Use PyO3 abi3-py38 feature for ABI stable wheels

Produces ABI stable wheels for Python >=3.8. This simplifies the build/distribution by generating wheels that are forward compatible.
abdenlab · Dec 1, 2024 · 97db077 · 97db077
1 parent 6ea712f
commit 97db077
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Showing 4 changed files with 26 additions and 23 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,29 +1,30 @@
-permissions:
-  contents: read
+name: Test
 
 on:
   push:
     branches: [main]
   pull_request:
 
-name: Test
+permissions:
+  contents: read
+
+env:
+  # Disable incremental compilation for faster from-scratch builds
+  CARGO_INCREMENTAL: 0
 
 jobs:
   Test:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - run: rustup update
 
       - name: Check formatting
-        run: cargo fmt --all --manifest-path ./oxbow/Cargo.toml -- --check
+        run: cargo fmt --all --check
 
       - name: Download fixtures
         run: cd fixtures && wget -i list.txt
 
       - name: Run cargo test
-        uses: actions-rs/cargo@v1
-        with:
-          command: test
-          args: --manifest-path ./oxbow/Cargo.toml
+        run: cargo test
diff --git a/py-oxbow/Cargo.toml b/py-oxbow/Cargo.toml
@@ -11,4 +11,4 @@ crate-type = ["cdylib"]
 
 [dependencies]
 oxbow = { workspace = true }
-pyo3 = { version = "0.23.2", features = ["extension-module"] }
+pyo3 = { version = "0.23.2", features = ["abi3-py38"] }
diff --git a/py-oxbow/pyproject.toml b/py-oxbow/pyproject.toml
@@ -10,7 +10,7 @@ authors = [
     { name = "Oxbow Developers", email = "[email protected]" }
 ]
 license = { text = "MIT OR Apache-2.0" }
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Rust",
     "Programming Language :: Python :: Implementation :: CPython",

diff --git a/py-oxbow/src/lib.rs b/py-oxbow/src/lib.rs
@@ -48,7 +48,7 @@ fn read_fasta(path: &str, region: Option<&str>) -> Vec<u8> {
 fn read_fastq(py: Python, path_or_file_like: PyObject) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it like a path
-        let mut reader = FastqReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = FastqReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc().unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -69,7 +69,7 @@ fn read_bam(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = BamReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = BamReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc(region).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -94,7 +94,7 @@ fn read_bam_vpos(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = BamReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = BamReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc_from_vpos(pos_lo, pos_hi).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -118,7 +118,7 @@ fn read_vcf(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = VcfReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = VcfReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc(region).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -143,7 +143,7 @@ fn read_vcf_vpos(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = VcfReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = VcfReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc_from_vpos(pos_lo, pos_hi).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -167,7 +167,7 @@ fn read_bcf(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = BcfReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = BcfReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc(region).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -192,7 +192,7 @@ fn read_bcf_vpos(
 ) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = VcfReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = VcfReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc_from_vpos(pos_lo, pos_hi).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -220,7 +220,8 @@ fn read_bigwig(
         .map(|h| h.iter().map(String::as_str).collect::<HashSet<&str>>());
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = BigWigReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader =
+            BigWigReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         match zoom_level {
             Some(zoom_level) => reader
                 .zoom_records_to_ipc(region, zoom_level, zoom_summary_columns_ref)
@@ -254,7 +255,8 @@ fn read_bigbed(
         .map(|h| h.iter().map(String::as_str).collect::<HashSet<&str>>());
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = BigBedReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader =
+            BigBedReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc(region, fields_ref).unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -269,7 +271,7 @@ fn read_bigbed(
 fn read_gff(py: Python, path_or_file_like: PyObject) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = GffReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = GffReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc().unwrap()
     } else {
         // Otherwise, treat it as file-like
@@ -284,7 +286,7 @@ fn read_gff(py: Python, path_or_file_like: PyObject) -> Vec<u8> {
 fn read_gtf(py: Python, path_or_file_like: PyObject) -> Vec<u8> {
     if let Ok(string_ref) = path_or_file_like.downcast_bound::<PyString>(py) {
         // If it's a string, treat it as a path
-        let mut reader = GtfReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
+        let mut reader = GtfReader::new_from_path(string_ref.to_string_lossy().as_ref()).unwrap();
         reader.records_to_ipc().unwrap()
     } else {
         // Otherwise, treat it as file-like