environment.yml

name: stat159-s23

channels:
  - conda-forge

dependencies:
  # Base language runtimes
  - python==3.11.*
  - nodejs=16 # VS code-server requires node < 17

  # Other user-facing Python packages
  - altair==4.2.2
  - bash_kernel==0.9.3
  - beautifulsoup4==4.11.1
  - black==22.12.0
  - bokeh==2.4.3
  - bqplot==0.12.36
  - cartopy==0.21.1
  - coverage==7.0.5
  - cython==0.29.33
  - dask==2023.1.1
  - dask-labextension==6.0.0
  - datascience==0.17.6
  - fortran-magic==0.7
  - gh-scoped-creds==4.1
  - h5netcdf==1.1.0
  - h5py==3.7.0
  - hdf4==4.2.15
  - hdf5==1.12.2
  - hypothesis==6.70.0
  - intake==0.6.6
  - intake-esm==2022.9.18
  - intake-xarray==0.6.1
  - ipycanvas==0.13.1
  - ipydatagrid==1.1.14
  - ipympl==0.9.2
  - ipyparallel==8.4.1
  - ipywidgets==8.0.7
  - jupyter-resource-usage==0.7.1
  # commented out by sknapp 2024.01.11 due to JL4 incompatibility
  #
  # we can revisit once this class is taught again
  #
  # - jupyter_bokeh==3.0.5
  - jupyter_server==2.7.0
  - jupyterlab==4.0.11
  # commented out by sknapp 2024.01.11 due to JL4 incompatibility
  #
  # we can revisit once this class is taught again
  #
  # - jupyterlab-drawio==0.9.0
  - jupyterlab-favorites==3.1.1
  - jupyterlab-geojson==3.3.1
  - jupyterlab-git==0.41.0

  # LSP for JupyterLab/Python - enhanced completions/language support
  - jupyterlab-lsp==5.0.0
  - python-lsp-server==1.7.0

  - jupyterlab-variableinspector==3.0.9
  - jupyterlab-myst==2.1.0
  - jupyterlab_pygments==0.2.2
  - jupyterlab_server==2.19.0
  - jupyterlab-spellchecker==0.8.3
  - jupyter_server_ydoc==0.8.0
  - jupytext==1.14.4
  - mamba==1.2.0
  - matplotlib==3.8.*
  - matplotlib-inline==0.1.6
  - mock==5.0.1
 
  # nbdime 3.1.1 is incompatible with jupyter server 2.0
  # See https://github.com/jupyter/nbdime/pull/649.
  # Use manual pip install from git (see below), revert once
  # official compatible release is available.
  #- nbdime==3.1.1
 
  - nbgitpuller==1.2.1
  - networkx==3.0
  - numba==0.59.1
  - numpy==1.23.5
  - pandas==1.5.3
  - pep8==1.7.1
  - pillow==9.4.0
  - pip==22.3.1
  - plotly==5.12.0
  - pooch==1.6.0
  - prettytable==3.6.0
  - pyarrow==10.0.1
  - pypdf2==2.11.1
  - pytables==3.7.0
  - pytest==7.2.1
  - pytest-cov==4.0.0
  - pytest-notebook==0.6.1
  - requests==2.28.2
  - ruyaml==0.91.0
  - scikit-image==0.19.3
  - scikit-learn==1.2.0
  - scipy==1.10.0
  - seaborn==0.12.2
  - sqlparse==0.4.3
  - statsmodels==0.13.5
  - sympy==1.11.1
  - tk==8.6.12
  - tornado==6.2.0
  - tqdm==4.64.1
  - xarray==2023.1.0
  - xlrd==2.0.1

  # Packages for Jupyter book. These are normal packages, but we put them in a
  # separate section so they are easier to manually sync between the main
  # environment.yml file and a pip requirements file that _only_ builds
  # jupyterbook sites using Github Actions.
  - jupyter-book==0.15.0
  - jupyter-sphinx==0.4.0
  - markdown-it-py==2.2.0
  - markupsafe==2.1.2
  - myst-nb==0.17.1

  # Userland small TeX (similar to tinytex)
  - tectonic==0.12.0

  # Packages that could be installed via the system package manager
  # (apt, homebrew, etc) but we bring them through here for better
  # reproducibility
  - git==2.39.1
  - pandoc==2.19.2
  - pandocfilters==1.5.0

  # ----------------- Hub-only section ----------------------------

  # Packages needed only on the hub (mostly linux)
  # If installing this environment on a personal machine,
  # comment these out (but not the pip section below)
  - micro==2.0.8
  - python-pdfkit==1.0.0
  - syncthing==1.23.0
  - websockify==0.11.0

  - jupyter-server-proxy==4.3.0
  # VS Code support
  - jupyter-vscode-proxy==0.2
  - code-server==4.10.1

  # Companions to tectonic, not yet available for desktop
  - texlab==5.4.0
  - chktex==1.7.8

# Packages not available on conda-forge, installed through pip
  - pip:
    - jupysql==0.10.5
    - ipytest==0.13.0
    - jupyterhub==4.1.6
    - nbval==0.10.0
    - nbdime==3.2.0

    # ----------------- Hub-only section ----------------------------

    # Packages needed only on the hub (mostly linux)
    # If installing this environment on a personal machine,
    # comment these out
    - jupyter-remote-desktop-proxy==2.0.0
    # syncthing for dropbox-like functionality
    - jupyter-syncthing-proxy==1.0.3
    # Needed for RTC on NFS-backed hubs
    - git+https://github.com/berkeley-dsep-infra/tmpystore.git@84765e1
    - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
    # for notebook exporting
    - nbconvert==7.6.0
    - nb2pdf==0.6.2
    - nbpdfexport==0.2.1
    # pulled in by ottr, if not pinned to 1.16.2, 1.16.3 causes DH-323
    - jupytext==1.16.2