Difference between revisions of "Osgeolive-jupyter"
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Revision as of 16:58, 26 July 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 1.3.5fundamental packages
- PostGIS writing done with pyscopg2
2.9.2(low-level) or geoalchemy20.10.2(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-1.8.0Fiona-1.8.21
- opendatacube core and Notebook client examples v1.8.7 -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-
- fsspec -LINK-
- geopython OWSLib, pygeoapi, pygeometa v0.9.1, others .. All -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 --LINK--
- 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 Notebooks
Notes: the demo material from Actinia/GRASS, opendatacube and others use an AWS connection. We want to demo without requiring a connection. There was an idea that a video could be a local file with the demo. Enock said he can edit video, and that some High School Summer of Code students submit their project this way, but the quality is not professional. Angelos suggested that any demo in a video should also be available to actually run, if the network is working; also the GRASS Notebooks download data, and then use that as the demo, instead of doing work only in the clouds. Brian said we should move to beta1 with ordinary Jupyter and then make changes to the details of the Notebooks and python stack.
opendatacube
26july2022
$ datacube product add /path/to/landsat-clip.yml
--- landsat-clip.yml
name: clip_landsat
description: example ortho imagery
metadata_type: eo3
license: CC-BY-4.0
metadata:
product:
name: clip_landsat
storage:
crs: EPSG:32619
resolution:
longitude: 28.497418829384827
latitude: -28.503958771796388
measurements:
- name: imagery
dtype: byte
nodata: -32768.0
units: "meter"
- ----------
25jul2022
user@osgeolive:~$ pip install --user lark-parser
Collecting lark-parser
Downloading lark_parser-0.12.0-py2.py3-none-any.whl (103 kB)
━---------------------------------━━━ 103.5/103.5 KB 352.8 kB/s eta 0:00:00
Installing collected packages: lark-parser
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
mappyfile 0.9.7 requires jsonref==0.2, but you have jsonref 0.1 which is incompatible.
Successfully installed lark-parser-0.12.0
$ createdb datacube
$ psql datacube -c 'create extension postgis'
$ mkdir ~/.config/datacube
$ cat << EOF > ~/.config/datacube/datacube.conf
[datacube]
db_database: datacube
# A blank host will use a local socket. Specify a hostname (such as localhost) to use TCP.
db_hostname:
# Credentials are optional: you might have other Postgres authentication configured.
# The default username otherwise is the current user id.
db_username: user
db_password: user
EOF
user@osgeolive:~$ DATACUBE_CONFIG_PATH=~/.config/datacube/datacube.conf datacube -v system init
2022-07-26 04:35:51,760 4663 datacube INFO Running datacube command: /usr/bin/datacube -v system init
Initialising database...
2022-07-26 04:35:52,213 4663 datacube.drivers.postgres._core INFO Ensuring user roles.
2022-07-26 04:35:52,270 4663 datacube.drivers.postgres._core INFO Creating schema.
2022-07-26 04:35:52,271 4663 datacube.drivers.postgres._core INFO Creating tables.
2022-07-26 04:35:53,006 4663 datacube.drivers.postgres._core INFO Creating triggers.
2022-07-26 04:35:53,015 4663 datacube.drivers.postgres._core INFO Creating added column.
2022-07-26 04:35:53,055 4663 datacube.drivers.postgres._core INFO Adding role grants.
2022-07-26 04:35:53,066 4663 datacube.index.postgres.index INFO Adding default metadata types.
Created.
Checking indexes/views.
2022-07-26 04:35:53,376 4663 datacube.drivers.postgres._api INFO Checking dynamic views/indexes. (rebuild views=True, indexes=False)
Done.
https://github.com/opendatacube/datacube-dataset-config https://github.com/opendatacube/datacube-dataset-config/tree/main/products
https://mybinder.org/v2/gh/opendatacube/odc-stac/develop?urlpath=lab/workspaces/demo
https://datacube-core.readthedocs.io/en/latest/installation/indexing-data/step-guide.html
18June2022 - opendatacube notebooks have very current software under development. Finding the stable parts is a challenge. #osgeolive alpha1 python-geo environment is surprisingly current, and matches a lot of ODC team dev environments including Folium. BUT two important parts are different: odc-devs have more DASK components (multi-processing chains); they have extended rasterio parts that I have not seen here yet. Others not present on alpha1 are JupyterLab parts - we are not going to use those (I read in the reviews late last year JupyterLab still has quality problems). ipyleaflet is developed with JupyterLab.. I am not confident ipyleaflet will work.. maybe. The alpha1 dot-deb packaging simplifies setup, MUCH simpler than their dev setup, and we have no DeepLearning ML GPU libs here.
Minimal datacube install from dot-deb
$apt install python3-xarray python3-cfgrib python3-datacube
Packages that will be installed: python3-cachetools python3-cloudpickle python3-dask python3-datacube python3-distributed python3-fsspec python3-heapdict python3-locket python3-msgpack python3-partd python3-psutil python3-sortedcontainers python3-tblib python3-toolz python3-tornado python3-zict
Jupyter jammy Install
dbb@x10jam:~$ sudo apt install jupyter 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 Get:1 http://mirrors.wikimedia.org/ubuntu jammy/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-2 [117 kB]
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
Get:1 http://mirrors.wikimedia.org/ubuntu jammy/main amd64 bzip2-doc all 1.0.8-5build1 [500 kB]
...
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%
Selecting previously unselected package bzip2-doc.
(Reading database ... 438665 files and directories currently installed.)
Setting up libjs-json (0~20210531+~1.0.8-1) ...
Setting up r-cran-bh (1.74.0-2) ...
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
Note: https://isciences.gitlab.io/exactextractr/
pangeo test install
$ pip install --user geocube
Collecting geocube
Downloading geocube-0.3.2-py3-none-any.whl (20 kB)
Requirement already satisfied: appdirs in /usr/lib/python3/dist-packages (from geocube) (1.4.4)
Requirement already satisfied: pyproj>=2 in /usr/lib/python3/dist-packages (from geocube) (3.3.0)
Requirement already satisfied: click>=6.0 in /usr/lib/python3/dist-packages (from geocube) (8.0.3)
Collecting rioxarray>=0.4
Downloading rioxarray-0.11.1.tar.gz (49 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.7/49.7 KB 283.0 kB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting xarray>=0.17
Downloading xarray-2022.3.0-py3-none-any.whl (870 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 870.9/870.9 KB 388.3 kB/s eta 0:00:00
Requirement already satisfied: numpy>=1.20 in /usr/lib/python3/dist-packages (from geocube) (1.21.5)
Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from geocube) (1.8.0)
Requirement already satisfied: geopandas>=0.7 in /usr/lib/python3/dist-packages (from geocube) (0.10.2)
Collecting odc-geo
Downloading odc_geo-0.2.1-py3-none-any.whl (102 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 102.8/102.8 KB 279.6 kB/s eta 0:00:00
Requirement already satisfied: rasterio in /usr/lib/python3/dist-packages (from geocube) (1.2.10)
Requirement already satisfied: packaging in /usr/lib/python3/dist-packages (from rioxarray>=0.4->geocube) (21.3)
Requirement already satisfied: pandas>=1.1 in /usr/lib/python3/dist-packages (from xarray>=0.17->geocube) (1.3.5)
Requirement already satisfied: affine in /usr/lib/python3/dist-packages (from odc-geo->geocube) (2.3.0)
Requirement already satisfied: cachetools in /usr/lib/python3/dist-packages (from odc-geo->geocube) (5.0.0)
Requirement already satisfied: shapely in /usr/lib/python3/dist-packages (from odc-geo->geocube) (1.8.0)
Building wheels for collected packages: rioxarray
Building wheel for rioxarray (pyproject.toml) ... done
Created wheel for rioxarray: filename=rioxarray-0.11.1-py2.py3-none-any.whl size=50942 sha256=61bb0bfd8815420dc5129f7c7a14afff11796b6978c976a5b3001e54b16ac5e4
Stored in directory: /home/dbb/.cache/pip/wheels/65/e9/a4/20811fc3ecaddf11c40d1e649d0d1bbe3cbbbd71559ca3cd9b
Successfully built rioxarray
Installing collected packages: xarray, odc-geo, rioxarray, geocube
WARNING: The script geocube is installed in '/home/dbb/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed geocube-0.3.2 odc-geo-0.2.1 rioxarray-0.11.1 xarray-2022.3.0
env
TODO pytest tests integration_tests in datacube-core
affine 2.3.0 appdirs 1.4.4 apt_xapian_index .49 asgiref 3.5.0 attrs 21.2.0 Babel 2.8.0 beniget 0.4.1 blinker 1.4 branca 0.4.2 Brotli 1.0.9 Cartopy 0.0.0 certifi 2020.6.20 cftime 1.5.2 chardet 4.0.0 click 8.0.3 click_plugins 1.1.1 cligj 0.7.2 colorama 0.4.4 command_not_found 0.3 cryptography 3.4.8 cupshelpers 1.0 cycler 0.11.0 dbus_python 1.2.18 decorator 4.4.2 defer 1.0.6 Deprecated 1.2.13 descartes 1.1.0 distro 1.7.0 distro_info 1.1 Django 3.2.12 django_model_utils 0.0.0 EOxServer 1.1.0 Fiona 1.8.21 Flask 2.0.1 folium 0.0.0 fonttools 4.29.1 fs 2.4.12 future 0.18.2 galternative 1.0.8 gast 0.5.2 GDAL 3.4.3 geographiclib 1.52 geojson 2.5.0 geolinks 0.2.0 geopandas 0.10.2 gps 3.22 greenlet 1.1.2 httplib2 0.20.2 humanize 0.0.0 idna 3.3 importlib_metadata 4.6.4 iotop 0.6 ipython_genutils 0.2.0 itsdangerous 2.1.0 jeepney 0.7.1 Jinja2 3.0.3 joblib 0.17.0 jsonref 0.1 jsonschema 3.2.0 jupyter_core 4.9.1 keyring 23.5.0 kiwisolver 1.3.2 language_selector 0.1 lark 1.1.1 launchpadlib 1.10.16 lazr.restfulclient 0.14.4 lazr.uri 1.0.6 lubuntu_update_notifier 0.4.dev0 lxml 4.8.0 lz4 3.1.3 mapnik 3.0.23 MapProxy 1.14.0 mappyfile 0.9.7 mapscript 7.6.4 MarkupSafe 2.0.1 matplotlib 3.5.1 meld 3.20.4 more_itertools 8.10.0 mpmath 0.0.0 munch 2.5.0 nbformat 5.1.3 netCDF4 1.5.8 netifaces 0.11.0 networkx 2.4 Nik4 1.7.0 numpy 1.21.5 oauthlib 3.2.0 osmapi 3.0.0 osmium 3.2.0 OWSLib 0.25.0 packaging 21.3 palettable 3.3.0 pandas 1.3.5 pbr 5.8.0 Pillow 9.0.1 plotly 5.4.0 ply 3.11 psycopg2 2.9.2 pycairo 1.20.1 pycql 0.0.8 pycups 2.0.1 pydantic 1.8.2 pygeoapi 0.12.0 Pygments 2.11.2 PyGObject 3.42.0 PyJWT 2.3.0 PyOpenGL 3.1.5 pyparsing 2.4.7 pyproj 3.3.0 PyQt5 5.15.6 PyQt5_sip 12.9.1 pyrsistent 0.18.1 pysal 2.1.0 pyserial 3.5 pyshp 2.2.0 python_apt 2.3.0 python_dateutil 2.8.1 python_debian 0.1.43 pythran 0.10.0 pytz 2022.1 pywps 4.5.1 pyxdg 0.27 PyYAML 5.4.1 QScintilla 2.11.6/ rasterio 1.2.10 requests 2.25.1 Rtree 0.9.7 scikit_learn 0.23.2 scipy 1.8.0 seaborn 0.11.2 SecretStorage 3.3.1 setuptools 59.6.0 Shapely 1.8.0 six 1.16.0 snuggs 1.4.7 SQLAlchemy 1.4.31 sqlparse 0.4.2 sympy 1.9 systemd_python 234 tenacity 6.3.1 threadpoolctl 3.1.0 tinydb 3.15.2 tqdm 4.57.0 traitlets 5.1.1 typing_extensions 3.10.0.2 ubuntu_advantage_tools 27.8 ubuntu_drivers_common 0.0.0 ufoLib2 0.13.1 ufw 0.36.1 unattended_upgrades 0.1 unicodecsv 0.14.1 unicodedata2 14.0.0 urllib3 1.26.5 usb_creator 0.3.7 wadllib 1.3.6 Werkzeug 2.0.2 wrapt 1.13.3 wxPython 4.0.7 xdg 5 xkit 0.0.0 xmltodict 0.12.0 zipp 1.0.0 zipstream 1.1.4 ---------------------------------------------------------- alpha1 Installed dist-packages
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 ----------------------------- ---------------------------- Package Version
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
DevInstall 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)
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Requirement already satisfied: affine in ./.local/lib/python3.8/site-packages (from odc-geo) (2.3.0)
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Downloading cachetools-5.0.0-py3-none-any.whl (9.1 kB)
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Installing collected packages: cachetools, odc-geo
Successfully installed cachetools-5.0.0 odc-geo-0.1.1
odc-stac
## from STAC-load-ms-S2.ipynb import dask.distributed import dask.utils import numpy as np import planetary_computer as pc import xarray as xr from IPython.display import display from pystac_client import Client from odc.stac import configure_rio, stac_load ## from STAC-load-e84-aws.ipynb import dask.distributed import folium import folium.plugins import geopandas as gpd import shapely.geometry from IPython.display import HTML, display from pystac_client import Client from odc.stac import configure_rio, stac_load
$ 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)
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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)
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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)
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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)
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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)
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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)
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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