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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 8f97d9940cab1fd53fb95ef9cc893a2c
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/analysis.doctree b/.doctrees/analysis.doctree
diff --git a/.doctrees/analysis/calibration.doctree b/.doctrees/analysis/calibration.doctree
diff --git a/.doctrees/analysis/coincidence_queries.doctree b/.doctrees/analysis/coincidence_queries.doctree
diff --git a/.doctrees/analysis/coincidences.doctree b/.doctrees/analysis/coincidences.doctree
diff --git a/.doctrees/analysis/core_reconstruction.doctree b/.doctrees/analysis/core_reconstruction.doctree
diff --git a/.doctrees/analysis/direction_reconstruction.doctree b/.doctrees/analysis/direction_reconstruction.doctree
diff --git a/.doctrees/analysis/event_utils.doctree b/.doctrees/analysis/event_utils.doctree
diff --git a/.doctrees/analysis/find_mpv.doctree b/.doctrees/analysis/find_mpv.doctree
diff --git a/.doctrees/analysis/landau.doctree b/.doctrees/analysis/landau.doctree
diff --git a/.doctrees/analysis/process_events.doctree b/.doctrees/analysis/process_events.doctree
diff --git a/.doctrees/analysis/process_traces.doctree b/.doctrees/analysis/process_traces.doctree
diff --git a/.doctrees/analysis/reconstructions.doctree b/.doctrees/analysis/reconstructions.doctree
diff --git a/.doctrees/analysis/signal_calibration.doctree b/.doctrees/analysis/signal_calibration.doctree
diff --git a/.doctrees/analysis/time_deltas.doctree b/.doctrees/analysis/time_deltas.doctree
diff --git a/.doctrees/api.doctree b/.doctrees/api.doctree
diff --git a/.doctrees/clusters.doctree b/.doctrees/clusters.doctree
diff --git a/.doctrees/configuration.doctree b/.doctrees/configuration.doctree
diff --git a/.doctrees/corsika.doctree b/.doctrees/corsika.doctree
diff --git a/.doctrees/corsika/blocks.doctree b/.doctrees/corsika/blocks.doctree
diff --git a/.doctrees/corsika/corsika_queries.doctree b/.doctrees/corsika/corsika_queries.doctree
diff --git a/.doctrees/corsika/generate_corsika_overview.doctree b/.doctrees/corsika/generate_corsika_overview.doctree
diff --git a/.doctrees/corsika/particles.doctree b/.doctrees/corsika/particles.doctree
diff --git a/.doctrees/corsika/qsub_corsika.doctree b/.doctrees/corsika/qsub_corsika.doctree
diff --git a/.doctrees/corsika/qsub_store_corsika_data.doctree b/.doctrees/corsika/qsub_store_corsika_data.doctree
diff --git a/.doctrees/corsika/reader.doctree b/.doctrees/corsika/reader.doctree
diff --git a/.doctrees/corsika/store_corsika_data.doctree b/.doctrees/corsika/store_corsika_data.doctree
diff --git a/.doctrees/corsika/units.doctree b/.doctrees/corsika/units.doctree
diff --git a/.doctrees/data.doctree b/.doctrees/data.doctree
diff --git a/.doctrees/data/extend_local_data.doctree b/.doctrees/data/extend_local_data.doctree
diff --git a/.doctrees/data/update_local_data.doctree b/.doctrees/data/update_local_data.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/esd.doctree b/.doctrees/esd.doctree
diff --git a/.doctrees/examples.doctree b/.doctrees/examples.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/installation.doctree b/.doctrees/installation.doctree
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diff --git a/.doctrees/publicdb.doctree b/.doctrees/publicdb.doctree
diff --git a/.doctrees/qsub.doctree b/.doctrees/qsub.doctree
diff --git a/.doctrees/sapphire.doctree b/.doctrees/sapphire.doctree
diff --git a/.doctrees/simulations.doctree b/.doctrees/simulations.doctree
diff --git a/.doctrees/simulations/base.doctree b/.doctrees/simulations/base.doctree
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diff --git a/.doctrees/simulations/groundparticles.doctree b/.doctrees/simulations/groundparticles.doctree
diff --git a/.doctrees/simulations/ldf.doctree b/.doctrees/simulations/ldf.doctree
diff --git a/.doctrees/simulations/showerfront.doctree b/.doctrees/simulations/showerfront.doctree
diff --git a/.doctrees/storage.doctree b/.doctrees/storage.doctree
diff --git a/.doctrees/tests.doctree b/.doctrees/tests.doctree
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diff --git a/.doctrees/transformations/base.doctree b/.doctrees/transformations/base.doctree
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diff --git a/.doctrees/tutorial.doctree b/.doctrees/tutorial.doctree
diff --git a/.doctrees/utils.doctree b/.doctrees/utils.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_images/github-zipball.png b/_images/github-zipball.png
diff --git a/_images/tutorial-hist-better.png b/_images/tutorial-hist-better.png
diff --git a/_images/tutorial-hist-simple.png b/_images/tutorial-hist-simple.png
diff --git a/_sources/analysis.rst.txt b/_sources/analysis.rst.txt
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+Data analysis
+=============
+
+.. automodule:: sapphire.analysis
+   :members:
+   :undoc-members:
+
+.. toctree::
+   :hidden:
+
+   analysis/calibration
+   analysis/coincidence_queries
+   analysis/coincidences
+   analysis/core_reconstruction
+   analysis/direction_reconstruction
+   analysis/event_utils
+   analysis/find_mpv
+   analysis/landau
+   analysis/process_events
+   analysis/process_traces
+   analysis/reconstructions
+   analysis/signal_calibration
+   analysis/time_deltas
diff --git a/_sources/analysis/calibration.rst.txt b/_sources/analysis/calibration.rst.txt
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+.. include:: ../subst.inc
+
+Data timing and signal calibration
+==================================
+
+.. automodule:: sapphire.analysis.calibration
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/coincidence_queries.rst.txt b/_sources/analysis/coincidence_queries.rst.txt
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+.. include:: ../subst.inc
+
+Query coincidences from a datafile
+==================================
+
+.. automodule:: sapphire.analysis.coincidence_queries
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/coincidences.rst.txt b/_sources/analysis/coincidences.rst.txt
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+.. include:: ../subst.inc
+
+Search for coincidences between |hisparc| stations
+==================================================
+
+.. automodule:: sapphire.analysis.coincidences
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/core_reconstruction.rst.txt b/_sources/analysis/core_reconstruction.rst.txt
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+Reconstruction of EAS core and size
+===================================
+
+.. automodule:: sapphire.analysis.core_reconstruction
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/direction_reconstruction.rst.txt b/_sources/analysis/direction_reconstruction.rst.txt
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+Reconstruction of EAS direction
+===============================
+
+.. automodule:: sapphire.analysis.direction_reconstruction
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/event_utils.rst.txt b/_sources/analysis/event_utils.rst.txt
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+.. include:: ../subst.inc
+
+Get signal and timing values from events
+========================================
+
+.. automodule:: sapphire.analysis.event_utils
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/find_mpv.rst.txt b/_sources/analysis/find_mpv.rst.txt
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+MPV fit
+=======
+
+.. automodule:: sapphire.analysis.find_mpv
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/landau.rst.txt b/_sources/analysis/landau.rst.txt
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+Landau distribution
+===================
+
+.. automodule:: sapphire.analysis.landau
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/process_events.rst.txt b/_sources/analysis/process_events.rst.txt
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+Processing of HiSPARC events
+============================
+
+.. automodule:: sapphire.analysis.process_events
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/process_traces.rst.txt b/_sources/analysis/process_traces.rst.txt
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+Processing of HiSPARC traces
+============================
+
+.. automodule:: sapphire.analysis.process_traces
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/reconstructions.rst.txt b/_sources/analysis/reconstructions.rst.txt
@@ -0,0 +1,6 @@
+Reconstructions 
+===============
+
+.. automodule:: sapphire.analysis.reconstructions
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/signal_calibration.rst.txt b/_sources/analysis/signal_calibration.rst.txt
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+.. include:: ../subst.inc
+
+Detector signal calibration
+===========================
+
+.. automodule:: sapphire.analysis.signal_calibration
+   :members:
+   :undoc-members:
diff --git a/_sources/analysis/time_deltas.rst.txt b/_sources/analysis/time_deltas.rst.txt
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+Time deltas 
+===========
+
+.. automodule:: sapphire.analysis.time_deltas
+   :members:
+   :undoc-members:
diff --git a/_sources/api.rst.txt b/_sources/api.rst.txt
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+HiSPARC API
+===========
+
+.. automodule:: sapphire.api
+   :members:
+   :undoc-members:
diff --git a/_sources/clusters.rst.txt b/_sources/clusters.rst.txt
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+HiSPARC clusters
+================
+
+.. automodule:: sapphire.clusters
+   :members:
+   :undoc-members:
diff --git a/_sources/configuration.rst.txt b/_sources/configuration.rst.txt
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+.. include:: subst.inc
+
+Configuration
+*************
+
+Various modules (:mod:`sapphire.api`, :mod:`sapphire.esd`, and :mod:`sapphire.publicdb`)
+connect to the |hisparc| Public Database to download data, metadata, configurations, etc.
+Normally you will want to use the official |hisparc| Public Database, which is hosted
+at `https://data.hisparc.nl`. However, during development, tests or other occasions you
+may want to use a different server, for example when running a local version of the
+publicdb. In that case you can overwrite the base url used. This overwrite is done
+using an environment variable: ``PUBLICDB_BASE``. This can be easily set when starting
+your Python environment, for example::
+
+    $ PUBLICDB_BASE=http://localhost:8000 python
+
+Or while already running Python::
+
+    from os import environ
+    environ['PUBLICDB_BASE'] = 'http://localhost:8000'
diff --git a/_sources/corsika.rst.txt b/_sources/corsika.rst.txt
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+.. include:: subst.inc
+
+CORSIKA simulations
+===================
+
+`CORSIKA <https://web.ikp.kit.edu/corsika/>`_ is an Air Shower
+Simulation Program. To be used for detailed simulation of
+extensive air showers initiated by high-energy cosmic-ray particles.
+
+This module makes it easy to work with CORSIKA output, it was
+original written by Javier Gonzalez and adapted for `HiSPARC
+<www.hisparc.nl>`_ by Arne de Laat.
+
+This documentation sometimes refers to the CORSIKA users manual, this
+users manual can be found here `CORSIKA User's Guide
+<https://www.ikp.kit.edu/corsika/70.php>`_
+
+In addition to reading CORSIKA output, functionally is provided to
+easily submit many CORSIKA jobs to the Nikhef batch facility
+(Stoomboot).
+
+
+CORSIKA Module
+--------------
+
+.. automodule:: sapphire.corsika
+   :members:
+
+
+Contents
+--------
+
+.. toctree::
+   :hidden:
+
+   corsika/blocks
+   corsika/corsika_queries
+   corsika/generate_corsika_overview
+   corsika/particles
+   corsika/qsub_corsika
+   corsika/qsub_store_corsika_data
+   corsika/reader
+   corsika/store_corsika_data
+   corsika/units
diff --git a/_sources/corsika/blocks.rst.txt b/_sources/corsika/blocks.rst.txt
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+CORSIKA Blocks
+==============
+
+.. automodule:: sapphire.corsika.blocks
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/corsika_queries.rst.txt b/_sources/corsika/corsika_queries.rst.txt
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+Query CORSIKA overview for simulations
+======================================
+
+.. automodule:: sapphire.corsika.corsika_queries
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/generate_corsika_overview.rst.txt b/_sources/corsika/generate_corsika_overview.rst.txt
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+Create an overview of CORSIKA simulations
+=========================================
+
+.. automodule:: sapphire.corsika.generate_corsika_overview
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/particles.rst.txt b/_sources/corsika/particles.rst.txt
@@ -0,0 +1,6 @@
+CORSIKA Particles
+=================
+
+.. automodule:: sapphire.corsika.particles
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/qsub_corsika.rst.txt b/_sources/corsika/qsub_corsika.rst.txt
@@ -0,0 +1,6 @@
+CORSIKA on Stoomboot
+====================
+
+.. automodule:: sapphire.corsika.qsub_corsika
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/qsub_store_corsika_data.rst.txt b/_sources/corsika/qsub_store_corsika_data.rst.txt
@@ -0,0 +1,6 @@
+Convert CORSIKA simulations on Stoomboot
+========================================
+
+.. automodule:: sapphire.corsika.qsub_store_corsika_data
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/reader.rst.txt b/_sources/corsika/reader.rst.txt
@@ -0,0 +1,6 @@
+CORSIKA Reader
+==============
+
+.. automodule:: sapphire.corsika.reader
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/store_corsika_data.rst.txt b/_sources/corsika/store_corsika_data.rst.txt
@@ -0,0 +1,6 @@
+Store CORSIKA data as HDF5
+==========================
+
+.. automodule:: sapphire.corsika.store_corsika_data
+   :members:
+   :undoc-members:
diff --git a/_sources/corsika/units.rst.txt b/_sources/corsika/units.rst.txt
@@ -0,0 +1,6 @@
+CORSIKA Units
+=============
+
+.. automodule:: sapphire.corsika.units
+   :members:
+   :undoc-members:
diff --git a/_sources/data.rst.txt b/_sources/data.rst.txt
@@ -0,0 +1,12 @@
+Updating and extending local data
+=================================
+
+.. automodule:: sapphire.data
+   :members:
+   :undoc-members:
+
+.. toctree::
+   :hidden:
+
+   data/extend_local_data
+   data/update_local_data
diff --git a/_sources/data/extend_local_data.rst.txt b/_sources/data/extend_local_data.rst.txt
@@ -0,0 +1,6 @@
+Download additional local data
+==============================
+
+.. automodule:: sapphire.data.extend_local_data
+   :members:
+   :undoc-members:
diff --git a/_sources/data/update_local_data.rst.txt b/_sources/data/update_local_data.rst.txt
@@ -0,0 +1,6 @@
+Update default local data with latest data from Publicdb
+========================================================
+
+.. automodule:: sapphire.data.update_local_data
+   :members:
+   :undoc-members:
diff --git a/_sources/esd.rst.txt b/_sources/esd.rst.txt
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+Event Summary Data
+==================
+
+.. automodule:: sapphire.esd
+   :members:
+   :undoc-members: