Comments (4)
M0hammadL
commented on August 26, 2024
Could you explain with more details?
from cpa.
bitcometz
commented on August 26, 2024
Hello, Thanks for your reply.
First, I run:
import sys
#if branch is stable, will install via pypi, else will install from source
branch = "stable"
IN_COLAB = "google.colab" in sys.modules
if IN_COLAB and branch == "stable":
!pip install cpa-tools
elif IN_COLAB and branch != "stable":
!pip install --quiet --upgrade jsonschema
!pip install --quiet git+https://github.com/theislab/cpa
got ouputs:
Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Requirement already satisfied: cpa-tools in /usr/local/lib/python3.7/dist-packages (0.2.11)
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Requirement already satisfied: importlib-metadata<2.0,>=1.0 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (1.7.0)
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Requirement already satisfied: notebook>=4.4.1 in /usr/local/lib/python3.7/dist-packages (from widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (5.3.1)
Requirement already satisfied: jinja2 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.11.3)
Requirement already satisfied: nbconvert in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (5.6.1)
Requirement already satisfied: Send2Trash in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.8.0)
Requirement already satisfied: terminado>=0.8.1 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.13.3)
Requirement already satisfied: pyzmq>=13 in /usr/local/lib/python3.7/dist-packages (from jupyter-client->ipykernel>=4.5.1->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (23.1.0)
Requirement already satisfied: ptyprocess in /usr/local/lib/python3.7/dist-packages (from terminado>=0.8.1->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.7.0)
Requirement already satisfied: MarkupSafe>=0.23 in /usr/local/lib/python3.7/dist-packages (from jinja2->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.0.1)
Requirement already satisfied: bleach in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (5.0.0)
Requirement already satisfied: entrypoints>=0.2.2 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.5.0)
Requirement already satisfied: testpath in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.6.0)
Requirement already satisfied: defusedxml in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.7.1)
Requirement already satisfied: mistune<2,>=0.8.1 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.8.4)
Requirement already satisfied: webencodings in /usr/local/lib/python3.7/dist-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.5.1)
Then I run
from sklearn.metrics import r2_score
import numpy as np
import os
os.environ['CUDA_VISIBLE_DEVICES'] = '1'
import cpa
import scanpy as sc
I got errors:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
[<ipython-input-5-429404895d3d>](https://localhost:8080/#) in <module>()
----> 1 import cpa
2 import scanpy as sc
12 frames
[/usr/local/lib/python3.7/dist-packages/torchtext/vocab.py](https://localhost:8080/#) in <module>()
11 from typing import Dict, List, Optional, Iterable
12 from collections import Counter, OrderedDict
---> 13 from torchtext._torchtext import (
14 Vocab as VocabPybind,
15 )
ImportError: /usr/local/lib/python3.7/dist-packages/torchtext/_torchtext.so: undefined symbol: _ZNK3c104Type14isSubtypeOfExtERKSt10shared_ptrIS0_EPSo
Thanks !!!
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Naghipourfar
commented on August 26, 2024
Hi @bitcometz,
Can you please try now with the latest CPA version (v0.3.3)?
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bitcometz
commented on August 26, 2024
Thanks and sorry for late reply，I will try ！！！
Best
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