From ca96421a35995c183d120da62e550116a7a32331 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Thu, 4 Apr 2024 10:39:09 -0600
Subject: [PATCH] Adding code coverage workflow (#64)

---
 .github/workflows/test_model.yaml             | 26 -----------
 .github/workflows/test_model.yml              | 46 +++++++++++++++++++
 .../{test_pipeline.yaml => test_pipeline.yml} |  2 +-
 .../workflows/{sphinx.yaml => website.yaml}   |  2 +-
 README.md                                     |  7 +--
 5 files changed, 52 insertions(+), 31 deletions(-)
 delete mode 100755 .github/workflows/test_model.yaml
 create mode 100644 .github/workflows/test_model.yml
 rename .github/workflows/{test_pipeline.yaml => test_pipeline.yml} (93%)
 mode change 100755 => 100644
 rename .github/workflows/{sphinx.yaml => website.yaml} (98%)

diff --git a/.github/workflows/test_model.yaml b/.github/workflows/test_model.yaml
deleted file mode 100755
index f849b20a..00000000
--- a/.github/workflows/test_model.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: installation and testing 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: run tests
-        run: poetry run -C model pytest model
diff --git a/.github/workflows/test_model.yml b/.github/workflows/test_model.yml
new file mode 100644
index 00000000..b735a3d4
--- /dev/null
+++ b/.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
diff --git a/.github/workflows/test_pipeline.yaml b/.github/workflows/test_pipeline.yml
old mode 100755
new mode 100644
similarity index 93%
rename from .github/workflows/test_pipeline.yaml
rename to .github/workflows/test_pipeline.yml
index c195c936..bcd3287c
--- a/.github/workflows/test_pipeline.yaml
+++ b/.github/workflows/test_pipeline.yml
@@ -1,4 +1,4 @@
-name: installation and testing pipeline
+name: pipeline
 
 on:
   pull_request:
diff --git a/.github/workflows/sphinx.yaml b/.github/workflows/website.yaml
similarity index 98%
rename from .github/workflows/sphinx.yaml
rename to .github/workflows/website.yaml
index c5f16946..d6bdc36a 100644
--- a/.github/workflows/sphinx.yaml
+++ b/.github/workflows/website.yaml
@@ -1,4 +1,4 @@
-name: "Sphinx: Render docs"
+name: website
 
 on:
   push:
diff --git a/README.md b/README.md
index 0be64ea3..ff18b029 100755
--- a/README.md
+++ b/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.