actionet-python/environment-gpu.yml at main · KellisLab/actionet-python · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
# Conda environment for GPU testing on Ubuntu 22+ (native / WSL2).
# CUDA >= 12.2 required; targets Ampere+ (SM 80+).
#
# Usage:
#   conda env create -f environment-gpu.yml
#   conda activate actionet-gpu
#
# Then build the package with GPU support:
#   LIBACTIONET_ENABLE_NVIDIA_GPU=ON pip install -e .

name: actionet-gpu

channels:
  - conda-forge
  - nvidia
  - defaults

dependencies:
  # ---------- Python ----------
  - python=3.12

  # ---------- Build toolchain ----------
  - cmake>=3.19
  - ninja
  - compilers
  - cxx-compiler
  - pybind11>=2.13.0
  - scikit-build-core>=0.10.0

  # ---------- CUDA toolkit ----------
  - cuda-toolkit=12.2
  - cuda-cudart-dev
  - cuda-nvcc
  - libcublas-dev
  - libcusolver-dev

  # ---------- Intel MKL (BLAS/LAPACK) ----------
  - mkl>=2024.0
  - mkl-devel
  - mkl-include
  - libblas=*=*mkl*
  - liblapack=*=*mkl*
  - libcblas=*=*mkl*

  # ---------- HDF5 (C library) ----------
  - hdf5>=1.12

  # ---------- OpenMP (GNU libgomp — single runtime to avoid mixing) ----------
  - libgomp

  # ---------- Python runtime dependencies ----------
  - numpy>=2.0.0
  - scipy>=1.11.0
  - pandas>=2.0.0
  - h5py>=3.9.0
  - anndata>=0.12.10
  - python-igraph>=1.0.0

  # ---------- Dev / test ----------
  - pytest>=8.0.0
  - pytest-cov>=5.0.0
  - black>=24.0.0
  - ruff>=0.1.0
  - pip

  # ---------- pip-only packages ----------
  - pip:
      - -e .