environment.yml

# conda env create -f environment.yml
name: birdy
channels:
  - conda-forge
  - cdat
  - bokeh
    # - plotly  # for jupyter-dash
    #  - pyston
  - pyviz/label/dev  # for jupyter-panel-proxy, panel
  - defaults

dependencies:

  # Do not put xclim and ravenpy direct dependencies here to let xclim and ravenpy
  # manage their own dependencies pinning.
  #
  # xclim direct dependencies: https://github.com/conda-forge/xclim-feedstock/blob/master/recipe/meta.yaml
  # ravenpy direct dependencies: https://github.com/conda-forge/ravenpy-feedstock/blob/master/recipe/meta.yaml

  # Pin latest xclim and ravenpy to avoid downgrading during the second installation phase.
  # Mamba is quicker to solve dependencies than conda, but it is less precise so accidental downgrades can happen.
  - xclim >= 0.53.2
  - ravenpy >= 0.16.0

  # https://anaconda.org/conda-forge/xscen
  # A climate change scenario-building analysis framework, built with xclim/xarray.
  - xscen >= 0.10.1

    #- dask  # from xclim and ravenpy
  - dask != 2024.11.0  # bug in this specific version broke Raven nb
    #- distributed

  # flox: fast & furious GroupBy reductions for dask.array
  # https://flox.readthedocs.io/en/latest/
  # https://anaconda.org/conda-forge/flox
  - flox
  - matplotlib
    # - xarray  # from xclim and ravenpy
    # - numpy  # from xclim and ravenpy
  - numpy
  # TODO: unpin cf_xarray due to https://github.com/xarray-contrib/cf-xarray/issues/442
  - cf_xarray != 0.8.1
  - birdy >= 0.8.7
    # - owslib>=0.23.0  # from ravenpy
    # - netcdf4  # from ravenpy
  - libnetcdf
  # https://github.com/ecmwf/cfgrib
  # Python interface to map GRIB files to the Unidata's Common Data Model v4
  # following the CF Conventions.
  - cfgrib
  - pydap
  - cartopy >= 0.21.0
  # Fixes cartopy bug arising with scipy 1.11.
  # https://github.com/Ouranosinc/pavics-sdi/pull/298
  # https://github.com/Ouranosinc/pavics-sdi/issues/294
  - pykdtree
  - descartes # Is this really needed???
    # - rasterio  # from ravenpy
    # - gdal  # for osgeo, from ravenpy
    # - geopandas  # from ravenpy
    # - pandas  # from xclim and ravenpy
    # - rioxarray  # from ravenpy
  # https://anaconda.org/conda-forge/pyogrio
  # Vectorized vector I/O using GDAL
  - pyogrio
  - scikit-image
  - ipyleaflet
  - threddsclient >= 0.4.5
  - bokeh
  - regionmask
  - siphon
  - jupyter_bokeh
  - pscript
  - h5netcdf
  - panel >= 1.2.2
  # https://github.com/holoviz/panel
  - pyviz_comms  # (was labextension pyviz/jupyterlab_pyviz in jupyterlab v2)
  - holoviews
  - geoviews >= 1.9.6
  # this might still be relevant https://github.com/holoviz/hvplot/issues/498
  # (violin plot not working with hvplot 0.6.0).
  # Per this comment
  # https://github.com/bird-house/birdhouse-deploy/pull/63#issuecomment-668270608
  # pinning hvplot did not solve the problem with violin plot.
  - hvplot
  # https://anaconda.org/conda-forge/dash
  - dash >= 2.16.1
  # https://streamlit.io/
  # https://anaconda.org/conda-forge/streamlit
  - streamlit
  # https://anaconda.org/conda-forge/seaborn
  # Statistical data visualization
  - seaborn
  # python-pptx is a Python library for creating and updating PowerPoint (.pptx) files.
  # https://python-pptx.readthedocs.io/en/latest/
  # https://anaconda.org/conda-forge/python-pptx
  - python-pptx
  # openpyxl: library to read/write Excel 2010 xlsx/xlsm files
  # https://anaconda.org/conda-forge/openpyxl
  - openpyxl
  - nc-time-axis
    # - cftime  # from xclim and ravenpy
    # - statsmodels  # for ravenpy
  # for error 'ImportError: HTTPFileSystem requires "requests" and "aiohttp" to
  # be installed' with call 'fsspec.filesystem('https')'
  - aiohttp
    # - pydantic  # from ravenpy
  # Intake is a lightweight set of tools for loading and sharing data in data science projects
  - intake
  # https://intake.readthedocs.io/en/latest/plugin-directory.html
  # Plugin for building and loading intake catalogs for earth system data sets
  # holdings, such as CMIP (Coupled Model Intercomparison Project) and CESM
  # Large Ensemble datasets.
  - intake-esm >= 2023.6.14
  # load netCDF, Zarr and other multi-dimensional data (xarray_image, netcdf,
  # grib, opendap, rasterio, remote-xarray, zarr)
  - intake-xarray
  # load from ESRI Shape Files, GeoJSON, and geospatial databases with
  # geopandas (geojson, postgis, shapefile, spatialite) and regionmask for
  # opening shapefiles into regionmask.
  - intake-geopandas
  # Intake interface to THREDDS data catalogs (thredds_cat, thredds_merged_source)
  - intake-thredds
  - gcsfs
  - zarr
  # https://github.com/dask/s3fs/
  - s3fs
    # - shapely  # from ravenpy
  # https://github.com/roocs/clisops
  - clisops >= 0.9.2
  # Universal Regridder for Geospatial Data
  # https://github.com/pangeo-data/xESMF
  # xesmf-0.6.2 requires clisops>=0.8.0
  - xesmf >= 0.6.2
  # Sensitivity Analysis Library
  # https://anaconda.org/conda-forge/salib
  - salib
  # https://anaconda.org/conda-forge/geopy
  - geopy
  # https://anaconda.org/anaconda/memory_profiler
  # Monitor memory consumption of a process as well as line-by-line analysis
  # of memory consumption for Python programs.
  - memory_profiler
  # for esgf notebooks
  - esgf-compute-api
  # https://anaconda.org/conda-forge/esgf-pyclient (for pavics-sdi esgf-dap.ipynb)
  - esgf-pyclient
  # Disable cdms2 because it was forcing python downgrade to 3.10 and below.
  #- cdms2
  # Disable vcs because it was forcing python downgrade to below 3.9.
  # See https://github.com/CDAT/vcs/issues/457
  #   package vcs-8.1-py_0 requires vtk-cdat >8.1, but none of the providers can be installed
  #   package vtk-cdat-8.2.0.8.2.1-py38hbc81915_0 requires python >=3.8,<3.9.0a0 *_cpython
  #- vcs
  - mesalib
  # tests
  - pytest
  - pytest-xdist
  - nbval
  # to edit .ipynb
  - jupyter
  # to be launched by image jupyterhub/jupyterhub
  - notebook
  - jupyterlab
  - jupyterhub
  # https://ipywidgets.readthedocs.io/en/latest/user_install.html
  - ipywidgets
  # https://github.com/jupyter-widgets/ipyleaflet
  - ipyleaflet
  # https://github.com/mamba-org/gator (was jupyter_conda)
  - mamba_gator
  # to diff .ipynb files
  - nbdime
  # extension to produce .py files from notebook .ipynb files
  - jupytext
  # jupyterlab extension for git
  - jupyterlab-git >= 0.44.0
  # Voilà turns Jupyter notebooks into standalone web applications
  - voila
  # TODO: UNPIN jupyter-archive due to
  # https://github.com/jupyterlab-contrib/jupyter-archive/issues/132
  - jupyter-archive <= 3.3.4
  # https://github.com/jtpio/jupyterlab-topbar
  - jupyterlab-topbar
  # https://github.com/jtpio/jupyterlab-system-monitor (was from jupyterlab-topbar)
  - jupyterlab-system-monitor
  - jupyter-resource-usage  # needed by jupyterlab-system-monitor
  - nbresuse  # needed by jupyterlab-system-monitor
  # xeus-python: back-end kernel implementing the Jupyter Debug Protocol
  - xeus-python
  # https:://github.com/jupyterhub/jupyter-server-proxy
  - jupyter-server-proxy
  # https://github.com/dask/dask-labextension
  - dask-labextension
  # https://github.com/holoviz/jupyter-panel-proxy
  # DISABLE: seems to interfere with 'panel serve' command
  #- jupyter-panel-proxy >= 0.2.0a2
  # Force newer nodejs for 'jupyter lab build' issue
  # https://github.com/jupyterlab/jupyterlab/issues/11726#issuecomment-998901247
  # TODO: remove nodejs once all extensions move to prebuilt extensions, see comment
  # https://github.com/jupyterlab/jupyterlab/issues/11726#issuecomment-998917305
  - nodejs >= 16.0
  # utilities
  - curl
  - wget
  - nested_dict
  # https://anaconda.org/conda-forge/urlpath
  # https://github.com/brandonschabell/urlpath
  - urlpath
  - paramiko
  - pymetalink  # for Raven notebook Extract_geographical_watershed_properties.ipynb
  - requests-magpie
  - scp
  - selenium
  - geckodriver
  - xlrd
  - pre-commit
  # pyston_lite_autoload blocked us from using newer Python than 3.8
  #   package pyston_lite_autoload-2.3.4-pyh44b312d_0 requires pyston_lite
  #   2.3.4 py38h0a891b7_0, but none of the providers can be installed
  # https://github.com/pyston/pyston/
  #  - pyston_lite_autoload
  # for pip packages
  - pip
  - pip:
    # https://pypi.org/project/xncml/
    # Tools for manipulating and opening NCML (NetCDF Markup) files with/for xarray
    - xncml
    # https://pypi.org/project/hsclient/
    # A python client for managing HydroShare resources, replaces hs_restclient
    - hsclient
    # https://pypi.org/project/fstd2nc/
    # Converts RPN standard files (from Environment Canada) to netCDF files.
    - fstd2nc
    # https://pypi.org/project/figanos/
    # Outils pour produire des graphiques informatifs sur les impacts des
    # changements climatiques.
    - figanos
    # visual debugger for Jupyter Notebook, not working with JupyterLab at this moment
    - pixiedust
    # block execution of 'run_all_cells' until user input finished
    - ipython_blocking
    # Mimics how one might format their calculation if it were written with a
    # pencil: write the symbolic formula, followed by numeric substitutions,
    # and then the result.
    # DISABLE handcalcs, interfere with "Panel preview" button
    # See comment https://github.com/holoviz/panel/issues/3440#issuecomment-1112182170
    # - handcalcs
    # https://github.com/ShopRunner/jupyter-notify
    # Jupyter Magic For Browser Notifications of Cell Completion.
    - jupyternotify
    # https://github.com/jupyterlab-contrib/jupyterlab-logout (was from jupyterlab-topbar)
    - jupyterlab-logout
    # https://github.com/jupytercalpoly/jupyterlab-tabular-data-editor
    - jupyterlab-tabular-data-editor
    # Needed to run notebook tests.  Missing indirect recursive dependencies
    # somewhere, should not need to manually add it here.
    - pytest-tornasync