From 075e95bd6ffd1a2bb4728868beb20b9a132bb935 Mon Sep 17 00:00:00 2001
From: Thomas Kiley <thomas.kiley@ukaea.uk>
Date: Thu, 27 Jul 2023 14:24:36 +0100
Subject: [PATCH 1/3] Add implementation of standard deviation on data

---
 inflammation-analysis.py |  3 ++-
 inflammation/models.py   | 10 ++++++++++
 tests/test_models.py     | 13 ++++++++++++-
 3 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/inflammation-analysis.py b/inflammation-analysis.py
index e1564317..4c612feb 100644
--- a/inflammation-analysis.py
+++ b/inflammation-analysis.py
@@ -27,7 +27,8 @@ def main(args):
     for filename in InFiles:
         inflammation_data = models.load_csv(filename)
 
-        view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data)}
+        view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data), **(models.s_dev(inflammation_data))}
+
 
         views.visualize(view_data)
 
diff --git a/inflammation/models.py b/inflammation/models.py
index 94387ee3..89cfd31e 100644
--- a/inflammation/models.py
+++ b/inflammation/models.py
@@ -54,3 +54,13 @@ def daily_min(data):
     """Calculate the daily min of a 2d inflammation data array."""
     return np.min(data, axis=0)
 
+
+def s_dev(data):
+    """Computes and returns standard deviation for data."""
+    mmm = np.mean(data, axis=0)
+    devs = []
+    for entry in data:
+        devs.append((entry - mmm) * (entry - mmm))
+
+    s_dev2 = sum(devs) / len(data)
+    return {'standard deviation': s_dev2}
diff --git a/tests/test_models.py b/tests/test_models.py
index 292d00c4..b8adbfb0 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -3,7 +3,7 @@
 import numpy as np
 import numpy.testing as npt
 import os
-
+import pytest
 
 def test_daily_mean_zeros():
     """Test that mean function works for an array of zeros."""
@@ -37,3 +37,14 @@ def test_load_from_json(tmpdir):
         temp_json_file.write('[{"observations":[1, 2, 3]},{"observations":[4, 5, 6]}]')
     result = load_json(example_path)
     npt.assert_array_equal(result, [[1, 2, 3], [4, 5, 6]])
+
+
+@pytest.mark.parametrize('data, expected_standard_deviation', [
+    ([0, 0, 0], 0.0),
+    ([1.0, 1.0, 1.0], 0),
+    ([0.0, 2.0], 1.0)
+])
+def test_daily_standard_deviation(data, expected_standard_deviation):
+    from inflammation.models import s_dev
+    result_data = s_dev(data)['standard deviation']
+    npt.assert_approx_equal(result_data, expected_standard_deviation)

From 179c581ae14737d9eea9a06cf74c36c082801f5e Mon Sep 17 00:00:00 2001
From: clmould <86794332+clmould@users.noreply.github.com>
Date: Thu, 23 Nov 2023 16:06:14 +0000
Subject: [PATCH 2/3] Update models.py

---
 inflammation/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inflammation/models.py b/inflammation/models.py
index 89cfd31e..bafeafae 100644
--- a/inflammation/models.py
+++ b/inflammation/models.py
@@ -57,7 +57,7 @@ def daily_min(data):
 
 def s_dev(data):
     """Computes and returns standard deviation for data."""
-    mmm = np.mean(data, axis=0)
+    mean_data = daily_mean(data)
     devs = []
     for entry in data:
         devs.append((entry - mmm) * (entry - mmm))

From 23f6700bc67f53eb0a03ef89ac2450584f158e3b Mon Sep 17 00:00:00 2001
From: clmould <86794332+clmould@users.noreply.github.com>
Date: Fri, 24 Nov 2023 13:15:48 +0000
Subject: [PATCH 3/3] Update models.py

---
 inflammation/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inflammation/models.py b/inflammation/models.py
index 6a23e357..6b1318e4 100644
--- a/inflammation/models.py
+++ b/inflammation/models.py
@@ -75,7 +75,7 @@ def s_dev(data):
     mean_data = daily_mean(data)
     devs = []
     for entry in data:
-        devs.append((entry - mmm) * (entry - mmm))
+        devs.append((entry - mean_data) * (entry - mean_data))
 
     s_dev2 = sum(devs) / len(data)
     return {'standard deviation': s_dev2}