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Fail to Install tombo using venv3 Ubuntu18.04
Hey, I am trying to install tombo using pip and or the git repository and I get the same error. Below you can find the details:
OS: Ubuntu18.04 Python: 3.8 numpy: 1.24.4
Using pip
mkdir tombo
python3 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install numpy
pip install ont-tombo[full]
Using github
git clone https://github.com/nanoporetech/tombo
cd tombo/
python3 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install numpy
pip install -e .
I get the following error:
Obtaining file:///home/workspaces/benchmark/tombo/tombo
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) ... error
error: subprocess-exited-with-error
× Preparing editable metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [34 lines of output]
************************************************************
INSTALLATION ERROR:
Need to install numpy before tombo installation.
This is required in order to get maximum efficincy from cython code optimizations.
To install run:
$ pip install numpy
************************************************************
/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py:487: SetuptoolsDeprecationWarning: Running `setup.py` directly as CLI tool is deprecated.
!!
********************************************************************************
Please avoid using `sys.exit(0)` or similar statements that don't fit in the paradigm of a configuration file.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
super().run_setup(setup_script=setup_script)
Traceback (most recent call last):
File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 181, in prepare_metadata_for_build_editable
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 453, in prepare_metadata_for_build_editable
return self.prepare_metadata_for_build_wheel(
File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 368, in prepare_metadata_for_build_wheel
self._bubble_up_info_directory(metadata_directory, ".egg-info")
File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 337, in _bubble_up_info_directory
info_dir = self._find_info_directory(metadata_directory, suffix)
File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 348, in _find_info_directory
assert len(candidates) == 1, f"Multiple {suffix} directories found"
AssertionError: Multiple .egg-info directories found
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.