fixed unit tests

.github/workflows/python-package.yml

@@ -10,30 +10,24 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
-
+  uv-example:
+    name: python
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.6, 3.7, 3.8]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        # For example, using `pytest`
+        run: uv run pytest tests

README.md

@@ -14,6 +14,7 @@ Simple SIR simulation
 
 ```python
 from epimodels.continuous.models import SIR
+
 model = SIR()
 model([1000, 1, 0], [0, 50], 1001, {'beta': 2, 'gamma': .1})
 model.plot_traces()

docs/Examples/Continuous_models.ipynb

@@ -17,7 +17,8 @@
    },
    "outputs": [],
    "source": [
-    "import epimodels.continuous.models as CM"
+    "\n",
+    "import epimodels as CM"
    ]
   },
   {

src/epimodels/discrete/__init__.py → epimodels/continuous/__init__.py

@@ -1,6 +1,6 @@
-u"""
+"""
 Created on 29/10/18
 by fccoelho
 license: GPL V3 or Later
 """
-
+from .models import *

src/epimodels/continuous/__init__.py → epimodels/discrete/__init__.py

@@ -3,4 +3,5 @@
 by fccoelho
 license: GPL V3 or Later
 """
+from .models import *
 

pyproject.toml

@@ -24,10 +24,12 @@ dependencies = [
     "sphinx>=8.1.3",
     "sympy>=1.13.3",
 ]
+packages = ["epimodels"]
+
 [project.urls]
 Homepage = "https://github.com/fccoelho/epimodels"
 Documentation = "https://epimodels.readthedocs.io"
-#packages = [{ include = "epimodels" }]
+
 
 [tool.uv]
 dev-dependencies = [

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+pythonpath = .

tests/test_base.py

@@ -1,4 +1,6 @@
 import unittest
+import sys
+sys.path.append('..')
 from epimodels.continuous import models as cm
 from epimodels.discrete import models as dm
 

tests/test_continuous_models.py

@@ -1,10 +1,8 @@
 __author__ = 'fccoelho'
-
-import unittest
-import pytest
+import sys
+sys.path.append('..')
 from matplotlib import pyplot as P
-
-from epimodels.continuous.models import *
+from epimodels.continuous import (SIS, SIR, SIR1D, SIRS, SEIR, SEQIAHR)
 
 
 def test_SIR():
@@ -13,7 +11,7 @@ def test_SIR():
     assert len(model.traces) == 4
     # assert len(model.traces['time']) == 50
     model.plot_traces()
-    P.show()
+    # P.show()
 
 def test_SIR_with_t_eval():
     model = SIR()
@@ -27,15 +25,15 @@ def test_SIR1D():
     # assert len(model.traces['R']) == 500
     assert len(model.traces) == 2
     model.plot_traces()
-    P.show()
+    # P.show()
 
 def test_SIS():
     model = SIS()
     model([1000, 1], [0, 50], 1001, {'beta': 2, 'gamma': .1})
     assert len(model.traces) == 3
     # assert len(model.traces['time']) == 50
     model.plot_traces()
-    P.show()
+    # P.show()
 
 
 def test_SIRS():
@@ -44,7 +42,7 @@ def test_SIRS():
     assert len(model.traces) == 4
     # assert len(model.traces['time']) == 50
     model.plot_traces()
-    P.show()
+    # P.show()
 
 
 def test_SEIR():
@@ -54,7 +52,7 @@ def test_SEIR():
     assert len(model.traces) == 5  # state variables plus time
     # assert len(model.traces['time']) == 50
     model.plot_traces()
-    P.show()
+    # P.show()
 
 
 def test_SEQIAHR():
@@ -68,7 +66,7 @@ def test_SEQIAHR():
     assert len(model.traces) == 9  # state variables plus time
     # assert len(model.traces['time']) == 50
     model.plot_traces()
-    P.show()
+    # P.show()
 
 # def test_SIS_with_cache():
 #     model = SIS()

tests/test_discrete_models.py

@@ -1,9 +1,10 @@
 __author__ = 'fccoelho'
 
-import pytest
 # import pyximport; pyximport.install(pyimport=True)
-from epimodels.discrete.models import (DiscreteModel, Influenza, SIS, SIR, SEIS, SEIR,
-                                       SIpRpS, SEIpRpS, SIpR, SEIpR, SIRS, SEQIAHR)
+import sys
+sys.path.append('..')
+from epimodels.discrete import (DiscreteModel, Influenza, SIS, SIR, SEIS, SEIR,
+                                SIpRpS, SEIpRpS, SIpR, SEIpR, SIRS, SEQIAHR)
 from matplotlib import pyplot as P
 
 
@@ -13,7 +14,7 @@ def test_SIS():
     assert len(modelsis.traces) == 3
     assert len(modelsis.traces['time']) == 50
     modelsis.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelsis, DiscreteModel)
 
 
@@ -23,7 +24,7 @@ def test_SIR():
     assert len(modelsir.traces) == 4
     assert len(modelsir.traces['time']) == 500
     modelsir.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelsir, DiscreteModel)
 
 
@@ -52,7 +53,7 @@ def test_FLU():
     assert len(modelflu.traces['time']) == 50
     print(list(modelflu.traces.keys()))
     modelflu.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelflu, DiscreteModel)
 
 
@@ -62,7 +63,7 @@ def test_SEIS():
     assert len(modelseis.traces) == 4
     assert len(modelseis.traces['time']) == 50
     modelseis.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelseis, DiscreteModel)
 
 
@@ -73,7 +74,7 @@ def test_SEIR():
     assert len(modelseir.traces) == 5
     assert len(modelseir.traces['time']) == tsteps[1]
     modelseir.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelseir, DiscreteModel)
 
 
@@ -84,7 +85,7 @@ def test_SIpRpS():
     assert len(modelsiprps.traces) == 4
     assert len(modelsiprps.traces['time']) == tsteps[1]
     modelsiprps.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelsiprps, DiscreteModel)
 
 
@@ -95,7 +96,7 @@ def test_SEIpRpS():
     assert len(modelseiprps.traces) == 5
     assert len(modelseiprps.traces['time']) == tsteps[1]
     modelseiprps.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelseiprps, DiscreteModel)
 
 
@@ -105,7 +106,7 @@ def test_SIpR():
     assert len(modelsipr.traces) == 4
     assert len(modelsipr.traces['time']) == 50
     modelsipr.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelsipr, DiscreteModel)
 
 def test_SEIpR():
@@ -115,7 +116,7 @@ def test_SEIpR():
     assert len(modelseipr.traces) == 5
     assert len(modelseipr.traces['time']) == tsteps[1]
     modelseipr.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelseipr, DiscreteModel)
 
 def test_SIRS():
@@ -124,7 +125,7 @@ def test_SIRS():
     assert len(modelsirs.traces) == 4
     assert len(modelsirs.traces['time']) == 50
     modelsirs.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(modelsirs, DiscreteModel)
 
 def test_SEQIAHR():
@@ -135,5 +136,5 @@ def test_SEQIAHR():
                                                     })
     assert len(model.traces) == 9
     model.plot_traces()
-    P.show()
+    # P.show()
     assert isinstance(model, DiscreteModel)