From d630a5cad0557ea2ed49b1bd6e2dc23e26fa3571 Mon Sep 17 00:00:00 2001
From: Nels Schimek <nlsschim@uw.edu>
Date: Thu, 18 Apr 2024 17:33:42 -0700
Subject: [PATCH] code coverage

---
 .github/workflows/python-package.yml | 35 +++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 524134c..27295d3 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,12 +30,31 @@ jobs:
         python -m pip install flake8 pytest
         pip install -e .
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     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: Lint with flake8
       run: |
-        pytest
+         # stop the build if there are Python syntax errors or undefined names
+         #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 and coverage
+      run: |
+        coverage run -m pytest
+        coverage report -m
+        coverage report -m --fail-under=50 --skip-covered
+        COVERAGE_PERCENT=$(coverage report -m --skip-covered | awk '/TOTAL/ { print $4 }' | sed 's/%$//' | awk '{ printf "%d\n", $1 }')
+        echo "COVERAGE_PERCENT=${COVERAGE_PERCENT}" >> $GITHUB_ENV
+
+    - name: Save coverage report as an artifact
+      uses: actions/upload-artifact@v2
+      with:
+        name: coverage-report
+        path: coverage.xml
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4.0.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: Nance-Lab/diff_classifier
+
+
+