Add Codecov

.github/workflows/testsuite.yml

@@ -1,4 +1,4 @@
-name: run tests
+name: testsuite
 
 on:
   push:
@@ -34,8 +34,9 @@ jobs:
           module restore pymbe
           source venv/bin/activate
           make pylint
-          make tests
+          make unit_tests COVERAGE=1
           make docs
+          make coverage_xml
         shell: bash
       - name: Upload artifact
         uses: actions/upload-artifact@v4
@@ -44,3 +45,14 @@ jobs:
           name: documentation
           retention-days: 2
           if-no-files-found: error
+      - name: Upload coverage to Codecov
+        if: ${{ github.repository == 'pyMBE-dev/pyMBE' }}
+        uses: codecov/codecov-action@v4
+        with:
+          file: "./coverage.xml"
+          disable_search: true
+          env_vars: OS,PYTHON
+          fail_ci_if_error: false
+          flags: unittests
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

Makefile

@@ -3,7 +3,17 @@
 .PHONY: visual 
 .PHONY: clean
 
+# whether to run unit tests with code coverage
+COVERAGE = 0
+
+# output directory for the code coverage HTML files
+COVERAGE_HTML = coverage
+
+# Python executable or launcher, possibly with command line arguments
 PYTHON = python3
+ifeq ($(COVERAGE),1)
+PYTHON := ${PYTHON} -m coverage run --parallel-mode --source=$(CURDIR)
+endif
 
 docs:
 	mkdir -p ./documentation
@@ -30,6 +40,15 @@ functional_tests:
 
 tests: unit_tests functional_tests
 
+coverage_xml:
+	${PYTHON} -m coverage combine .
+	${PYTHON} -m coverage report
+	${PYTHON} -m coverage xml
+
+coverage_html:
+	${PYTHON} -m coverage combine .
+	${PYTHON} -m coverage html --directory="${COVERAGE_HTML}"
+
 sample:
 	${PYTHON} samples/peptide.py
 

README.md

@@ -1,5 +1,8 @@
 # pyMBE: the Python-based Molecule Builder for ESPResSo 
 
+![GitHub Actions](https://github.com/pyMBE-dev/pyMBE/actions/workflows/testsuite.yml/badge.svg)
+[![codecov](https://codecov.io/gh/pyMBE-dev/pyMBE/branch/codecov/graph/badge.svg)](https://codecov.io/gh/pyMBE-dev/pyMBE)
+
 pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software [ESPResSo](https://espressomd.org/wordpress/). Some examples of molecules that can be set up with pyMBE are polyelectrolytes, peptides and proteins. pyMBE bookkeeps all the information about the molecule topology, permitting to link each particle to its corresponding residue and molecule. pyMBE uses the [Pint](https://pint.readthedocs.io/en/stable/) library to enable input parameters in any arbitrary unit system, which is later transformed in the reduced unit system used in ESPResSo.
 
 ## Dependencies