Merge pull request #8 from aertslab/fix_linux_ppc64le_build

Fix linux ppc64le build
aertslab · Jul 8, 2024 · 615c76b · 615c76b
2 parents 908396a + 472a3cf
commit 615c76b
Show file tree

Hide file tree

Showing 4 changed files with 84 additions and 36 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,7 +1,7 @@
-# This file is autogenerated by maturin v1.4.0
+# This file is autogenerated by maturin v1.7.0
 # To update, run
 #
-#    maturin generate-ci github
+#    maturin generate-ci github --zig --pytest --platform manylinux macos
 #
 name: CI
 
@@ -20,79 +20,117 @@ permissions:
 
 jobs:
   linux:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, aarch64, ppc64le]
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: aarch64
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --zig --find-interpreter
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --zig
           sccache: 'true'
           manylinux: auto
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-linux-${{ matrix.platform.target }}
           path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install scatac_fragment_tools --find-links dist --force-reinstall
+          pip install pytest
+          pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') && matrix.platform.target != 'ppc64' }}
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: ${{ matrix.platform.target }}
+          distro: ubuntu22.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-dev python3-pip gcc zlib1g-dev
+            pip3 install -U pip pytest
+          run: |
+            set -e
+            pip3 install scatac_fragment_tools --find-links dist --force-reinstall
+            pytest
 
   macos:
-    runs-on: macos-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, aarch64]
+        platform:
+          - runner: macos-12
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
           sccache: 'true'
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-macos-${{ matrix.platform.target }}
           path: dist
+      - name: pytest
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install scatac_fragment_tools --find-links dist --force-reinstall
+          pip install pytest
+          pytest
 
   sdist:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:
           command: sdist
           args: --out dist
       - name: Upload sdist
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-sdist
           path: dist
 
   release:
     name: Release
-    environment: release
     runs-on: ubuntu-latest
     if: "startsWith(github.ref, 'refs/tags/')"
     needs: [linux, macos, sdist]
-    permissions:
-      id-token: write
     steps:
-      - uses: actions/download-artifact@v3
-        with:
-          name: wheels
+      - uses: actions/download-artifact@v4
       - name: Publish to PyPI
         uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         with:
           command: upload
-          args: --non-interactive --skip-existing *
+          args: --non-interactive --skip-existing wheels-*/*
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,10 +4,16 @@
 
 ### Updated
 
-- **[27b3a059](https://github.com/aertslab/scatac_fragment_tools/commit/27b3a059c23462ebdb7240d10ce4be171cd67ce0)**: Update polars groupby syntax to group_by
+- **[27b3a059](https://github.com/aertslab/scatac_fragment_tools/commit/27b3a059c23462ebdb7240d10ce4be171cd67ce0)**: Update Polars `groupby` syntax to `group_by`.
+- **[98a55b0d](https://github.com/aertslab/scatac_fragment_tools/commit/98a55b0de121883fca3660a9128871b67e3deead)**: Update pyo3 and itertools dependencies.
+
+### Fixed
+
+- **[65381a76](https://github.com/aertslab/scatac_fragment_tools/commit/65381a76adb07c3a657f325bb7bfcd06f636b244)**: Fix building for Linux ppc64le.
+
 
 ## v0.1.1
 
 ### Added
 
-- **[004a265](https://github.com/aertslab/scatac_fragment_tools/commit/004a2654ecd5ed0a33be78f6fa5789c0a41deafb)**: Allow barcodes to map to multiple cell types while splitting fragments by cell type.
+- **[004a265](https://github.com/aertslab/scatac_fragment_tools/commit/004a2654ecd5ed0a33be78f6fa5789c0a41deafb)**: Allow barcodes to map to multiple cell types while splitting fragments by cell type.
diff --git a/rust/Cargo.toml b/rust/Cargo.toml
@@ -11,6 +11,10 @@ crate-type = ["cdylib"]
 
 [dependencies]
 bgzip = { git = "https://github.com/informationsea/bgzip-rs/", rev = "4492b5d6abb3e191c2eb007f148b704b654d528e", default-features = false, features = ["rust_backend", "rayon", "log"] }
-itertools = "0.12.1"
-pyo3 = { version = "0.20.2", features = ["abi3-py38", "extension-module"] }
-rust-htslib = { version = "0.45.0", default-features = false, features = ["libdeflate"] }
+itertools = "0.13.0"
+pyo3 = { version = "0.22.1", features = ["abi3-py38", "extension-module"] }
+
+[target.'cfg(not(all(target_os = "linux", target_arch = "powerpc64")))'.dependencies]
+rust-htslib = { version = "0.47.0", default-features = false, features = ["libdeflate"] }
+[target.'cfg(all(target_os = "linux", target_arch = "powerpc64"))'.dependencies]
+rust-htslib = { version = "0.47.0", default-features = false }
diff --git a/rust/src/lib.rs b/rust/src/lib.rs
@@ -105,7 +105,7 @@ fn merge_fragment_files(
 }
 
 #[pymodule]
-fn _rust_scatac_fragment_tools(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
+fn _rust_scatac_fragment_tools(m: &Bound<'_, PyModule>) -> PyResult<()> {
     // set version dunder
     m.add("__version__", env!("CARGO_PKG_VERSION"))?;
     // add functions