bed-reader 1.0.4b1__tar.gz → 1.0.4b2__tar.gz

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/Cargo.lock

@@ -136,7 +136,7 @@ checksum = "9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567"
 
 [[package]]
 name = "bed-reader"
-version = "1.0.4-beta.1"
+version = "1.0.4-beta.2"
 dependencies = [
  "anyhow",
  "anyinput",

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-version = "1.0.4-beta.1"
+version = "1.0.4-beta.2"
 name = "bed-reader"
 description = "Read and write the PLINK BED format, simply and efficiently."
 repository = "https://github.com/fastlmm/bed-reader"

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bed-reader
-Version: 1.0.4b1
+Version: 1.0.4b2
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/bed_reader/_open_bed.py

@@ -1345,20 +1345,28 @@ class open_bed:
         if len(input.shape) != 1:
             raise ValueError(f"{key} should be one dimensional")
 
-        if not np.issubdtype(input.dtype, dtype):
+        do_missing_values = True
+        if np.issubdtype(input.dtype, np.floating) and np.issubdtype(dtype, int):
+            input[input != input] = missing_value
+            old_settings = np.seterr(invalid="warn")
+            try:
+                output = np.array(input, dtype=dtype)
+            finally:
+                np.seterr(**old_settings)
+        elif not np.issubdtype(input.dtype, dtype):
             # This will convert, for example, numerical sids to string sids or
             # floats that happen to be integers into ints,
             # but there will be a warning generated.
+            old_settings = np.seterr(invalid="warn")
             try:
-                np.seterr(invalid="warn")
                 output = np.array(input, dtype=dtype)
             finally:
-                np.seterr(invalid="raise")
+                np.seterr(**old_settings)
         else:
             output = input
 
         # Change NaN in input to correct missing value
-        if np.issubdtype(input.dtype, np.floating):
+        if do_missing_values and np.issubdtype(input.dtype, np.floating):
             output[input != input] = missing_value
 
         return output

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/bed_reader/tests/test_open_bed.py

@@ -880,11 +880,10 @@ def test_coverage2(shared_datadir, tmp_path):
 
 
 def test_coverage3(shared_datadir, tmp_path):
-    with pytest.warns(RuntimeWarning, match="invalid value encountered in cast"):
-        with open_bed(
-            shared_datadir / "small.bed", properties={"sex": [1.0, np.nan, 1.0, 2.0]}
-        ) as bed:
-            assert np.array_equal(bed.sex, np.array([1, 0, 1, 2]))
+    with open_bed(
+        shared_datadir / "small.bed", properties={"sex": [1.0, np.nan, 1.0, 2.0]}
+    ) as bed:
+        assert np.array_equal(bed.sex, np.array([1, 0, 1, 2]))
 
     with open_bed(
         shared_datadir / "small.bed",

{bed_reader-1.0.4b1 → bed_reader-1.0.4b2}/bed_reader/tests/test_open_bed_cloud.py

@@ -712,12 +712,11 @@ def test_cloud_coverage2(shared_datadir, tmp_path):
 
 
 def test_cloud_coverage3(shared_datadir, tmp_path):
-    with pytest.warns(RuntimeWarning, match="invalid value encountered in cast"):
-        with open_bed(
-            file_to_url(shared_datadir / "small.bed"),
-            properties={"sex": [1.0, np.nan, 1.0, 2.0]},
-        ) as bed:
-            assert np.array_equal(bed.sex, np.array([1, 0, 1, 2]))
+    with open_bed(
+        file_to_url(shared_datadir / "small.bed"),
+        properties={"sex": [1.0, np.nan, 1.0, 2.0]},
+    ) as bed:
+        assert np.array_equal(bed.sex, np.array([1, 0, 1, 2]))
 
     with open_bed(
         file_to_url(shared_datadir / "small.bed"),