Add support for label properties in zattrs and plugin

[DragaDoncila]

Add support for label properties of the form

        "properties": [
            {
                "label-value": 1,
                "class": "Urban",
                "m2": "100"
            },
            {
                "label-value": 2,
                "class": "Water",
                "m2": "200"

            },
            {
                "label-value": 3,
                "class": "Deciduous Woody Horticulture"

            },
            {
                "label-value": 4,
                "class": "Evergreen Woody Horticulture"

            },
            ...

as discussed in #60 .

Read these properties in as dictionary of label-value to properties.

Transform these properties in the napari reader to:

{
    "index": [
        1,
        2,
        3,
        4,
       ...
    ],
    "class": [
        "Urban",
        "Water",
        "Deciduous Woody Horticulture",
        "Evergreen Woody Horticulture",
        ...
    ],
    "m2": [
        "100",
        "200",
        "None",
        "None",
        "None",
       ...
    ]
}

This is the very first pass, so would appreciate feedback on the general approach before I move on to updating spec, documentation, tests, etc.

We probably also wish to consider what types of property keys and values we want to accept.

[manics]

Could you explain what's happening here? We'll need to check whether the underlying dictionary is a deep-copy of the original, or whether it returns a reference which means this may update the properties seen by other code.

[will-moore]

Yes, if I do image_label.get('properties', []) after this for loop, I get the properties without the label-values so you probably should create a copy of the props before editing.
This seems to work:

                properties[label_val] = dict(props)
                del properties[label_val]['label-value']

[will-moore]

This can probably be an actual None value here instead of a string "None" (unless it has to be a string for some reason). Since if some code is testing for the value being None, then the string won't be recognised as None.

[will-moore]

This works fine for me. Can see the values in napari (bottom left) when hovering over the mask:

Few minor comments but generally looking good.

[joshmoore]

Pushed a commit to update the miniconda action since it looks like your PR was running into:

Error: Unable to process command '::set-env name=CONDA_PKGS_DIR::/home/runner/conda_pkgs_dir' successfully.
25
Error: The `set-env` command is disabled. Please upgrade to using Environment Files or opt into unsecure command execution by setting the `ACTIONS_ALLOW_UNSECURE_COMMANDS` environment variable to `true`. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

[DragaDoncila]

Pushed a commit to update the miniconda action since it looks like your PR was running into:

Error: Unable to process command '::set-env name=CONDA_PKGS_DIR::/home/runner/conda_pkgs_dir' successfully.
25
Error: The `set-env` command is disabled. Please upgrade to using Environment Files or opt into unsecure command execution by setting the `ACTIONS_ALLOW_UNSECURE_COMMANDS` environment variable to `true`. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

Thanks for this, pre-commit was giving me the run around...

[DragaDoncila]

@joshmoore I've added a test to test_napari.py for label properties. I was going to add one to test_reader.py as well but it looks like that doesn't really check metadata. Is there anywhere else I should add tests?

Aside from tests I've now also added a PR for the spec update - I hope that's the right approach. What else needs doing to fully incorporate the label properties into the package?

[joshmoore]

Ah, @DragaDoncila. Sorry, I see I owe(d) you a comment regarding the spec & more tests. Your PR against omero-ms-zarr was perfect and against the right repo at the time. 💯 You saw that I migrated it. Further PRs welcome against ome/zarr. 😄 Regarding tests, I imagine there will need to be a new file created for what you were wanted to accomplish. Feel free to open a new PR if you're interested. All the best, ~Josh

Merging along with ome/ngff#3