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Installing using pip inside a virtual environment complains about mpi4py while it is installed #1296

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kasra-keshavarz opened this issue Nov 28, 2023 · 2 comments

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@kasra-keshavarz
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Installing netCDF4 (GitHub version with commit f9dc8b2) inside a virtual environment using pip install causes an error complaining about the lack of mpi4py package. This error is thrown at the user regardless whether the mpi4py is installed within the same virtual environment or not. This is not limited to this version of netcdf4-python, as a few latest releases that I have tried, also demonstrate the same behaviour. Here is an example:

(test2) [netcdf4-python]$ pip install --no-binary mpi4py --no-cache mpi4py
Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2020/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2020/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
Collecting mpi4py
  Downloading mpi4py-3.1.5.tar.gz (2.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 68.8 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mpi4py
  Building wheel for mpi4py (pyproject.toml) ... done
  Created wheel for mpi4py: filename=mpi4py-3.1.5-cp310-cp310-linux_x86_64.whl size=3365058 sha256=114d79ee629f43bafeb69a273c25984db3a644dd64ea57b47c84c7a058c0b7a9
  Stored in directory: /tmp/pip-ephem-wheel-cache-o8sr3xtk/wheels/18/2b/7f/c852523089e9182b45fca50ff56f49a51eeb6284fd25a66713
Successfully built mpi4py
Installing collected packages: mpi4py
Successfully installed mpi4py-3.1.5

(test2) [netcdf4-python]$ pip install -v .
Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2020/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2020/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo/generic, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
Processing /home/user/github-repos/netcdf4-python
  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
  ╰─> [28 lines of output]
      -L/home/user/.local/lib64 -lnetcdf
      -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/lib -lhdf5 -lsz
      reading from setup.cfg...
      using nc-config...
      checking /home/user/.local/include...
      hdf5 headers not found in /home/user/.local/include
      nc-config did provide path to HDF5 headers, search standard locations...
      checking /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/include...
      HDF5 library version: 1.12.1 headers found in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/include
      HDF5 library version: 1.12.1 found in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1
      using netcdf library version b'4.9.3-development'
      using Cython to compile netCDF4.pyx...
      netcdf lib has parallel functions
      Traceback (most recent call last):
        File "/home/user/virtual-envs/test2/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/user/virtual-envs/test2/lib/python3.10/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/user/virtual-envs/test2/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-ifjbt4w7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "/tmp/pip-build-env-ifjbt4w7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-ifjbt4w7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 395, in <module>
      ModuleNotFoundError: No module named 'mpi4py'
      [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.

(test2) [netcdf4-python]$ python
Python 3.10.2 (main, Feb  4 2022, 19:10:35) [GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mpi4py
>>> mpi4py.__file__
'/home/user/virtual-envs/test2/lib/python3.10/site-packages/mpi4py/__init__.py'

However, if the installation proceeds with using the setup.py, it works smoothly and there won't be any problem:

(test2) [netcdf4-python]$ python -m setup install
reading from setup.cfg...
-L/home/user/.local/lib64 -lnetcdf
-L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/lib -lhdf5 -lsz
using nc-config...
checking /home/user/.local/include...
hdf5 headers not found in /home/user/.local/include
nc-config did provide path to HDF5 headers, search standard locations...
checking /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/include...
HDF5 library version: 1.12.1 headers found in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/include
HDF5 library version: 1.12.1 found in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1
using netcdf library version b'4.9.3-development'
using Cython to compile netCDF4.pyx...
netcdf lib has parallel functions
NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed
running install
/home/user/virtual-envs/test2/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/home/user/virtual-envs/test2/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
running bdist_egg
running egg_info
writing src/netCDF4.egg-info/PKG-INFO
writing dependency_links to src/netCDF4.egg-info/dependency_links.txt
writing entry points to src/netCDF4.egg-info/entry_points.txt
writing requirements to src/netCDF4.egg-info/requires.txt
writing top-level names to src/netCDF4.egg-info/top_level.txt
reading manifest file 'src/netCDF4.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'examples/data'
warning: no previously-included files found matching 'src/netCDF4/_netCDF4.c'
adding license file 'LICENSE'
writing manifest file 'src/netCDF4.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
Compiling src/netCDF4/_netCDF4.pyx because it changed.
[1/1] Cythonizing src/netCDF4/_netCDF4.pyx
building 'netCDF4._netCDF4' extension
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/home/user/.local/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/include -I/home/user/virtual-envs/test2/lib/python3.10/site-packages/numpy/core/include -I/home/user/virtual-envs/test2/lib/python3.10/site-packages/mpi4py/include -Iinclude -I/home/user/virtual-envs/test2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/include/python3.10 -c src/netCDF4/_netCDF4.c -o build/temp.linux-x86_64-cpython-310/src/netCDF4/_netCDF4.o
src/netCDF4/_netCDF4.c: In function ‘__pyx_pf_7netCDF4_8_netCDF4_7_MemBuf_4__dealloc__’:
src/netCDF4/_netCDF4.c:13413:20: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
13413 |   free(__pyx_v_self->memory);
      |        ~~~~~~~~~~~~^~~~~~~~
In file included from /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/include/python3.10/Python.h:34,
                 from src/netCDF4/_netCDF4.c:65:
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const void *’
  565 | extern void free (void *__ptr) __THROW;
      |                   ~~~~~~^~~~~
src/netCDF4/_netCDF4.c: In function ‘__pyx_f_7netCDF4_8_netCDF4__set_att’:
src/netCDF4/_netCDF4.c:18963:106: warning: passing argument 5 of ‘nc_put_att_string’ from incompatible pointer type [-Wincompatible-pointer-types]
18963 |               __pyx_v_ierr = nc_put_att_string(__pyx_v_grpid, __pyx_v_varid, __pyx_v_attname, __pyx_v_N, __pyx_v_string_ptrs);
      |                                                                                                          ^~~~~~~~~~~~~~~~~~~
      |                                                                                                          |
      |                                                                                                          char **
In file included from src/netCDF4/_netCDF4.c:1249:
/home/user/.local/include/netcdf.h:1091:44: note: expected ‘const char **’ but argument is of type ‘char **’
 1091 |                   size_t len, const char **op);
      |                               ~~~~~~~~~~~~~^~
src/netCDF4/_netCDF4.c:19490:103: warning: passing argument 5 of ‘nc_put_att_string’ from incompatible pointer type [-Wincompatible-pointer-types]
19490 |                   __pyx_v_ierr = nc_put_att_string(__pyx_v_grpid, __pyx_v_varid, __pyx_v_attname, 1, (&__pyx_v_datstring));
      |                                                                                                      ~^~~~~~~~~~~~~~~~~~~
      |                                                                                                       |
      |                                                                                                       char **
In file included from src/netCDF4/_netCDF4.c:1249:
/home/user/.local/include/netcdf.h:1091:44: note: expected ‘const char **’ but argument is of type ‘char **’
 1091 |                   size_t len, const char **op);
      |                               ~~~~~~~~~~~~~^~
src/netCDF4/_netCDF4.c: In function ‘__pyx_f_7netCDF4_8_netCDF4__read_compound’:
src/netCDF4/_netCDF4.c:85513:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
85513 |   for (__pyx_v_nf = 0; __pyx_v_nf < __pyx_t_7; __pyx_v_nf++) {
      |                                   ^
src/netCDF4/_netCDF4.c: In function ‘__pyx_f_7netCDF4_8_netCDF4__read_enum’:
src/netCDF4/_netCDF4.c:89720:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
89720 |   for (__pyx_v_nmem = 0; __pyx_v_nmem < __pyx_t_11; __pyx_v_nmem++) {
      |                                       ^
src/netCDF4/_netCDF4.c: In function ‘__pyx_pw_7netCDF4_8_netCDF4_8Variable_1__init__’:
src/netCDF4/_netCDF4.c:49807:28: warning: ‘__pyx_v_dimids’ may be used uninitialized in this function [-Wmaybe-uninitialized]
49807 |             __pyx_v_ierr = nc_def_var(__pyx_v_self->_grpid, __pyx_v_varname, __pyx_v_xtype, __pyx_v_ndims, __pyx_v_dimids, (&__pyx_v_self->_varid));
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:48022:8: note: ‘__pyx_v_dimids’ was declared here
48022 |   int *__pyx_v_dimids;
      |        ^~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c: In function ‘__pyx_f_7netCDF4_8_netCDF4__get_types’:
src/netCDF4/_netCDF4.c:19952:12: warning: ‘__pyx_v_typeids’ may be used uninitialized in this function [-Wmaybe-uninitialized]
19952 |   nc_type *__pyx_v_typeids;
      |            ^~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c: In function ‘__pyx_pw_7netCDF4_8_netCDF4_7Dataset_1__init__’:
src/netCDF4/_netCDF4.c:25956:30: warning: ‘__pyx_v_mpiinfo’ may be used uninitialized in this function [-Wmaybe-uninitialized]
25956 |               __pyx_v_ierr = nc_create_par(__pyx_v_path, (__pyx_v_cmode | __pyx_v_parmode), __pyx_v_mpicomm, __pyx_v_mpiinfo, (&__pyx_v_grpid));
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:24839:12: note: ‘__pyx_v_mpiinfo’ was declared here
24839 |   MPI_Info __pyx_v_mpiinfo;
      |            ^~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:25956:30: warning: ‘__pyx_v_mpicomm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
25956 |               __pyx_v_ierr = nc_create_par(__pyx_v_path, (__pyx_v_cmode | __pyx_v_parmode), __pyx_v_mpicomm, __pyx_v_mpiinfo, (&__pyx_v_grpid));
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:24838:12: note: ‘__pyx_v_mpicomm’ was declared here
24838 |   MPI_Comm __pyx_v_mpicomm;
      |            ^~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:25956:30: warning: ‘__pyx_v_parmode’ may be used uninitialized in this function [-Wmaybe-uninitialized]
25956 |               __pyx_v_ierr = nc_create_par(__pyx_v_path, (__pyx_v_cmode | __pyx_v_parmode), __pyx_v_mpicomm, __pyx_v_mpiinfo, (&__pyx_v_grpid));
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/netCDF4/_netCDF4.c:24837:7: note: ‘__pyx_v_parmode’ was declared here
24837 |   int __pyx_v_parmode;
      |       ^~~~~~~~~~~~~~~
gcc -shared -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/libffi/3.3/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/libffi/3.3/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/libffi/3.3/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/libffi/3.3/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib build/temp.linux-x86_64-cpython-310/src/netCDF4/_netCDF4.o -L/home/user/.local/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/lib -Wl,--enable-new-dtags,-R/home/user/.local/lib64 -Wl,--enable-new-dtags,-R/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/hdf5-mpi/1.12.1/lib -lnetcdf -lhdf5_hl -lhdf5 -o build/lib.linux-x86_64-cpython-310/netCDF4/_netCDF4.cpython-310-x86_64-linux-gnu.so
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/netCDF4
creating build/bdist.linux-x86_64/egg/netCDF4/plugins
copying build/lib.linux-x86_64-cpython-310/netCDF4/plugins/empty.txt -> build/bdist.linux-x86_64/egg/netCDF4/plugins
copying build/lib.linux-x86_64-cpython-310/netCDF4/_netCDF4.cpython-310-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/netCDF4
copying build/lib.linux-x86_64-cpython-310/netCDF4/_netCDF4.pyx -> build/bdist.linux-x86_64/egg/netCDF4
copying build/lib.linux-x86_64-cpython-310/netCDF4/utils.py -> build/bdist.linux-x86_64/egg/netCDF4
copying build/lib.linux-x86_64-cpython-310/netCDF4/__init__.py -> build/bdist.linux-x86_64/egg/netCDF4
byte-compiling build/bdist.linux-x86_64/egg/netCDF4/utils.py to utils.cpython-310.pyc
byte-compiling build/bdist.linux-x86_64/egg/netCDF4/__init__.py to __init__.cpython-310.pyc
creating stub loader for netCDF4/_netCDF4.cpython-310-x86_64-linux-gnu.so
byte-compiling build/bdist.linux-x86_64/egg/netCDF4/_netCDF4.py to _netCDF4.cpython-310.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying src/netCDF4.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
netCDF4.__pycache__.__init__.cpython-310: module references __path__
netCDF4.__pycache__._netCDF4.cpython-310: module references __file__
creating 'dist/netCDF4-1.7.0-py3.10-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing netCDF4-1.7.0-py3.10-linux-x86_64.egg
removing '/home/user/virtual-envs/test2/lib/python3.10/site-packages/netCDF4-1.7.0-py3.10-linux-x86_64.egg' (and everything under it)
creating /home/user/virtual-envs/test2/lib/python3.10/site-packages/netCDF4-1.7.0-py3.10-linux-x86_64.egg
Extracting netCDF4-1.7.0-py3.10-linux-x86_64.egg to /home/user/virtual-envs/test2/lib/python3.10/site-packages
Adding netCDF4 1.7.0 to easy-install.pth file
Installing nc3tonc4 script to /home/user/virtual-envs/test2/bin
Installing nc4tonc3 script to /home/user/virtual-envs/test2/bin
Installing ncinfo script to /home/user/virtual-envs/test2/bin

Installed /home/user/virtual-envs/test2/lib/python3.10/site-packages/netCDF4-1.7.0-py3.10-linux-x86_64.egg
Processing dependencies for netCDF4==1.7.0
Searching for numpy==1.25.2+computecanada
Best match: numpy 1.25.2+computecanada
Adding numpy 1.25.2+computecanada to easy-install.pth file
Installing f2py script to /home/user/virtual-envs/test2/bin
Installing f2py3 script to /home/user/virtual-envs/test2/bin
Installing f2py3.10 script to /home/user/virtual-envs/test2/bin

Using /home/user/virtual-envs/test2/lib/python3.10/site-packages
Searching for certifi==2023.11.17
Best match: certifi 2023.11.17
Processing certifi-2023.11.17-py3.10.egg
Adding certifi 2023.11.17 to easy-install.pth file

Using /home/user/virtual-envs/test2/lib/python3.10/site-packages/certifi-2023.11.17-py3.10.egg
Searching for cftime==1.6.3
Best match: cftime 1.6.3
Processing cftime-1.6.3-py3.10-linux-x86_64.egg
Adding cftime 1.6.3 to easy-install.pth file

Using /home/user/virtual-envs/test2/lib/python3.10/site-packages/cftime-1.6.3-py3.10-linux-x86_64.egg
Finished processing dependencies for netCDF4==1.7.0

Wondering if anybody has dealt with this issue?

@francesco-ballarin
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You need to install with pip install --no-build-isolation

@stubbiali
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You may want to have a look at #1307.

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