ClearMapUi39.yml

# ClearMap.yml 
#
# ClearMap2.0 Toolbox
# © Christoph Kirst
# https://github.com/ChristophKirst/ClearMap2
#
# Licensed under GNU General Public License v3.0
#
# ClearMap anaconda environment
#
# install: conda env create -f ClearMap.yml 
# update:  conda env update -f ClearMap.yml 
name: ClearMapUi39
channels:
  - nvidia
  - pytorch
  - conda-forge
  - defaults

dependencies:
  - python=3.9  # constraining seems to speed up resolution
  - pip
  - ipython
  - vispy
  - pyopengl
  - pyqt<6
  - pyqtwebengine
  - pyqtgraph=0.12  # Problem with pyqtgraph import of QWidgets with 0.13
  - opencv
  - cython<3
  - numpy
  - scipy
  - pandas<2  # Groupby syntax changes
  - pyarrow
  - matplotlib
  - scikit-image
  - scikit-learn
  - graph-tool<=2.45  # Cannot remove self loops with later versions
  - pytorch<=1.11  # could probably upgrade
  - mkl<2024.1  # Breaks pytorch (https://github.com/pytorch/pytorch/issues/123097)
  - cudatoolkit=11.6
  - configobj
  - natsort
  - tifffile<2020.9.22  # Adds "Use DimensionOrder to determine axes order in OmeXml." which breaks ClearMap.IO
  - xmltodict  # to compensate for old tifffile
  - pygments
  - qdarkstyle
  - qtpy  # for qdarkstyle
  - psutil  # required for python < 3.9 for cancelable ProcessPoolExecutors
  - tqdm
  - mpld3  # WARNING Maybe pip
#  - pip:
#    - lxml
variables:
  PYTHONNOUSERSITE: 1
#  TMPDIR: /data/tmp  # FIXME: add option to script