Notebook

Commands for Ubuntu installation of notes¶

Uses sudo, but might not be necessary
Sets environment, to keep seperate buyt might not be needed eg for google colab.

In [31]:

%%bash
rm -rf ~/geog0111
cd ~ && git clone https://github.com/UCL-EO/geog0111.git
cd ~/geog0111
cd notebooks && tar xzf data/cacheData.tar.Z

Cloning into 'geog0111'...
Updating files: 100% (696/696), done.

In [1]:

%%bash

pip install virtualenv --quiet
mkdir -p ~/envs
virtualenv ~/envs/geog0111
source ~/envs/geog0111/bin/activate

created virtual environment CPython3.10.12.final.0-64 in 974ms
  creator CPython3Posix(dest=/root/envs/geog0111, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/root/.local/share/virtualenv)
    added seed packages: GDAL==3.3.2, pip==23.1.2, setuptools==67.8.0, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

In [25]:

%%bash
# delete unwanted packages
cd ~/geog0111
awk < environment.yml -F= '{print $1}' | sed 's/-//' | sed 's/ //g' | grep -v 'pip:' | \
      grep -v 'channels:' | grep -v 'dependencies:' | grep -v 'conda-forge' | \
      grep -v 'defaults' | grep -v '#' | grep -vi conda | grep -v libmambapy | \
      grep -vi gdal  | grep -v git  | grep -vi python | grep -v nomkl | \
      grep -vi matplotlib | grep -vi hdf5 | grep -vi libnetcdf > requirements.txt

# look for gdal, matplotlib, hdf5, libnetcdf, libmambapy versions outside this
# nomkl, python, git not needed

In [26]:

%%bash
source ~/envs/geog0111/bin/activate

cd ~/geog0111
pip install -r requirements.txt
#pip install GDAL==`ogrinfo --version | awk -F, '{print $1}' | awk '{print $2}'`

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Building wheels for collected packages: pyephem, cartopy, jupyter_contrib_nbextensions, pandoc, mkdocs-exclude, earthengine-api, jupyter_contrib_core, pyperclip, future
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  Stored in directory: /root/.cache/pip/wheels/5e/a9/47/f118e66afd12240e4662752cc22cefae5d97275623aa8ef57d
Successfully built pyephem cartopy jupyter_contrib_nbextensions pandoc mkdocs-exclude earthengine-api jupyter_contrib_core pyperclip future
Installing collected packages: webencodings, wcwidth, snowballstemmer, pytz, pyperclip, pure-eval, ptyprocess, ply, pickleshare, libclang, jupyter_highlight_selected_word, json5, ipython_genutils, flatbuffers, fastjsonschema, executing, ephem, colour, backcall, args, zipp, xyzservices, wrapt, widgetsnbextension, websocket-client, webcolors, watchdog, urllib3, uritemplate, uri-template, tzdata, typing-extensions, traitlets, tornado, tomli, toml, tinycss2, threadpoolctl, termcolor, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, tenacity, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, smmap, six, send2trash, scooby, rpds-py, rfc3986-validator, regex, pyzmq, PyYAML, python-json-logger, python-box, pyshp, pyparsing, pygments, pyflakes, pyephem, pycparser, pycodestyle, pyasn1, py, psutil, protobuf, prompt-toolkit, prometheus-client, plumbum, pluggy, platformdirs, pillow, pexpect, pathspec, parso, pandocfilters, packaging, overrides, oauthlib, numpy, networkx, nest-asyncio, mypy-extensions, mkdocs-material-extensions, mistune, mergedeep, mdurl, mccabe, markupsafe, markdown, lxml, lazy_loader, kiwisolver, keras, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, joblib, iniconfig, imagesize, idna, grpcio, google-crc32c, gast, future, fsspec, fqdn, fonttools, exceptiongroup, docutils, defusedxml, decorator, debugpy, cycler, coverage, colorama, clint, click, charset-normalizer, certifi, cachetools, babel, attrs, alabaster, affine, absl-py, werkzeug, traittypes, tifffile, terminado, snuggs, shapely, scipy, rsa, rfc3339-validator, retry, requests, referencing, ratelim, qtpy, pyyaml-env-tag, PyWavelets, python-dateutil, pytest, pyproj, pymdown-extensions, pyerfa, pyasn1-modules, plotly, patsy, pandoc, opt-einsum, matplotlib-inline, markdown-it-py, mamba, jupyter-core, Jinja2, jedi, importlib-metadata, imageio, httplib2, h5py, googleapis-common-protos, google-resumable-media, google-pasta, gitdb, flake8, contourpy, comm, cligj, click-plugins, cftime, cffi, bleach, black, beautifulsoup4, autopep8, async-lru, astunparse, asttokens, anyio, yapf, urlpath, stack-data, sphinx, scikit-learn, scikit-image, requests-oauthlib, rasterio, pandas, netcdf4, mdit-py-plugins, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, google-auth, gitpython, ghp-import, geocoder, fiona, branca, astropy, arrow, argon2-cffi-bindings, xarray, statsmodels, seaborn, numpydoc, mkdocs, jsonschema, isoduration, ipython, google-auth-oauthlib, google-auth-httplib2, google-api-core, geopandas, folium, cartopy, argon2-cffi, tensorboard, nbformat, mkdocs-material, mkdocs-exclude, ipykernel, google-cloud-core, google-api-python-client, tensorflow, qtconsole, nbclient, jupytext, jupyter-events, jupyter_console, ipywidgets, google-cloud-storage, nbconvert, ipytree, ipympl, ipyleaflet, ipyfilechooser, ipyevents, earthengine-api, bqplot, nbsphinx, mknotebooks, mkdocs-jupyter, jupyter-server, eerepr, notebook-shim, jupyterlab-server, jupyter-lsp, geemap, nbclassic, jupyterlab, notebook, jupyter_contrib_core, jupyter, jupyter_nbextensions_configurator, jupyter_contrib_nbextensions
Successfully installed Jinja2-3.1.2 PyWavelets-1.4.1 PyYAML-6.0 absl-py-1.4.0 affine-2.4.0 alabaster-0.7.13 anyio-3.7.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 args-0.1.0 arrow-1.2.3 astropy-5.3.1 asttokens-2.2.1 astunparse-1.6.3 async-lru-2.0.3 attrs-23.1.0 autopep8-2.0.2 babel-2.12.1 backcall-0.2.0 beautifulsoup4-4.12.2 black-23.7.0 bleach-6.0.0 bqplot-0.12.40 branca-0.6.0 cachetools-5.3.1 cartopy-0.21.1 certifi-2023.5.7 cffi-1.15.1 cftime-1.6.2 charset-normalizer-3.2.0 click-8.1.5 click-plugins-1.1.1 cligj-0.7.2 clint-0.5.1 colorama-0.4.6 colour-0.1.5 comm-0.1.3 contourpy-1.1.0 coverage-7.2.7 cycler-0.11.0 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 docutils-0.20.1 earthengine-api-0.1.358 eerepr-0.0.4 ephem-4.1.4 exceptiongroup-1.1.2 executing-1.2.0 fastjsonschema-2.17.1 fiona-1.9.4.post1 flake8-6.0.0 flatbuffers-23.5.26 folium-0.14.0 fonttools-4.41.0 fqdn-1.5.1 fsspec-2023.6.0 future-0.18.3 gast-0.4.0 geemap-0.24.3 geocoder-1.38.1 geopandas-0.13.2 ghp-import-2.1.0 gitdb-4.0.10 gitpython-3.1.32 google-api-core-2.11.1 google-api-python-client-2.93.0 google-auth-2.22.0 google-auth-httplib2-0.1.0 google-auth-oauthlib-1.0.0 google-cloud-core-2.3.3 google-cloud-storage-2.10.0 google-crc32c-1.5.0 google-pasta-0.2.0 google-resumable-media-2.5.0 googleapis-common-protos-1.59.1 grpcio-1.56.0 h5py-3.9.0 httplib2-0.22.0 idna-3.4 imageio-2.31.1 imagesize-1.4.1 importlib-metadata-6.8.0 iniconfig-2.0.0 ipyevents-2.0.1 ipyfilechooser-0.6.0 ipykernel-6.24.0 ipyleaflet-0.17.3 ipympl-0.9.3 ipython-8.14.0 ipython_genutils-0.2.0 ipytree-0.2.2 ipywidgets-8.0.7 isoduration-20.11.0 jedi-0.18.2 joblib-1.3.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.18.3 jsonschema-specifications-2023.6.1 jupyter-1.0.0 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyter-events-0.6.3 jupyter-lsp-2.2.0 jupyter-server-2.7.0 jupyter-server-terminals-0.4.4 jupyter_console-6.6.3 jupyter_contrib_core-0.4.2 jupyter_contrib_nbextensions-0.7.0 jupyter_highlight_selected_word-0.2.0 jupyter_nbextensions_configurator-0.6.3 jupyterlab-4.0.3 jupyterlab-pygments-0.2.2 jupyterlab-server-2.23.0 jupyterlab-widgets-3.0.8 jupytext-1.14.7 keras-2.13.1 kiwisolver-1.4.4 lazy_loader-0.3 libclang-16.0.0 lxml-4.9.3 mamba-0.11.2 markdown-3.3.7 markdown-it-py-3.0.0 markupsafe-2.1.3 matplotlib-3.7.2 matplotlib-inline-0.1.6 mccabe-0.7.0 mdit-py-plugins-0.4.0 mdurl-0.1.2 mergedeep-1.3.4 mistune-3.0.1 mkdocs-1.4.3 mkdocs-exclude-1.0.2 mkdocs-jupyter-0.24.2 mkdocs-material-9.1.18 mkdocs-material-extensions-1.1.1 mknotebooks-0.7.1 mypy-extensions-1.0.0 nbclassic-1.0.0 nbclient-0.8.0 nbconvert-7.6.0 nbformat-5.9.1 nbsphinx-0.9.2 nest-asyncio-1.5.6 netcdf4-1.6.4 networkx-3.1 notebook-6.5.4 notebook-shim-0.2.3 numpy-1.24.3 numpydoc-1.5.0 oauthlib-3.2.2 opt-einsum-3.3.0 overrides-7.3.1 packaging-23.1 pandas-2.0.3 pandoc-2.3 pandocfilters-1.5.0 parso-0.8.3 pathspec-0.11.1 patsy-0.5.3 pexpect-4.8.0 pickleshare-0.7.5 pillow-10.0.0 platformdirs-3.8.1 plotly-5.15.0 pluggy-1.2.0 plumbum-1.8.2 ply-3.11 prometheus-client-0.17.1 prompt-toolkit-3.0.39 protobuf-4.23.4 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 py-1.11.0 pyasn1-0.5.0 pyasn1-modules-0.3.0 pycodestyle-2.10.0 pycparser-2.21 pyephem-9.99 pyerfa-2.0.0.3 pyflakes-3.0.1 pygments-2.15.1 pymdown-extensions-10.1 pyparsing-3.0.9 pyperclip-1.8.2 pyproj-3.6.0 pyshp-2.3.1 pytest-7.4.0 python-box-7.0.1 python-dateutil-2.8.2 python-json-logger-2.0.7 pytz-2023.3 pyyaml-env-tag-0.1 pyzmq-25.1.0 qtconsole-5.4.3 qtpy-2.3.1 rasterio-1.3.8 ratelim-0.1.6 referencing-0.29.1 regex-2023.6.3 requests-2.31.0 requests-oauthlib-1.3.1 retry-0.9.2 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.8.10 rsa-4.9 scikit-image-0.21.0 scikit-learn-1.3.0 scipy-1.11.1 scooby-0.7.2 seaborn-0.12.2 send2trash-1.8.2 shapely-2.0.1 six-1.16.0 smmap-5.0.0 sniffio-1.3.0 snowballstemmer-2.2.0 snuggs-1.4.7 soupsieve-2.4.1 sphinx-7.0.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 stack-data-0.6.2 statsmodels-0.14.0 tenacity-8.2.2 tensorboard-2.13.0 tensorboard-data-server-0.7.1 tensorflow-2.13.0 tensorflow-estimator-2.13.0 tensorflow-io-gcs-filesystem-0.32.0 termcolor-2.3.0 terminado-0.17.1 threadpoolctl-3.2.0 tifffile-2023.7.10 tinycss2-1.2.1 toml-0.10.2 tomli-2.0.1 tornado-6.3.2 traitlets-5.9.0 traittypes-0.2.1 typing-extensions-4.5.0 tzdata-2023.3 uri-template-1.3.0 uritemplate-4.1.1 urllib3-1.26.16 urlpath-1.2.0 watchdog-3.0.0 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.1 werkzeug-2.3.6 widgetsnbextension-4.0.8 wrapt-1.15.0 xarray-2023.6.0 xyzservices-2023.7.0 yapf-0.40.1 zipp-3.16.1

In [32]:

%%bash
# look for gdal, matplotlib, hdf5, libnetcdf, libmambapy versions outside this
# codes for gdal

# https://gis.stackexchange.com/questions/370736/installing-gdal-on-ubuntu-20-04-unmet-dependencies
sudo add-apt-repository ppa:ubuntugis/ppa
sudo apt-get update
sudo apt-get install gdal-bin
#sudo apt install libpq5=12.10-0ubuntu0.20.04.1
sudo apt install libpq-dev

ogrinfo --version
sudo apt-get install libgdal-dev
export CPLUS_INCLUDE_PATH=/usr/include/gdal
export C_INCLUDE_PATH=/usr/include/gdal
pip install GDAL==`ogrinfo --version | awk -F, '{print $1}' | awk '{print $2}'`

 Official stable UbuntuGIS packages.


 More info: https://launchpad.net/~ubuntugis/+archive/ubuntu/ppa
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Reading package lists...
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
gdal-bin is already the newest version (3.3.2+dfsg-2~focal2).
0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
libpq-dev is already the newest version (12.15-0ubuntu0.20.04.1).
0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
GDAL 3.3.2, released 2021/09/01
Reading package lists...
Building dependency tree...
Reading state information...
libgdal-dev is already the newest version (3.3.2+dfsg-2~focal2).
0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Requirement already satisfied: GDAL==3.3.2 in /usr/local/lib/python3.10/dist-packages (3.3.2)

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

In [27]:

%%bash
# look for gdal, matplotlib, hdf5, libnetcdf, libmambapy versions outside this

source ~/envs/geog0111/bin/activate
pip install GDAL==`ogrinfo --version | awk -F, '{print $1}' | awk '{print $2}'`

Requirement already satisfied: GDAL==3.3.2 in /root/envs/geog0111/lib/python3.10/site-packages (3.3.2)

In [ ]: