fix: Do not require schema_version field in h5ad uns for validation (#…

…601)

* fix: do not require schema_version in uns for validating h5ads

* Bump version: 3.1.1 → 3.1.2-rc.0

* Bump version: 3.1.2-rc.0 → 3.1.2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.1
+current_version = 3.1.2
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

cellxgene_schema_cli/cellxgene_schema/__init__.py

@@ -1 +1 @@
-__version__ = "3.1.1"
+__version__ = "3.1.2"

cellxgene_schema_cli/cellxgene_schema/schema_definitions/3_0_0.yaml

@@ -36,8 +36,6 @@ components:
         keys:
             schema_version:
                 type: string
-                # If "required" is present, then the key/value are required
-                required: null
             title:
                 type: string
                 required: null

cellxgene_schema_cli/setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="cellxgene-schema",
-    version="3.1.1",
+    version="3.1.2",
     url="https://github.com/chanzuckerberg/single-cell-curation",
     license="MIT",
     author="Chan Zuckerberg Initiative",

cellxgene_schema_cli/tests/fixtures/examples_validate.py

@@ -155,6 +155,13 @@
 # ---
 # 3. Creating individual uns component
 good_uns = {
+    "title": "A title",
+    "default_embedding": "X_umap",
+    "X_approximate_distribution": "normal",
+    "batch_condition": ["is_primary_data"],
+}
+
+good_uns_with_labels = {
     "schema_version": SCHEMA_VERSION,
     "title": "A title",
     "default_embedding": "X_umap",
@@ -213,7 +220,7 @@
     X=sparse.csr_matrix(X),
     obs=pd.concat([good_obs, obs_expected], axis=1),
     var=var_expected,
-    uns=good_uns,
+    uns=good_uns_with_labels,
     obsm=good_obsm,
 )
 
@@ -270,7 +277,7 @@
 adata_with_lables_unmigrated = anndata.AnnData(
     X=sparse.csr_matrix(unmigrated_X),
     obs=umigrated_obs,
-    uns=good_uns,
+    uns=good_uns_with_labels,
     var=var_unmigrated,
     obsm={"X_umap": numpy.zeros([unmigrated_X.shape[0], 2])},
 )

cellxgene_schema_cli/tests/test_schema_compliance.py

@@ -1043,7 +1043,6 @@ def test_optional_fields_schema_version_is_old(self):
     def test_optional_fields_schema_version_is_missing(self):
         latest_version = "1.0.0"
         self.validator.schema_version = None
-        del self.validator.adata.uns["schema_version"]
         with patch(
             "cellxgene_schema.validate.schema.get_schema_versions_supported", return_value=[latest_version]
         ) as mock_supported_versions, patch(