Environnment issues on Linux

[Hierakonpolis]

Trying to set up a conda environment on a Linux Mint 22 system, the installation fails at the pip dependencies stage:

FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
  action(self, namespace, argument_values, option_string)
Channels:
 - conda-forge
 - mrtrix3
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:
                                                                                
Preparing transaction: done                                                     
Verifying transaction: done                                                     
Executing transaction: \                                                        
\                                                                               
done                                                                            
Installing pip dependencies: \ Ran pip subprocess with arguments:               
['/home/riccardo/anaconda3/envs/py39cmp-gui/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/riccardo/condaenv.cpcqg3w7.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting numpy==1.21.6
  Using cached numpy-1.21.6-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting matplotlib==3.5.2
  Using cached matplotlib-3.5.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
Collecting configparser==5.2.0
  Using cached configparser-5.2.0-py3-none-any.whl (19 kB)
Collecting nibabel==3.2.2
  Using cached nibabel-3.2.2-py3-none-any.whl (3.3 MB)
Collecting nipype==1.8.0
  Using cached nipype-1.8.0-py3-none-any.whl (3.2 MB)
Collecting traits==6.3.2
  Using cached traits-6.3.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (5.1 MB)
Collecting traitsui==7.2.0
  Using cached traitsui-7.2.0-py3-none-any.whl
Collecting duecredit==0.9.1
  Using cached duecredit-0.9.1-py3-none-any.whl (86 kB)
Collecting obspy==1.2.2
  Using cached obspy-1.2.2.zip (24.7 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'error'

Pip subprocess error:
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [31 lines of output]
      <string>:48: DeprecationWarning:
      
        `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
        of the deprecation of `distutils` itself. It will be removed for
        Python >= 3.12. For older Python versions it will remain present.
        It is recommended to use `setuptools < 60.0` for those Python versions.
        For more details, see:
          https://numpy.org/devdocs/reference/distutils_status_migration.html
      
      
      Traceback (most recent call last):
        File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 48, in <module>
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/numpy/distutils/core.py", line 24, in <module>
          from numpy.distutils.command import config, config_compiler, \
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/numpy/distutils/command/config.py", line 19, in <module>
          from numpy.distutils.mingw32ccompiler import generate_manifest
        File "/tmp/pip-build-env-wz66h3r2/overlay/lib/python3.9/site-packages/numpy/distutils/mingw32ccompiler.py", line 27, in <module>
          from distutils.msvccompiler import get_build_version as get_build_msvc_version
      ModuleNotFoundError: No module named 'distutils.msvccompiler'
      [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.

failed

CondaEnvException: Pip failed

If I try to move obspy to the list of packages installed by anaconda I can get the environment setup to complete successfully. After pip install connectomemapper (and pip install future which seems to be also missing) both connectomemapper3 and cmpbidsappmanager evenutally fail with:

~$ connectomemapper3
RuntimeError: module was compiled against NumPy C-API version 0x10 (NumPy 1.23) but the running NumPy has C-API version 0xe. Check the section C-API incompatibility at the Troubleshooting ImportError section at https://numpy.org/devdocs/user/troubleshooting-importerror.html#c-api-incompatibility for indications on how to solve this problem.
Traceback (most recent call last):
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/bin/connectomemapper3", line 5, in <module>
    from cmp.cli.connectomemapper3 import main
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/cmp/cli/connectomemapper3.py", line 16, in <module>
    import cmp.project
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/cmp/project.py", line 25, in <module>
    from cmp.pipelines.functional import eeg as EEG_pipeline
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/cmp/pipelines/functional/eeg.py", line 25, in <module>
    from cmp.stages.eeg.esi import EEGSourceImagingStage
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/cmp/stages/eeg/esi.py", line 29, in <module>
    from cmtklib.interfaces.mne import (
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/cmtklib/interfaces/mne.py", line 25, in <module>
    import mne_connectivity as mnec
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/mne_connectivity/__init__.py", line 11, in <module>
    from .base import (Connectivity, EpochConnectivity, EpochSpectralConnectivity,
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/mne_connectivity/base.py", line 4, in <module>
    import xarray as xr
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/__init__.py", line 3, in <module>
    from xarray import testing, tutorial
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/testing.py", line 11, in <module>
    from xarray.core.coordinates import Coordinates
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/core/coordinates.py", line 16, in <module>
    from xarray.core.alignment import Aligner
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/core/alignment.py", line 24, in <module>
    from xarray.core.variable import Variable, as_compatible_data, calculate_dimensions
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/core/variable.py", line 48, in <module>
    from xarray.namedarray.core import NamedArray
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/namedarray/core.py", line 24, in <module>
    from xarray.namedarray._typing import (
  File "/home/riccardo/anaconda3/envs/py39cmp-gui/lib/python3.9/site-packages/xarray/namedarray/_typing.py", line 28, in <module>
    _DType = TypeVar("_DType", bound=np.dtype[Any])
TypeError: 'numpy._DTypeMeta' object is not subscriptable

Incidentally, because the docker container is likely going to work anyway, I might also just do with instructions on how to build the configuration json files myself if these are available anywhere.