Update documentation

specsanalyzer/latest/_sources/getting_started.rst.txt

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+..  include:: ../README.md
+    :parser: myst_parser.sphinx_

specsanalyzer/latest/_sources/index.rst.txt

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+.. specsanalyzer documentation master file, created by
+   sphinx-quickstart on Wed Jul 27 16:11:48 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to specsanalyzer's documentation!
+=========================================
+Concept description. TODO
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Getting Started
+
+   getting_started
+   specsanalyzer/config
+   tutorial/1_specsanalyzer_conversion_examples
+   tutorial/2_specsscan_example
+   tutorial/3_specsscan_conversion_to_NeXus
+   tutorial/4_specsscan_load_sweep_scan
+
+.. toctree::
+   :maxdepth: 1
+   :numbered:
+   :caption: SpecsAnalyzer Core Modules
+
+   specsanalyzer/core
+   specsanalyzer/convert
+   specsanalyzer/img_tools
+   specsanalyzer/io
+
+.. toctree::
+   :maxdepth: 1
+   :numbered:
+   :caption: SpecsScan Core Modules
+
+   specsscan/core
+   specsscan/helpers
+
+.. toctree::
+   :maxdepth: 2
+   :numbered:
+   :caption: Contributing
+
+   misc/maintain
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

specsanalyzer/latest/_sources/misc/maintain.rst.txt

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+How to maintain
+===================================================
+
+refer to github wiki as well

specsanalyzer/latest/_sources/specsanalyzer/config.rst.txt

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+Config
+===================================================
+The config module contains a mechanics to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary.
+It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
+
+* ``folder_config``: A config file of name :file:`specs_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.
+* ``user_config``: A config file provided by the user, stored as :file:`.specsanalyzer/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
+* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/specsanalyzer/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/specsanalyzer/config.yaml` on Windows. This should provide all necessary default parameters for using the specsanalyzer processor with a given setup. For an example for the setup at the Fritz Haber Institute setup, see :ref:`example_config`
+* ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files.
+
+The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary).
+
+
+API
+***************************************************
+.. automodule:: specsanalyzer.config
+   :members:
+   :undoc-members:
+
+
+.. _example_config:
+
+Default specsanalyzer configuration settings
+***************************************************
+
+.. literalinclude:: ../../src/specsanalyzer/config/default.yaml
+   :language: yaml
+
+Default specsscan configuration settings
+***************************************************
+
+.. literalinclude:: ../../src/specsscan/config/default.yaml
+   :language: yaml
+
+Example configuration file for the trARPES setup at FHI-Berlin
+*********************************************************************************
+
+.. literalinclude:: ../../src/specsscan/config/example_config_FHI.yaml
+   :language: yaml

specsanalyzer/latest/_sources/specsanalyzer/convert.rst.txt

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+convert functions ``(specsanalyzer.convert)``
+=============================================
+convert functions for the specsanalyzer package
+
+.. automodule:: specsanalyzer.convert
+   :members:
+   :private-members:

specsanalyzer/latest/_sources/specsanalyzer/core.rst.txt

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+Core functions  ``(specsanalyzer.core)``
+========================================
+Core class functions for the specsanalyzer package
+
+.. automodule:: specsanalyzer.core
+   :members:
+   :private-members:

specsanalyzer/latest/_sources/specsanalyzer/img_tools.rst.txt

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+image tool functions ``(specsanalyzer.img_tools)``
+===================================================
+image tool functions for the specsanalyzer package
+
+.. automodule:: specsanalyzer.img_tools
+   :members:
+   :private-members:

specsanalyzer/latest/_sources/specsanalyzer/io.rst.txt

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+io functions  ``(specsanalyzer.io)``
+=====================================
+io functions for the specsanalyzer package
+
+.. automodule:: specsanalyzer.io
+   :members:
+   :private-members:

specsanalyzer/latest/_sources/specsscan/core.rst.txt

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+Core functions  ``(specsscan.core)``
+========================================
+Core class functions for the specsscan package
+
+.. automodule:: specsscan.core
+   :members:
+   :private-members:

specsanalyzer/latest/_sources/specsscan/helpers.rst.txt

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+Helpers
+===================================================
+.. automodule:: specsscan.helpers
+   :members:
+   :undoc-members: