🐛 Fix git action

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
  strategy:
  matrix:
  fast_finish: [false]
- python-version: [3.8]
+ python-version: [3.10]
 
  steps:
  - uses: actions/checkout@v2
@@ -31,7 +31,7 @@ jobs:
  curl -sSL https://install.python-poetry.org | python3 -
  pip install --upgrade pip
  pip install -e ".[docs, dev]"
- pip install pyg_lib torch_scatter==2.1.1 torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cpu.html
+ install_pyg_dependencies
  
  - name: Build documentation
  run: |

pyproject.toml

@@ -50,6 +50,7 @@ pynvml = "*"
 scikit-misc = "*"
 opencv-python = "*"
 harmonypy = "*"
+loguru = "*"
 
 torch = {version = ">=2.0.0"}
 torchvision = {version = "*"}
@@ -85,4 +86,7 @@ dev = ["pytest", "pytest-cov", "papermill", "ipython", "jupyter", "parse", "nbfo
 [tool.pyright]
 include = ["scSLAT"]
 exclude = ["**/conda", "**/__pycache__", "**/.**"]
-ignore = ["resource/"]
+ignore = ["resource/"]
+
+[tool.poetry.scripts]
+install_pyg_dependencies = "scSLAT.utils:install_pyg_dep"

scSLAT/utils.py

@@ -2,10 +2,12 @@
 Miscellaneous utilities
 """
 import random
+from subprocess import run
 
 from pynvml import *
 from anndata import AnnData
 from typing import List, Optional, Union
+from loguru import logger
 
 import numpy as np
 import torch
@@ -96,4 +98,65 @@ def global_seed(seed: int) -> None:
  torch.manual_seed(seed)
  if torch.cuda.is_available():
  torch.cuda.manual_seed_all(seed)
- print(f"Global seed set to {seed}.")
+ print(f"Global seed set to {seed}.")
+
+
+def install_pyg_dep(torch_version: str = None, cuda_version: str = None):
+ r"""
+ Automatically install PyG dependencies
+
+ Parameters
+ ----------
+ torch_version
+ torch version, e.g. 2.2.1
+ cuda_version
+ cuda version, e.g. 12.1
+ """
+ if torch_version is None:
+ torch_version = torch.__version__
+ torch_version = torch_version.split("+")[0]
+
+ if cuda_version is None:
+ cuda_version = torch.version.cuda
+
+ if torch_version < "2.0":
+ raise ValueError(f"PyG only support torch>=2.0, but get {torch_version}")
+ elif "2.0" <= torch_version < "2.1":
+ torch_version = "2.0.0"
+ elif "2.1" <= torch_version < "2.2":
+ torch_version = "2.1.0"
+ elif "2.2" <= torch_version < "2.3":
+ torch_version = "2.2.0"
+
+ if "cu" in cuda_version and not torch.cuda.is_available():
+ logger.warning(
+ "CUDA is not available, try install CPU version, but may raise error."
+ )
+ cuda_version = "cpu"
+ elif cuda_version >= "12.1":
+ cuda_version = "cu121"
+ elif "11.8" <= cuda_version < "12.1":
+ cuda_version = "cu118"
+ elif "11.7" <= cuda_version < "11.8":
+ cuda_version = "cu117"
+ else:
+ raise ValueError(f"PyG only support cuda>=11.7, but get {cuda_version}")
+
+ if torch_version == "2.2.0" and cuda_version == "cu117":
+ raise ValueError(
+ "PyG not support torch-2.2.* with cuda-11.7, please check https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html"
+ )
+ if torch_version == "2.1.0" and cuda_version == "cu117":
+ raise ValueError(
+ "PyG not support torch-2.1.* with cuda-11.7, please check https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html"
+ )
+ if torch_version == "2.0.0" and cuda_version == "cu121":
+ raise ValueError(
+ "PyG not support torch-2.0.* with cuda-12.1, please check https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html"
+ )
+
+ logger.info(
+ f"Installing PyG dependencies for torch-{torch_version} and cuda-{cuda_version}"
+ )
+ cmd = f"pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-{torch_version}+{cuda_version}.html"
+ run(cmd, shell=True)