Fix_dependency

[pr4deepr]

Modified pyproject.toml files

• added back napari-aicsimageio constraint
  linked PR was merged: Improve handling of constraints on requirements with extras pypa/pip#12095

• added napari[all] so pyqt5 is installed by default

• added numpy<2 constraint

[pr4deepr]

There are issues with Python 3.11 which is to do with incompatibility with
Pillow==8.4.0, (needed for napari 0.4.17). This pillow version does not have a python 3.11 wheel.
This also has to do with

• aicsimageio[all] being installed with napari-aicsimageio
• tifffile pin in aicsimageio

aicsimageio is being deprecated to bioio and this may help with dependency issues.
Considering adding a reader for napari instead of depending on napari-aicsimageio.

I reccomend we remove 3.11 from testing and mention compatibility with python 3.10 for now.

[pr4deepr]

@multimeric ,

Does this need to be Python 3.11 in test and deploy workflow?

    uses: actions/setup-python@v4
    with:
      python-version: "3.11"

[multimeric]

Can you show me the error with pillow etc? Even if there isn't a wheel it should be possible to install somehow. I'm very wary of pulling support for Python 3.11 fully. If anything we should add 3.12 and 3.13 to the tests.

[pr4deepr]

uv pip install lls-core napari-lattice "napari-aicsimageio>0.7" napari[all]

Using Python 3.11.11 environment at: .conda\envs\nap_py311
Resolved 200 packages in 1.96s
  x Failed to build `pillow==8.4.0`
  |-> The build backend returned an error
  `-> Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit code:
      1)        

      <string>:46: RuntimeWarning: Pillow 8.4.0 does not support Python 3.11 and
      does not provide prebuilt Windows binaries. We do not recommend building
      from source on Windows.

      hint: This usually indicates a problem with the package or the build
      environment.
  help: `pillow` (v8.4.0) was included because `napari` (v0.4.17) depends on
        `pillow`

If I just try without napari:

uv pip install lls-core napari-lattice "napari-aicsimageio>0.7"

      hint: This usually indicates a problem with the package or the build
      environment.
  help: `pillow` (v8.4.0) was included because `napari-aicsimageio` (v0.7.2)
        depends on `readlif` (v0.6.5) which depends on `pillow`

Its got to do with some of the packages in napari-aicsimageio, aicsimageio.
I believe this is also why aicsimageio was deprecated in favour of bioio so we minimize conflicts between packages

I'm very wary of pulling support for Python 3.11 fully. If anything we should add 3.12 and 3.13 to the tests.

This will be temporary, until we remove napari-aicsimageio as a dependency and implement our own reader.
I'd like to prioritize having a working plugin for now

[pr4deepr]

Will merge this today and #93

[multimeric]

I've looked into this issue, and as far as I can tell it only affects Windows. This means that changing the package metadata and the CI aren't necessary.

I would prefer we just add a Windows-specific note in the docs that explain the issue and how to resolve it.