✨ feat: add Python deep learning API with PyTorch and Lightning integ…

.github/workflows/release-python.yml

@@ -9,10 +9,12 @@ on:
   push:
     branches:
       - main
-      - master
     tags:
       - "*"
   pull_request:
+    branches:
+      - main
+
   workflow_dispatch:
 
 permissions:
@@ -49,39 +51,6 @@ jobs:
         with:
           name: wheels-linux-${{ matrix.platform.target }}
           path: dist
-      - name: Test wheel install
-        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
-        shell: bash
-        run: |
-          set -e
-          python3 -m pip install --upgrade pip
-          python3 -m pip install numpy pytest pytest-sugar
-          python3 -m pip install deepbiop --find-links dist --force-reinstall --no-deps --no-cache-dir
-          # Remove source deepbiop directory to prevent import conflicts
-          mv py-deepbiop/deepbiop py-deepbiop/deepbiop.bak
-          cd py-deepbiop && python3 -m pytest -vls
-          # Restore source directory
-          mv deepbiop.bak deepbiop
-      - name: Test wheel install
-        if: ${{ !startsWith(matrix.platform.target, 'x86') }}
-        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-pip
-            pip3 install -U pip
-            pip3 install numpy pytest pytest-sugar
-          run: |
-            set -e
-            pip3 install deepbiop --find-links dist --force-reinstall --no-deps --no-cache-dir
-            # Remove source deepbiop directory to prevent import conflicts
-            mv py-deepbiop/deepbiop py-deepbiop/deepbiop.bak
-            cd py-deepbiop && pytest -vls
-            # Restore source directory
-            mv deepbiop.bak deepbiop
 
   windows:
     runs-on: ${{ matrix.platform.runner }}
@@ -107,18 +76,6 @@ jobs:
         with:
           name: wheels-windows-${{ matrix.platform.target }}
           path: dist
-      - name: Test wheel install
-        shell: bash
-        run: |
-          set -e
-          python3 -m pip install --upgrade pip
-          python3 -m pip install numpy pytest pytest-sugar
-          python3 -m pip install deepbiop --find-links dist --force-reinstall --no-deps --no-cache-dir
-          # Remove source deepbiop directory to prevent import conflicts
-          mv py-deepbiop/deepbiop py-deepbiop/deepbiop.bak
-          cd py-deepbiop && python3 -m pytest -vls
-          # Restore source directory
-          mv deepbiop.bak deepbiop
 
   macos:
     runs-on: ${{ matrix.platform.runner }}
@@ -145,18 +102,6 @@ jobs:
         with:
           name: wheels-macos-${{ matrix.platform.target }}
           path: dist
-      - name: Test wheel install
-        if: ${{ !startsWith(matrix.platform.target, 'x86_64') }}
-        run: |
-          set -e
-          python3 -m pip install --upgrade pip
-          python3 -m pip install numpy pytest pytest-sugar
-          python3 -m pip install deepbiop --find-links dist --force-reinstall --no-deps --no-cache-dir
-          # Remove source deepbiop directory to prevent import conflicts
-          mv py-deepbiop/deepbiop py-deepbiop/deepbiop.bak
-          cd py-deepbiop && python3 -m pytest -vls
-          # Restore source directory
-          mv deepbiop.bak deepbiop
 
   sdist:
     runs-on: ubuntu-latest

.github/workflows/test-python.yml

@@ -0,0 +1,142 @@
+name: Test-Python
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  RUSTFLAGS: -C debuginfo=0 # Do not produce debug symbols to keep memory usage down
+
+jobs:
+  test:
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          profile: minimal
+
+      - name: Install uv (Linux/macOS)
+        if: runner.os != 'Windows'
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Install uv (Windows)
+        if: runner.os == 'Windows'
+        run: irm https://astral.sh/uv/install.ps1 | iex
+        shell: powershell
+
+      - name: Cache Rust dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/bin/
+            ~/.cargo/registry/index/
+            ~/.cargo/registry/cache/
+            ~/.cargo/git/db/
+            target/
+          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+
+      - name: Cache Python dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/uv
+            py-deepbiop/.venv
+          key: ${{ runner.os }}-py${{ matrix.python-version }}-uv-${{ hashFiles('py-deepbiop/uv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-py${{ matrix.python-version }}-uv-
+
+      - name: Build Python package
+        working-directory: py-deepbiop
+        run: |
+          uv sync
+          uv tool run maturin develop --release
+
+      - name: Run Python tests
+        working-directory: py-deepbiop
+        run: uv run pytest -vls --tb=short
+
+      - name: Run Python tests with coverage (Linux only)
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
+        working-directory: py-deepbiop
+        run: |
+          uv run pytest --cov=deepbiop --cov-report=xml --cov-report=term
+
+      - name: Upload coverage to Codecov (Linux only)
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
+        uses: codecov/codecov-action@v5
+        with:
+          files: py-deepbiop/coverage.xml
+          flags: python
+          name: python-${{ matrix.python-version }}
+          fail_ci_if_error: false
+
+  lint:
+    name: Lint Python code
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 1
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.10"
+
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          profile: minimal
+
+      - name: Install uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Install dependencies
+        working-directory: py-deepbiop
+        run: |
+          uv sync
+          uv tool run maturin develop --release
+
+      - name: Run ruff check
+        working-directory: py-deepbiop
+        run: uvx ruff check .
+
+      - name: Run ruff format check
+        working-directory: py-deepbiop
+        run: uvx ruff format --check .
+
+      - name: Run interrogate (docstring coverage)
+        working-directory: py-deepbiop
+        run: uv run interrogate deepbiop/ tests/ -vv

.github/workflows/test.yml → .github/workflows/test-rust.yml

@@ -1,25 +1,10 @@
-name: CI-rust
+name: Test-rust
 
 on:
   push:
     branches:
       - main
-    paths:
-      - src/**
-      - examples/**
-      - Cargo.toml
-      - .github/workflows/test.yml
-      - crates/*
-
   pull_request:
-    branches:
-      - main
-    paths:
-      - src/**
-      - examples/**
-      - Cargo.toml
-      - .github/workflows/test.yml
-      - crates/*
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.pre-commit-config.yaml

@@ -23,17 +23,13 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/doublify/pre-commit-rust
-    rev: v1.0
-    hooks:
-      - id: fmt
-      - id: cargo-check
-
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.14.3
+    rev: v0.14.4
     hooks:
-      - id: ruff
-        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      # Run the linter.
+      - id: ruff-check
+        args: [--fix, --unsafe-fixes]
+      # Run the formatter.
       - id: ruff-format
 
     # python docstring coverage checking

Cargo.toml

@@ -61,6 +61,7 @@ pyo3-stub-gen = "0.17.0"
 rand = "0.9"
 rand_distr = "0.5"
 rayon = { version = "1.11" }
+rust-numpy = "0.22"
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 tempfile = "3.23"

crates/deepbiop-bam/Cargo.toml

@@ -15,6 +15,7 @@ anyhow = { workspace = true }
 noodles = { workspace = true }
 pyo3 = { workspace = true, optional = true }
 pyo3-stub-gen = { workspace = true, optional = true }
+numpy = { workspace = true, optional = true }
 flate2 = { workspace = true }
 bstr = { workspace = true }
 rayon = { workspace = true }
@@ -23,6 +24,7 @@ log = { workspace = true }
 lexical = { workspace = true }
 
 derive_builder = { workspace = true }
+deepbiop-core = { workspace = true }
 deepbiop-utils = { workspace = true }
 deepbiop-fq = { workspace = true }
 
@@ -32,4 +34,4 @@ tempfile = { workspace = true }
 
 
 [features]
-python = ["dep:pyo3", "dep:pyo3-stub-gen"]
+python = ["dep:pyo3", "dep:pyo3-stub-gen", "dep:numpy"]