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update env for hub-image and book #100

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merged 3 commits into from
Jul 2, 2024
Merged

update env for hub-image and book #100

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18253ec
update env for hub-image and book
tsnow03 Jun 24, 2024
5900eb1
remove nbcovert per hub-image
tsnow03 Jun 25, 2024
6324a21
Merge branch 'main' into booky
tsnow03 Jun 25, 2024
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175 changes: 110 additions & 65 deletions conda/environment.yml
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Expand Up @@ -10,105 +10,150 @@ channels:
- conda-forge

dependencies:
- python==3.10.8
- python~=3.11.0
# Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged
- jupyterhub-singleuser>=3.0,<4.0
- jupyterhub-singleuser~=4.0.1
# nbgitpuller is very helpful when distributing user content
- nbgitpuller==1.1.1
- nbgitpuller~=1.2.0
# Specify major version of jupyterlab to use. Manually bump it when you want to upgrade
# jupyterlab version
- jupyterlab>=3.0,<4.0
- jupyterlab>=4.0,<4.1
# This provides memory usage stats on JupyterLab and classic notebook
- jupyter-resource-usage==0.6.4
- jupyter-resource-usage~=1.0.1
# https://syncthing.net/ provides a dropbox-like interface for syncing directories across users,
# hubs and machines. Used along with `jupyter-syncthing-proxy` from pip.
- syncthing==1.22.1
# hubs and machines. Used along with `jupyter-syncthing-proxy`.
- jupyter-syncthing-proxy==1.0.3
- syncthing~=1.22.1
# gh-scoped-creds allows users to securely push to GitHub from their repo.
# https://blog.jupyter.org/securely-pushing-to-github-from-a-jupyterhub-3ee42dfdc54f has
# some more information
- gh-scoped-creds==4.1
# needed for Linux desktop to work
- websockify>=0.10
# Cloud access tools and libraries
# Access S3 easily from python
- s3fs==2022.11.0
# handle login and similar details for accessing earthdata protected data
# https://github.com/nsidc/earthaccess
- earthaccess~=0.8.2
# Access datasets exposed via STAC
- pystac-client==0.5.1
# Access datasets exposed via intake catalogs
- intake==0.6.6
- intake-esm==2022.9.18
- intake-xarray==0.6.1
# More git tools from github-cli
- gh~=2.32.1

# Jupyter tools
- ipython~=8.20.0
- ipywidgets~=8.1.1
- jupyter-book~=1.0.0
- jupyterlab-favorites~=3.2.1
- jupyterlab-geojson~=3.4.0
- jupyterlab-git~=0.50.0
- jupyterlab-h5web~=11.1.0
- jupyterlab-myst~=2.4.2
- jupyterlab_pygments~=0.3.0 # To bring extension uptodate
- jupytext~=1.16.1
- nbdime~=4.0.1
# JupyterBook Addons
- sphinxcontrib-bibtex
# dashboards
- voila~=0.5

# JupyterBook packages
- jupytext
# For building Team Splashpage
- cookiecutter
# Dependencies of jinja-markdown
- jinja2>=2.11
- pygments>=2.6.1
- pymdown-extensions>=7.1

# Core scientific python stack
- numpy==1.23.5
- scipy==1.9.3
- matplotlib==3.6.2
- pandas==1.5.2
- cython==0.29.32 # optimization, C API access
- flox~=0.9.7 # optimization, xarray operations
- hypothesis==6.58.0 # needed by numpy testing tools
- networkx==2.8.8
- numba~=0.58.1 # high-performance numerics
- numpy==1.23.5
- pandas>=2.0.1,<3.0
- scikit-image==0.19.3
- scikit-learn==1.1.3
- sympy==1.11.1
- scikit-learn>=1.2.2,<2.0.0
- scipy>=1.10
- statsmodels==0.13.5
- xarray==2022.11.0
- hypothesis==6.58.0 # needed by numpy testing tools
- cython==0.29.32 # optimization, C API access
- numba==0.56.4 # high-performance numerics

# Jupyter tools
- ipython==8.6.0
- ipywidgets==7.7.2
- jupyterlab-favorites==3.1.0
- jupyterlab-geojson==3.3.1
- jupyterlab-git==0.39.3
- jupyter-book==0.13.1
- nbconvert==6.5.3
- nbdime==3.1.1
- sympy~=1.12
- xarray>=2024.05.0

# Visualization packages
- cartopy==0.20.2 # geospatial plotting with matplotlib
- bokeh~=3.2.2
- cartopy~=0.22.0 # geospatial plotting with matplotlib
- geemap~=0.32
- geoviews~=1.10.1
- hvplot~=0.8.4
- ipyleaflet~=0.17.3
- ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets
- leafmap~=0.31
- matplotlib~=3.8.0
- plotly~=5.18.0
- seaborn==0.12.1 # statistical plotting with matplotlib
- ipympl==0.9.2 # This enables matplotlib interaction with jupyter widgets
- ipyleaflet==0.17.2
- bokeh==3.0.2
- plotly==5.11.0

# Geospatial data packages
- geopandas==0.12.1
- rasterio==1.2.10
- rioxarray==0.13.1
- xarray-datatree==0.0.9

- geopandas~=0.13.2
- pygmt~=0.10.0
- rasterio~=1.3
- rioxarray~=0.15.5
# File formats and file management, download, dataset caching
- h5py==3.7.0
- hdf5==1.12.1
- h5netcdf==1.1.0
- h5py~=3.8
- hdf5~=1.14
- h5netcdf~=1.3.0
- nco~=5.1.6
- pooch==1.6.0
- zarr~=2.18
- kerchunk~=0.2

# Cloud access tools and libraries
- awscli~=1.27.76
- boto3
- s3fs>=2023.6.0
# handle login and similar details for accessing earthdata protected data
# https://github.com/nsidc/earthaccess
- earthaccess~=0.9.0
# Access datasets exposed via STAC
- pystac-client==0.5.1
# Access datasets exposed via intake catalogs
- intake==0.6.6
- intake-esm>=2023.7.7
- intake-stac==0.4.0
- intake-xarray==0.6.1
- gcsfs>=2023.5.0

# Distributed computing
- dask==2022.11.0
- dask-labextension==6.0.0
- dask>=2023.12.1
- dask-labextension~=7.0.0
- dask-geopandas~=0.3.1

# Other useful generic python packages
- pillow==9.2.0 # Python imaging library, useful for many image-related tasks
- tqdm==4.64.1 # progress bars, with notebook support
- pillow~=10.2.0 # Python imaging library, useful for many image-related tasks
- pytest==7.2.0
- pytest-cov==4.0.0
- pep8==1.7.1
- flake8==5.0.4
- tqdm==4.64.1 # progress bars, with notebook support

# Packages specific to climate work
- esmpy~=8.4.2
- xmip~=0.7.1

# Packages specific to cryo work
- icepyx~=0.8.1
- h5coro~=0.0.6
- icepyx~=1.1.0
- itslive~=0.3.2
- is2view~=0.0.8
- sliderule~=4.0.0

# Desktop tools whose versions are more recent on conda-forge than ubuntu
- qgis==3.18.3
- qgis~=3.34.0
# Maybe needed for qgis? https://github.com/conda-forge/qgis-feedstock/issues/263
- pyopencl
# needed for Linux desktop to work
- websockify>=0.10
# Includes new subcommands (`switch` & `restore`) and vulnerability fixes
# over the version available via ubuntu sources
- git>=2.39

# Not all packages will be available from conda-forge, we install from pip when we need to.
- pip==22.3.1
- pip~=23.3.2
- pip:
- jupyter-syncthing-proxy

# Access linux desktop from inside JupyterHub
- jupyter-desktop-server
# Access linux desktop from inside JupyterHub
- jupyter-desktop-server==0.1.3
# For JupyterBook
- jinja-markdown==1.210911
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