[BUG]Installation issue: ModuleNotFoundError: No module named 'setuptools.dep_util' #187
Description
Describe the bug
Installation issue: ModuleNotFoundError: No module named 'setuptools.dep_util'
Steps to reproduce
Your script/notebook including the command and error that is produced.
Data Inspection (recommended)
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# Output here
Expected behavior
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Screenshots
Here is the trace back from "pip install bento-tools":
Collecting bento-tools
Using cached bento_tools-2.1.4.post2-py3-none-any.whl.metadata (3.5 kB)
Collecting adjusttext>=1.1.1 (from bento-tools)
Using cached adjustText-1.3.0-py3-none-any.whl.metadata (3.1 kB)
Collecting astropy>=6.0.1 (from bento-tools)
Using cached astropy-7.1.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting decoupler>=1.7.0 (from bento-tools)
Using cached decoupler-2.0.6-py3-none-any.whl.metadata (8.0 kB)
Collecting emoji>=2.11.0 (from bento-tools)
Using cached emoji-2.14.1-py3-none-any.whl.metadata (5.7 kB)
Collecting ipywidgets>=8.1.5 (from bento-tools)
Using cached ipywidgets-8.1.7-py3-none-any.whl.metadata (2.4 kB)
Collecting kneed>=0.8.5 (from bento-tools)
Using cached kneed-0.8.5-py3-none-any.whl.metadata (5.5 kB)
Collecting matplotlib-scalebar>=0.8.1 (from bento-tools)
Using cached matplotlib_scalebar-0.9.0-py3-none-any.whl.metadata (18 kB)
Collecting minisom>=2.3.2 (from bento-tools)
Using cached minisom-2.3.5.tar.gz (12 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pandas>=2.2.2 in ./scverse/lib/python3.13/site-packages (from bento-tools) (2.3.0)
Collecting rasterio>=1.3.9 (from bento-tools)
Using cached rasterio-1.4.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Collecting rtree>=1.2.0 (from bento-tools)
Using cached rtree-1.4.0-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.1 kB)
Collecting scikit-learn<1.6.0 (from bento-tools)
Using cached scikit_learn-1.5.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
INFO: pip is looking at multiple versions of bento-tools to determine which version is compatible with other requirements. This could take a while.
Collecting bento-tools
Using cached bento_tools-2.1.3-py3-none-any.whl.metadata (3.5 kB)
Requirement already satisfied: scikit-learn>=1.4.2 in ./scverse/lib/python3.13/site-packages (from bento-tools) (1.7.0)
Using cached bento_tools-2.1.2-py3-none-any.whl.metadata (3.3 kB)
Collecting decoupler~=1.4.0 (from bento-tools)
Using cached decoupler-1.4.0-py3-none-any.whl.metadata (3.2 kB)
Collecting pandas<2.0.0 (from bento-tools)
Using cached pandas-1.5.3.tar.gz (5.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting bento-tools
Using cached bento_tools-2.1.1-py3-none-any.whl.metadata (3.3 kB)
Collecting pytest>=8.2.1 (from bento-tools)
Using cached pytest-8.4.1-py3-none-any.whl.metadata (7.7 kB)
Collecting bento-tools
Using cached bento_tools-2.1-py3-none-any.whl.metadata (3.1 kB)
Using cached bento_tools-0.1.0-py3-none-any.whl.metadata (1.3 kB)
Collecting anndata<0.8.0,>=0.7.1 (from bento-tools)
Using cached anndata-0.7.8-py3-none-any.whl.metadata (4.2 kB)
Collecting astropy<5.0.0,>=4.0.1 (from bento-tools)
Using cached astropy-4.3.1.tar.gz (7.6 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [32 lines of output]
Traceback (most recent call last):
File "/home/hhao/mambaforge-pypy3/envs/scverse/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in
main()
~~~~^^
File "/home/hhao/mambaforge-pypy3/envs/scverse/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/hhao/mambaforge-pypy3/envs/scverse/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 143, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
self.run_setup()
~~~~~~~~~~~~~~^^
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 317, in run_setup
exec(code, locals())
~~~~^^^^^^^^^^^^^^^^
File "", line 70, in
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/extension_helpers/_setup_helpers.py", line 68, in get_extensions
for setuppkg in iter_setup_packages(srcdir, packages):
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/extension_helpers/_setup_helpers.py", line 179, in iter_setup_packages
module = import_file(setup_package, name=packagename + ".setup_package")
File "/tmp/pip-build-env-j8_m9p0l/overlay/lib/python3.13/site-packages/extension_helpers/_utils.py", line 147, in import_file
loader.exec_module(mod)
~~~~~~~~~~~~~~~~~~^^^^^
File "", line 1026, in exec_module
File "", line 488, in _call_with_frames_removed
File "astropy/wcs/setup_package.py", line 12, in
from setuptools.dep_util import newer_group
ModuleNotFoundError: No module named 'setuptools.dep_util'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.