fix: Native builds for Linux/Windows (#70)

* chore: Performance wrong caption

* Info about benchmarking

* fix: Setting target arch for Linux/Windows to skylake

.github/workflows/publish_to_pypi.yml

@@ -31,8 +31,8 @@ permissions:
 
 # Make sure CI fails on all warnings, including Clippy lints
 env:
-  RUSTFLAGS: "-Dwarnings -Ctarget-cpu=native"
   POETRY_VERSION: 1.8.4
+  TARGET_CPU: skylake
 
 jobs:
   linux_tests:
@@ -74,10 +74,11 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-
           args: --release --out dist --find-interpreter
           sccache: 'true'
           manylinux: auto
+        env:
+          RUSTFLAGS: "-Dwarnings -Ctarget-cpu=${{ env.TARGET_CPU }}"
 
       - name: Upload wheels
         uses: actions/upload-artifact@v4
@@ -101,12 +102,11 @@ jobs:
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-
           target: ${{ matrix.target }}
-
           args: --release --out dist --find-interpreter
           sccache: 'true'
-
+        env:
+          RUSTFLAGS: "-Dwarnings -Ctarget-cpu=${{ env.TARGET_CPU }}"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
@@ -118,6 +118,11 @@ jobs:
     strategy:
       matrix:
         target: [x86_64, aarch64]
+        include:
+          - target: x86_64
+            apple_cpu_target: "skylake"
+          - target: aarch64
+            apple_cpu_target: "apple-m1"
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -137,8 +142,8 @@ jobs:
         with:
           name: wheels-macos-${{ matrix.target }}
           path: dist
-    env:
-      RUSTFLAGS: "-Clink-arg=-undefined -Clink-arg=dynamic_lookup"
+        env:
+          RUSTFLAGS: "-Dwarnings -Clink-arg=-undefined -Clink-arg=dynamic_lookup -Ctarget-cpu=${{ matrix.apple_cpu_target }}"
 
   sdist:
     runs-on: ubuntu-latest

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "polars_bio"
-version = "0.5.2"
+version = "0.5.3"
 edition = "2021"
 
 [lib]

docs/performance.md

@@ -1138,7 +1138,7 @@ the `parallel` dataset was used (see [Test datasets](#test-datasets))
 ###### Memory characteristic polars_bio_pandas_pd
 ![polars-bio-overlap-pd-mem.png](assets/memory/dataframes/polars-bio-overlap-pd-mem.png)
 
-###### Memory characteristic polars_bio_pandas_eager
+###### Memory characteristic polars_bio_polars_eager
 
 ![polars-bio-overlap-pl-mem.png](assets/memory/dataframes/polars-bio-overlap-pl-mem.png)
 
@@ -1319,15 +1319,7 @@ pyranges1    | 35,940           | 2.45x    |
 ![pyranges](assets/memory/pyranges1_sink.png)
 
 ## How to run the benchmarks
-```bash
-poetry env use python3.12
-poetry update
-poetry shell
-RUSTFLAGS="-Ctarget-cpu=native" maturin develop --release  -m Cargo.toml
-## export path with benchmark datasets, e.g.
-export BENCH_DATA_ROOT=/Users/mwiewior/research/databio/
-## other test also in benchmark/src directory
-python benchmark/src/bench_overlap.py
+Check the [repository](https://github.com/biodatageeks/polars-bio-bench) for more details on how to run the benchmarks.
 ```
 
 !!! todo

docs/quickstart.md

@@ -3,18 +3,15 @@
 pip install polars-bio
 ```
 There are binary versions for Linux (x86_64), MacOS (x86_64 and arm64) and Windows (x86_64).
-!!! Note
-    In case of Xeon processors, you are advised to build the package from source to avoid `Illegal instruction (core dumped)` errors.
-
 In case of other platforms (or errors indicating incompatibilites between Python's ABI), it is fairly easy to build polars-bio from source with [maturin](https://github.com/PyO3/maturin):
 ```shell
 RUSTFLAGS="-Ctarget-cpu=native" maturin build --release -m Cargo.toml
 ```
 and you should see the following output:
 ```shell
-Compiling polars_bio v0.2.11 (/Users/mwiewior/research/git/polars-bio)
+Compiling polars_bio v0.5.2 (/Users/mwiewior/research/git/polars-bio)
 Finished `release` profile [optimized] target(s) in 1m 25s
-📦 Built wheel for abi3 Python ≥ 3.8 to /Users/mwiewior/research/git/polars-bio/target/wheels/polars_bio-0.2.11-cp38-abi3-macosx_11_0_arm64.whl
+📦 Built wheel for abi3 Python ≥ 3.8 to /Users/mwiewior/research/git/polars-bio/target/wheels/polars_bio-0.5.2-cp38-abi3-macosx_11_0_arm64.whl
 ```
 and finally install the package with pip:
 ```bash

polars_bio/__init__.py

@@ -16,7 +16,7 @@
 POLARS_BIO_MAX_THREADS = "datafusion.execution.target_partitions"
 
 
-__version__ = "0.5.2"
+__version__ = "0.5.3"
 __all__ = [
     "overlap",
     "nearest",

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "polars-bio"
-version = "0.5.2"
+version = "0.5.3"
 description = "Blazing fast genomic operations on large Python dataframes"
 authors = []
 requires-python = ">=3.9"