sctl.yaml

name: sctl                         # conda activate sctl
channels:
  - conda-forge
dependencies:
  # ─── core Python stack ──────────────────────────────────────────
  - python =3.10                    # keep 3.10 to avoid RC builds
  - pip
  # numba 0.61 supports NumPy <2.3; keep on conda-forge/openblas
  - numpy >=1.24,<2.3
  - pandas >=2.2
  - scipy >=1.14
  - scikit-learn >=1.5
  - scikit-image >=0.21
  - scikit-misc >=0.5
  - statsmodels >=0.14
  - matplotlib >=3.9
  - seaborn >=0.13
  - numba =0.61.*
  - llvmlite =0.44.*               # matched to numba 0.61

  # ─── single-cell / graph stack ─────────────────────────────────
  - scanpy >=1.11
  - anndata >=0.10
  - python-igraph >=0.11
  - leidenalg >=0.10
  - pynndescent >=0.5
  - umap-learn >=0.5
  - gseapy >=1.1.9
  - bbknn >=1.6

  # ─── misc utilities ────────────────────────────────────────────
  - requests >=2.32
  - tqdm >=4.67
  - ipython >=8.35
  - ipykernel >=6.29
  - ipywidgets >=8.1
  - jupyterlab_widgets >=3.0
  - widgetsnbextension
  - session-info
  - psutil

  # ─── install your package in editable mode ─────────────────────
  - pip:
      - -e .     # assumes you run 'conda env create -f sctl.yaml' in repo root