Python 3.9.10 pipenv install errors: 461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates

[SomePersonSomeWhereInTheWorld]

Python 3.9.10 on RHEL 9.0 is there a fix for this? I see Python lower than 3.8 is needed?

~/.local/bin/pipenv install
Installing dependencies from Pipfile.lock (66950d)...
[pipenv.exceptions.InstallError]: Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
[pipenv.exceptions.InstallError]: Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment
[pipenv.exceptions.InstallError]: Ignoring typed-ast: markers 'implementation_name == "cpython" and python_version < "3.8"' don't match your environment
[pipenv.exceptions.InstallError]: Collecting astroid==2.4.2 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 1))
[pipenv.exceptions.InstallError]: Downloading astroid-2.4.2-py3-none-any.whl (213 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 214.0/214.0 kB 49.9 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting attrs==19.3.0 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 2))
[pipenv.exceptions.InstallError]: Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB)
[pipenv.exceptions.InstallError]: Collecting biopython==1.68 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 3))
[pipenv.exceptions.InstallError]: Downloading biopython-1.68.tar.gz (14.4 MB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.4/14.4 MB 117.3 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): started
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): finished with status 'done'
[pipenv.exceptions.InstallError]: Collecting certifi==2020.4.5.2 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 4))
[pipenv.exceptions.InstallError]: Downloading certifi-2020.4.5.2-py2.py3-none-any.whl (157 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 157.7/157.7 kB 248.8 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting chardet==3.0.4 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 5))
[pipenv.exceptions.InstallError]: Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.4/133.4 kB 249.5 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting click==7.1.2 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 6))
[pipenv.exceptions.InstallError]: Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 kB 278.1 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting flask==1.1.1 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 7))
[pipenv.exceptions.InstallError]: Downloading Flask-1.1.1-py2.py3-none-any.whl (94 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.5/94.5 kB 267.0 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting flask-cors==3.0.8 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 8))
[pipenv.exceptions.InstallError]: Downloading Flask_Cors-3.0.8-py2.py3-none-any.whl (14 kB)
[pipenv.exceptions.InstallError]: Collecting future==0.18.2 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 9))
[pipenv.exceptions.InstallError]: Downloading future-0.18.2.tar.gz (829 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 129.5 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): started
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): finished with status 'done'
[pipenv.exceptions.InstallError]: Collecting h5py==2.10.0 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 10))
[pipenv.exceptions.InstallError]: Downloading h5py-2.10.0.tar.gz (301 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 301.1/301.1 kB 296.3 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): started
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): finished with status 'done'
[pipenv.exceptions.InstallError]: Collecting idna==2.8 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 11))
[pipenv.exceptions.InstallError]: Downloading idna-2.8-py2.py3-none-any.whl (58 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.6/58.6 kB 23.6 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting isort==4.3.21 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 13))
[pipenv.exceptions.InstallError]: Downloading isort-4.3.21-py2.py3-none-any.whl (42 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.3/42.3 kB 120.3 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting itsdangerous==1.1.0 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 14))
[pipenv.exceptions.InstallError]: Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
[pipenv.exceptions.InstallError]: Collecting jinja2==2.11.2 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 15))
[pipenv.exceptions.InstallError]: Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.8/125.8 kB 301.1 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting lazy-object-proxy==1.4.3 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 16))
[pipenv.exceptions.InstallError]: Downloading lazy-object-proxy-1.4.3.tar.gz (34 kB)
[pipenv.exceptions.InstallError]: Installing build dependencies: started
[pipenv.exceptions.InstallError]: Installing build dependencies: finished with status 'done'
[pipenv.exceptions.InstallError]: Getting requirements to build wheel: started
[pipenv.exceptions.InstallError]: Getting requirements to build wheel: finished with status 'done'
[pipenv.exceptions.InstallError]: Preparing metadata (pyproject.toml): started
[pipenv.exceptions.InstallError]: Preparing metadata (pyproject.toml): finished with status 'done'
[pipenv.exceptions.InstallError]: Collecting markupsafe==1.1.1 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 17))
[pipenv.exceptions.InstallError]: Downloading MarkupSafe-1.1.1.tar.gz (19 kB)
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): started
[pipenv.exceptions.InstallError]: Preparing metadata (setup.py): finished with status 'done'
[pipenv.exceptions.InstallError]: Collecting mccabe==0.6.1 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 18))
[pipenv.exceptions.InstallError]: Downloading mccabe-0.6.1-py2.py3-none-any.whl (8.6 kB)
[pipenv.exceptions.InstallError]: Collecting more-itertools==8.3.0 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 19))
[pipenv.exceptions.InstallError]: Downloading more_itertools-8.3.0-py3-none-any.whl (44 kB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.7/44.7 kB 210.6 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Collecting numpy==1.18.5 (from -r /local/pipenv-pq6e4pl6-requirements/pipenv-rl4pj7lz-hashed-reqs.txt (line 20))
[pipenv.exceptions.InstallError]: Downloading numpy-1.18.5.zip (5.4 MB)
[pipenv.exceptions.InstallError]: ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 121.2 MB/s eta 0:00:00
[pipenv.exceptions.InstallError]: Installing build dependencies: started
[pipenv.exceptions.InstallError]: Installing build dependencies: finished with status 'done'
[pipenv.exceptions.InstallError]: Getting requirements to build wheel: started
[pipenv.exceptions.InstallError]: Getting requirements to build wheel: finished with status 'done'
[pipenv.exceptions.InstallError]: Preparing metadata (pyproject.toml): started
[pipenv.exceptions.InstallError]: Preparing metadata (pyproject.toml): finished with status 'error'
[pipenv.exceptions.InstallError]: error: subprocess-exited-with-error
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: × Preparing metadata (pyproject.toml) did not run successfully.
[pipenv.exceptions.InstallError]: │ exit code: 1
[pipenv.exceptions.InstallError]: ╰─> [54 lines of output]
[pipenv.exceptions.InstallError]: Running from numpy source directory.
[pipenv.exceptions.InstallError]: :461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
[pipenv.exceptions.InstallError]: /local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
[pipenv.exceptions.InstallError]: required_version = LooseVersion('0.29.14')
[pipenv.exceptions.InstallError]: /local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
[pipenv.exceptions.InstallError]: if LooseVersion(cython_version) < required_version:
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: Error compiling Cython file:
[pipenv.exceptions.InstallError]: ------------------------------------------------------------
[pipenv.exceptions.InstallError]: ...
[pipenv.exceptions.InstallError]: for i in range(1, RK_STATE_LEN):
[pipenv.exceptions.InstallError]: self.rng_state.key[i] = val[i]
[pipenv.exceptions.InstallError]: self.rng_state.pos = i
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: self._bitgen.state = &self.rng_state
[pipenv.exceptions.InstallError]: self._bitgen.next_uint64 = &mt19937_uint64
[pipenv.exceptions.InstallError]: ^
[pipenv.exceptions.InstallError]: ------------------------------------------------------------
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: _mt19937.pyx:138:35: Cannot assign type 'uint64_t (*)(void ) except? -1 nogil' to 'uint64_t ()(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'uint64_t (void *) except? -1 nogil'.
[pipenv.exceptions.InstallError]: Processing numpy/random/_bounded_integers.pxd.in
[pipenv.exceptions.InstallError]: Processing numpy/random/_mt19937.pyx
[pipenv.exceptions.InstallError]: Traceback (most recent call last):
[pipenv.exceptions.InstallError]: File "/local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py", line 238, in
[pipenv.exceptions.InstallError]: main()
[pipenv.exceptions.InstallError]: File "/local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py", line 234, in main
[pipenv.exceptions.InstallError]: find_process_files(root_dir)
[pipenv.exceptions.InstallError]: File "/local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py", line 225, in find_process_files
[pipenv.exceptions.InstallError]: process(root_dir, fromfile, tofile, function, hash_db)
[pipenv.exceptions.InstallError]: File "/local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py", line 191, in process
[pipenv.exceptions.InstallError]: processor_function(fromfile, tofile)
[pipenv.exceptions.InstallError]: File "/local/pip-install-lw4evu5t/numpy_9a03571d21dc4a8981a9247675648988/tools/cythonize.py", line 80, in process_pyx
[pipenv.exceptions.InstallError]: subprocess.check_call(
[pipenv.exceptions.InstallError]: File "/cm/shared/apps/anaconda3-2022.10/lib/python3.9/subprocess.py", line 373, in check_call
[pipenv.exceptions.InstallError]: raise CalledProcessError(retcode, cmd)
[pipenv.exceptions.InstallError]: subprocess.CalledProcessError: Command '['/burg/home/rk3199/.local/share/virtualenvs/openprotein-PnNMcUVz/bin/python', '-m', 'cython', '-3', '--fast-fail', '-o', '_mt19937.c', '_mt19937.pyx']' returned non-zero exit status 1.
[pipenv.exceptions.InstallError]: Cythonizing sources
[pipenv.exceptions.InstallError]: Traceback (most recent call last):
[pipenv.exceptions.InstallError]: File "/burg/home/rk3199/.local/lib/python3.9/site-packages/pipenv/patched/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
[pipenv.exceptions.InstallError]: main()
[pipenv.exceptions.InstallError]: File "/burg/home/rk3199/.local/lib/python3.9/site-packages/pipenv/patched/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
[pipenv.exceptions.InstallError]: json_out['return_val'] = hook(**hook_input['kwargs'])
[pipenv.exceptions.InstallError]: File "/burg/home/rk3199/.local/lib/python3.9/site-packages/pipenv/patched/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
[pipenv.exceptions.InstallError]: return hook(metadata_directory, config_settings)
[pipenv.exceptions.InstallError]: File "/local/pip-build-env-7ik93v8v/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 396, in prepare_metadata_for_build_wheel
[pipenv.exceptions.InstallError]: self.run_setup()
[pipenv.exceptions.InstallError]: File "/local/pip-build-env-7ik93v8v/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 507, in run_setup
[pipenv.exceptions.InstallError]: super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
[pipenv.exceptions.InstallError]: File "/local/pip-build-env-7ik93v8v/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 341, in run_setup
[pipenv.exceptions.InstallError]: exec(code, locals())
[pipenv.exceptions.InstallError]: File "", line 488, in
[pipenv.exceptions.InstallError]: File "", line 469, in setup_package
[pipenv.exceptions.InstallError]: File "", line 275, in generate_cython
[pipenv.exceptions.InstallError]: RuntimeError: Running cythonize failed!
[pipenv.exceptions.InstallError]: [end of output]
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: note: This error originates from a subprocess, and is likely not a problem with pip.
[pipenv.exceptions.InstallError]: error: metadata-generation-failed
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: × Encountered error while generating package metadata.
[pipenv.exceptions.InstallError]: ╰─> See above for output.
[pipenv.exceptions.InstallError]:
[pipenv.exceptions.InstallError]: note: This is an issue with the package mentioned above, not pip.
[pipenv.exceptions.InstallError]: hint: See above for details.
ERROR: Couldn't install package: {}
Package installation failed...
/cm/shared/apps/anaconda3-2022.10/lib/python3.9/subprocess.py:1052: ResourceWarning: subprocess 3699277 is still running
_warn("subprocess %s is still running" % self.pid,
ResourceWarning: Enable tracemalloc to get the object allocation traceback
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name=4 encoding='utf-8'>
ResourceWarning: Enable tracemalloc to get the object allocation traceback
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name=7 encoding='utf-8'>
ResourceWarning: Enable tracemalloc to get the object allocation traceback