Merge branch 'main' into gafBinding

Author: JerryJi0730

.github/workflows/build.yml

@@ -58,7 +58,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions-rust-lang/setup-rust-toolchain@v1
+      - run: rustup toolchain install stable --no-self-update
 
       # Install slow-odgi.
       - uses: actions/cache@v4

.github/workflows/code-quality.yml

@@ -1,16 +1,49 @@
-name: CodeQuality
-on: [pull_request]
+name: quality
+on:
+  push:
+  pull_request:
+    branches: [main]
 
 jobs:
-  build:
+  python:
     runs-on: ubuntu-latest
-    name: CodeQuality
+    name: Python
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+
+    - name: ruff check
+      uses: astral-sh/ruff-action@v3
+      with:
+        src: >-
+          mygfa
+          slow_odgi
+          pollen_data_gen
+          flatgfa-py
+
+    - name: ruff format
+      uses: astral-sh/ruff-action@v3
       with:
-        python-version: 3.x
-    - run: pip install --upgrade pip
-    - run: pip install "black<24" mypy==v1.3
-    - run: black --diff --check $(git ls-files '*.py')
-    - run: MYPYPATH=mygfa mypy --no-namespace-packages --disallow-untyped-defs mygfa slow_odgi pollen_data_gen
+        args: "format --check --diff"
+        src: >-
+          mygfa
+          slow_odgi
+          pollen_data_gen
+          flatgfa-py
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+    - name: mypy
+      run: MYPYPATH=mygfa uv tool run mypy --no-namespace-packages --disallow-untyped-defs mygfa slow_odgi pollen_data_gen
+
+  rust:
+    runs-on: ubuntu-latest
+    name: Rust
+    env:
+      RUSTFLAGS: "-Dwarnings"
+    steps:
+    - uses: actions/checkout@v4
+    - run: rustup toolchain install stable --no-self-update
+    - uses: Swatinem/rust-cache@v2
+    - run: cargo check
+    - run: cargo clippy
+    - run: cargo fmt --check

.gitignore

@@ -18,8 +18,7 @@ __pycache__/
 og_to_gfa.py
 compute_maxes.py
 
-flatgfa/target
-flatgfa-py/target
+target/
 pollen/*.rlib
 
 slow_odgi/dist/