environment-gpu.yaml

####################################################################
# faketGPU Conda Environment (modified for cryo-ET simulation pipeline)
# Approx size: ~9 GB
#
# Original environment from: 
#   https://github.com/paloha/faket/blob/master/environment-gpu.yml
# Modified by: Sage Martineau
# Date modified: 11-02-2026
#
# Purpose:
#   GPU-enabled environment for noise addition with FakET style transfer, 
#   adapted for cryo-ET simulation pipeline with PolNet.

####################################################################
# TESTED ON:
#   Driver Version: 570.211.01
#   CUDA Version: 12.8
#   GPU: NVIDIA A100-SXM4 40GB
#   Python: 3.11.8
#
####################################################################
# MODIFICATIONS FROM ORIGINAL faketGPU:
#    - numpy
#    - pandas
#    - scikit-learn
#    - toml
#
#   Versions pinned for reproducibility on HPC.
#
####################################################################
# NOTES:
#  PyTorch will warn about depricated "pretrained" param but its OK
####################################################################

name: simulation-main
channels:
  - nvidia
  - conda-forge 
dependencies:
  - python=3.11.8  
  - pytorch::pytorch-cuda=12.1
  - conda-forge::cudnn=8.9.7.29
  - pytorch::pytorch=2.2.1                                 
  - pytorch::torchvision=0.17.1
  - conda-forge::mrcfile=1.5.0
  - scikit-image=0.22.0
  - jupyter==1.0.0
  - scipy==1.11.4
  - numpy=1.26.4 
  - pandas=2.3.3 
  - scikit-learn=1.8.0
  - matplotlib=3.8.0
  - pillow=10.2.0
  - ipyfilechooser==0.6.0
  - pynrrd==1.0.0
  - mrcfile=1.5.0 
  - jax==0.4.23
  - vtk==9.3.0
  - tqdm=4.67.3 
  - pip>=23.3
  - pip:
    - configargparse==1.7.1
    - toml==0.10.2
    - wget==3.2
  # - radontea==0.4.9 # reconstruction package used by faket, we use IMOD instead