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Merge pull request #21 from CardiacModelling/docs
Added documentation, tests, and more
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‎.flake8‎

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# missing whitespace around arithmetic operator
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# Import sorting
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exclude=
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.git,
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.github,
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.venv,
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venv,
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tests/test_data,

‎README.md‎

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[![codecov](https://codecov.io/gh/CardiacModelling/syncropatch_export/graph/badge.svg?token=HOL0FrpGqs)](https://codecov.io/gh/CardiacModelling/syncropatch_export)
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This repository contains a python package and scripts for processing data outputted from Nanion SynroPatch 384.
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With this package you can export each sweep of each protocol for each well as individual files (.csv).
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Meta-data describing the protocol, and variables such as membrance capacitance (Cm), Rseries and Rseal can be exported.
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```
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python3 -m unittest
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```
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## Usage example
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...TODO
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## Development
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Commits should be merged in via pull requests.
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Tests are written using the standard [unittest](https://docs.python.org/3.13/library/unittest.html) framework.
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Online testing, style-checking, and coverage testing is set up using GitHub actions.
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Coverage testing is handled via [Codecov](https://about.codecov.io/).
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Style testing is done with `flake8`. For example, to test with 4 subprocesses use
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```
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flake8 -j4
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```
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Import sorting can be checked with `isort`:
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```
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isort --verbose --check-only --diff syncropatch_export tests setup.py
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```
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Documentation is implemented using [Sphinx](https://www.sphinx-doc.org/).
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To compile locally, first install the required dependencies
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```
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pip install -e .'[docs]'
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```
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and then use Make
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```
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cd docs
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make html
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```
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‎docs/.gitignore‎

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build/*

‎docs/Makefile‎

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

‎docs/make.bat‎

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

‎docs/source/_static/placeholder‎

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Images etc. can be placed here

‎docs/source/conf.py‎

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# -*- coding: utf-8 -*-
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#
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# This file is execfile()d with the current directory set to its
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# containing dir.
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#
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# Note that not all possible configuration values are present in this
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# autogenerated file.
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#
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# All configuration values have a default; values that are commented out
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# serve to show the default.
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import syncropatch_export
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# -- General configuration ----------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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# needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.doctest',
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'sphinx.ext.mathjax',
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'sphinx.ext.napoleon',
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]
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# Autodoc defaults
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autodoc_default_options = {
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'members': None,
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# 'inherited-members': None,
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}
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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# General information about the project.
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project = u'Syncropatch export'
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# copyright = syncropatch_export.COPYRIGHT
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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#
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# The short X.Y version.
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version = syncropatch_export.__version__
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# The full version, including alpha/beta/rc tags.
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release = syncropatch_export.__version__
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = 'en'
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This patterns also effect to html_static_path and html_extra_path
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exclude_patterns = []
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'default'
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = False
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# -- Options for HTML output ----------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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html_theme = 'alabaster'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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# html_theme_options = {}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# Add any paths that contain custom themes here, relative to this directory.
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html_theme_path = ['_templates']
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# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
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html_show_sphinx = False
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# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
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html_show_copyright = False
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# -- Options for HTMLHelp output ------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'SyncropatchExpertDoc'
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# -- Options for LaTeX output ---------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title, author, documentclass[howto/manual]).
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latex_documents = [(
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'index', 'syncropatch_export.tex', u'Syncropatch Export Documentation',
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u'Mixed', 'manual'
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)]
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# -- Options for manual page output ---------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [(
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'index', 'syncropatch_export', u'Syncropatch Export Documentation',
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[u'Syncropatch Export Team'], 1
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)]
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# -- Options for Texinfo output -------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'syncropatch_export', u'Syncropatch Export Documentation',
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'Syncropatch Export Team', 'Syncropatch Export',
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'Exports Nanion Syncropatch data to CSV.',
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'Miscellaneous'),
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]
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‎docs/source/index.rst‎

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*****************
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Table of contents
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*****************
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.. module:: syncropatch_export
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This module contains methods to export data from the Nanion SynroPatch 384.
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.. toctree::
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:maxdepth: 2
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self
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trace
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voltage_protocols
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‎docs/source/trace.rst‎

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.. currentmodule:: syncropatch_export.trace
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**************
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Accessing data
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**************
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Data is accessed and exported via the :class:`Trace` class.
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.. autoclass:: Trace
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‎docs/source/voltage_protocols.rst‎

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.. currentmodule:: syncropatch_export.voltage_protocols
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***************************
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Accessing voltage protocols
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***************************
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Voltage protocols can be parsed from the JSON data using the
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:class:`VoltageProtocol` class.
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.. autoclass:: VoltageProtocol
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