Added docs

.gitignore

+docs/build
+.vscode

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_build/html/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: ae4434aa08c681ca92badba252b9ae4e
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/source/_build/html/_sources/index.rst.txt

+.. Python front-end for MDC PASTTRECs documentation master file, created by
+   sphinx-quickstart on Mon Jan  3 15:10:45 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Python front-end for MDC PASTTRECs documentation!
+==============================================================
+
+The source code can be found on my `GitLab <http://github.com/ericholscher/django-kong>`_.
+
+The basic idea is to let the user manipulate both virtual configuration objects and real hardware via Jupyter Notebook.
+The system uses the pasttrec_ctrl module as a port for physical interaction with real hardware using trbnet library.
+The passtrec_conf module created for simpler handling of different configurations and control the PASTTREC chips. 
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   pasttrec_ctrl
+   pasttrec_conf
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/_build/html/_sources/mdctdc_fpga.rst.txt

+MDCTDC_FPGA
+===========

docs/source/_build/html/_sources/mdctdc_oep.rst.txt

+MDCTDC_OEP
+==========
\ No newline at end of file

docs/source/_build/html/_sources/mdctdc_pt.rst.txt

+MDCTDC_PT
+=========
+
+A class for handling the individual configurations for each PASTTREC.
+
+Attributes:
+
+gain : float
+    Value of gain for this PASTTREC. Acceptable values is only: 0.67, 1, 2, 4. 
+pt : float
+    Value of peaking time for this PASTTREC. Acceptable values is only: 10, 15, 20, 35.
+thr : float
+    Value of threshold for this PASTTREC. Acceptable values is any one in range from 0 to 2^7.
+baselines : array(float)
+    Values of baseline for each channel of this PASTTREC. Acceptable values is any one in range from 0 to 31.
+gain_map : dict(float, int)
+    Bit mask for each value of gain. Not for end user.
+pt_map : dict(float, int)
+    Bit mask for each value of peaking time. Not for end user.
+
+
+``__init__``
+------------
+
+Parameters:
+
+gain : float, optional (default is 4)
+    Pasttrec gain
+peaktime : float, optional (default is 10)
+    Pasttrec peaking time
+thr : float, optional (default is 8)
+    Pasttrec threshold
+baselines : array(float), optional (default is [0x0f,0x0f,0x0f,0x0f,0x0f,0x0f,0x0f,0x0f])
+    Pasttrec baselines
+
+``setBaselines``
+----------------
+
+Set a new values for baselines. Automatically checks validity.
+
+Parameters:
+
+new : array(float)
+    New baselines
+
+``setBaseline``
+---------------
+
+Set a new value for one specific baseline. Automatically checks validity.
+
+Parameters:
+
+ch : float
+    Number of channel
+value: float
+    New value of baseline for channel ch
+
+
+
+
+
+
+
+
+
+
+
+
+    
\ No newline at end of file

docs/source/_build/html/_sources/passtrec_conf.rst.txt

+PASTTREC configuration module (pasttrec_ctrl.py)
+================================================
+
+Contain the mechanisms for handling virtual PASTTREC configurations and effective flashing them.
+
+.. toctree::
+    MDCTDC_PT - Virtual PASTTREC objects <mdctdc_pt>
+    MDCTDC_FPGA - Virtual PASTTREC objects <mdctdc_fpga>
+    MDCTDC_OEP - Virtual PASTTREC objects <mdctdc_oep>
+

docs/source/_build/html/_sources/pasttrec_conf.rst.txt

+PASTTREC configuration module (pasttrec_ctrl.py)
+================================================
+
+Contain the mechanisms for handling virtual PASTTREC configurations and effective flashing them.
+
+.. toctree::
+    MDCTDC_PT - Virtual PASTTREC object <mdctdc_pt>
+    MDCTDC_FPGA - Virtual FPGA object <mdctdc_fpga>
+    MDCTDC_OEP - Virtual OEP object <mdctdc_oep>
+    Configuration - Python object for handling PASTTREC configurations <configuration>
+    ConfStorage - One place for storing default PASTTREC configurations.

docs/source/_build/html/_sources/pasttrec_ctrl.rst.txt

+PASTTREC control module (pasttrec_ctrl.py)
+==========================================
+
+Contain all methods for physical interaction with actual boards.
+
+.. contents::
+    :local:
+    :depth: 1
+
+
+
+``spi_mdc_mbo``
+---------------
+
+#TODO lorem impsum
+
+``spi_set_pasttrec_register``
+-----------------------------
+
+Set a value to a specific PASTTREC register.
+
+Parameters:
+
+TDC_str : str
+  Address of associated TDC
+
+pasttrec : int
+  Number of PASTTREC ASIC [0-3].
+
+reg : int
+  Address of PASTTREC register [0x0 - 0xD]
+
+data : int
+  Data to be written [0x00 - 0xFF].
+  See details in the PASTTREC docs.
+
+``spi_set_pasttrecs_register``
+------------------------------
+
+Set a value to a specific PASTTREC register for all associated PASTTRECs with specified TDC.
+
+Parameters:
+
+TDC_str : str
+  Address of associated TDC
+
+reg : int
+  Address of PASTTREC register [0x0 - 0xD]
+
+data : int
+  Data to be written [0x00 - 0xFF].
+  See details in the PASTTREC docs.
+
+``reset_board``
+---------------
+
+Performs a soft reset of PASTTREC FPGA module (without interruption of all other systems)
+
+Parameters:
+
+TDC_str : str
+  Address of associated TDC
+
+CONN : int, optional (default is 0)
+  Not used. For back compatibility only.
+
+``reset_boards``
+----------------
+
+Performs a soft reset of PASTTREC FPGA module (without interruption of all other systems)
+
+Parameters:
+
+TDC_strs : array(str)
+  An array of associated TDC's addresses.
+CONN : int, optional (default is 0)
+  Not used. For back compatibility only.
+
+``reset_board_by_name``
+-----------------------
+
+Performs a soft reset of PASTTREC FPGA module (without interruption of all other systems)
+
+Parameters:
+
+board_name : str
+  Board name
+
+``set_threshold``
+-----------------
+
+Set threshold value of specific PASTTREC
+
+Parameters:
+
+TDC : str
+  Assosiated TDC
+CONN : int
+  PASTTREC's number of connection.
+CHIP : int
+  PASTTREC's chip number
+THR : int
+  New threshold value
+
+``set_threshold_for_board``
+---------------------------
+
+Set threshold value of specific PASTTRECs.
+
+Parameters:
+
+TDC : str
+  Assosiated TDC
+CONN : int
+  PASTTREC's number of connection. Not used if new style is active.
+thresh : int
+  New threshold value
+new_style : boolean, optional (default is false)
+  If new_style is false, only PASTTRECs assosiated with specific connection are affected. (for back compability)
+  If new_style is true, all PASTTRECs assosiated with specific TDC are affected.
+
+``set_threshold_for_board_by_name``
+-----------------------------------
+
+Set threshold value of all PASTTREC assosiated with specific board.
+
+Parameters:
+
+board_name : str
+  Name of assosiated board.
+thresh : int
+  New threshold value
+new_style : boolean, optional (default is false)
+  If new_style is false, only PASTTRECs assosiated with specific connection (specified by board_name) are affected. (for back compability)
+  If new_style is true, all PASTTRECs assosiated with specific TDC are affected.
+
+``slow_control_test``
+
+#TODO have no idea what is this for 
+
+``slow_control_test_boards``
+----------------------------
+
+#TODO have no idea what is this for 
+
+``set_baseline``
+----------------
+
+Set a baseline level for one of TDC channels.
+
+Parameters:
+
+TDC : str
+  A TDC's address.
+channel : int
+  Number of channel [0 - 31].
+value : int
+  New value of baseline level [-15,15].
+
+``set_all_baselines``
+---------------------
+
+Set a baseline level for an array of TDC channels.
+
+Parameters:
+
+TDC : str
+  A TDC's address.
+channels : array(int)
+  Array of channel's numbers.
+values : array(int)
+  Array of new values of baseline levels.
+
+``set_all_baselines_to_same_value``
+-----------------------------------
+
+Set a baseline level for all channels of specified TDC.
+
+Parameters:
+
+TDC : str
+  A TDC address.
+value : int
+  New value of baseline levels.
+
+``init_chip``
+-------------
+
+#TODO
+
+``init_board``
+--------------
+
+#TODO
+
+``init_active_boards``
+----------------------
+
+#TODO
+
+``init_boards_by_name``
+-----------------------
+
+#TODO
+
+``init_board_by_name``
+----------------------
+
+#TODO
+
+``found_baselines_for_board``
+-----------------------------
+
+Found a baseline level for all channels of specific board with noize method.
+
+Parameters:
+
+board : str
+  A TDC address.
+scaning_time : float, optional (default is 0.2)
+  Duration of each step during data aqusition
+plot : boolean, optional (default is False)
+  if true, plots the noize level versus baseline for each channel.
+apply_res : boolean, optional (default is False)
+  if true, after the baselines will be found, they will be applyed for each channel.
+
+``found_baselines_for_boards``
+------------------------------
+
+The same as found_baselines_for_board but for a list of boards.
+
+Parameters:
+
+boards : array(str)
+  A list of TDC's addresses.
+scaning_time : float, optional (default is 0.2)
+  Duration of each step during data aqusition
+plot : boolean, optional (default is False)
+  if true, plots the noize level versus baseline for each channel.
+apply_res : boolean, optional (default is False)
+  if true, after the baselines will be found, they will be applyed for each channel.
+
+``read_PASTTREC_regs``
+----------------------
+
+Read the values of PASTTREC registers.
+
+Parameters:
+
+TDC_str : str
+  A TDC address.
+pasttrec : int
+  Number of PASTTREC

docs/source/_build/html/_static/alabaster.css

+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
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+    font-family: Georgia, serif;
+    font-size: 17px;
+    background-color: #fff;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+
+div.document {
+    width: 940px;
+    margin: 30px auto 0 auto;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 220px;
+}
+
+div.sphinxsidebar {
+    width: 220px;
+    font-size: 14px;
+    line-height: 1.5;
+}
+
+hr {
+    border: 1px solid #B1B4B6;
+}
+
+div.body {
+    background-color: #fff;
+    color: #3E4349;
+    padding: 0 30px 0 30px;
+}
+
+div.body > .section {
+    text-align: left;
+}
+
+div.footer {
+    width: 940px;
+    margin: 20px auto 30px auto;
+    font-size: 14px;
+    color: #888;
+    text-align: right;
+}
+
+div.footer a {
+    color: #888;
+}
+
+p.caption {
+    font-family: inherit;
+    font-size: inherit;
+}
+
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+div.relations {
+    display: none;
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+
+
+div.sphinxsidebar a {
+    color: #444;
+    text-decoration: none;
+    border-bottom: 1px dotted #999;
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+    text-align: center;
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