NickAkhmetov/HMP-159 Upgrade vitessce-python dependency

[NickAkhmetov]

This PR updates the vitessce-python dependency from 1.0.9 to 3.0.5; this was done as part of troubleshooting HMP-296. There are still failing tests etc, which will be updated accordingly once the core issue in 296 is resolved.

[NickAkhmetov]

Current state:

• All the assays on the portal which have vitessce hints display identical to prod
• Potential issue: I can't get the obsLabelsType coordination that's supposed to take the place of the factors to work as expected right now. When the related code is uncommented and the duplicate obs sets are removed, the tooltips show up with blank values for all marker genes, regardless of whether the coordination value is prefixed with obs. Continuing to investigate this a bit further.

Without obs/:

With obs/:

Sample vitessce config with the marker genes issue

{
  "coordinationSpace": {
    "dataset": {
      "A": "A"
    },
    "embeddingType": {
      "A": "UMAP"
    },
    "obsLabelsType": {
      "A": "marker_gene_0",
      "B": "marker_gene_1",
      "C": "marker_gene_2",
      "D": "marker_gene_3",
      "E": "marker_gene_4"
    }
  },
  "datasets": [
    {
      "files": [
        {
          "fileType": "anndata.zarr",
          "options": {
            "featureLabels": {
              "path": "var/hugo_symbol"
            },
            "obsEmbedding": [
              {
                "dims": [
                  0,
                  1
                ],
                "embeddingType": "UMAP",
                "path": "obsm/X_umap"
              }
            ],
            "obsFeatureMatrix": {
              "initialFeatureFilterPath": "var/marker_genes_for_heatmap",
              "path": "X"
            },
            "obsSets": [
              {
                "name": "Leiden",
                "path": "obs/leiden"
              }
            ]
          },
          "url": "https://assets.hubmapconsortium.org/6c57274e7a40413dc042ec32442a228b/hubmap_ui/anndata-zarr/secondary_analysis.zarr"
        }
      ],
      "name": "6c57274e7a40413dc042ec32442a228b",
      "uid": "A"
    }
  ],
  "description": "",
  "initStrategy": "auto",
  "layout": [
    {
      "component": "scatterplot",
      "coordinationScopes": {
        "dataset": "A",
        "embeddingType": "A",
        "obsLabelsType": [
          "A",
          "B",
          "C",
          "D",
          "E"
        ]
      },
      "h": 6,
      "w": 9,
      "x": 0,
      "y": 0
    },
    {
      "component": "obsSets",
      "coordinationScopes": {
        "dataset": "A",
        "obsLabelsType": [
          "A",
          "B",
          "C",
          "D",
          "E"
        ]
      },
      "h": 3,
      "w": 3,
      "x": 9,
      "y": 0
    },
    {
      "component": "featureList",
      "coordinationScopes": {
        "dataset": "A",
        "obsLabelsType": [
          "A",
          "B",
          "C",
          "D",
          "E"
        ]
      },
      "h": 3,
      "w": 3,
      "x": 9,
      "y": 4
    },
    {
      "component": "obsSetFeatureValueDistribution",
      "coordinationScopes": {
        "dataset": "A",
        "obsLabelsType": [
          "A",
          "B",
          "C",
          "D",
          "E"
        ]
      },
      "h": 4,
      "w": 5,
      "x": 7,
      "y": 6
    },
    {
      "component": "heatmap",
      "coordinationScopes": {
        "dataset": "A",
        "obsLabelsType": [
          "A",
          "B",
          "C",
          "D",
          "E"
        ]
      },
      "h": 4,
      "w": 7,
      "x": 0,
      "y": 6
    }
  ],
  "name": "6c57274e7a40413dc042ec32442a228b",
  "version": "1.0.15"
}

[NickAkhmetov]

I put together a local draft release of vitessce-python 3.0.7 using some of my pending PR's:

• NickAkhmetov/Add support for obs_labels_names and obs_labels_paths arrays vitessce/vitessce-python#272
• NickAkhmetov/Update CoordinationType and FileType to match docs vitessce/vitessce-python#273
• NickAkhmetov/Add allow_multiple_scopes_per_type boolean arg to use_coordination and link_views vitessce/vitessce-python#274

I verified these changes work as expected locally; CI fails for this branch because 3.0.7 is not yet a released Vitessce version. Once those three PR's are merged and a new release is made, I will update the test fixtures again and open this PR for review.

I've also preemptively pushed a portal-visualization package version bump as part of this PR given the change in dependency version.

[NickAkhmetov]

• Vitessce 3.0.7 is released
• Fixtures are updated
• Tests pass
• Smoke test of portal visualizations loaded as expected

Ergo, I'm opening this for review.

[NickAkhmetov]

I added this .vscode config as a guide to avoid long comment lines that broke lint

[john-conroy]

Not sure if my review is valuable here, but looks good to me!

[john-conroy]

Can we define schema_version somewhere for reuse?

[NickAkhmetov]

Great call! I've added this as a private field in the BaseBuilder which allows for overrides to be done (if ever needed) by passing schema_version to the args of any builder.

[john-conroy]

Could it be worth introducing a util or similar for coordination_values? There is a bit of repetition.

[NickAkhmetov]

I added a create_coordination_values util which:

• Returns `{ "obsType": "cell" } by default (most common case)
• Can have a different obs_type specified by passing an arg (first positional arg or named obs_type)
• Can have other keys specified as named args, e.g. embeddingType="UMAP"

[NickAkhmetov]

After resolving John's comments above and getting verbal approval from Mark via slack, I'm merging these changes in 🙌