environment.yaml

name: spatialdata-workshop
channels:
  - conda-forge
dependencies:
  - python=3.11
  - jupyterlab
  - ipykernel
  - pip
  - numpy
  - pandas
  - matplotlib
  - notebook
  - jupyter
  - jupyter_contrib_nbextensions # for auto-completion 
  - squidpy
  - pytest
  - pip:
    # install method 1: latest pip release (recommended)
    - spatialdata
    - spatialdata-io
    - napari-spatialdata
    - spatialdata-plot
    #
    # install method 2: latest unreleased version (includes all latest bugfixes, but since it's not released code it may also introduce new bugs)
    # - git+https://github.com/scverse/spatialdata
    # - git+https://github.com/scverse/spatialdata-io
    # - git+https://github.com/scverse/napari-spatialdata
    # - git+https://github.com/scverse/spatialdata-plot
    #
    # install method 3: pinned release (guaranteed to work, does not include the latest bugfixes)
    # - spatialdata==0.2.3
    # - spatialdata-io==0.1.5
    # - napari-spatialdata==0.5.3
    # - spatialdata-plot==0.2.6
    #
    # install method 4: pinned unreleased version (not recommended, please use if the above does not work and you want unreleased bugfixes)
    # - git+https://github.com/scverse/spatialdata@a126e5804b8c982d9386703f6a108f8b078263a5
    # - git+https://github.com/scverse/spatialdata-io@6d20d76233cdc4d439dee7ec759f6420109de68f
    # - git+https://github.com/scverse/napari-spatialdata@a38e2866c9195866fecf1eca0f911d52587b163a
    # - git+https://github.com/scverse/spatialdata-plot@80c6f7774add354657a1e6b7fed28e162d614584
    #
    # additional packages
    - spatial-image==1.1.0
    - PyQt5 # for napari
    - lxml_html_clean # for napari
    - jupyter-black