feat(repo, grz-check) V2: Build and publish grz-check as pyproject as well (#543)

## Summary
- Package `grz-check` as a Python extension via maturin (PyO3/Bound
API).
- Add streaming interfaces for FASTQ and BAM checks.
- Unify path-based and stream-based APIs into a single set of functions.
- CI: workflow to build and publish maturin wheels (pinned action hash).
- Tests: 11 Python binding tests (path/stream parity, gzip streams,
input validation).

This PR supercedes PR #509: feat(repo, grz-check) : Build and publish
grz-check as pyproject as well
Closes #509

---------

Co-authored-by: Eckart Bindewald <eckart.bindewald@uni-tuebingen.de>
Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de>

Author: 3 people

.github/workflows/pypi-rust.yml

@@ -0,0 +1,78 @@
+name: Publish Rust Package to PyPI
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'grz-check-v[0-9]+.[0-9]+.[0-9]+*'
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      # actions/checkout v6.0.2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+      # actions/setup-python v6.2.0
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: '3.12'
+      - name: Build wheels
+        # PyO3/maturin-action v1.51.0
+        uses: PyO3/maturin-action@3e2bdf6ba6453a61e649744019b8a2d906c7eb38
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+          manylinux: auto
+          working-directory: packages/grz-check
+      - name: Upload wheels
+        # actions/upload-artifact v7.0.1
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      # actions/checkout v6.0.2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+      - name: Build sdist
+        # PyO3/maturin-action v1.51.0
+        uses: PyO3/maturin-action@3e2bdf6ba6453a61e649744019b8a2d906c7eb38
+        with:
+          command: sdist
+          args: --out dist
+          working-directory: packages/grz-check
+      - name: Upload sdist
+      # actions/upload-artifact v7.0.1
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release to PyPI
+    runs-on: ubuntu-latest
+    needs: [linux, sdist]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/grz-check
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      # actions/download-artifact v8.0.1
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+      - name: Publish to PyPI
+        # pypa/gh-action-pypi-publish release/v1
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b
+        with:
+          packages-dir: dist

packages/grz-check/Cargo.lock

@@ -10,18 +10,32 @@ repository = "https://github.com/BfArM-MVH/grz-tools"
 readme = "README.md"
 categories = ["command-line-utilities"]
 
+[lib]
+name = "grz_check"
+crate-type = ["cdylib"]
+
+[[bin]]
+name = "grz-check"
+path = "src/main.rs"
+
 [dependencies]
 anyhow = "1.0.98"
-clap = { version = "4.5.40", features = ["derive"] }
+clap = { version = "4.5.40", features = ["derive"], optional = true }
 noodles = { version = "0.100.0", features = ["sam", "bam", "fastq", "bgzf"] }
 niffler = "3.0.0"
-rayon = "1.10.0"
+rayon = { version = "1.10.0", optional = true }
 indicatif = { version = "0.18.0", features = ["rayon", "improved_unicode"] }
 serde = { version = "1.0.219", features = ["derive"] }
 sha2 = "0.10.9"
 serde_json = "1.0.140"
 itertools = "0.14.0"
-ctrlc = "3.4.7"
+ctrlc = { version = "3.4.7", optional = true }
+pyo3 = { version = "0.23", features = ["extension-module"], optional = true }
+
+[features]
+default = ["cli"]
+cli = ["clap", "rayon", "ctrlc"]
+python = ["pyo3"]
 
 [dev-dependencies]
 tempfile = "3.20"

packages/grz-check/Cargo.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = ["maturin>=1.0,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "grz-check"
+version = "0.2.1"
+description = "Fast validation of sequencing files (FASTQ, BAM) powered by Rust"
+readme = "README.md"
+requires-python = ">=3.12"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Rust",
+]
+
+[project.optional-dependencies]
+dev = ["pytest", "maturin"]
+
+[dependency-groups]
+test = ["pytest >=8,<9"]
+dev = ["tox >=4.23", "tox-uv"]
+
+[tool.maturin]
+features = ["python"]
+python-source = "python"
+module-name = "grz_check"
+
+[tool.tox]
+requires = ["tox>=4.23", "tox-uv"]
+env_list = ["3.12", "3.13"]
+
+[tool.tox.env_run_base]
+runner = "uv-venv-lock-runner"
+dependency_groups = ["test"]
+commands = [["pytest", { replace = "posargs", default = ["tests"], extend = true }]]