environment.yml

# Dependencies marked with "(optional)" are not required for core functionality
# and can be commented out if there are conflicts.

name: test
channels:
  - pytorch
  - conda-forge
  - defaults
  - menpo
  - open3d-admin
  # - pyg
dependencies:
  - cudatoolkit=11.6
  # From -c pytorch
  - pytorch::pytorch=1.12.1  # can be > 1.9 if glibc >=2.27 is available
  - torchvision
  # - pyg
  # - pytorch-sparse

  # From conda-forge and defaults
  - python >= 3.9  # (3.6 should also work)
  - pip
  - lemon
  - vigra
  - freeglut
  - pyopengl=3.1.5
  # highest available version for pyopengl-accelerate is 3.1.3 (pyopengl 3.1.5 is being used right now)
  #  - pyopengl-accelerate
  - python-snappy
  - ipython
  - h5py > 3
  - matplotlib
  - tqdm
  - networkx <= 2.5.1
  - m2r
  - lz4
  - flask
  - fasteners
  - numpy
  - coloredlogs
  - scipy < 1.9   # <1.9 because n_jobs parameter in every tree query was removed. Can be >=1.9 if refactored in the whole project
  - termcolor
  # fix version due to stored RFC models.
  - scikit-learn >= 0.24.1
  - scikit-image
  - opencv
  - numba >0.48  # =0.48 led to freeze when importing elektronn3.data
  - openmesh-python
  - prompt_toolkit
  - dill
  - joblib
  - seaborn >= 0.11
  - pyyaml
  - cython
  - colorlog
  # for pandas xls support
  - xlrd >= 1.0.0
   # >= 7 raises "cannot import name 'PILLOW_VERSION' from 'PIL'" with torchvision=0.3.0
  - pillow

  # From -c menpo
  - menpo::osmesa
  - conda-forge::mesalib

  # From -c open3d-admin; >0.9.0 throws /lib64/libm.so.6: version `GLIBC_2.27' not found
  #- open3d-admin::open3d

  # For tests (optional):
  - pytest
  - pytest-cov

  # For docs (optional):
  - sphinx
  - sphinx_rtd_theme
  - sphinx-autodoc-typehints

  # Required dependencies that are not yet available via conda:
  - pip:
    - open3d
    - zmesh
    - plyfile
    - torch_geometric == 2.0.2  # 2.0.3 is incompatible with lcp.knn.quantized_sampling
    - --find-links https://data.pyg.org/whl/torch-1.12.0+cu116.html
    - torch-sparse
    - torch-scatter
    # Pre-release packages
    - git+https://github.com/ELEKTRONN/elektronn3.git@syconn2#egg=elektronn3
    - git+https://github.com/knossos-project/knossos_utils.git@syconn2#egg=knossos_utils
    - git+https://github.com/StructuralNeurobiologyLab/MorphX.git@v0.1#egg=MorphX

    # cloud-volume >=4 throws an error in simple_merge during np.concatenate if any skeleton has no vertices
    - git+https://github.com/StructuralNeurobiologyLab/kimimaro.git

    # point models
    - git+https://github.com/StructuralNeurobiologyLab/LightConvPoint.git

#    # training scripts
#    - git+https://github.com/StructuralNeurobiologyLab/NeuronX.git

    #for skeletonisation
    - fill-voids