It seems that new test runner for PyCharm 2017.1 changed default behavior comparing to previous releases. When running py.test tests using PyCharm generated run configuration all tests were run inside project test directory. In 2017 py.test runs in project root (just like being called from command line). The previous behavior broke some CI systems defaults that expected py.test standard behavior.
Now it breaks all our test configs generated by previous PyCharm versions. It also seems to be ignoring py.test path setting in run configuration making it all pretty useless for running test suite.