dawe
commented
5 days ago What version of schist were you installing using conda? It seems to me this has been addressed in cf657f603b301b91986903cc29b193461be05dbc, so it should have been ok since v0.8.4.
Hello,
I installed schist with conda. When I imported the package I had the following error: ---------------------------------------------------------------------------AttributeError Traceback (most recent call last) Cell In[66], line 1----> 1 import schist as scs 3 #scs.inference.fit_model(adata) File ~/.conda/envs/visium-env/lib/python3.11/site-packages/schist/init.py:1----> 1 from . import inference 2 from . import tools as tl 3 from . import plotting as pl File ~/.conda/envs/visium-env/lib/python3.11/site-packages/schist/inference/init.py:4 2 from ._flat_model import flat_model 3 from ._planted_model import planted_model----> 4 from ._pmleiden import leiden 5 from ._multi_nested import nested_model_multi File ~/.conda/envs/visium-env/lib/python3.11/site-packages/schist/inference/_pmleiden.py:45 29 except ImportError: 30 raise ImportError( 31 """Please install the graph-tool>=2.33 library either visiting 32 (...) 36 """ 37 ) 39 def leiden( 40 adata: AnnData, 41 resolution: float = 1, 42 n_init: int = 100, 43 *, 44 restrict_to: Optional[Tuple[str, Sequence[str]]] = None,---> 45 random_state: _utils.AnyRandom = 0, 46 key_added: str = 'leiden', 47 adjacency: Optional[sparse.spmatrix] = None, 48 directed: bool = True, 49 use_weights: bool = True, 50 n_iterations: int = -1, 51 partition_type: Optional[Type[MutableVertexPartition]] = None, 52 neighbors_key: Optional[str] = None, 53 obsp: Optional[str] = None, 54 collect_marginals: bool = True, 55 n_jobs: int = -1, 56 copy: bool = False, 57 save_model: Union[str, None] = None, 58 dispatch_backend: Optional[str] = 'threads', 59 **partitionkwargs, 60 ) -> Optional[AnnData]: 61 """\ 62 Cluster cells into subgroups [Traag18]. 63 (...) 136 and
n_iterations. 137 """ 138 try: AttributeError: module 'scanpy._utils' has no attribute 'AnyRandom'In my environment I have the version 1.10.2 of scanpy. I had no problem with the installation of schist by git. Thank you Lucrezia