Fixes to PopV.

YosefLab · Jun 19, 2023 · 6b95ddf · 6b95ddf
1 parent af1a9d2
commit 6b95ddf
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/popv/algorithms/_onclass.py b/popv/algorithms/_onclass.py
@@ -86,11 +86,15 @@ def make_cell_ontology_id(self, adata, celltype_dict, ontology_key):
             Default will be <labels_key>_cell_ontology_id
         """
         ontology_id = []
+        single_warning = []  # print a single warning per missing cell-type
 
         for label in adata.obs[self.labels_key]:
             if label != adata.uns["unknown_celltype_label"]:
                 if label not in celltype_dict:
-                    logging.warning("Following label not in celltype_dict ", label)
+                    if label not in single_warning:
+                        logging.warning("Following label not in celltype_dict ", label)
+                        single_warning.append(label)
+                    ontology_id.append("unknown")
                 ontology_id.append(celltype_dict[label])
             else:
                 ontology_id.append("unknown")

diff --git a/pyproject.toml b/pyproject.toml
@@ -22,7 +22,7 @@ description = "Automatic annotation of single cell data using a labelled referen
 packages = [
   {include = "popv"},
 ]
-version = "0.3.1"
+version = "0.3.2"
 readme = "README.md"
 
 [tool.poetry.dependencies]
@@ -48,7 +48,7 @@ nbformat = {version = ">=4.4.0", optional = true}
 nbsphinx = {version = "*", optional = true}
 nbsphinx-link = {version = "*", optional = true}
 onclass = "^1.2"
-pandas = ">=1.4"
+pandas = ">=1.4,<2.0"
 pre-commit = {version = ">=2.7.1", optional = true}
 pytest = {version = ">=4.4", optional = true}
 rich = ">=9.1.0"