Km3pipe

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* add a makefile
* flake8 all the things
* make compatible for upcoming numpy 1.14
* add ``nb2shpx`` util for notebook -> sphinx gallery exampe
* some pandas bits and bobs

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* Improved CLB raw data readout
* Pipelines now return a ``finish blob`` which contains the return values
of each modules finish method (this is for Tommaso)
* ``TimesliceParser`` now reads all timeslice streams (L0, L1, L2, SN)
* ``TimesliceParser`` now returns the blob even if it was not able to parse
the data
* ``TMCHRepump`` now has an iterator interface
* Fixed bug in ``StreamDS`` where it tried to create a session in Lyon and
failed. Now it uses the permanent session which was created by Cristiano
* Some smaller bugfixes and name-consistency-changes

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* ``kp.math``: ``zenith, azimuth, phi, theta`` now follow the correct
km3net definitions (finally)
* JFit pump now follows multipump paradigm
* improved logging in IO

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* Added preliminary ``kp.io.jpp.FitPump``, which reads ``JFit`` objects.
However, it does not yet read the ``fitinf`` vector, yet.
* ``Calibration`` moved to ``kp.calib``, since core.pyx was Cython and numba
does not like cython files.
* ``streamds`` now requires the ``get`` command to retrieve info on command
line
* ``streamds`` can now upload to runsummary tables
* remove obsolete ``kp.dev`` (now resides in ``kp.tools``
* fixes EOF hang in ``kp.io.daq.TMCHRepump``

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* Hotfix of the SummaryslicePump (rates/fifos/hrvs reference issue)
* ``Geometry`` has been renamed to ``Calibration``
* aanetpump now does not convert MC times by default

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* JPPPump removed
* New ``k40calib`` command line tool to calibrate DOMs using the K40
method
* ``TimeslicePump`` and ``SummaryslicePump`` now add meta information about
the slices to the blob: ``blob['TimesliceInfo']`` and
``blob['SummarysliceInfo']``
* ``SummaryslicePump`` now reads out FIFO status and HRV for each PMT
* ``kp.shell.qsub()`` can be used to submit jobs to SGE clusters