Fix all doc warnings

beat/core/algorithm.py

beat/core/database.py

beat/core/dataformat.py

beat/core/dock.py

beat/core/execution/base.py

beat/core/execution/docker.py

beat/core/execution/local.py

beat/core/execution/remote.py

beat/core/execution/subprocess.py

beat/core/experiment.py

beat/core/hash.py

beat/core/library.py

beat/core/plotter.py

beat/core/stats.py

beat/core/toolchain.py

doc/api.rst

doc/conf.py

doc/dataformats.rst

doc/nitpick-exceptions.txt