Fixed tests

.github/workflows/test.yaml

@@ -25,6 +25,8 @@ jobs:
         include:
           - os: ubuntu-latest
             python: "3.9"
+          - os: ubuntu-latest
+            python: "3.10"
           - os: ubuntu-latest
             python: "3.11"
           - os: ubuntu-latest

.github/workflows/test.yml

@@ -29,6 +29,8 @@ jobs:
             python: "3.9"
           - os: ubuntu-latest
             python: "3.10"
+          - os: ubuntu-latest
+            python: "3.11"
 
     env:
       OS: ${{ matrix.os }}

docs/notebooks/tabula_sapiens_tutorial.ipynb

@@ -566,7 +566,7 @@
         "    ref_batch_key=ref_batch_key,\n",
         "    unknown_celltype_label=unknown_celltype_label,\n",
         "    save_path_trained_models=output_model_fn,\n",
-        "    cl_obo_folder=\"./PopV/popv/ontology/\",\n",
+        "    cl_obo_folder=\"./PopV/resources/ontology/\",\n",
         "    prediction_mode=\"inference\",  # 'fast' mode gives fast results (does not include BBKNN and Scanorama and makes more inaccurate predictions)\n",
         "    n_samples_per_label=n_samples_per_label,\n",
         "    accelerator=\"cuda\",\n",

popv/_settings.py

@@ -1,6 +1,7 @@
+from __future__ import annotations
+
 import logging
 from pathlib import Path
-from typing import Union
 
 import torch
 from rich.console import Console
@@ -48,7 +49,7 @@ def logging_dir(self) -> Path:
         return self._logging_dir
 
     @logging_dir.setter
-    def logging_dir(self, logging_dir: Union[str, Path]):
+    def logging_dir(self, logging_dir: str | Path):
         self._logging_dir = Path(logging_dir).resolve()
 
     @property
@@ -80,7 +81,7 @@ def verbosity(self) -> int:
         return self._verbosity
 
     @verbosity.setter
-    def verbosity(self, level: Union[str, int]):
+    def verbosity(self, level: str | int):
         """
         Sets logging configuration for popv based on chosen level of verbosity.
 

popv/_utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import networkx as nx

popv/algorithms/_bbknn.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numpy as np

popv/algorithms/_celltypist.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import celltypist

popv/algorithms/_harmony.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numpy as np

popv/algorithms/_onclass.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numpy as np

popv/algorithms/_rf.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import pickle
 

popv/algorithms/_scaffold_algorithm.py

@@ -1,4 +1,5 @@
 # Method that hightlights how to implement a new classifier. All class items are necessary but can contain Pass as only function argument.
+from __future__ import annotations
 
 import logging
 

popv/algorithms/_scanorama.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import anndata

popv/algorithms/_scanvi.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numpy as np

popv/algorithms/_scvi.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import pickle
 

popv/algorithms/_svm.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import pickle
 

popv/annotation.py

@@ -1,5 +1,7 @@
 """Helper function to execute cell-type annotation and accumulate results."""
 
+from __future__ import annotations
+
 import inspect
 import logging
 import os