bed-reader 1.0.3__tar.gz → 1.0.4__tar.gz

{bed_reader-1.0.3 → bed_reader-1.0.4}/.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-12, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
@@ -39,7 +39,7 @@ jobs:
   
   
   macos:
-    runs-on: macos-latest
+    runs-on: macos-12
     strategy:
       matrix:
         target: [x86_64, aarch64]
@@ -75,11 +75,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.7
             3.8
             3.9
             3.10
             3.11
+            3.12
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -103,11 +103,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.7
             3.8
             3.9
             3.10
             3.11
+            3.12
           architecture: ${{ matrix.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
@@ -142,7 +142,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-12, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout

{bed_reader-1.0.3 → bed_reader-1.0.4}/CHANGELOG.md

@@ -5,13 +5,17 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0.2] - 2024-4-17
+## [1.0.4] - 2024-4-24
+
+- Fix a minor bug in helper functions used by PySnpTools.
+
+## [1.0.3] - 2024-4-17
 
 - On the Python file, add `create-bed`, a method for writing large
   bed files SNP-by-SNP (or individual-by-individual).
   Also, add full support for the less common individual-major files.
 
-## [1.0.1] - 2024-3-16
+## [1.0.2] - 2024-3-16
 
 - Add support for cloud files to both Rust and Python.
 

{bed_reader-1.0.3 → bed_reader-1.0.4}/Cargo.lock

@@ -136,7 +136,7 @@ checksum = "9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567"
 
 [[package]]
 name = "bed-reader"
-version = "1.0.3"
+version = "1.0.4"
 dependencies = [
  "anyhow",
  "anyinput",

{bed_reader-1.0.3 → bed_reader-1.0.4}/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-version = "1.0.3"
+version = "1.0.4"
 name = "bed-reader"
 description = "Read and write the PLINK BED format, simply and efficiently."
 repository = "https://github.com/fastlmm/bed-reader"

{bed_reader-1.0.3 → bed_reader-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bed-reader
-Version: 1.0.3
+Version: 1.0.4
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10

{bed_reader-1.0.3 → bed_reader-1.0.4}/bed_reader/_open_bed.py

@@ -1345,16 +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.
-            output = np.array(input, dtype=dtype)
+            old_settings = np.seterr(invalid="warn")
+            try:
+                output = np.array(input, dtype=dtype)
+            finally:
+                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-1.0.3 → bed_reader-1.0.4}/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-1.0.3 → bed_reader-1.0.4}/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"),

{bed_reader-1.0.3 → bed_reader-1.0.4}/src/python_module.rs

@@ -448,7 +448,7 @@ fn bed_reader(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();
 
-        let val_in = val_in.readwrite();
+        let val_in = val_in.readonly();
         let val_in = val_in.as_array();
         let mut val_out = val_out.readwrite();
         let mut val_out = val_out.as_array_mut();
@@ -473,7 +473,7 @@ fn bed_reader(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();
 
-        let val_in = val_in.readwrite();
+        let val_in = val_in.readonly();
         let val_in = val_in.as_array();
         let mut val_out = val_out.readwrite();
         let mut val_out = val_out.as_array_mut();
@@ -498,7 +498,7 @@ fn bed_reader(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();
 
-        let val_in = val_in.readwrite();
+        let val_in = val_in.readonly();
         let val_in = val_in.as_array();
         let mut val_out = val_out.readwrite();
         let mut val_out = val_out.as_array_mut();