Added documentation, tests, and more

.flake8

@@ -9,10 +9,10 @@ ignore =
     W504,
     # missing whitespace around arithmetic operator
     E226,
-    # Import sorting
-    I201
-    I100
 
 exclude=
     .git,
+    .github,
+    .venv,
     venv,
+    tests/test_data,

README.md

@@ -2,6 +2,7 @@
 [![codecov](https://codecov.io/gh/CardiacModelling/syncropatch_export/graph/badge.svg?token=HOL0FrpGqs)](https://codecov.io/gh/CardiacModelling/syncropatch_export)
 
 This repository contains a python package and scripts for processing data outputted from Nanion SynroPatch 384.
+
 With this package you can export each sweep of each protocol for each well as individual files (.csv). 
 Meta-data describing the protocol, and variables such as membrance capacitance (Cm), Rseries and Rseal can be exported.
 
@@ -41,3 +42,39 @@ Then you can run the tests.
 ```
 python3 -m unittest
 ```
+
+## Usage example
+
+...TODO
+
+
+## Development
+
+Commits should be merged in via pull requests.
+
+Tests are written using the standard [unittest](https://docs.python.org/3.13/library/unittest.html) framework.
+
+Online testing, style-checking, and coverage testing is set up using GitHub actions.
+Coverage testing is handled via [Codecov](https://about.codecov.io/).
+
+Style testing is done with `flake8`. For example, to test with 4 subprocesses use
+```
+flake8 -j4
+```
+Import sorting can be checked with `isort`:
+```
+isort --verbose --check-only --diff syncropatch_export tests setup.py
+```
+
+Documentation is implemented using [Sphinx](https://www.sphinx-doc.org/).
+To compile locally, first install the required dependencies
+```
+pip install -e .'[docs]'
+```
+and then use Make
+```
+cd docs
+make html
+```
+
+

docs/.gitignore

@@ -0,0 +1 @@
+build/*

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = syncropatch_export
+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

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=syncropatch_export
+
+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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/_static/placeholder

@@ -0,0 +1 @@
+Images etc. can be placed here

docs/source/conf.py

@@ -0,0 +1,163 @@
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import syncropatch_export
+
+
+# -- General configuration ----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+]
+
+# Autodoc defaults
+autodoc_default_options = {
+    'members': None,
+    # 'inherited-members': None,
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Syncropatch export'
+# copyright = syncropatch_export.COPYRIGHT
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = syncropatch_export.__version__
+# The full version, including alpha/beta/rc tags.
+release = syncropatch_export.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'default'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any paths that contain custom themes here, relative to this directory.
+html_theme_path = ['_templates']
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SyncropatchExpertDoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass[howto/manual]).
+latex_documents = [(
+    'index', 'syncropatch_export.tex', u'Syncropatch Export Documentation',
+    u'Mixed', 'manual'
+)]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(
+    'index', 'syncropatch_export', u'Syncropatch Export Documentation',
+    [u'Syncropatch Export Team'], 1
+)]
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'syncropatch_export', u'Syncropatch Export Documentation',
+     'Syncropatch Export Team', 'Syncropatch Export',
+     'Exports Nanion Syncropatch data to CSV.',
+     'Miscellaneous'),
+]
+

docs/source/index.rst

@@ -0,0 +1,15 @@
+*****************
+Table of contents
+*****************
+
+.. module:: syncropatch_export
+
+This module contains methods to export data from the Nanion SynroPatch 384.
+
+..  toctree::
+    :maxdepth: 2
+
+    self
+    trace
+    voltage_protocols
+

docs/source/trace.rst

@@ -0,0 +1,10 @@
+.. currentmodule:: syncropatch_export.trace
+
+**************
+Accessing data
+**************
+
+Data is accessed and exported via the :class:`Trace` class.
+
+.. autoclass:: Trace
+

docs/source/voltage_protocols.rst

@@ -0,0 +1,11 @@
+.. currentmodule:: syncropatch_export.voltage_protocols
+
+***************************
+Accessing voltage protocols
+***************************
+
+Voltage protocols can be parsed from the JSON data using the
+:class:`VoltageProtocol` class.
+
+.. autoclass:: VoltageProtocol
+

setup.py

@@ -4,14 +4,17 @@
 with open('README.md') as f:
     readme = f.read()
 
-# Load version number
-# with open('version.txt', 'r') as f:
-#     version = f.read()
 
-# Go!
+# Load version number
+import os   # isort:skip
+import sys  # isort:skip
+sys.path.append(os.path.abspath('syncropatch_export'))
+from _version import __version__ as version  # noqa isort:skip
+sys.path.pop()
+del os, sys
 
-version = '0.0.1'
 
+# Go!
 setup(
     # Module name (lowercase)
     name='syncropatch_export',
@@ -57,5 +60,8 @@
             'mock>=3.0.5',         # For mocking command line args etc.
             'codecov>=2.1.3',
         ],
+        'docs': [
+            'sphinx>=1.7.4',
+        ],
     },
 )

syncropatch_export/__init__.py

@@ -0,0 +1,5 @@
+#
+# Syncropatch, main module
+#
+from ._version import __version__  # noqa
+

syncropatch_export/_version.py

@@ -0,0 +1,4 @@
+#
+# Syncropatch_export version number
+#
+__version__ = '0.0.1'