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theislab / graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
MIT License
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ImportError: cannot import name 'scalar_search_armijo' from 'scipy.optimize.linesearch' #66

Closed spatts14 closed 2 weeks ago

spatts14 commented 2 months ago

Hi,

I followed the update instructions detailed in #61 but Ive gotten a new issue importing now...

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/ot/optim.py:21
     20 try:
---> 21     from scipy.optimize import scalar_search_armijo
     22 except ImportError:

ImportError: cannot import name 'scalar_search_armijo' from 'scipy.optimize' (/rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/scipy/optimize/__init__.py)

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
Cell In[1], line 8
      5 warnings.filterwarnings("ignore")
      7 import scanpy as sc
----> 8 import graphcompass as gc
      9 import numpy as np
     10 import anndata as ad

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/__init__.py:2
      1 """Graph-COMPASS."""
----> 2 from graphcompass import pl
      3 from graphcompass import tl
      4 from graphcompass import datasets

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/pl/__init__.py:2
      1 """The plotting module."""
----> 2 from . import _distance as distance
      3 from . import _WLkernel as wlkernel
      4 from . import _filtration_curves as filtration_curves

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/pl/_distance.py:14
     11 from matplotlib.figure import Figure
     13 from tqdm import tqdm
---> 14 from graphcompass.tl._distance import compare_groups
     16 from typing import Any, Sequence, Tuple, Union
     19 def convert_dataframe(df_ct, samples):

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/tl/__init__.py:3
      1 """The spatial DE methods module."""
      2 from . import _distance as distance
----> 3 from . import _WLkernel as wlkernel
      4 from . import _filtration_curves as filtration_curves
      5 from . import utils

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:11
      9 from anndata import AnnData
     10 from graphcompass.tl.utils import _calculate_graph, _get_igraph
---> 11 from graphcompass.imports.wwl_package import wwl, pairwise_wasserstein_distance 
     14 def compare_conditions(
     15     adata: AnnData,
     16     library_key: str = "sample",
   (...)
     24     **kwargs,
     25 ) -> AnnData:
     26     """
     27     Compares conditions based on entire spatial graphs using the WWL Kernel.
     28 
   (...)
     49         Whether to return a copy of the Wasserstein distance object.
     50     """

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/imports/wwl_package/__init__.py:2
      1 """The spatial DE methods module."""
----> 2 from .wwl import pairwise_wasserstein_distance, wwl

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/graphcompass/imports/wwl_package/wwl.py:12
      9 import sys
     10 import logging
---> 12 import ot
     13 import numpy as np
     14 from sklearn.metrics.pairwise import laplacian_kernel

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/ot/__init__.py:23
     21 from . import lp
     22 from . import bregman
---> 23 from . import optim
     24 from . import utils
     25 from . import datasets

File ~/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/ot/optim.py:23
     21         from scipy.optimize import scalar_search_armijo
     22     except ImportError:
---> 23         from scipy.optimize.linesearch import scalar_search_armijo
     25 # The corresponding scipy function does not work for matrices
     28 def line_search_armijo(
     29     f, xk, pk, gfk, old_fval, args=(), c1=1e-4,
     30     alpha0=0.99, alpha_min=0., alpha_max=None, nx=None, **kwargs
     31 ):

ImportError: cannot import name 'scalar_search_armijo' from 'scipy.optimize.linesearch' (/rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages/scipy/optimize/linesearch.py)
spatts14 commented 2 months ago

I also got this error about numpy during the install if that is helpful

(graphcompass_HPC) [sep22@login-a GitHub]$ git clone https://github.com/theislab/graphcompass.git
Cloning into 'graphcompass'...
remote: Enumerating objects: 502, done.
remote: Counting objects: 100% (69/69), done.
remote: Compressing objects: 100% (51/51), done.
remote: Total 502 (delta 20), reused 31 (delta 11), pack-reused 433 (from 1)
Receiving objects: 100% (502/502), 2.91 MiB | 11.74 MiB/s, done.
Resolving deltas: 100% (239/239), done.
(graphcompass_HPC) [sep22@login-a GitHub]$ cd graphcompass/
(graphcompass_HPC) [sep22@login-a graphcompass]$ pip install -e .['development']
Obtaining file:///rds/general/user/sep22/home/Other/GitHub/graphcompass
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Installing backend dependencies ... done
  Preparing editable metadata (pyproject.toml) ... done
Requirement already satisfied: aiohttp>=3.8.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from graphcompass==0.2.4) (3.10.5)
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WARNING: graphcompass 0.2.4 does not provide the extra 'development'
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Collecting multiscale-spatial-image==0.11.2 (from spatialdata->graphcompass==0.2.4)
  Using cached multiscale_spatial_image-0.11.2-py3-none-any.whl.metadata (21 kB)
Requirement already satisfied: ome-zarr>=0.7.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (0.9.0)
Requirement already satisfied: pyarrow in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (17.0.0)
Requirement already satisfied: pygeos in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (0.14)
Requirement already satisfied: rich in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (13.7.1)
Requirement already satisfied: shapely>=2.0.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (2.0.3)
Collecting spatial-image==0.3.0 (from spatialdata->graphcompass==0.2.4)
  Using cached spatial_image-0.3.0-py3-none-any.whl.metadata (5.5 kB)
Requirement already satisfied: xarray-schema in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (0.0.3)
Requirement already satisfied: xarray-spatial>=0.3.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatialdata->graphcompass==0.2.4) (0.4.0)
Requirement already satisfied: xarray-datatree>=0.0.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from multiscale-spatial-image==0.11.2->spatialdata->graphcompass==0.2.4) (0.0.14)
Requirement already satisfied: xarray-dataclasses>=1.1.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from spatial-image==0.3.0->spatialdata->graphcompass==0.2.4) (1.7.0)
Requirement already satisfied: dask-expr<1.2,>=1.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from dask[array,dataframe]>=2024.4.1->dask-image>=0.5.0->graphcompass==0.2.4) (1.1.11)
Requirement already satisfied: zipp>=0.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from importlib-metadata>=4.13.0->dask>=2021.02.0->dask[array]>=2021.02.0->graphcompass==0.2.4) (3.20.1)
Requirement already satisfied: more-itertools>=8.5.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from inflect>=4.1.0->omnipath>=1.0.7->graphcompass==0.2.4) (10.4.0)
Requirement already satisfied: typeguard>=4.0.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from inflect>=4.1.0->omnipath>=1.0.7->graphcompass==0.2.4) (4.3.0)
Requirement already satisfied: distributed in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (2024.8.1)
Requirement already satisfied: locket in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from partd>=1.4.0->dask>=2021.02.0->dask[array]>=2021.02.0->graphcompass==0.2.4) (1.0.0)
Requirement already satisfied: slicerator>=0.9.8 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from pims>=0.4.1->dask-image>=0.5.0->graphcompass==0.2.4) (1.1.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from requests>=2.24.0->omnipath>=1.0.7->graphcompass==0.2.4) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from requests>=2.24.0->omnipath>=1.0.7->graphcompass==0.2.4) (3.8)
Requirement already satisfied: certifi>=2017.4.17 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from requests>=2.24.0->omnipath>=1.0.7->graphcompass==0.2.4) (2024.8.30)
Collecting numpy>=1.23.0 (from graphcompass==0.2.4)
  Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Requirement already satisfied: datashader>=0.15.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from xarray-spatial>=0.3.5->spatialdata->graphcompass==0.2.4) (0.16.3)
Requirement already satisfied: fiona>=1.8.21 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from geopandas->spatialdata->graphcompass==0.2.4) (1.9.6)
Requirement already satisfied: pyproj>=3.3.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from geopandas->spatialdata->graphcompass==0.2.4) (3.6.1)
Requirement already satisfied: markdown-it-py>=2.2.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from rich->spatialdata->graphcompass==0.2.4) (3.0.0)
Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from rich->spatialdata->graphcompass==0.2.4) (2.18.0)
Requirement already satisfied: stdlib-list in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from session-info->scanpy>=1.9.3->graphcompass==0.2.4) (0.10.0)
Requirement already satisfied: colorcet in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata->graphcompass==0.2.4) (3.1.0)
Requirement already satisfied: multipledispatch in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata->graphcompass==0.2.4) (1.0.0)
Requirement already satisfied: param in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata->graphcompass==0.2.4) (2.1.1)
Requirement already satisfied: pyct in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata->graphcompass==0.2.4) (0.5.0)
Requirement already satisfied: click-plugins>=1.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from fiona>=1.8.21->geopandas->spatialdata->graphcompass==0.2.4) (1.1.1)
Requirement already satisfied: cligj>=0.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from fiona>=1.8.21->geopandas->spatialdata->graphcompass==0.2.4) (0.7.2)
Requirement already satisfied: s3fs in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (2023.6.0)
Requirement already satisfied: mdurl~=0.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from markdown-it-py>=2.2.0->rich->spatialdata->graphcompass==0.2.4) (0.1.2)
Requirement already satisfied: jinja2>=2.10.3 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (3.1.4)
Requirement already satisfied: msgpack>=1.0.2 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (1.0.8)
Requirement already satisfied: psutil>=5.8.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (6.0.0)
Requirement already satisfied: sortedcontainers>=2.0.5 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (2.4.0)
Requirement already satisfied: tblib>=1.6.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (3.0.0)
Requirement already satisfied: tornado>=6.2.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (6.4.1)
Requirement already satisfied: zict>=3.0.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (3.0.0)
Requirement already satisfied: MarkupSafe>=2.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from jinja2>=2.10.3->distributed->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (2.1.5)
Requirement already satisfied: aiobotocore~=2.5.0 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (2.5.4)
Requirement already satisfied: botocore<1.31.18,>=1.31.17 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from aiobotocore~=2.5.0->s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (1.31.17)
Requirement already satisfied: aioitertools<1.0.0,>=0.5.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from aiobotocore~=2.5.0->s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (0.11.0)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (from botocore<1.31.18,>=1.31.17->aiobotocore~=2.5.0->s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.7.0->spatialdata->graphcompass==0.2.4) (1.0.1)
Using cached multiscale_spatial_image-0.11.2-py3-none-any.whl (24 kB)
Using cached spatial_image-0.3.0-py3-none-any.whl (7.8 kB)
Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)
Building wheels for collected packages: graphcompass
  Building editable for graphcompass (pyproject.toml) ... done
  Created wheel for graphcompass: filename=graphcompass-0.2.4-py3-none-any.whl size=4323 sha256=2cec6bd320e837fde7e1005e0f594d81b3aa0b3d6639841e65d513c134560c84
  Stored in directory: /rds/general/ephemeral/user/sep22/ephemeral/pip-ephem-wheel-cache-vi4ppl6t/wheels/f3/2c/61/54e93c0ebeada9b662d1bbaeb8472353bbae0eb31889a55dc3
Successfully built graphcompass
Installing collected packages: numpy, spatial-image, multiscale-spatial-image, graphcompass
  Attempting uninstall: numpy
    Found existing installation: numpy None
error: uninstall-no-record-file

× Cannot uninstall numpy None
╰─> The package's contents are unknown: no RECORD file was found for numpy.

hint: You might be able to recover from this via: pip install --force-reinstall --no-deps numpy==1.23.4
(graphcompass_HPC) [sep22@login-a graphcompass]$ pip install --force-reinstall --no-deps numpy==1.23.4
Collecting numpy==1.23.4
  Using cached numpy-1.23.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Using cached numpy-1.23.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy None
error: uninstall-no-record-file

× Cannot uninstall numpy None
╰─> The package's contents are unknown: no RECORD file was found for numpy.

hint: You might be able to recover from this via: pip install --force-reinstall --no-deps numpy==1.23.4
(graphcompass_HPC) [sep22@login-a graphcompass]$ pip install numpy
Requirement already satisfied: numpy in /rds/general/user/sep22/home/anaconda3/envs/graphcompass_HPC/lib/python3.11/site-packages (1.23.4)
merelkuijs commented 2 months ago

Hm... That looks like a pretty nasty dependency issue. I think the issue here is that some versions of numpy, scipy, and pot play together nicely and some don't, but I don't know why the issue hasn't appeared before.

I'll try to replicate the issue and get back to you.

merelkuijs commented 2 months ago

The issue occurs when you try to import graphcompass, right?

spatts14 commented 2 months ago

yes when I try to import

mayarali commented 1 month ago

Hi @spatts14, can you please confirm that this has been solved with the latest release?

merelkuijs commented 1 month ago

As a reminder, the latest release can be installed with pip install --upgrade graphcompass If the issue persists, could you try to create a new environment?

mayarali commented 2 weeks ago

Closing this issue due to inactivity.

@spatts14, feel free to reopen or create a new issue if you encounter further errors or have additional questions. Thanks!