add github actions

Author: RGB43

.github/workflows/main.yml

@@ -0,0 +1,34 @@
+name: CI
+
+# We can specify which Github events will trigger a CI build
+on: push
+
+# now define a single job 'build' (but could define more)
+jobs:
+
+  build:
+
+    # we can also specify the OS to run tests on
+    runs-on: ubuntu-latest
+
+    # a job is a seq of steps
+    steps:
+
+    # Next we need to checkout out repository, and set up Python
+    # A 'name' is just an optional label shown in the log - helpful to clarify progress - and can be anything
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install Python dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        python3 -m pip install -r requirements.txt
+
+    - name: Test with PyTest
+      run: |
+        python3 -m pytest --cov=inflammation.models tests/test_models.py

requirements.txt

@@ -1,6 +1,7 @@
 astroid==3.3.5
 colorama==0.4.6
 contourpy==1.3.1
+coverage==7.6.8
 cycler==0.12.1
 dill==0.3.9
 fonttools==4.55.0
@@ -17,6 +18,7 @@ pluggy==1.5.0
 pylint==3.3.1
 pyparsing==3.2.0
 pytest==8.3.3
+pytest-cov==6.0.0
 python-dateutil==2.9.0.post0
 six==1.16.0
 tomlkit==0.13.2

tests/test_models.py

@@ -2,10 +2,22 @@
 
 import numpy as np
 import numpy.testing as npt
+import pytest
 
-from inflammation.models import daily_mean
+from inflammation.models import daily_mean, daily_max, daily_min
 
-def test_daily_mean_zeros():
+@pytest.mark.parametrize(
+    "test, expected",
+    [
+        ([[0,0],[0,0],[0,0]],[0,0]),
+        ([[0, 0],[0, 0],[0, 0]], [0, 0]),
+        ([[-1, -1],[-1, -1],[-1, -1]],[-1, -1]),
+        ([[1, 2],[3, 4],[5, 6]],[3, 4]),
+        ([[1, 2],[3, 4],[5, 6]], [6, 7])
+    ]
+)
+#not sure why pytest seems to be required here. error says it should be test but doesn't seem to work
+def pytest_daily_mean_zeros():
     """Test that mean function works for an array of zeros."""
 
     test_input = np.array([[0, 0],
@@ -46,3 +58,34 @@ def test_daily_mean():
     test_result = np.array([3, 4])
 
     npt.assert_array_equal(daily_mean(test_input), test_result)
+"""
+def test_daily_mean_string():
+    test_input = np.array([["this is something incorrect", 2],
+                           [3, 4],
+                           [5, 6]])
+    test_result = np.array([3, 4])
+
+    npt.assert_array_equal(daily_mean(test_input), test_result)
+"""
+
+
+"""
+def test_daily_min_string():
+    #test for typeerror when passing strings
+
+    #with pytest.raises(TypeError):
+     #   error_expected = daily_min([["one", "two"],["3","4"]])
+"""
+
+
+"""Tests for the Patient model - class/file in this folder
+
+from inflammation.models import Patient
+
+def test_create_patient():
+
+    name = 'Alice'
+    p = Patient(name=name)
+
+    assert p.name == name
+"""