Workflow enabled

.github/workflows/coverage.yml

@@ -0,0 +1,40 @@
+name: Coverage
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install .[dev]
+        python -m pip install coverage codecov
+
+    - name: Run coverage
+      run: |
+        coverage run epios/run_tests.py --unit
+
+    - name: Upload coverage reports to Codecov
+      if: success()
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        files: coverage.xml
+      run: |
+        codecov

.github/workflows/os_versions.yml

@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of operating systems
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Operating systems
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python --version
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install .[dev]
+    - name: Run unit tests
+      run: |
+        python epios/run_tests.py --unit

.github/workflows/python_versions.yml

@@ -0,0 +1,35 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install .[dev]
+    - name: Run unit tests
+      run: |
+        python epios/run_tests.py --unit
+

.github/workflows/style.yml

@@ -0,0 +1,31 @@
+name: Style tests (flake8)
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+  workflow_dispatch:
+
+jobs:
+
+  build-and-test:
+    name: style test
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install .[dev]
+      - name: Run style tests
+        run: |
+          python -m flake8 --max-line-length=120

epios/tests/test_age_region.py

@@ -25,9 +25,6 @@ def setUp(self) -> None:
 
         self.expected_age_dist = [1 / 6, 0.0, 0.0, 0.0, 1 / 6, 0.0, 1 / 6, 0.0, 0.0, 1 / 6, 0.0, 0.0, 1 / 6, 0.0, 0.0, 0.0, 1 / 6]
         self.expected_region_dist = [5 / 6, 1 / 6]
-        # self.expected_json = [1 / 6, 0.0, 0.0, 0.0, 1 / 6, 0.0, 1 / 6, 0.0, 0.0, 1 / 6, 0.0, 0.0, 1 / 6, 0.0, 0.0, 0.0, 1 / 6]
-        # self.expected_df_microcell = pd.DataFrame({'cell': [0, 0, 0, 0, 1], 'microcell': [0, 0, 1, 2, 0], 'household': [0, 1, 0, 0, 0], 'Susceptible': [2, 1, 1, 1, 1]})
-        # self.expected_df_population = pd.DataFrame({'ID': ['0.0.0.0', '0.0.0.1', '0.0.1.0', '0.1.0.0', '0.2.0.0', '1.0.0.0'], 'age': [1, 81, 45, 33, 20, 60], 'cell': [0, 0, 0, 0, 0, 1], 'microcell': [0, 0, 0, 1, 2, 0], 'household': [0, 0, 1, 0, 0, 0]})
 
     def test_get_age_dist(self):
         self.assertEqual(self.sampler.get_age_dist(), self.expected_age_dist)