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theislab / cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
BSD 3-Clause "New" or "Revised" License
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Failed to run the notebook in colab #5

Closed bitcometz closed 9 months ago

bitcometz commented 2 years ago

hello, Thanks for develop the cpa software.

But I cannot run the provided notebook in colab due to the failed installation of CPA.

Could you help with this problem ?

Thanks !!!

M0hammadL commented 2 years ago

Could you explain with more details?

bitcometz commented 2 years ago

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)
Requirement already satisfied: adjustText in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (0.7.3)
Requirement already satisfied: llvmlite<0.39.0,>=0.38.0 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (0.38.1)
Requirement already satisfied: matplotlib<4.0.0,>=3.5.1 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (3.5.2)
Requirement already satisfied: scvi-tools<0.15.0,>=0.14.6 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (0.14.6)
Requirement already satisfied: importlib-metadata<2.0,>=1.0 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (1.7.0)
Requirement already satisfied: scipy<2.0.0,>=1.7.3 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (1.7.3)
Requirement already satisfied: numpy<2.0.0,>=1.21.5 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (1.21.6)
Requirement already satisfied: seaborn<0.12.0,>=0.11.2 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (0.11.2)
Requirement already satisfied: scikit-learn<2.0.0,>=1.0.2 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (1.0.2)
Requirement already satisfied: anndata>=0.7.5 in /usr/local/lib/python3.7/dist-packages (from cpa-tools) (0.8.0)
Requirement already satisfied: typing_extensions in /usr/local/lib/python3.7/dist-packages (from anndata>=0.7.5->cpa-tools) (4.1.1)
Requirement already satisfied: natsort in /usr/local/lib/python3.7/dist-packages (from anndata>=0.7.5->cpa-tools) (5.5.0)
Requirement already satisfied: pandas>=1.1.1 in /usr/local/lib/python3.7/dist-packages (from anndata>=0.7.5->cpa-tools) (1.3.5)
Requirement already satisfied: h5py>=3 in /usr/local/lib/python3.7/dist-packages (from anndata>=0.7.5->cpa-tools) (3.1.0)
Requirement already satisfied: packaging>=20 in /usr/local/lib/python3.7/dist-packages (from anndata>=0.7.5->cpa-tools) (21.3)
Requirement already satisfied: cached-property in /usr/local/lib/python3.7/dist-packages (from h5py>=3->anndata>=0.7.5->cpa-tools) (1.5.2)
Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.7/dist-packages (from importlib-metadata<2.0,>=1.0->cpa-tools) (3.8.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.5.1->cpa-tools) (0.11.0)
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Requirement already satisfied: pyparsing>=2.2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.5.1->cpa-tools) (3.0.9)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.5.1->cpa-tools) (1.4.3)
Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.1.1->anndata>=0.7.5->cpa-tools) (2022.1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7->matplotlib<4.0.0,>=3.5.1->cpa-tools) (1.15.0)
Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.7/dist-packages (from scikit-learn<2.0.0,>=1.0.2->cpa-tools) (1.1.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from scikit-learn<2.0.0,>=1.0.2->cpa-tools) (3.1.0)
Requirement already satisfied: openpyxl>=3.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.0.10)
Requirement already satisfied: torchmetrics>=0.6.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.6.0)
Requirement already satisfied: numba>=0.41.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.55.2)
Requirement already satisfied: ipywidgets in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (7.7.0)
Requirement already satisfied: pytorch-lightning<1.4,>=1.3 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.3.8)
Requirement already satisfied: tqdm>=4.56.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (4.64.0)
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Requirement already satisfied: torch>=1.8.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.11.0)
Requirement already satisfied: pyro-ppl>=1.6.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.8.1)
Requirement already satisfied: setuptools<=59.5.0 in /usr/local/lib/python3.7/dist-packages (from scvi-tools<0.15.0,>=0.14.6->cpa-tools) (57.4.0)
Requirement already satisfied: et-xmlfile in /usr/local/lib/python3.7/dist-packages (from openpyxl>=3.0->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.1.0)
Requirement already satisfied: opt-einsum>=2.3.2 in /usr/local/lib/python3.7/dist-packages (from pyro-ppl>=1.6.0->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.3.0)
Requirement already satisfied: pyro-api>=0.1.1 in /usr/local/lib/python3.7/dist-packages (from pyro-ppl>=1.6.0->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.1.2)
Requirement already satisfied: PyYAML<=5.4.1,>=5.1 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (5.4.1)
Requirement already satisfied: fsspec[http]!=2021.06.0,>=2021.05.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2022.5.0)
Requirement already satisfied: pyDeprecate==0.3.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.3.0)
Requirement already satisfied: future>=0.17.1 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.18.2)
Requirement already satisfied: tensorboard!=2.5.0,>=2.2.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.8.0)
Requirement already satisfied: requests in /usr/local/lib/python3.7/dist-packages (from fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.23.0)
Requirement already satisfied: aiohttp in /usr/local/lib/python3.7/dist-packages (from fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.8.1)
Requirement already satisfied: pygments<3.0.0,>=2.6.0 in /usr/local/lib/python3.7/dist-packages (from rich>=9.1.0->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.6.1)
Requirement already satisfied: commonmark<0.10.0,>=0.9.0 in /usr/local/lib/python3.7/dist-packages (from rich>=9.1.0->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.9.1)
Requirement already satisfied: absl-py>=0.4 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.1.0)
Requirement already satisfied: werkzeug>=0.11.15 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.0.1)
Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.6.1)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.4.6)
Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.8.1)
Requirement already satisfied: wheel>=0.26 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.37.1)
Requirement already satisfied: protobuf>=3.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.17.3)
Requirement already satisfied: google-auth<3,>=1.6.3 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.35.0)
Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.3.4)
Requirement already satisfied: grpcio>=1.24.3 in /usr/local/lib/python3.7/dist-packages (from tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.46.3)
Requirement already satisfied: cachetools<5.0,>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from google-auth<3,>=1.6.3->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (4.2.4)
Requirement already satisfied: rsa<5,>=3.1.4 in /usr/local/lib/python3.7/dist-packages (from google-auth<3,>=1.6.3->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (4.8)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /usr/local/lib/python3.7/dist-packages (from google-auth<3,>=1.6.3->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.2.8)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /usr/local/lib/python3.7/dist-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.3.1)
Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /usr/local/lib/python3.7/dist-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.4.8)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2.10)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.24.3)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (2022.6.15)
Requirement already satisfied: oauthlib>=3.0.0 in /usr/local/lib/python3.7/dist-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (3.2.0)
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Requirement already satisfied: frozenlist>=1.1.1 in /usr/local/lib/python3.7/dist-packages (from aiohttp->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (1.3.0)
Requirement already satisfied: asynctest==0.13.0 in /usr/local/lib/python3.7/dist-packages (from aiohttp->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning<1.4,>=1.3->scvi-tools<0.15.0,>=0.14.6->cpa-tools) (0.13.0)
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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 !!!

Naghipourfar commented 1 year ago

Hi @bitcometz,

Can you please try now with the latest CPA version (v0.3.3)?

bitcometz commented 1 year ago

Thanks and sorry for late reply，I will try ！！！

Best