From 6bc47dfbf9b4525b58c7acceaf83942177a9b316 Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Mon, 12 May 2025 13:26:23 +0100
Subject: [PATCH 1/6] Add basic pytest infrastructure

---
 pyproject.toml            |  6 ++++++
 tests/test_placeholder.py | 21 +++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 tests/test_placeholder.py

diff --git a/pyproject.toml b/pyproject.toml
index 5c5957f..3c8646a 100644
--- a/pyproject.toml
+++ b/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"
diff --git a/tests/test_placeholder.py b/tests/test_placeholder.py
new file mode 100644
index 0000000..9f1e034
--- /dev/null
+++ b/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

From d277ec6da90770db085a97e781a7074274d54ace Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Mon, 12 May 2025 14:20:54 +0100
Subject: [PATCH 2/6] Add workflow to run tests using github actions

---
 .github/workflows/testing.yaml | 36 ++++++++++++++++++++++++++++++++++
 .gitignore                     |  4 +++-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/testing.yaml

diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
new file mode 100644
index 0000000..024b2d5
--- /dev/null
+++ b/.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
diff --git a/.gitignore b/.gitignore
index be2c700..6a58192 100644
--- a/.gitignore
+++ b/.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/
\ No newline at end of file
+DEMENTpy_notebooks/

From e0d6092439ddb3f4a7b85665cd0ae148264eaeca Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Mon, 19 May 2025 15:13:44 +0100
Subject: [PATCH 3/6] Fix testing workflow

---
 .github/workflows/testing.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
index 024b2d5..e8935bf 100644
--- a/.github/workflows/testing.yaml
+++ b/.github/workflows/testing.yaml
@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.10, 3.11, 3.12]
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4

From 8620f424583742dd02b2afb16d6a36870ea8184c Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Mon, 19 May 2025 15:50:27 +0100
Subject: [PATCH 4/6] Added test for the initialize_data function

---
 tests/conftest.py            |  5 +++++
 tests/test_initialization.py | 14 ++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 tests/conftest.py
 create mode 100644 tests/test_initialization.py

diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..5c86ec6
--- /dev/null
+++ b/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')))
diff --git a/tests/test_initialization.py b/tests/test_initialization.py
new file mode 100644
index 0000000..b05d95e
--- /dev/null
+++ b/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)

From 4885fa4490ca9651c40a8872184ef5bcb3258765 Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Tue, 20 May 2025 09:14:24 +0100
Subject: [PATCH 5/6] Added simple tests for the Grid class

---
 tests/test_grid.py | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 tests/test_grid.py

diff --git a/tests/test_grid.py b/tests/test_grid.py
new file mode 100644
index 0000000..b3cf6be
--- /dev/null
+++ b/tests/test_grid.py
@@ -0,0 +1,46 @@
+"""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.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)

From ffd60716870d721abeebd8906a26fda9b521f927 Mon Sep 17 00:00:00 2001
From: Sam Avis <avissam96@gmail.com>
Date: Tue, 20 May 2025 09:41:37 +0100
Subject: [PATCH 6/6] Fix Grid.uptake test by making sure variables are
 initialized

---
 tests/test_grid.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_grid.py b/tests/test_grid.py
index b3cf6be..ae0b128 100644
--- a/tests/test_grid.py
+++ b/tests/test_grid.py
@@ -28,6 +28,7 @@ def test_degradation_runs(grid):
 
 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)