env_mixed.yaml

name: ghent_hackathon_mixed
channels:
  - conda-forge
  - bioconda
  - r
  - defaults
dependencies:
  # R
  # R 4.3 and Bioconductor 3.17 seem to have some package issues, so pin to 4.2 and 3.16 for now
  - r-base=4.2
  - r-irkernel
  - r-recommended
  - r-devtools
  - r-ggplot2
  - r-patchwork
  - r-biocmanager
  - r-quarto
  - bioconductor-biobase
  - bioconductor-experimenthub
  - bioconductor-annotationhub
  - bioconductor-rhdf5
  - bioconductor-ebimage
  - bioconductor-biocstyle
  - bioconductor-spatialexperiment
  - bioconductor-zellkonverter
  ## cytoviewer
  # pre-unlink script failed for package bioconda/noarch::bioconductor-imcdatasets-1.6.0-r42hdfd78af_0
  - bioconductor-imcdatasets
  # package bioconductor-cytoviewer-1.0.0-r43hdfd78af_0 requires bioconductor-s4vectors >=0.38.0,<0.39.0, but none of the providers can be installed
  # - bioconductor-cytoviewer
  - bioconductor-cytomapper
  ## moleculeexperiment
  # package bioconductor-moleculeexperiment-1.0.1-r43hdfd78af_0 requires bioconductor-spatialexperiment >=1.10.0,<1.11.0, but none of the providers can be installed
  # - bioconductor-moleculeexperiment
  ## anndataR
  - r-r6
  - r-anndata
  - r-knitr
  - r-reticulate
  - bioconductor-rhdf5
  - r-rmarkdown
  - r-seuratobject
  - bioconductor-singlecellexperiment
  - bioconductor-summarizedexperiment
  - bioconductor-s4vectors
  - r-withr
  # Jupyter
  - jupyterlab
  - nb_conda_kernels
  # Python
  - python=3.10
  - napari=0.4.18
  - pyqt
  - zarr
  - anndata>=0.9.1
  - pyarrow
  - pip
  - pip:
    # git repo
    - git+https://github.com/scverse/spatialdata.git@main
    # dependencies from spatialdata[extra]
    - napari-spatialdata>=0.2.4
    - spatialdata-plot
    - spatialdata-io