Removed manual channel mapping for EPICs (#99)

* Removed manual channel mapping for EPICs * Updated vitessce and fixed builder * Fixed python version and configs * Updated readme * Updated pytest version * Updated python version * Fixed np.str_ issue during test * Bumped version
hubmapconsortium · Dec 18, 2024 · 12dbd45 · 12dbd45
1 parent e84b829
commit 12dbd45
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Showing 9 changed files with 152 additions and 163 deletions.
diff --git a/.github/workflows/portal-ci.yml b/.github/workflows/portal-ci.yml
@@ -14,10 +14,10 @@ jobs:
       with:
         submodules: 'recursive'
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.10'
         architecture: 'x64'
 
     - name: Install python main dependencies

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ usage: vis-preview.py [-h] (--url URL | --json JSON) [--assets_url URL]
 
 Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
 
-optional arguments:
+options:
   -h, --help          show this help message and exit
   --url URL           URL which returns Dataset JSON
   --json JSON         File containing Dataset JSON

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.3.6
+0.3.7
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,4 +1,4 @@
-pytest==5.2.1
+pytest==7.0.0
 flake8==7.0.0
 autopep8==2.0.4
 pytest-mock==3.7.0

diff --git a/setup.cfg b/setup.cfg
@@ -18,11 +18,11 @@ scripts =
 package_dir =
     = src
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.10
 install_requires =
     # Currently pinned due to the added `spatialdata` dependency 
     # having a lot of uncapped dependencies that are causing conflicts with search-api downstream.
-    vitessce==3.4.0
+    vitessce==3.5.0
     hubmap-commons>=2.0.15
     requests>=2.27.1
     nbformat==5.1.3

diff --git a/src/portal_visualization/builders/anndata_builders.py b/src/portal_visualization/builders/anndata_builders.py
@@ -132,7 +132,7 @@ def _set_up_marker_gene(self, marker):
             # Future improvement to be implemented in CAT-137
             # elif (encoding_version == "0.2.0"):
             #     print('TODO - Encoding Version 0.2.0 support')
-        self._marker = marker
+        self._marker = str(marker) if marker is not None else None
         self._gene_alias = gene_alias
 
     def _set_up_dataset(self, vc):
@@ -600,7 +600,6 @@ def _setup_anndata_view_config(self, vc, dataset, column_name, column_label):
         obs_set_coordination, obs_color_coordination = vc.add_coordination(
             ct.OBS_SET_SELECTION, ct.OBS_COLOR_ENCODING)
         genomic_profiles.use_coordination(obs_set_coordination, obs_color_coordination)
-
         obs_set_coordination.set_value(obs_set_coordinations)
         obs_color_coordination.set_value('cellSetSelection')
 

diff --git a/src/portal_visualization/builders/epic_builders.py b/src/portal_visualization/builders/epic_builders.py
@@ -169,14 +169,9 @@ def read_segmentation_scale(self):  # pragma: no cover
 
 
 def create_segmentation_objects(base_url, mask_names):  # pragma: no cover
-    spatialTargetCMapping = {
-        'arteries-arterioles': 4,
-        'glomeruli': 2,
-        'tubules': 3,
-    }
     segmentation_objects = []
     segmentations_CL = []
-    for index, mask_name in enumerate(mask_names):
+    for mask_name in mask_names:
         color_channel = generate_unique_color()
         mask_url = f'{base_url}/{mask_name}.zarr'
         segmentations_zarr = AnnDataWrapper(
@@ -187,13 +182,8 @@ def create_segmentation_objects(base_url, mask_names):  # pragma: no cover
                 "obsType": mask_name
             }
         )
-        # TODO: manually adjusted for the test dataset, need to be fixed on Vitessce side
-        if all(mask in mask_names for mask in spatialTargetCMapping.keys()):
-            channelIndex = spatialTargetCMapping[mask_name]
-        else:
-            channelIndex = index
         seg_CL = {
-            "spatialTargetC": channelIndex,
+            "spatialTargetC": mask_name,
             "obsType": mask_name,
             "spatialChannelOpacity": 1,
             "spatialChannelColor": color_channel,

diff --git a/test/good-fixtures/MultiomicAnndataZarrViewConfBuilder/fake-multiome-conf.json b/test/good-fixtures/MultiomicAnndataZarrViewConfBuilder/fake-multiome-conf.json
@@ -179,13 +179,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 0.0,
-        "y": 0.0
+        "w": 3,
+        "x": 0,
+        "y": 0
       },
       {
         "component": "scatterplot",
@@ -200,13 +200,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 3.0,
-        "y": 0.0
+        "w": 3,
+        "x": 3,
+        "y": 0
       },
       {
         "component": "scatterplot",
@@ -219,13 +219,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 6.0,
-        "y": 0.0
+        "w": 3,
+        "x": 6,
+        "y": 0
       },
       {
         "component": "featureList",
@@ -238,10 +238,10 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 9.0,
-        "y": 6.0
+        "h": 6,
+        "w": 3,
+        "x": 9,
+        "y": 6
       },
       {
         "component": "featureList",
@@ -254,10 +254,10 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 6.0,
-        "y": 6.0
+        "h": 6,
+        "w": 3,
+        "x": 6,
+        "y": 6
       },
       {
         "component": "genomicProfiles",
@@ -266,13 +266,13 @@
           "obsColorEncoding": "B",
           "obsSetSelection": "B"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "title": "Leiden (Weighted Nearest Neighbor) Genomic Profiles"
         },
-        "w": 6.0,
-        "x": 0.0,
-        "y": 6.0
+        "w": 6,
+        "x": 0,
+        "y": 6
       },
       {
         "component": "obsSets",
@@ -283,10 +283,10 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 9.0,
-        "y": 0.0
+        "h": 6,
+        "w": 3,
+        "x": 9,
+        "y": 0
       }
     ],
     "name": "Leiden (Weighted Nearest Neighbor)",
@@ -472,13 +472,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 0.0,
-        "y": 0.0
+        "w": 3,
+        "x": 0,
+        "y": 0
       },
       {
         "component": "scatterplot",
@@ -493,13 +493,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 3.0,
-        "y": 0.0
+        "w": 3,
+        "x": 3,
+        "y": 0
       },
       {
         "component": "scatterplot",
@@ -512,13 +512,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "embeddingCellSetLabelsVisible": false
         },
-        "w": 3.0,
-        "x": 6.0,
-        "y": 0.0
+        "w": 3,
+        "x": 6,
+        "y": 0
       },
       {
         "component": "featureList",
@@ -531,10 +531,10 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 9.0,
-        "y": 6.0
+        "h": 6,
+        "w": 3,
+        "x": 9,
+        "y": 6
       },
       {
         "component": "featureList",
@@ -547,10 +547,10 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 6.0,
-        "y": 6.0
+        "h": 6,
+        "w": 3,
+        "x": 6,
+        "y": 6
       },
       {
         "component": "genomicProfiles",
@@ -559,13 +559,13 @@
           "obsColorEncoding": "B",
           "obsSetSelection": "B"
         },
-        "h": 6.0,
+        "h": 6,
         "props": {
           "title": "Leiden (RNA) Genomic Profiles"
         },
-        "w": 6.0,
-        "x": 0.0,
-        "y": 6.0
+        "w": 6,
+        "x": 0,
+        "y": 6
       },
       {
         "component": "obsSets",
@@ -576,13 +576,13 @@
           "obsColorEncoding": "A",
           "obsSetSelection": "A"
         },
-        "h": 6.0,
-        "w": 3.0,
-        "x": 9.0,
-        "y": 0.0
+        "h": 6,
+        "w": 3,
+        "x": 9,
+        "y": 0
       }
     ],
     "name": "Leiden (RNA)",
     "version": "1.0.15"
   }
-]
+]