nf1_cellpainting_env.yml

name: nf1_cellpainting_data

channels:
- conda-forge

dependencies:
# this is restricted to Python 3.8 at this time due to other conflicts
- conda-forge::python=3.8
- conda-forge::ipykernel
- conda-forge::jupyterlab
- conda-forge::nbconvert=6.4.4
- conda-forge::pip
- conda-forge::numpy
- conda-forge::pyyaml
- conda-forge::matplotlib
- conda-forge::seaborn
- conda-forge::pandas
# this package must be hardcoded to work with Mac 
- conda-forge::mysqlclient=1.4.6
- conda-forge::openjdk
# must specifiy scikit-image to avoid error in MeasureGranularity
- conda-forge::scikit-image=0.19.3
- conda-forge::scikit-learn
- conda-forge::mahotas
- conda-forge::gtk2
- conda-forge::typing-extensions
# these are strict because that is how it is on the CellProfiler wiki (Jinja updated for nbconvert)
- conda-forge::Jinja2=3.0.3
- conda-forge::inflect=5.3.0
- conda-forge::wxpython=4.2.0
- conda-forge::sentry-sdk=0.18.0
- pip:
    # Install CellProfiler (do not install higher due to possible differences in output)
    - cellprofiler==4.2.4
    - CytoTable
    - pycytominer