Merging main branch into staging branch

chanzuckerberg · Aug 22, 2024 · 6d33571 · 6d33571
2 parents 0c386de + db2cc47
commit 6d33571
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 9 deletions.
diff --git a/python_dependencies/processing/requirements.txt b/python_dependencies/processing/requirements.txt
@@ -1,13 +1,13 @@
-anndata==0.8.0
+anndata==0.10.8
 awscli
 boto3>=1.11.17
 botocore>=1.14.17
 cellxgene-schema
 dataclasses-json
 ddtrace==2.1.4
 numba==0.59.1
-numpy==1.26.4
-pandas==1.4.4
+numpy<2
+pandas>2,<3
 psutil>=5.9.0
 psycopg2-binary==2.*
 pyarrow>=1.0

diff --git a/tests/unit/processing/test_h5ad_data_file.py b/tests/unit/processing/test_h5ad_data_file.py
@@ -304,7 +304,7 @@ def _write_anndata_to_file(self, anndata):
 
     def _create_sample_anndata_dataset(self):
         # Create X
-        X = np.random.rand(3, 4)
+        X = np.random.rand(3, 4).astype(np.float32)
 
         # Create obs
         random_string_category = Series(data=["a", "b", "b"], dtype="category")

diff --git a/tests/unit/processing/test_type_conversion_utils.py b/tests/unit/processing/test_type_conversion_utils.py
@@ -128,7 +128,7 @@ def __exit__(self, exc_type, exc_val, exc_tb):
         "expected_schema_hint": {"type": "float32"},
         "logs": None if data.dtype != np.float64 else {"level": logging.WARNING, "output": "may lose precision"},
     }
-    for dtype in [np.float16, np.float32, np.float64]
+    for dtype in [np.float32, np.float64]
     for data in [
         np.arange(-128, 1000, dtype=dtype),
         pd.Series(np.arange(-128, 1000, dtype=dtype)),
@@ -201,9 +201,9 @@ def __exit__(self, exc_type, exc_val, exc_tb):
             "data": data,
             "expected_encoding_dtype": np.float32,
             "expected_schema_hint": {"type": "categorical"},
-            "logs": {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
         }
-        for dtype in [np.float16, np.float32, np.float64]
+        for dtype in [np.float32, np.float64]
         for data in [
             pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category"),
             pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category").cat.remove_categories([1]),
@@ -216,7 +216,7 @@ def __exit__(self, exc_type, exc_val, exc_tb):
             "data": data,
             "expected_encoding_dtype": np.float32,
             "expected_schema_hint": {"type": "categorical"},
-            "logs": {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
         }
         for dtype in [
             np.int8,
@@ -227,7 +227,6 @@ def __exit__(self, exc_type, exc_val, exc_tb):
             np.uint32,
             np.int64,
             np.uint64,
-            np.float16,
             np.float32,
             np.float64,
         ]