Age-region sampling enabled and other modifies

.coveragerc

@@ -1,7 +1,7 @@
 [run]
-source = sampling
+source = epios
 omit =
-    sampling/tests/*
-    sampling/version_info.py
-    sampling/__init__.py
-    sampling/run_tests.py
+    epios/tests/*
+    epios/version_info.py
+    epios/__init__.py
+    epios/run_tests.py

.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

age_region.ipynb

@@ -0,0 +1,171 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "import os\n",
+    "from pathlib import Path\n",
+    "sys.path.append(str(Path.cwd().parent))\n",
+    "import epios\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a = epios.Sampler('./input/Luxembourg_microcells.csv', './input/Luxembourg_pop_dist.json', './input/Luxembourg_data.csv')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "res = a.sample(10000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "age_dist = a.get_age_dist()\n",
+    "region_dist = a.get_region_dist()\n",
+    "ar_dist = np.array(age_dist) * np.array(region_dist).reshape((-1, 1))\n",
+    "ar_dist = ar_dist.reshape((1, -1))[0]\n",
+    "size = 1000\n",
+    "num_sample, cap = a.multinomial_draw(size, ar_dist)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "b = np.array(num_sample).reshape((-1, len(age_dist))) > cap\n",
+    "sum(b)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "10000"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(res)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "b = np.sum(np.array(num_sample).reshape((-1, len(age_dist))), axis=1) > np.array(cap).reshape((1, -1))[0]\n",
+    "sum(b)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# df = pd.read_csv('./input/Luxembourg_microcells.csv')\n",
+    "# with open('./input/Luxembourg_pop_dist.json', 'r') as f:\n",
+    "#     config = json.loads(f.read())\n",
+    "# id_counter = 0\n",
+    "# for ind, row in df.iterrows():\n",
+    "#     household = 1\n",
+    "#     for i in range(int(row['Susceptible'])):\n",
+    "#         draw = list(np.random.multinomial(1, config))\n",
+    "#         index = draw.index(max(draw))\n",
+    "#         age = index * 5 + np.random.randint(0, 4)\n",
+    "#         text = '\\n' + str(id_counter) + ',' + str(age) + ',' + str(int(row['cell'])) + ',' + str(int(row['microcell'])) + ',' + str(household)\n",
+    "#         household = min(household + 1, int(row['household_number']))\n",
+    "#         id_counter += 1\n",
+    "#         with open('./input/data.csv', 'a') as f:\n",
+    "#             f.write(text)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import epios\n",
+    "# import pandas as pd\n",
+    "# a = pd.DataFrame({'ID': ['0.0.0.0','0.1.0.0','1.0.0.0','0.2.0.0','0.0.0.1','0.0.1.0'], 'age': [1, 81, 45, 33, 20, 60]})\n",
+    "# pro = epios.DataProcess(a)\n",
+    "# pro.pre_process()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

epios/__init__.py

@@ -0,0 +1,3 @@
+from .age_region import Sampler # noqa
+from .non_responders import NonResponder # noqa
+from .data_process import DataProcess # noqa