chore: update workflow permissions and fix paths in settings (#2227)

* chore: update workflow permissions and fix paths in settings

* dep

* dep upgraes

.github/workflows/pytest.yml

@@ -1,5 +1,9 @@
 name: Run python tests with pytest
 on: [push, pull_request]
+
+permissions:
+  contents: read
+
 jobs:
   pytest_and_coverage:
     name: Run tests and count coverage