Pyproject.toml & setuptools_scm support

[joshmoore]

As a follow on from #325, this moves ome-zarr-py to the use of setuptools_scm (like ome/omero-cli-zarr#159) so that tags with their releases can be created directly from the GitHub UI. cc: @dstansby

To simplify this, I've gone ahead and migrated setup.py to pyproject.toml. I imagine this is a template that we can follow elsewhere. The major discrepancy in the mapping between the two was that test_requires is now an optional dependencies key which may require some adjustments.

Major question from my side is which python version to pin to. Note that zarr-python has dropped 3.8 for the next release and there is already discussion about dropping 3.9 too based on SPEC-0000.

A minor question is whether or not we still want to write the version number to a file or to just leave folks to use importlib.metadata.version("ome_zarr").

[joshmoore]

Still needs a replacement for bsdist & wheel creation, e.g., https://stackoverflow.com/questions/58753970/how-to-build-a-source-distribution-without-using-setup-py-file

[joshmoore]

Trying to get this green to see if it addresses @akhanf's issues in #353.

[joshmoore]

Reviewers requested, largely with an OR.

[will-moore]

Re: minor question - we haven't previously written the version number to a file, right?

[will-moore]

Reviewers requested, largely with an OR.

What's an OR?

[joshmoore]

Sorry, I mentioned recently elsewhere to Seb, that I'm not expecting all of these reviewers (i.e. with an AND), but any of you would be great (OR).

[joshmoore]

Re: minor question - we haven't previously written the version number to a file, right?

I'm not sure what you're asking. Previously, we've hard-coded the version in setup.py: zarr-developers/zarr-developers.github.io#105 (comment)

[will-moore]

Ah, understood. With "write the version number to a file" I was thinking of the functionality like in omero-cli-zarr where the version is importable by the code and is written to a file (https://github.com/ome/omero-cli-zarr/blob/75ab185a184410aa408772e12315ba9cbf209b36/src/omero_zarr/raw_pixels.py#L350).
But in ome-zarr-py we've never needed the ability for the code to access the version (Could you previously import it from setup.py?).
If you can get it with importlib.metadata.version("ome_zarr") anyway then 👍

[will-moore]

With this branch...

pip install -e .
...
Successfully built ome-zarr
Installing collected packages: ome-zarr
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
napari-ome-zarr 0.5.2 requires ome-zarr>=0.3.0, but you have ome-zarr 0.0.0 which is incompatible.
omero-cli-zarr 0.5.5.dev10+g893d4ee requires ome-zarr>=0.5.0, but you have ome-zarr 0.0.0 which is incompatible.
Successfully installed ome-zarr-0.0.0

Tried getting version number as described:

>>> import importlib
>>> importlib.metadata.version("ome_zarr")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'importlib' has no attribute 'metadata'

After googling alternative approach:

>>> import pkg_resources
>>> pkg_resources.get_distribution("ome_zarr").version
'0.0.0'

[sbesson]

At the code level, the changes look reasonable.

On the build system, I am not strongly opinionated about either form and would need to read more to have an informed view. My primary feedback is practical as updating the style/layout can introduce some churn with effectively zero value for end-users and additional burden for maintainers e.g. when looking at the code history. This is mostly related to the suggestion that the template could be followed elsewhere. Only suggestion is that I would weigh the impact before rolling out the new style to all OME Python repositories.

On the bumpversion vs setuptools-scm (or similar) workflow, it all boils down to the usual trade-off between a quick release workflow via a tag only vs managing the version lifecycle explicitly. Here again, I don't have a strong opinion as we already have a mixture of workflows. The biggest caveats of the setuptools-scm approach that I remember is the requirement for a Git checkout and also tags (esp. for forks).
The readme section about the release process should likely be updated accordingly.

[dstansby]

I see a ping to me from many months ago! This looks great to me, and as well as hopefully helping with #353 would also help for folks using uv (including myself), that needs a pyproject.toml to read from.

On Python support, I think SPEC-0 forces that hand of any package that depends on numpy (or other scientific python packages) to follow it, so I'd advocate for >=3.11 here.

[dstansby]

Suggested change

	"zarr>=2.8.1",
	"zarr>=2.8.1,<3",

[dstansby]

Suggested change

"tifffile",

This doesn't seem to be an actual dependency?