feat: comprehensive biological data preprocessing library

.github/workflows/release-python.yml

@@ -9,10 +9,12 @@ on:
   push:
     branches:
       - main
-      - master
     tags:
       - "*"
   pull_request:
+    branches:
+      - main
+
   workflow_dispatch:
 
 permissions:
@@ -30,8 +32,8 @@ jobs:
             target: x86
           - runner: ubuntu-latest
             target: aarch64
-          - runner: ubuntu-latest
-            target: armv7
+          # armv7 removed due to cross-compilation issues with PyO3/maturin
+          # Most modern ARM devices use aarch64 (ARM64) instead
     steps:
       - uses: actions/checkout@v5
       - uses: actions/setup-python@v6
@@ -49,92 +51,6 @@ jobs:
         with:
           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 deepbiop --find-links dist --force-reinstall
-          pip install pytest
-          cd py-deepbiop && pytest  -vls
-      - 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-pip
-            pip3 install -U pip pytest
-          run: |
-            set -e
-            pip3 install deepbiop --find-links dist --force-reinstall
-            cd py-deepbiop && pytest  -vls
-
-  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@v5
-      - uses: actions/setup-python@v6
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --manifest-path py-deepbiop/Cargo.toml
-          sccache: "true"
-          manylinux: musllinux_1_2
-      - name: Upload wheels
-        uses: actions/upload-artifact@v5
-        with:
-          name: wheels-musllinux-${{ matrix.platform.target }}
-          path: dist
-      - name: pytest
-        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
-        uses: addnab/docker-run-action@v3
-        with:
-          image: alpine:latest
-          options: -v ${{ github.workspace }}:/io -w /io
-          run: |
-            set -e
-            apk add py3-pip py3-virtualenv
-            python3 -m virtualenv .venv
-            source .venv/bin/activate
-            pip install deepbiop --no-index --find-links dist --force-reinstall
-            pip install pytest
-            cd py-deepbiop && pytest  -vls
-      - name: pytest
-        if: ${{ !startsWith(matrix.platform.target, 'x86') }}
-        uses: uraimo/run-on-arch-action@v2
-        with:
-          arch: ${{ matrix.platform.target }}
-          distro: alpine_latest
-          githubToken: ${{ github.token }}
-          install: |
-            apk add py3-virtualenv
-          run: |
-            set -e
-            python3 -m virtualenv .venv
-            source .venv/bin/activate
-            pip install pytest
-            pip install deepbiop --find-links dist --force-reinstall
-            cd py-deepbiop && pytest -vls
 
   windows:
     runs-on: ${{ matrix.platform.runner }}
@@ -160,23 +76,13 @@ jobs:
         with:
           name: wheels-windows-${{ matrix.platform.target }}
           path: dist
-      - name: pytest
-        if: ${{ !startsWith(matrix.platform.target, 'aarch64') }}
-        shell: bash
-        run: |
-          set -e
-          python3 -m venv .venv
-          source .venv/Scripts/activate
-          pip install deepbiop --find-links dist --force-reinstall
-          pip install pytest
-          cd py-deepbiop && pytest  -vls
 
   macos:
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
         platform:
-          - runner: macos-13
+          - runner: macos-14
             target: x86_64
           - runner: macos-14
             target: aarch64
@@ -196,14 +102,6 @@ jobs:
         with:
           name: wheels-macos-${{ matrix.platform.target }}
           path: dist
-      - name: pytest
-        run: |
-          set -e
-          python3 -m venv .venv
-          source .venv/bin/activate
-          pip install deepbiop --find-links dist --force-reinstall
-          pip install pytest
-          cd py-deepbiop && pytest  -vls
 
   sdist:
     runs-on: ubuntu-latest
@@ -228,7 +126,7 @@ jobs:
     name: Release
     runs-on: ubuntu-latest
     if: ${{ startsWith(github.ref, 'refs/tags/py-deepbiop-v') }}
-    needs: [linux, musllinux, windows, macos, sdist]
+    needs: [linux, windows, macos, sdist]
     steps:
       - uses: actions/download-artifact@v6
       - name: Publish to PyPI

.github/workflows/test-python.yml

@@ -0,0 +1,130 @@
+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: 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: 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 }}
@@ -111,7 +96,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: test
-          args: --all --no-fail-fast
+          args: --workspace --exclude py-deepbiop --no-fail-fast
 
   MSRV:
     needs: Formatting
@@ -137,4 +122,4 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: test
-          args: --all --no-fail-fast
+          args: --workspace --exclude py-deepbiop --no-fail-fast

.gitignore

@@ -13,6 +13,21 @@ Cargo.lock
 # MSVC Windows builds of rustc generate these, which store debugging information
 *.pdb
 
+# Rust profiling and benchmarking
+*.prof
+*.profdata
+flamegraph.svg
+
+# Rust release artifacts
+release/
+
+# Rust library files
+*.rlib
+
+# Environment files
+.env*
+!.env.example
+
 # RustRover
 #  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
@@ -193,12 +208,19 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
-# End of https://www.toptal.com/developers/gitignore/api/python
 .ltex/
 libcairo*
-uv.lock
 _build
 CLAUDE.md
 .claude
 .specify
 specs
+
+# Claude Code development artifacts
+claudedoc
+claudedocs
+.mcp.json
+.serena
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+#