Adding code coverage workflow (#64)

.github/workflows/test_model.yml

@@ -0,0 +1,46 @@
+name: model
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+      - name: install poetry
+        run: pip install poetry
+
+      - name: install package
+        run: poetry install -C model
+
+      - name: install pytest-cov
+        run: poetry run -C model pip install pytest-cov
+
+      - name: run tests
+        run: |
+          poetry run -C model pytest \
+            --cov=pyrenew --cov-report term --cov-report xml model
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          flags: unittests
+          file: coverage.xml
+          plugin: pycoverage
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.github/workflows/test_pipeline.yaml → .github/workflows/test_pipeline.yml

@@ -1,4 +1,4 @@
-name: installation and testing pipeline
+name: pipeline
 
 on:
   pull_request:

.github/workflows/sphinx.yaml → .github/workflows/website.yaml

@@ -1,4 +1,4 @@
-name: "Sphinx: Render docs"
+name: website
 
 on:
   push:

README.md

@@ -3,9 +3,10 @@
 ⚠️ This is a work in progress ⚠️
 
 [![Pre-commit](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit.yaml)
-[![installation and testing model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_model.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_model.yaml)
-[![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_pipeline.yaml)
-[![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/sphinx.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/sphinx.yaml)
+[![installation and testing model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/model.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/model.yaml)
+[![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml)
+[![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml)
+[![codecov (model)](https://codecov.io/gh/CDCgov/multisignal-epi-inference/graph/badge.svg?token=7Z06HOMYR1)](https://codecov.io/gh/CDCgov/multisignal-epi-inference)
 
 This repo hosts the multisignal (*a.k.a.* signal fusion) renewal project: an internal forecasting model that leverages multiple data sources for enhancing epidemiological modeling of infectious disease outbreaks.