Package discovery error with new setuptools

[kaitsull]

Hi all!

When I try to download napari-lattice via:
pip install git+https://github.com/BioimageAnalysisCoreWEHI/napari_lattice.git

I receive the following error:

error: subprocess-exited-with-error  

  × Getting requirements to build wheel did not run successfully.  
  │ exit code: 1  
  ╰─> [14 lines of output]  
      error: Multiple top-level packages discovered in a flat-layout: ['core', 'plugin', 'notebooks', 'resources', 'sample_data', 'workflow_examples'].  

      To avoid accidental inclusion of unwanted files or directories,
      setuptools will not proceed with this build.  

      If you are trying to create a single distribution with multiple packages
      on purpose, you should not rely on automatic discovery.
      Instead, consider the following options:  

      1. set up custom discovery ('find' directive with 'include' or 'exclude')  
      2. use a 'src-layout'  
      3. explicitly set 'py_modules' or 'packages' with a list of names  

      To find more information, look for "package discovery" on setuptools docs.  
      [end of output]  

  note: This error originates from a subprocess, and is likely not a problem with pip.

After perusing the internet I found that this error can be circumvented by either:

1. This answer on stackoverflow suggested adding the following lines to the pyproject.toml:

   [tool.setuptools]  
   py-modules = []

2. Since I don't have access to the repo, I tried downgrading setuptools via:
   pip install setuptools==version#

Unfortunately downgrading setuptools still causes a host of errors to occur. Any suggestions?

Thank you so much :octocat: !!!

[multimeric]

This is caused by the project being split into two Python packages. This affects only the case where you install directly from GitHub, so I would suggest using the standard PyPI version unless you need a specific change that's only on the Git master.

That said, you can still install from GitHub, using pip install git+https://github.com/BioimageAnalysisCoreWEHI/napari_lattice.git#subdirectory=core git+https://github.com/BioimageAnalysisCoreWEHI/napari_lattice.git#subdirectory=plugin. We will need to update our documentation about this.

[kaitsull]

Wow thank you so so much for such a quick response!

This fix worked perfectly :)

[multimeric]

This seems to be resolved. Also, the new packages are now published on PyPI, so you no longer need to install from GitHub at all!