Codecov integrated (#63)

NEW: Codecov integrated

UPDATED: Additional JS files added to ‘.gitignore’
UPDATED: Python version of the Lint step changed to Python 3.12

.github/workflows/test-build-and-publish.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: "3.12"
       - name: Install dependencies
         run: python -m pip install tox
       - name: Linter
@@ -117,6 +117,12 @@ jobs:
       - name: Run test suite
         run: tox --skip-pkg-install
 
+      - name: Upload coverage reports to Codecov
+        if: ${{ ( matrix.python-version == '3.12' ) && ( runner.os == 'Linux' ) }}
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
   publish-to-pypi:
     needs: [unittest]
     name: >-

.gitignore

@@ -16,6 +16,11 @@ docs/source/summary.txt
 # node_modules
 node_modules/
 
+# JS Build Files
+src/cobramod/static/escher.mjs
+src/cobramod/static/force_graph.mjs
+src/cobramod/static/LICENSES.txt
+
 # ui test results
 ui-tests/playwright-report
 ui-tests/test-results

README.md

@@ -8,7 +8,7 @@
 ![Version](https://img.shields.io/pypi/v/cobramod?label=version)
 ![Read the Docs (version)](https://img.shields.io/readthedocs/cobramod/latest)
 ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Toepfer-lab/cobramod/test-build-and-publish.yml)
-![Coverage Status](./docs/source/img/coverage.svg)
+![Coverage Status](https://img.shields.io/codecov/c/gh/Toepfer-Lab/cobramod)
 
 CobraMod: A pathway-centric curation tool for constraint-based metabolic models
 ===============================================================================

tox.ini

@@ -11,6 +11,14 @@ deps =
     pytest
 commands = pytest {posargs}
 
+[testenv:py312]
+description = "Runs test suite"
+download = true
+deps =
+    pytest
+    pytest-cov
+commands = pytest --cov=cobramod --cov-report xml {posargs}
+
 [testenv:ui]
 description = "Runs ui tests"
 download = true