From a9d3e69f092858bc0a397dae23cfd83d3aa963f4 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 1 Jul 2024 11:55:58 +0200
Subject: [PATCH] Adding code coverage (#1)

---
 .github/workflows/python-package.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index ba59677..9c5f7f4 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -34,7 +34,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |
@@ -45,6 +45,11 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+    - name: Test with pytest and coverage
       run: |
-        pytest
+        pytest --cov=pCRscore
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: ./coverage/reports/