.2
thunder_registration-1.0.1
tifffile-2022.2.9
tqdm-4.62.3
traittypes-0.2.1
typing_extensions-4.1.1
typing_inspect-0.7.1
utm-0.7.0
widgetsnbextension-3.5.2
wrapt-1.13.3
xarray-0.21.1
xyzservices-2022.2.0
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