Set the source on pyproject and add a paths config

If using relative paths, the `source` argument needs to passed on the
config file instead of the command line (don't know why but says so in
the docs). We can also set patterns for paths that should be considered
the same by the reporting.

Author: leouieda

Makefile

@@ -1,7 +1,7 @@
 # Build, package, test, and clean
 PROJECT=harmonica
 TESTDIR=tmp-test-dir-with-unique-name
-PYTEST_ARGS=--cov-report=term-missing --cov=$(PROJECT) --doctest-modules --doctest-continue-on-failure -v --pyargs
+PYTEST_ARGS=--cov-report=term-missing --cov --doctest-modules --doctest-continue-on-failure -v --pyargs
 NUMBATEST_ARGS=--doctest-modules -v --pyargs -m use_numba
 STYLE_CHECK_FILES=$(PROJECT) examples doc
 GITHUB_ACTIONS=.github/workflows

pyproject.toml

@@ -80,13 +80,21 @@ notice = '''
 #'''
 
 [tool.coverage.run]
-branch = true
+source = ["harmonica"]
 omit = [
     "**/_version.py",
     "**/__init__.py",
 ]
+branch = true
 # Needed to combine coverage data from multiple OSs on CI
 relative_files = true
 
+[tool.coverage.paths]
+source = [
+    "harmonica",
+    "*/harmonica",
+    "*\\harmonica",
+]
+
 [tool.coverage.report]
 show_missing = true