Fail to Install tombo using venv3 Ubuntu18.04
abadouh opened this issue · comments
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.
It appears as though pip is not finding the numpy install. This may be an issue with your python environment or the way Tombo runs setup. Tombo is deprecated and I would recommend moving to Remora for raw signal analysis.