Python bindings

.github/workflows/clippy_check.yml

@@ -1,6 +1,11 @@
-on: push
 name: Clippy check
 
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]    
+
 # Make sure CI fails on all warnings, including Clippy lints
 env:
   RUSTFLAGS: "-Dwarnings"

.github/workflows/coverage.yml

@@ -1,4 +1,4 @@
-name: coverage
+name: Code coverage
 
 on:
   push:

.github/workflows/pypi.yml

@@ -0,0 +1,157 @@
+name: Upload to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+          - runner: ubuntu-latest
+            target: s390x
+          - runner: ubuntu-latest
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-12
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path ./pykmertools/Cargo.toml
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    needs: [linux, musllinux, windows, macos, sdist]
+    steps:
+      - 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 wheels-*/*

Cargo.toml

@@ -1,7 +1,10 @@
 [workspace]
 package.version = "0.1.0"
 package.edition = "2021"
-package.authors = ["Anuradha Wickramarachchi [email protected]", "Vijini Mallawaarachchi [email protected]"]
+package.authors = ["Anuradha Wickramarachchi <[email protected]>", "Vijini Mallawaarachchi <[email protected]>"]
+package.description = "kmertools is a k-mer based feature extraction tool designed to support metagenomics and other bioinformatics analytics."
+package.readme = "README.md"
+package.license-file = "LICENSE"
 
-members = ["composition", "coverage", "kmertools", "kmer", "ktio", "counter", "misc"]
+members = ["composition", "coverage", "kmertools", "kmer", "ktio", "counter", "misc", "pykmertools"]
 resolver = "2"

composition/Cargo.toml

@@ -3,6 +3,7 @@ name = "composition"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 [dependencies]
 kmer = { path = "../kmer" }
@@ -12,3 +13,6 @@ rayon = "1.10.0"
 
 [lib]
 doctest = false
+
+[lints.rust]
+unexpected_cfgs = { level = "warn", check-cfg = ["cfg(tarpaulin_include)"] }

counter/Cargo.toml

@@ -3,6 +3,7 @@ name = "counter"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 

coverage/Cargo.toml

@@ -3,6 +3,7 @@ name = "coverage"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 

kmer/Cargo.toml

@@ -3,6 +3,7 @@ name = "kmer"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 [dependencies]
 indicatif = "0.17.8"

kmertools/Cargo.toml

@@ -3,6 +3,7 @@ name = "kmertools"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 [dependencies]
 clap = { version = "4.5.4", features = ["derive"] }
@@ -11,3 +12,6 @@ coverage = { path = "../coverage" }
 counter = { path = "../counter" }
 misc = { path = "../misc" }
 ktio = { path = "../ktio" }
+
+[lints.rust]
+unexpected_cfgs = { level = "warn", check-cfg = ["cfg(tarpaulin_include)"] }

ktio/Cargo.toml

@@ -3,6 +3,7 @@ name = "ktio"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
+description.workspace = true
 
 [dependencies]
 bio = "1.6.0"