environment.yml

name: cryocloud

channels:
  - conda-forge
  - nodefaults

dependencies:
  - python~=3.11.0
  # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged
  - jupyterhub-singleuser~=4.0.1
  # nbgitpuller is very helpful when distributing user content
  - nbgitpuller~=1.2.0
  # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade
  # jupyterlab version
  - jupyterlab>=4.0,<4.1
  # This provides memory usage stats on JupyterLab and classic notebook
  - 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`.
  - 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
  # More git tools from github-cli
  - gh~=2.32.1

  # VS Code support
  - jupyter-vscode-proxy~=0.5
  - code-server~=4.23

  # Jupyter tools
  - ipython~=8.17
  - ipywidgets~=8.1.1
  - jupyter-ai~=2.20
  - jupyter-book~=1.0.0
  # - jupyter-collaboration~=2.0.1
  - jupyter-offlinenotebook~=0.3.1
  - jupyter-sshd-proxy~=0.2
  - 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 up-to-date
  - jupytext~=1.16.1
  - nbdime~=4.0.1
  # JupyterBook Addons
  - sphinx~=7.3
  - sphinxcontrib-bibtex
  # Interactive apps
  - itables~=2.1
  - voila~=0.5

  # Core scientific python stack
  - cython~=3.0.10 # 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~=0.60.0 # high-performance numerics
  - numpy==1.26.4
  - pandas>=2.0.1,<3.0
  - scikit-image~=0.24.0
  - scikit-learn>=1.2.2,<2.0.0
  - scipy>=1.10
  - statsmodels==0.13.5
  - sympy~=1.12
  - xarray>=2024.05.0

  # Visualization packages
  - bokeh~=3.2.2
  - cartopy~=0.23.0 # geospatial plotting with matplotlib
  - geemap~=0.32
  - geoviews~=1.10.1
  - hvplot~=0.10.0
  - ipyleaflet~=0.19.2
  - ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets
  - leafmap~=0.36
  - lonboard~=0.9
  - matplotlib~=3.9.0
  - plotly~=5.18.0
  - seaborn~=0.13.2 # statistical plotting with matplotlib

  # Machine Learning packages
  - py-xgboost~=2.1.1=cpu*

  # Geospatial data packages
  - geopandas>=0.14.4
  - pygmt~=0.12.0
  - rasterio~=1.3
  - rioxarray~=0.17.0

  # File formats and file management, download, dataset caching
  - h5py~=3.11
  - h5netcdf~=1.3.0
  - nco~=5.1.6
  - pooch~=1.8.0
  - zarr~=2.18
  - kerchunk~=0.2

  # Cloud access tools and libraries
  - awscli~=2.17
  - boto3
  - s3fs>=2023.6.0
  # handle login and similar details for accessing earthdata protected data
  # https://github.com/nsidc/earthaccess
  - earthaccess~=0.10.0
  # Access datasets exposed via STAC
  - pystac-client~=0.8.3
  - stackstac~=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>=2023.12.1
  - dask-labextension~=7.0.0
  - dask-geopandas~=0.4.1

  # Other useful generic python packages
  - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks
  - pytest~=8.3
  - pytest-cov~=5.0
  - pep8~=1.7
  - flake8~=7.1
  - tqdm~=4.66 # progress bars, with notebook support

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

  # Packages specific to cryo work
  - h5coro~=0.0.6
  - icepyx~=1.2.0
  - itslive~=0.3.2
  - is2view~=0.0.8
  - sliderule~=4.5
  - snowexsql~=0.5

  # Desktop tools whose versions are more recent on conda-forge than ubuntu
  - qgis~=3.38.0
  # Maybe needed for qgis? https://github.com/conda-forge/qgis-feedstock/issues/263
  - pyopencl
  # Resolves warning "No ICDs were found": https://github.com/CryoInTheCloud/hub-image/issues/50
  - ocl-icd-system
  # 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~=23.3.2
  - pip:
    # Access linux desktop from inside JupyterHub
    - jupyter-desktop-server==0.1.3