Dockerfile

.github/workflows/tests.yml

@@ -29,11 +29,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev]
+        pip install -e .[dev]
 
     - name: Run tests with coverage
       run: |
-        pytest --cov=pyphenopop --cov-report xml:coverage.xml
+        pytest --cov=./ --cov-report xml:coverage.xml
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4

README.md

@@ -2,7 +2,7 @@ Mixed Cell Population Identification Package
 =======================
 [![PyPI version](https://badge.fury.io/py/pyphenopop.svg)](https://badge.fury.io/py/pyphenopop)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7323577.svg)](https://doi.org/10.5281/zenodo.7323577)
-
+[![codecov](https://codecov.io/gh/ocbe-uio/pyPhenoPop/graph/badge.svg?token=fihRjmYkMy)](https://codecov.io/gh/ocbe-uio/pyPhenoPop)
 
 
 This package contains methods designed to determine the existance of

docker/Dockerfile

@@ -0,0 +1,17 @@
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Europe/Berlin
+
+RUN apt-get update \
+    && apt-get install -y \
+    git \
+    python-is-python3 \
+    python3 \
+    python3-dev \
+    python3-pip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install --no-cache-dir -U --upgrade pip wheel \
+    && pip3 install --no-cache-dir pyphenopop

docker/README.md

@@ -0,0 +1,7 @@
+# AMICI & pyPESTO with Docker
+
+## Create image
+
+```bash
+cd <path to pyphenopop base directory>/docker && docker build -t $USER/pyphenopop:latest .
+```

pyproject.toml

@@ -8,4 +8,4 @@ build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]
 testpaths = "tests"
-addopts = "--cov=pyphenopop --cov-report=xml"
+addopts = "--cov=./ --cov-report=xml"

setup.cfg

@@ -27,7 +27,7 @@ classifiers=
 install_requires =
     matplotlib == 3.5.3
     scipy >= 1.9.3
-    numpy >= 1.23.4
+    numpy >= 1.23.4, < 2.0
     pandas >= 1.5.1
     tqdm >= 4.64.1
 

tests/test_plotting.py

@@ -0,0 +1,140 @@
+import unittest
+from unittest.mock import patch
+from pyphenopop.plotting import plot_neg_llh, plot_bic, plot_aic, plot_gr50, plot_gr50_subplot
+
+import matplotlib.pyplot as plt
+
+
+class TestPlotting(unittest.TestCase):
+
+    def setUp(self):
+        self.results_dict = {
+            'summary': {
+                'estimated_num_populations': 3,
+                'final_parameters': [0.3, 0.5, 0.2]
+            },
+            '3_subpopulations': {
+                'gr50': [0.1, 1.0, 10.0]
+            }
+        }
+        self.results_list = [self.results_dict, self.results_dict]
+        self.concentrations = [0.01, 0.1, 1.0, 10.0, 100.0]
+        self.subpopulation_indices = [3, 3]
+
+    @patch('pyphenopop.plotting.plt.show')
+    def test_plot_neg_llh(self, mock_show):
+        # Mock data
+        results = {
+            '1_subpopulations': {'fval': [10, 12, 11, 13, 14]},
+            '2_subpopulations': {'fval': [8, 9, 7, 10, 6]},
+            '3_subpopulations': {'fval': [6, 5, 7, 8, 4]},
+            '4_subpopulations': {'fval': [4, 3, 5, 2, 1]},
+            'summary': {'estimated_num_populations': 4,
+                        'final_neg_llh': 1,
+                        'best_optimization_idx': 4}
+        }
+
+        # Call the function
+        fig = plot_neg_llh(results)
+
+        # Check if the figure is created
+        self.assertIsInstance(fig, plt.Figure)
+
+        # Check if the plot has the correct number of points
+        ax = fig.gca()
+        self.assertEqual(len(ax.lines[0].get_xdata()), len(results) - 1)
+        self.assertEqual(len(ax.lines[0].get_ydata()), len(results) - 1)
+
+        # Check if the y-data matches the expected negative log-likelihood values
+        expected_nllhs = [10, 6, 4, 1]
+        self.assertListEqual(list(ax.lines[0].get_ydata()), expected_nllhs)
+
+        # Check labels
+        self.assertEqual(ax.get_ylabel(), 'Negative log-likelihood')
+        self.assertEqual(ax.get_xlabel(), 'Number of inferred populations')
+
+    @patch('pyphenopop.plotting.plt.show')
+    def test_plot_bic(self, mock_show):
+        # Mock data
+        results = {
+            '1_subpopulations': {'BIC': 100},
+            '2_subpopulations': {'BIC': 80},
+            '3_subpopulations': {'BIC': 60},
+            '4_subpopulations': {'BIC': 40},
+            'summary': {'estimated_num_populations': 4,
+                        'final_neg_llh': 1,
+                        'best_optimization_idx': 4}
+        }
+
+        # Call the function
+        fig = plot_bic(results)
+
+        # Check if the figure is created
+        self.assertIsInstance(fig, plt.Figure)
+
+        # Check if the plot has the correct number of points
+        ax = fig.gca()
+        self.assertEqual(len(ax.lines[0].get_xdata()), len(results) - 1)
+        self.assertEqual(len(ax.lines[0].get_ydata()), len(results) - 1)
+
+        # Check if the y-data matches the expected BIC values
+        expected_bic = [100, 80, 60, 40]
+        self.assertListEqual(list(ax.lines[0].get_ydata()), expected_bic)
+
+        # Check labels
+        self.assertEqual(ax.get_ylabel(), 'BIC')
+        self.assertEqual(ax.get_xlabel(), 'Number of inferred populations')
+
+    @patch('pyphenopop.plotting.plt.show')
+    def test_plot_aic(self, mock_show):
+        # Mock data
+        results = {
+            '1_subpopulations': {'AIC': 90},
+            '2_subpopulations': {'AIC': 70},
+            '3_subpopulations': {'AIC': 50},
+            '4_subpopulations': {'AIC': 30},
+            'summary': {'estimated_num_populations': 4,
+                        'final_neg_llh': 1,
+                        'best_optimization_idx': 4}
+        }
+
+        # Call the function
+        fig = plot_aic(results)
+
+        # Check if the figure is created
+        self.assertIsInstance(fig, plt.Figure)
+
+        # Check if the plot has the correct number of points
+        ax = fig.gca()
+        self.assertEqual(len(ax.lines[0].get_xdata()), len(results) - 1)
+        self.assertEqual(len(ax.lines[0].get_ydata()), len(results) - 1)
+
+        # Check if the y-data matches the expected AIC values
+        expected_aic = [90, 70, 50, 30]
+        self.assertListEqual(list(ax.lines[0].get_ydata()), expected_aic)
+
+        # Check labels
+        self.assertEqual(ax.get_ylabel(), 'AIC')
+        self.assertEqual(ax.get_xlabel(), 'Number of inferred populations')
+
+    def test_plot_gr50_with_dict(self):
+        fig = plot_gr50(self.results_dict, self.concentrations, 'best')
+        self.assertIsInstance(fig, plt.Figure)
+
+    def test_plot_gr50_with_invalid_results(self):
+        with self.assertRaises(TypeError):
+            plot_gr50("invalid_results", self.concentrations, 'best')
+
+    def test_plot_gr50_with_mismatched_lengths(self):
+        with self.assertRaises(Exception):
+            plot_gr50(self.results_list, self.concentrations, [3])
+
+    def test_plot_gr50_subplot(self):
+        fig, (ax1, ax2) = plt.subplots(1, 2, gridspec_kw={'width_ratios': [1, 3]})
+        plot_gr50_subplot(ax1, ax2, self.results_dict, self.concentrations, 'best')
+        self.assertTrue(len(ax1.patches) > 0)  # Check if pie chart is plotted
+        self.assertTrue(len(ax2.lines) > 0)    # Check if GR50 lines are plotted
+
+
+if __name__ == '__main__':
+    unittest.main()