TypeError: _detect_vcs() missing 2 required positional arguments: 'expected_vcs' and 'path'

[pengpengyang94]

I installed the stitch3d package using conda, following the provided instructions. However, when importing stitch3d, I am getting a TypeError. How can I troubleshoot this issue?

[gefeiwang]

Hi there,

Thank you for your interest in our package. This error seems to arise from one of the package dependencies. Could you provide a complete error report so we can find the source of the issue? Besides using conda, you can also try pip install stitch3d for installation.

Best, Gefei

[pengpengyang94]

Hi there,

Thank you for your interest in our package. This error seems to arise from one of the package dependencies. Could you provide a complete error report so we can find the source of the issue? Besides using conda, you can also try pip install stitch3d for installation.

Best, Gefei

Attached is the full error report. Upon inspection, it appears the issue may be caused by an incompatibility with the scanpy package.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/data3/yangpp/soft/STitch3D/STitch3D/__init__.py", line 1, in <module>
    import STitch3D.utils
  File "/data3/yangpp/soft/STitch3D/STitch3D/utils.py", line 2, in <module>
    import scanpy as sc
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/scanpy/__init__.py", line 18, in <module>
    from . import datasets, logging, queries, external, get
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/scanpy/external/__init__.py", line 3, in <module>
    from . import pp
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/scanpy/external/pp/__init__.py", line 5, in <module>
    from ._magic import magic
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/scanpy/external/pp/_magic.py", line 7, in <module>
    from legacy_api_wrap import legacy_api
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/legacy_api_wrap.py", line 18, in <module>
    from get_version import get_version
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/get_version/__init__.py", line 287, in <module>
    __version__ = get_version(__file__)
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/get_version/__init__.py", line 270, in get_version
    version = method(parent)
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/get_version/__init__.py", line 117, in get_version_from_vcs
    vcs_root = find_vcs_root(parent, vcs=vcs)
  File "/data/anaconda3/envs/stitch3d/lib/python3.9/site-packages/get_version/__init__.py", line 148, in find_vcs_root
    vcs_e = _detect_vcs()
TypeError: _detect_vcs() missing 2 required positional arguments: 'expected_vcs' and 'path'

[pengpengyang94]

Hi there,

Thank you for your interest in our package. This error seems to arise from one of the package dependencies. Could you provide a complete error report so we can find the source of the issue? Besides using conda, you can also try pip install stitch3d for installation.

Best, Gefei

Installation via pip also produced errors. Therefore, I opted to use conda install instead.

[gefeiwang]

May I know which version of scanpy you are using?

[gefeiwang]

The scanpy version you installed has a conflict with other packages in your environment.

The error occurs when it tries to call from legacy_api_wrap import legacy_api in module scanpy/external/pp/_magic.py. This command has been deleted in an update for scanpy on June 29, 2021, so updating your scanpy to a newer version (e.g. 1.8.1 or later) might be helpful.

[pengpengyang94]

May I know which version of scanpy you are using? The software dependencies list indicates the installed version of the scanpy package.

$pip show scanpy
Name: scanpy
Version: 1.7.2

[pengpengyang94]

The scanpy version you installed has a conflict with other packages in your environment.

The error occurs when it tries to call from legacy_api_wrap import legacy_api in module scanpy/external/pp/_magic.py. This command has been deleted in an update for scanpy on June 29, 2021, so updating your scanpy to a newer version (e.g. 1.8.1 or later) might be helpful.

Following your recommendations resolved the issue. Thank you very much for your assistance.

pip install scanpy==1.8.1 -i https://pypi.tuna.tsinghua.edu.cn/simple