bed-reader 1.0.5__tar.gz → 1.0.5b2__tar.gz

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        os: [ubuntu-latest, macos-12, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
@@ -39,7 +39,7 @@ jobs:
   
   
   macos:
-    runs-on: macos-13
+    runs-on: macos-12
     strategy:
       matrix:
         target: [x86_64, aarch64]
@@ -48,6 +48,7 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
+            3.8
             3.9
             3.10
             3.11
@@ -57,6 +58,7 @@ jobs:
         with:
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
+          sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v3
         with:
@@ -67,42 +69,24 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        target: [x86_64, aarch64]
+        target: [x86_64]
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: |
+            3.8
             3.9
             3.10
             3.11
             3.12
-
-      - name: Install cross-compilation dependencies
-        if: matrix.target == 'aarch64'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y gcc-aarch64-linux-gnu
-          
-      - name: Build wheels for aarch64
-        if: matrix.target == 'aarch64'
-        env:
-          CC: aarch64-linux-gnu-gcc
-          CFLAGS: -march=armv8-a -D__ARM_ARCH=8
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.target }}
-          args: --release --out dist -i python3.9 -i python3.10 -i python3.11 -i python3.12
-          manylinux: auto
-
-      - name: Build wheels for x86_64
-        if: matrix.target == 'x86_64'
+      - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist -i python3.9 -i python3.10 -i python3.11 -i python3.12
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
           manylinux: auto
-
       - name: Upload wheels
         uses: actions/upload-artifact@v3
         with:
@@ -119,6 +103,7 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
+            3.8
             3.9
             3.10
             3.11
@@ -129,6 +114,7 @@ jobs:
         with:
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
+          sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v3
         with:
@@ -155,8 +141,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9, "3.10", "3.11", "3.12"]
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-12, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/Cargo.lock

@@ -142,7 +142,7 @@ checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
 
 [[package]]
 name = "bed-reader"
-version = "1.0.5"
+version = "1.0.5-beta.2"
 dependencies = [
  "anyhow",
  "anyinput",

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-version = "1.0.5"
+version = "1.0.5-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-1.0.5 → bed_reader-1.0.5b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bed-reader
-Version: 1.0.5
+Version: 1.0.5b2
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/bed_reader/_open_bed.py

@@ -2,6 +2,7 @@ import logging
 import multiprocessing
 import os
 import re
+import sys
 from dataclasses import dataclass
 from io import BytesIO
 from itertools import repeat, takewhile
@@ -1814,7 +1815,12 @@ def _read_csv(filepath, delimiter=None, dtype=None, usecols=None):
         col = transposed[output_index]
 
         # work around numpy/python bug
-        if len(col) > 0 and pattern.fullmatch(col[0]):
+        if (
+            (sys.version_info.major, sys.version_info.minor) <= (3, 9)
+            and int(np.__version__.split(".")[0]) >= 2
+            and len(col) > 0
+            and pattern.fullmatch(col[0])
+        ):
             col = np.array([pattern.fullmatch(x).group(1) for x in col])
 
         # Find the dtype for this column

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/src/python_module.rs

@@ -50,7 +50,7 @@ fn bed_reader(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
 
     #[pyfn(m)]
     fn url_to_bytes(location: &str, options: &Bound<'_, PyDict>) -> Result<Vec<u8>, PyErr> {
-        let options: HashMap<String, String> = options.extract()?;
+        let options: HashMap<String, String> = options.extract()?; // cmk
         let cloud_file = CloudFile::new_with_options(location, options)
             .map_err(|e| Box::new(BedErrorPlus::CloudFileError(e)))?;
         let rt = runtime::Runtime::new()?;
@@ -178,7 +178,7 @@ fn bed_reader(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
 
     #[pyfn(m)]
     fn check_file_cloud(location: &str, options: &Bound<'_, PyDict>) -> Result<(), PyErr> {
-        let options: HashMap<String, String> = options.extract()?;
+        let options: HashMap<String, String> = options.extract()?; // cmk
         runtime::Runtime::new()?.block_on(async {
             BedCloud::new_with_options(location, options).await?;
             Ok(())
@@ -200,7 +200,7 @@ fn bed_reader(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
         max_concurrent_requests: usize,
         max_chunk_bytes: usize,
     ) -> Result<(), PyErr> {
-        let options: HashMap<String, String> = options.extract()?;
+        let options: HashMap<String, String> = options.extract()?; // cmk
 
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();
@@ -247,7 +247,7 @@ fn bed_reader(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
         max_concurrent_requests: usize,
         max_chunk_bytes: usize,
     ) -> Result<(), PyErr> {
-        let options: HashMap<String, String> = options.extract()?;
+        let options: HashMap<String, String> = options.extract()?; // cmk
 
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();
@@ -294,7 +294,7 @@ fn bed_reader(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
         max_concurrent_requests: usize,
         max_chunk_bytes: usize,
     ) -> Result<(), PyErr> {
-        let options: HashMap<String, String> = options.extract()?;
+        let options: HashMap<String, String> = options.extract()?; // cmk
 
         let iid_index = iid_index.readonly();
         let sid_index = sid_index.readonly();

{bed_reader-1.0.5 → bed_reader-1.0.5b2}/useful.md

@@ -4,6 +4,7 @@
 
 To get some Rust PyO3 debugging to work I had to set this before starting vscode:
 
+<!-- cmk -->
 ```cmd
 set PYO3_PYTHON=C:/Users/carlk/OneDrive/programs/bed-reader/.venv\Scripts\python.exe
 ```