Add codecov integration for code coverage tracking

.codecov.yml

@@ -0,0 +1,32 @@
+
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default
+  require_changes: false
+  require_base: no
+  require_head: yes
+
+coverage:
+  status:
+    project:
+      default:
+        # basic
+        target: auto
+        threshold: 1%
+    patch:
+      default:
+        # basic
+        target: auto
+        threshold: 1%
+
+# Separate flags for C++ and Python coverage
+flags:
+  cpp:
+    paths:
+      - volesti/
+    carryforward: true
+  python:
+    paths:
+      - dingo/
+      - tests/
+    carryforward: true

.github/workflows/ubuntu.yml

@@ -46,17 +46,25 @@ jobs:
         source $(poetry env info --path)/bin/activate
         poetry install;
         pip3 install numpy scipy;
-    - name: Run tests
+        pip3 install pytest pytest-cov codecov;
+    - name: Run tests with coverage
       run: |
-        poetry run python3 tests/fba.py;
-        poetry run python3 tests/full_dimensional.py;
-        poetry run python3 tests/max_ball.py;
-        poetry run python3 tests/scaling.py;
-        poetry run python3 tests/sampling.py;
-        poetry run python3 tests/sampling_no_multiphase.py;
-        # currently we do not test with gurobi
-        # python3 tests/fast_implementation_test.py;
-
-        #run all tests
-        #python -m unittest discover test
-        #TODO: use pytest
+        # Legacy way - keep for compatibility
+        poetry run python3 tests/test_fba.py;
+        poetry run python3 tests/test_full_dimensional.py;
+        poetry run python3 tests/test_max_ball.py;
+        poetry run python3 tests/test_scaling.py;
+        poetry run python3 tests/test_sampling.py;
+        poetry run python3 tests/test_sampling_no_multiphase.py;
+
+        # New way - using pytest with coverage
+        poetry run pytest --cov=dingo --cov-report=xml --cov-report=term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        flags: python
+        fail_ci_if_error: false
+        name: codecov-umbrella
+        verbose: true

README.md

@@ -14,8 +14,7 @@ metabolic network, namely Flux Balance Analysis and Flux Variability Analysis.
 [![unit-tests](https://github.com/GeomScale/dingo/workflows/dingo-ubuntu/badge.svg)](https://github.com/GeomScale/dingo/actions?query=workflow%3Adingo-ubuntu)
 [![Tutorial In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeomScale/dingo/blob/develop/tutorials/dingo_tutorial.ipynb)
 [![Chat](https://badges.gitter.im/geomscale.png)](https://gitter.im/GeomScale/community?utm_source=share-link&utm_medium=link&utm_campaign=share-link)
-
-
+[![codecov](https://codecov.io/gh/GeomScale/dingo/branch/develop/graph/badge.svg)](https://codecov.io/gh/GeomScale/dingo)
 ## Installation
 
 **Note:** Python version should be 3.8.x. You can check this by running the following command in your terminal:

pytest.ini

@@ -0,0 +1,10 @@
+
+[pytest]
+testpaths = tests
+python_files = test_*.py
+python_functions = test_*
+addopts = 
+    --cov=dingo
+    --cov-report=xml:coverage.xml
+    --cov-report=term
+    --verbose

requirements-dev.txt

@@ -0,0 +1,3 @@
+pytest>=7.0.0
+pytest-cov>=4.1.0
+codecov>=2.1.13

tests/rounding.py → tests/test_rounding.py

@@ -15,7 +15,7 @@
 from dingo import MetabolicNetwork, PolytopeSampler
 from dingo.pyoptinterface_based_impl import set_default_solver
 
-def test_rounding(self, method_str):
+def rounding_test(self, method_str):
 
         input_file_json = os.getcwd() + "/ext_data/e_coli_core.json"
         model = MetabolicNetwork.from_json( input_file_json )
@@ -59,10 +59,10 @@ def test_rounding(self, method_str):
 class TestSampling(unittest.TestCase):
 
     def test_rounding_min_ellipsoid(self):
-        test_rounding(self, "min_ellipsoid")
+       rounding_test(self, "min_ellipsoid")
 
     def test_rounding_john_position(self):
-        test_rounding(self, "john_position")
+        rounding_test(self, "john_position")
 
 if __name__ == "__main__":
     if len(sys.argv) > 1: