utility/environment.yml at main · ncborcherding/utility · GitHub

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name: sc-integration-benchmark
channels:
  - conda-forge
  - pytorch
  - nvidia  # For CUDA support on Linux (ignored on macOS)
dependencies:
  # ─────────────────────────────────────────────────────────────────────────────
  # Core Python
  # ─────────────────────────────────────────────────────────────────────────────
  - python=3.10
  - pip

  # ─────────────────────────────────────────────────────────────────────────────
  # Scientific Stack
  # ─────────────────────────────────────────────────────────────────────────────
  - numpy>=1.25
  - pandas>=2.0
  - scipy>=1.10
  - h5py>=3.8
  - matplotlib>=3.7
  - seaborn>=0.12
  - scikit-learn>=1.2

  # ─────────────────────────────────────────────────────────────────────────────
  # Graph/Clustering (for Leiden, UMAP neighbors)
  # ─────────────────────────────────────────────────────────────────────────────
  - python-igraph>=0.10
  - leidenalg>=0.9

  # ─────────────────────────────────────────────────────────────────────────────
  # PyTorch - Choose ONE of the following options before creating the environment:
  #
  # Option A: CPU only (default, works everywhere)
  - pytorch>=2.2
  - cpuonly
  #
  # Option B: CUDA 11.8 (uncomment below, comment out cpuonly above)
  # - pytorch>=2.2
  # - pytorch-cuda=11.8
  #
  # Option C: CUDA 12.1 (uncomment below, comment out cpuonly above)
  # - pytorch>=2.2
  # - pytorch-cuda=12.1
  #
  # Option D: macOS MPS (Apple Silicon) - just use the CPU version; MPS is auto-detected
  # ─────────────────────────────────────────────────────────────────────────────

  # ─────────────────────────────────────────────────────────────────────────────
  # Pip-installed packages (versions pinned for reproducibility)
  # ─────────────────────────────────────────────────────────────────────────────
  - pip:
      # Core single-cell ecosystem
      - scvi-tools>=1.1,<1.4       # scVI, scANVI models
      - scanpy>=1.9,<1.12          # Preprocessing, HVG selection
      - anndata>=0.10              # AnnData I/O (zarr support included)

      # Multi-modal / TCR/BCR analysis (for export script)
      - muon>=0.1.5                # MuData for multi-modal
      - scirpy>=0.18               # TCR/BCR analysis

      # YAML config parsing
      - pyyaml>=6.0