ci: Add GitHub Actions workflow for code quality

.github/workflows/ci.yml

@@ -0,0 +1,37 @@
+name: Python Code Quality
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  code-quality-checks:
+    # Use the latest stable Ubuntu runner
+    runs-on: ubuntu-latest
+
+    steps:
+      # Step 1: Check out the repository's code
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Step 2: Set up a specific Python environment for consistency
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      # Step 3: Install linting and formatting tools
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black ruff
+
+      # Step 4: Check if code is formatted with Black
+      - name: Check formatting with Black
+        run: black --check .
+
+      # Step 5: Run Ruff to find potential errors
+      - name: Lint with Ruff
+        run: ruff check .

notebooks/01_simulation.ipynb

@@ -34,10 +34,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os, sys\n",
+    "import os\n",
+    "import sys\n",
     "sys.path.append(os.path.abspath(\"../src\"))\n",
     "import pandas as pd\n",
-    "import numpy as np\n",
     "import xarray as xr\n",
     "import warnings\n",
     "import matplotlib.pyplot as plt\n",
@@ -1583,7 +1583,7 @@
     "sns.barplot(x=avg_resistance_by_country.values, y=avg_resistance_by_country.index, palette=\"viridis\")\n",
     "plt.xlabel(\"Simulated Resistance Proportion\")\n",
     "plt.ylabel(\"Country\")\n",
-    "plt.title(f\"Simulated Insecticide Resistance by Country\")\n",
+    "plt.title(\"Simulated Insecticide Resistance by Country\")\n",
     "plt.tight_layout()\n",
     "plt.show()"
    ]

notebooks/02_mixed_effects_analysis.ipynb

@@ -32,15 +32,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os, sys\n",
+    "import os\n",
+    "import sys\n",
     "sys.path.append(os.path.abspath(\"../src\"))\n",
-    "import pandas as pd\n",
-    "import numpy as np\n",
     "import xarray as xr\n",
     "import matplotlib.pyplot as plt\n",
     "import seaborn as sns\n",
     "import warnings\n",
-    "from sklearn.metrics import roc_curve, roc_auc_score\n",
+    "from sklearn.metrics import roc_curve\n",
     "\n",
     "# Import our custom classes\n",
     "from data.simulation import ResistanceSimulator\n",