Update to work locally and on github actions

.github/workflows/run_coverage.yml

@@ -60,9 +60,8 @@ jobs:
 
       - name: Run tests and generate coverage report
         run: |
-          pytest
-          python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          # coverage is configured in pyproject.toml
+          pytest --cov=hdmf --cov-report=xml --cov-report=term  # codecov uploader requires xml format
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

pyproject.toml

@@ -77,7 +77,6 @@ packages = ["src/hdmf"]
 # verbose = 1
 
 [tool.pytest.ini_options]
-addopts = "--cov=hdmf --cov-report html"
 norecursedirs = "tests/unit/helpers"
 
 [tool.codespell]
@@ -86,17 +85,17 @@ ignore-words-list = "datas"
 
 [tool.coverage.run]
 branch = true
-source = ["src/"]
-omit = [
-    "src/hdmf/_due.py",
-    "src/hdmf/testing/*",
-]
+source = ["src"]
 
 [tool.coverage.report]
 exclude_lines = [
     "pragma: no cover",
     "@abstract"
 ]
+omit = [
+    "*/hdmf/_due.py",
+    "*/hdmf/testing/*",
+]
 
 # [tool.black]
 # line-length = 120