Closed Capiques closed 1 month ago
Hi! this issue seems to be associated with the version of the tool umap (https://github.com/lmcinnes/umap). You can try creating an environment following the instructions here: https://github.com/saezlab/ccc_protocols/tree/main/env_setup
Thank you!!
Hello,
I meet a conflict when I want to install cell2cell. Im not able to import it because during the import the module name import lib.metadata is not find. I tried to install this module on the side with pip
Requirement already satisfied: importlib.metadata in /home/miniconda3/envs/cell2cell/lib/python3.7/site-packages (4.11.3) Requirement already satisfied: zipp>=0.5 in /home/miniconda3/envs/cell2cell/lib/python3.7/site-packages (from importlib.metadata) (3.11.0) Requirement already satisfied: typing-extensions>=3.6.4 in /home/miniconda3/envs/cell2cell/lib/python3.7/site-packages (from importlib.metadata) (4.4.0)
but I still have this error
`ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_3722822/3261411870.py in
----> 1 import cell2cell as c2c
2 import scanpy as sc
3 import pandas as pd
4
5 get_ipython().run_line_magic('matplotlib', 'inline')
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/init.py in
1 # -- coding: utf-8 --
2
----> 3 from cell2cell import analysis
4 from cell2cell import clustering
5 from cell2cell import core
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/analysis/init.py in
1 from cell2cell.analysis.cell2cell_pipelines import (initialize_interaction_space, BulkInteractions, SingleCellInteractions)
----> 2 from cell2cell.analysis.tensor_pipelines import (run_tensor_cell2cell_pipeline)
3 import cell2cell.analysis.tensor_downstream as tensor_downstream
4
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/analysis/tensor_pipelines.py in
5 import tensorly as tl
6
----> 7 from cell2cell.plotting.tensor_plot import tensor_factors_plot
8
9
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/plotting/init.py in
5 from cell2cell.plotting.pval_plot import (dot_plot, generate_dot_plot)
6 from cell2cell.plotting.factor_plot import (context_boxplot, loading_clustermap, ccc_networks_plot)
----> 7 from cell2cell.plotting.pcoa_plot import (pcoa_3dplot)
8 from cell2cell.plotting.tensor_plot import (tensor_factors_plot, tensor_factors_plot_from_loadings)
9 from cell2cell.plotting.umap_plot import (umap_biplot)
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/plotting/pcoa_plot.py in
6 from mpl_toolkits.mplot3d import Axes3D
7
----> 8 from cell2cell.external import pcoa, _check_ordination
9 from cell2cell.plotting.aesthetics import get_colors_from_labels
10
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/external/init.py in
2 from cell2cell.external.goenrich import (goa, ontology)
3 from cell2cell.external.gseapy import (load_gmt, generate_lr_geneset, run_gsea)
----> 4 from cell2cell.external.umap import (run_umap)
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/cell2cell/external/umap.py in
1 # -- coding: utf-8 --
----> 2 import umap
3
4 import pandas as pd
5 import scipy.spatial as sp
~/miniconda3/envs/cell2cell/lib/python3.7/site-packages/umap/init.py in
34 import numba
35
---> 36 from importlib.metadata import version, PackageNotFoundError
37
38 try:
ModuleNotFoundError: No module named 'importlib.metadata'`
Do you have an idea of what can I do ?
Thanks !!