Test infrastructure

.github/workflows/testing.yaml

@@ -0,0 +1,36 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [ main ]
+
+  # Triggers the workflow on pushes to open pull requests with code changes
+  pull_request:
+    branches: [ main ]
+    paths:
+      - '**.py'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install uv
+          uv sync --dev
+
+      - name: Run tests
+        run: uv run pytest

.gitignore

@@ -1,6 +1,8 @@
 # vscode workspace
 .vscode/
 
+# Python module bytecode
+__pycache__
 
 # Jupyter Notebook
 */.ipynb_checkpoints
@@ -16,4 +18,4 @@ output/
 documentation/DEMENTpy_Documentation.*
 
 # DEMENTpy_notebooks
-DEMENTpy_notebooks/
+DEMENTpy_notebooks/

pyproject.toml

@@ -13,4 +13,10 @@ dependencies = [
 dev = [
     "pre-commit>=4.2.0",
     "ruff>=0.11.4",
+    "pytest>=7.0",
 ]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = "test_*.py"
+addopts = "-v"

tests/conftest.py

@@ -0,0 +1,5 @@
+import sys
+import os
+
+# Add the src/ directory to the pythonpath
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'src')))

tests/test_grid.py

@@ -0,0 +1,47 @@
+"""Tests for the Grid class."""
+
+import pandas as pd
+import pytest
+
+from initialization import initialize_data
+from grid import Grid
+
+
+@pytest.fixture
+def grid():
+    """Initialize a Grid object using the initialize_data function."""
+    input_dir = 'grassland'
+    runtime = pd.read_csv(input_dir+'/runtime.txt', header=None, index_col=0, sep='\t')
+    data = initialize_data(runtime, input_dir)
+    return Grid(runtime, data)
+
+
+def test_initialization_runs(grid):
+    """Test that the initialization of Grid works without an error."""
+    pass
+
+
+def test_degradation_runs(grid):
+    """Test that Grid.degradation works without an error."""
+    grid.degradation(0)
+
+
+def test_uptake_runs(grid):
+    """Test that Grid.uptake works without an error."""
+    grid.degradation(0) # degradation needs to run to initialize some DataFrames
+    grid.uptake(0)
+
+
+def test_metabolism_runs(grid):
+    """Test that Grid.metabolism works without an error."""
+    grid.metabolism(0)
+
+
+def test_mortality_runs(grid):
+    """Test that Grid.mortality works without an error."""
+    grid.mortality(0)
+
+
+def test_reproduction_runs(grid):
+    """Test that Grid.reproduction works without an error."""
+    grid.reproduction(0)

tests/test_initialization.py

@@ -0,0 +1,14 @@
+"""Tests for the initialization of the data."""
+
+import pandas as pd
+import pytest
+
+from initialization import initialize_data
+
+
+def test_initialize_data():
+    """Test that initialize_data works without an error."""
+    input_dir = 'grassland'
+    runtime = pd.read_csv(input_dir+'/runtime.txt', header=None, index_col=0, sep='\t')
+    data = initialize_data(runtime, input_dir)
+    assert isinstance(data, dict)

tests/test_placeholder.py

@@ -0,0 +1,21 @@
+"""Tests to show how to use pytest."""
+
+import numpy as np
+import pytest
+
+
+def test_basic():
+    """Illustrates how to write a simple test."""
+    assert 1 + 1 == 2
+
+
+def test_raises_exception():
+    """Illustrates how to write a test that checks for an exception."""
+    with pytest.raises(ZeroDivisionError):
+        1 / 0
+
+
+@pytest.mark.parametrize("x,y,r", [(3, 4, 5), (-5, -12, 13)])
+def test_multiple_parameters(x, y, r):
+    """Illustrates how to write a test to run with multiple input arguments."""
+    assert np.sqrt(x**2 + y**2) == r