Advice for M1 mac installation

[swilson27]

There are difficulties with installing navis on an M1 mac, with PyQt5 appearing to be the root. Running pip3 install navis in the terminal raiss the following error:

error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
Querying qmake about your Qt installation...
/opt/homebrew/bin/qmake -query
Traceback (most recent call last):
File "/Users/swilson/documents/devneurons/devenv/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 156, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'

  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/Users/swilson/documents/devneurons/devenv/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
      main()
    File "/Users/swilson/documents/devneurons/devenv/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/Users/swilson/documents/devneurons/devenv/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 160, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
    File "/private/var/folders/5h/ftvtllls0nj2xjm5r7fwj9qh0000gp/T/pip-build-env-da71a4tm/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 51, in build_wheel
      project = AbstractProject.bootstrap('pep517')
    File "/private/var/folders/5h/ftvtllls0nj2xjm5r7fwj9qh0000gp/T/pip-build-env-da71a4tm/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 83, in bootstrap
      project.setup(pyproject, tool, tool_description)
    File "/private/var/folders/5h/ftvtllls0nj2xjm5r7fwj9qh0000gp/T/pip-build-env-da71a4tm/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 610, in setup
      self.update(tool)
    File "/private/var/folders/5h/ftvtllls0nj2xjm5r7fwj9qh0000gp/T/pip-install-8r7dfzxu/pyqt5_31dd0b8a97e242c3bb9e37bb5de28680/project.py", line 160, in update
      raise UserException(
  sipbuild.exceptions.UserException
  [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 that this applies for python 3.8, .9 and .10. I previously managed to get this working, so there is definitely a means, but stupidly didn't note down which fix online worked. If anyone has any insights or has succeeded with installing navis on M1 recently, please do let me know

[schlegelp]

@dokato: any thoughts on that?

@swilson27: technically navis doesn't actually need pyqt5 anymore. It's only there as a backend for vispy which we use for 3D plotting from the terminal. What you could do is this:

1. Install navis without dependencies: pip3 install navis --no-deps
2. Install dependencies manually skipping pyqt5: pip3 install h5py>=3.1 matplotlib>=3.3 morphops>=0.1.11 ncollpyde>=0.18 networkx>=2.4 numpy>=1.16 pandas>=1.0 pint>=0.10 plotly>=4.9 pynrrd>=0.4.2 pypng>=0.0.18 requests>=2.20 seaborn>=0.10 setuptools>=50.6 scipy>=1.5 six>=1.11 tqdm>=4.45 typing-extensions>=3.7.4 trimesh>=3.8 vispy>=0.6.4 fuzzywuzzy>=0.18 molesq>=0.2.0 rdata>=0.5 skeletor>=1.0.0

Let me know if you run into any issues.

[clbarnes]

Could pyqt5 be moved into an optional dependency? I regularly have installation issues with it on x86 too.

[dokato]

I'm on Mac M1 and used to have much more problems with pyqt in the past. Recently, I succeeded with creating a conda environment like this:

conda install -c andfoy pyqt
conda install pandas numpy matplotlib scipy h5py
conda install -c anaconda scikit-learn scikit-image 
pip install git+git://github.com/schlegelp/clio-py@main 
conda install -c flyem-forge neuprint-python
pip install --verbose git+https://github.com/navis-org/navis

(some packages can be probably skipped, leaving for completeness, just in case)

[schlegelp]

Could pyqt5 be moved into an optional dependency? I regularly have installation issues with it on x86 too.

I was thinking about that too but just tried uninstalling my PyQt5 and then matplotlib.pyplot fails to import.

[schlegelp]

Hi @swilson27. Has any of the above helped you to install navis?

[clbarnes]

2. Install dependencies manually skipping pyqt5: `a long pip command`

In case it's useful for anyone else, a cheat code for this which will stay up to date with master is

wget -O - https://raw.githubusercontent.com/navis-org/navis/master/requirements.txt \
    | grep -v 'PyQt' \
    | pip install -r /dev/stdin

It'll also install the dev reqs, but that shouldn't be too much of a problem.

[clbarnes]

If pyqt5 is only used as a vispy backend, should we just use a different backend? Both pyqt6 and pyside6 have macos-universal2 wheels for py3.6+.

[clbarnes]

Progress: on master, no backend is installed if you just pip install navis - so more people can get most of navis' functionality without issue. You still need a backend if you want to do 3D plotting with vispy, and each of the available options are navis extras, e.g. pip install 'navis[vispy-pyside6]'. Which one works for you will be platform-dependent. The all extra includes vispy-default, which is currently pyside6, which seems to work from ipython terminals on most platforms.