GitHub Actions, Python 3.9+ Support, Jupyterlab Extensions

[srivarra]

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What is the purpose of this PR?

• Closes #965.
• Closes #899.
• Closes #954.

Adds a Conda environment using Python 3.11. The docker environment now uses a slim Python 3.11 Image.

How did you implement your changes

Environment Changes

Added the environment.yml file, adjusted the Dockerfile, made changes to the README and reformatted the setup.py file. Support for Python 3.9 to 3.11.

Added the following extensions:

• jupyterlab-lsp
• jupyterlab-git
• jupyterlab-skip-traceback
• lckr-jupyterlab-variableinspector

These extensions are not dependencies of Ark, they are installed alongside Ark in the Conda environment.yml and the Docker image Dockerfile, and can be optionally installed with pip install ark-analysis[lab_ext] or pip install .[lab_ext] if you are in the ark directory.

Testing Changes

• Added a Python Script which runs as the first job in the CI workflow. This will grab the huggingface-dataset cache, and will verify and update it if necessary. (In the future we can add a drop down menu for us to be able to select a specific commit when working with PRs which require dataset changes). The cache is now cross-os enabled, so 1 cache for all tests. Tests are only able to read the cache, not write to it.
• The fiber segmentation tests do not require the example dataset anymore, so these should be a bit faster.
• Reduced the cell count for dimensionality_reduction_test.py from 300 to 50.

Removed unused imports in src/ark/, tests/, and templates/

Sorted all imports with isort, removed unused imports.

Remaining issues Merge the following before this pr:

• [x] Merge #998
• [x] Merge #997
• [x] Merge #992
• [x] Merge #972 / #986

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[cliu72]

We should get the sequencing right for all of this. If @cliu72 wants the updated version for her paper to to be 3.9+, then we should wait on merging in #985 until after this.

If not, then we should make a new release once her other requests get merged in, then #985, then this.

Yeah I think it'd be good for the updated version of my paper to be 3.9+, since pip install doesn't work anymore with the old version. So I think we can merge this one now.

[srivarra]

@ngreenwald @cliu72 This is good to go.

@camisowers @alex-l-kong Added the fix in for watershed's argument dtype.