Cannot install conda env on Mac M1

[rly]

With the update to the conda environment file for Mac M1 to install the full version of neuroconv, pytables is installed. However, pytables has not released a macos arm64 wheel on PyPI, and building pytables on a Mac M1 results in a build error related to hdf5 because it is not yet installed:

Collecting tables (from neuroconv@ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]->-r /Users/rly/Documents/NWB/nwb-guide/environments/condaenv.6j96x3bd.requirements.txt (line 6))
  Using cached tables-3.8.0.tar.gz (8.0 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:
  Running command git clone --filter=blob:none --quiet https://github.com/catalystneuro/neuroconv.git /private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-install-1tdukxb1/neuroconv_852440243b6a40e1872cab98ef6f834f
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [12 lines of output]
      <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      ld: library not found for -lhdf5
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      cpuinfo failed, assuming no CPU features: 'flags'
      * Using Python 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:53:08)
      * Found cython 3.0.2
      * USE_PKGCONFIG: False
      * Found conda env: ``/Users/rly/mambaforge/envs/nwb-guide``
      .. ERROR:: Could not find a local HDF5 installation.
         You may need to explicitly state where your local HDF5 headers and
         library can be found by setting the ``HDF5_DIR`` environment
         variable or by using the ``--hdf5`` command-line option.
      [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

Installing HDF5 first does not resolve the error. I get a linking error from pytables instead.

Collecting tables (from neuroconv@ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]->-r /Users/rly/Documents/NWB/nwb-guide/environments/condaenv.044m0nux.requirements.txt (line 6))
  Using cached tables-3.8.0.tar.gz (8.0 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:
  Running command git clone --filter=blob:none --quiet https://github.com/catalystneuro/neuroconv.git /private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-install-wrclyt0f/neuroconv_398f117b8175446da0bf1f4223d6d088
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [55 lines of output]
      <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      ld: library not found for -llzo2
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      ld: library not found for -llzo
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      ld: library not found for -lblosc
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
      
      def _dump_h5_backtrace():
          cdef object bt = []
      
          if H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, e_walk_cb, <void*>bt) < 0:
                                                     ^
      ------------------------------------------------------------
      
      tables/utilsextension.pyx:384:47: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'. Exception values are incompatible. Suggest adding 'noexcept' to type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil'.
      cpuinfo failed, assuming no CPU features: 'flags'
      * Using Python 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:53:08)
      * Found cython 3.0.2
      * USE_PKGCONFIG: False
      * Found conda env: ``/Users/rly/mambaforge/envs/nwb-guide``
      * Found HDF5 headers at ``/Users/rly/mambaforge/envs/nwb-guide/include``, library at ``/Users/rly/mambaforge/envs/nwb-guide/lib``.
      * Could not find LZO 2 headers and library; disabling support for it.
      * Could not find LZO 1 headers and library; disabling support for it.
      * Found bzip2 headers at ``/Users/rly/mambaforge/envs/nwb-guide/include``, library at ``/Users/rly/mambaforge/envs/nwb-guide/lib``.
      * Could not find blosc headers and library; using internal sources.
      * Found blosc2 headers at ``/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/include``, library at ``/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib``.
        * Copying blosc2 runtime library to 'tables' dir because it was not found in standard locations
      Compiling tables/utilsextension.pyx because it changed.
      [1/1] Cythonizing tables/utilsextension.pyx
      Traceback (most recent call last):
        File "/Users/rly/mambaforge/envs/nwb-guide/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/rly/mambaforge/envs/nwb-guide/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Users/rly/mambaforge/envs/nwb-guide/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 928, in <module>
        File "<string>", line 923, in get_cython_extfiles
        File "/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
          cythonize_one(*args)
        File "/private/var/folders/cp/nh4x2lls1qq03jh58crvh8t00000gp/T/pip-build-env-jwqxo1tp/overlay/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: tables/utilsextension.pyx
      [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

To resolve this, we should install pytables from conda-forge in the conda env file.