yeast_fusion_segmenter/environment.yml at main · DessimozLab/yeast_fusion_segmenter · GitHub

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name: yeast_fusion_segmenter
channels:
  - conda-forge
  - pytorch
  - nvidia
  - defaults
dependencies:
  # Core Python
  - python=3.9.23
  - pip=25.2

  # Scientific Computing
  - pandas=2.3.1
  - scipy=1.13.1
  - h5py=3.14.0
  - tqdm=4.67.1

  # Image Processing
  - matplotlib=3.9.4
  - pillow=11.3.0

  # CUDA Toolkit and GPU Support (CUDA 12.9)
  - cuda-toolkit=12.9.1
  - cuda-cudart=12.9.79
  - cuda-libraries=12.9.1
  - cuda-libraries-dev=12.9.1
  - cuda-nvcc=12.9.86
  - cudnn=9.10.2  # CUDA Deep Neural Network library

  # Jupyter Environment
  - jupyterlab=4.4.6
  - ipykernel=6.30.1
  - ipython=8.18.1
  - jupyter_client=8.6.3
  - jupyter_core=5.8.1
  - jupyter_server=2.16.0
  - nbconvert-core=7.16.6
  - nbformat=5.10.4

  # Bioinformatics Tools
  - mafft=7.526
  - raxml-ng=1.2.2
  - foldseek=10.941cd33

  # Graphics and Visualization
  - opencv-python=4.13.0.90
  - qt6-main=6.9.1
  - pyside6=6.9.1

  # System Libraries
  - openmpi=4.1.6
  - pytorch-mutex=1.0=cpu

  # pip-installed packages
  - pip:
    # Deep Learning - PyTorch with CUDA 12.8
    - torch==2.8.0
    - torchvision==0.23.0
    - torchaudio==2.8.0
    - torch-geometric==2.6.1
    - pytorch-lightning==2.6.0
    - torchmetrics==1.8.2
    - triton==3.4.0

    # NVIDIA CUDA Libraries (matching CUDA 12.8)
    - nvidia-cublas-cu12==12.8.4.1
    - nvidia-cuda-cupti-cu12==12.8.90
    - nvidia-cuda-nvrtc-cu12==12.8.93
    - nvidia-cuda-runtime-cu12==12.8.90
    - nvidia-cudnn-cu12==9.10.2.21
    - nvidia-cufft-cu12==11.3.3.83
    - nvidia-curand-cu12==10.3.9.90
    - nvidia-cusolver-cu12==11.7.3.90
    - nvidia-cusparse-cu12==12.5.8.93
    - nvidia-nccl-cu12==2.27.3
    - nvidia-nvjitlink-cu12==12.8.93
    - nvidia-nvtx-cu12==12.8.90

    # YOLO and Computer Vision
    - ultralytics==8.4.7
    - ultralytics-thop==2.0.18
    - opencv-python==4.13.0.90

    # Image Processing
    - scikit-image==0.24.0
    - imageio==2.37.2
    - tifffile==2024.8.30
    - pypng==0.20220715.0

    # ImageJ Integration
    - pyimagej==1.7.0
    - imagej==0.3.2
    - imglyb==2.1.0
    - jpype1==1.6.0
    - scyjava==1.12.1
    - jgo==1.1.0
    - cjdk==0.4.1

    # Machine Learning
    - scikit-learn==1.6.1
    - numpy==2.0.2
    - safetensors==0.7.0
    - transformers==4.57.3
    - tokenizers==0.22.1
    - huggingface-hub==0.36.0

    # Advanced ML Libraries
    - deepspeed==0.18.4
    - tensorboard==2.20.0
    - einops==0.8.1
    - opt-einsum==3.4.0

    # Data Science
    - polars==1.36.1
    - xarray==2024.7.0
    - seaborn==0.13.2
    - statsmodels==0.14.5

    # Utilities
    - colour==0.1.5
    - biopython==1.79
    - pyyaml==6.0.2
    - regex==2025.11.3
    - click==8.1.8
    - loguru==0.7.3
    - iprogress==0.4
    - progressbar2==4.5.0

    # Jupyter Widgets
    - ipywidgets==8.1.8
    - jupyterlab-widgets==3.0.16
    - widgetsnbextension==4.0.15
    - jupyterlab_pygments==0.3.0