Rt notebook example

.coveragerc

@@ -2,6 +2,7 @@
 source = pints
 omit =
     pints/tests/*
+    pints/functionaltests/*
 
 [report]
 exclude_lines =

.github/workflows/change-point-tests.yml

@@ -0,0 +1,58 @@
+name: Change-point testing
+
+on:
+  push:
+    branches:
+      - issue-1294-functional-testing-module
+
+jobs:
+
+  run-functional-testing:
+    name: Change-point testing
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out PINTS repository
+        uses: actions/checkout@v2
+        with:
+          path: 'pints'
+
+      - name: Check out functional-testing-2 repository
+        uses: actions/checkout@v2
+        with:
+          repository: 'pints-team/functional-testing-2'
+          ref: 'new-infra'
+          path: 'functional-testing-2'
+          token: ${{ secrets.FUNCTIONAL_TESTING_TOKEN }}
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+          architecture: x64
+
+      - name: install pints
+        run: |
+          python --version
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install .
+        working-directory: 'pints'
+
+      - name: install functional-testing-2
+        run: |
+          python -m pip install .
+        working-directory: 'functional-testing-2'
+
+      - name: run change-point testing
+        run: |
+          python run_all_the_things.py
+        working-directory: 'functional-testing-2'
+
+      - name: commit changes
+        run: |
+          git config user.name "github-workflow"
+          git config user.email "github-workflow"
+          git add --all
+          git commit -m "Run of change-point testing" || echo "No changes to commit"
+          git push
+        working-directory: 'functional-testing-2'

examples/README.md

@@ -119,6 +119,7 @@ relevant code.
 - [Logistic growth model](./toy/model-logistic.ipynb)
 - [Lotka-Volterra predator-prey model](./toy/model-lotka-volterra.ipynb)
 - [Repressilator model](./toy/model-repressilator.ipynb)
+- [Rt estimation Renewal Equation model](./toy/model-rt-estimation-renewal-equation.ipynb)
 - [Simple Harmonic Oscillator model](./toy/model-simple-harmonic-oscillator.ipynb)
 - [SIR Epidemiology model](./toy/model-sir.ipynb)
 

examples/toy/negbin_rt.csv

@@ -0,0 +1,101 @@
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examples/toy/pois_rt.csv

@@ -0,0 +1,101 @@
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