Add code coverage to CI (#694)

* Add code coverage to CI

* Use coverage.py for generating coverage report

* Trial: use "Cython" with a capital C

* Add Cython linetracing in CI

* Use scip.pxi file to avoid coverage error when using pyx

* Separate test coverage into its own CI workflow

* Rename test coverage job

* Add comment to make it clear why redirection to .pxi is needed

* Remove unneeded packages

* Trial: add back cython install

.coveragerc

@@ -1,6 +1,7 @@
 [run]
 plugins = Cython.Coverage
-#source = src/pyscipopt
-#omit =
-#    tests
-#    *__init__.py
+source = src/pyscipopt
+omit =
+    tests
+    __init__.py
+    scip.pyx

.github/workflows/coverage.yml

@@ -0,0 +1,50 @@
+name: Run tests with coverage
+env:
+  version: 8.0.3
+
+# runs on branches and pull requests; doesn't run on tags.
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+
+jobs:
+
+  test-coverage:
+    runs-on: ubuntu-20.04
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies (SCIPOptSuite)
+        run: |
+          wget --quiet --no-check-certificate https://scipopt.org/download/release/SCIPOptSuite-${{ env.version }}-Linux-ubuntu.deb
+          sudo apt-get update && sudo apt install -y ./SCIPOptSuite-${{ env.version }}-Linux-ubuntu.deb
+
+      - name: Setup python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Prepare python environment
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install networkx cython pytest-cov
+
+      - name: Install PySCIPOpt
+        run: python -m pip install .
+
+      - name: Run pyscipopt tests
+        run: |
+          coverage run -m pytest
+          coverage report -m
+          coverage xml
+      
+      - name: Upload to codecov.io
+        uses: codecov/codecov-action@v2
+        with:
+          fail_ci_if_error: true

README.md

@@ -72,7 +72,7 @@ from pyscipopt import Model
 model = Model("Example")  # model name is optional
 ```
 
-3)  Access the methods in the `scip.pyx` file using the solver/model
+3)  Access the methods in the `scip.pxi` file using the solver/model
     instance `model`, e.g.:
 
 ``` {.sourceCode .python}
@@ -108,7 +108,7 @@ may also extend it to increase the functionality of this interface. The
 following will provide some directions on how this can be achieved:
 
 The two most important files in PySCIPOpt are the `scip.pxd` and
-`scip.pyx`. These two files specify the public functions of SCIP that
+`scip.pxi`. These two files specify the public functions of SCIP that
 can be accessed from your python code.
 
 To make PySCIPOpt aware of the public functions you would like to
@@ -122,7 +122,7 @@ be done in order to properly add the functions:
 
 After following the previous two steps, it is then possible to create
 functions in python that reference the SCIP public functions included in
-`scip.pxd`. This is achieved by modifying the `scip.pyx` file to add the
+`scip.pxd`. This is achieved by modifying the `scip.pxi` file to add the
 functionality you require.
 
 We are always happy to accept pull request containing patches or

docs/maindoc.py

@@ -30,7 +30,7 @@
 #following will provide some directions on how this can be achieved:
 #
 #The two most important files in PySCIPOpt are the `scip.pxd` and
-#`scip.pyx`. These two files specify the public functions of SCIP that
+#`scip.pxi`. These two files specify the public functions of SCIP that
 #can be accessed from your python code.
 #
 #To make PySCIPOpt aware of the public functions you would like to
@@ -44,7 +44,7 @@
 #
 #After following the previous two steps, it is then possible to create
 #functions in python that reference the SCIP public functions included in
-#`scip.pxd`. This is achieved by modifying the `scip.pyx` file to add the
+#`scip.pxd`. This is achieved by modifying the `scip.pxi` file to add the
 #functionality you require.
 #
 #We are always happy to accept pull request containing patches or

setup.py

@@ -88,6 +88,8 @@
 
 ext = ".pyx" if use_cython else ".c"
 
+on_github_actions = os.getenv('GITHUB_ACTIONS') == 'true'
+
 extensions = [
     Extension(
         "pyscipopt.scip",
@@ -97,11 +99,12 @@
         libraries=[libname],
         extra_compile_args=extra_compile_args,
         extra_link_args=extra_link_args,
+        define_macros= [("CYTHON_TRACE_NOGIL", 1), ("CYTHON_TRACE", 1)] if on_github_actions else []
     )
 ]
 
 if use_cython:
-    extensions = cythonize(extensions, compiler_directives={"language_level": 3})
+    extensions = cythonize(extensions, compiler_directives={"language_level": 3, "linetrace": on_github_actions})
 
 with open("README.md") as f:
     long_description = f.read()