repeat_conversation_test.py: remove
test_dependencies.py: Update
test_pipeline.py: Include TRD results
logging.ini: Generalised paths
repeat.rst: repeat_conversation_test unmentioned
setup.py: Update requirements, etc
hmm_io: credentials
*_test.py: remove logging, slight updates
dependencies_test.py: Transform dependencies test to pytest
rm example_pipeline.py
sequence.py: shift repeat_in_sequence check from repeat to sequence class
update credentials, etc
Merge branch 'refactoring' into refactoring_w_data