Update pSA calculation

.github/workflows/lint.yml

@@ -0,0 +1,77 @@
+name: Lint
+on: [pull_request]
+
+env:
+  RUSTFLAGS: "-Dwarnings"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: chartboost/ruff-action@v1
+
+  clippy_check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Run Clippy
+        run: cargo clippy --all-targets --all-features
+
+  typecheck:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install project with types
+        run: uv sync --all-extras --dev
+
+      - name: Run type checking with ty
+        run: uv run ty check
+
+  dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      # Install uv
+      - uses: astral-sh/setup-uv@v4
+      # Install project
+      - run: uv sync --dev --all-extras
+      # Run deptry to check that all dependencies are present.
+      - run: uv run deptry . -ddg test,dev,types
+
+  numpydoc:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: fd-find
+          version: 1.0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.13"
+
+      - name: Install dependencies
+        run: |
+          pip install numpydoc
+
+      - name: Run Numpydoc Lint
+        run: |
+          fdfind . IM/ -E "__init__.py" --extension py | xargs numpydoc lint

.github/workflows/pytest.yml → .github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Pytest Check
+name: Tests
 
 on: [pull_request]
 
@@ -8,20 +8,19 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e ".[test]"
+          python-version: 3.13
+      - uses: astral-sh/setup-uv@v4
+      # Install project
+      - run: uv sync --dev --all-extras
 
       - name: Run tests
         run: |
-          pytest --cov=IM --cov-report=html tests
+          uv run pytest --cov=IM --cov-report=html tests
 
       - name: Upload coverage data
         uses: actions/upload-artifact@v4
@@ -37,12 +36,12 @@ jobs:
 
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.13
 
       - name: Install dependencies
         run: |
@@ -71,3 +70,10 @@ jobs:
           path: htmlcov
 
         if: ${{ failure() }}
+
+  cargo_test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Run cargo test
+        run: cargo test