From 34bfef6fb5b8bfc7025bff2f38965dc95d695db4 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:14:23 +0100
Subject: [PATCH 01/19] Added documentating. Added missing docstrings. Used
 single and double quotes consistently. Added developer info to README.md

---
 README.md                               |  28 ++++
 docs/.gitignore                         |   1 +
 docs/Makefile                           |  20 +++
 docs/make.bat                           |  36 ++++++
 docs/source/_static/bg.png              | Bin 0 -> 11174 bytes
 docs/source/conf.py                     | 163 ++++++++++++++++++++++++
 docs/source/index.rst                   |  15 +++
 docs/source/trace.rst                   |  10 ++
 docs/source/voltage_protocols.rst       |  11 ++
 setup.py                                |  16 ++-
 syncropatch_export/__init__.py          |   5 +
 syncropatch_export/_version.py          |   4 +
 syncropatch_export/trace.py             |  87 +++++++------
 syncropatch_export/voltage_protocols.py |  77 ++++++++---
 14 files changed, 407 insertions(+), 66 deletions(-)
 create mode 100644 docs/.gitignore
 create mode 100644 docs/Makefile
 create mode 100644 docs/make.bat
 create mode 100644 docs/source/_static/bg.png
 create mode 100644 docs/source/conf.py
 create mode 100644 docs/source/index.rst
 create mode 100644 docs/source/trace.rst
 create mode 100644 docs/source/voltage_protocols.rst
 create mode 100644 syncropatch_export/_version.py

diff --git a/README.md b/README.md
index 3d61d4f..ce1208d 100644
--- a/README.md
+++ b/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 +42,30 @@ 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/).
+
+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
+```
+
+
diff --git a/docs/.gitignore b/docs/.gitignore
new file mode 100644
index 0000000..a007fea
--- /dev/null
+++ b/docs/.gitignore
@@ -0,0 +1 @@
+build/*
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..ad732be
--- /dev/null
+++ b/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    = SyncropatchExport
+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)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..16faa53
--- /dev/null
+++ b/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=Myokit
+
+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
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diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..c5c072f
--- /dev/null
+++ b/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 = datkit.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'),
+]
+
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..f673e5c
--- /dev/null
+++ b/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
+
diff --git a/docs/source/trace.rst b/docs/source/trace.rst
new file mode 100644
index 0000000..083b087
--- /dev/null
+++ b/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
+
diff --git a/docs/source/voltage_protocols.rst b/docs/source/voltage_protocols.rst
new file mode 100644
index 0000000..0bab766
--- /dev/null
+++ b/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
+
diff --git a/setup.py b/setup.py
index 1d1727b..bdb0b74 100644
--- a/setup.py
+++ b/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
+import sys
+sys.path.append(os.path.abspath('syncropatch_export'))
+from _version import __version__ as version  # noqa
+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',
+        ],
     },
 )
diff --git a/syncropatch_export/__init__.py b/syncropatch_export/__init__.py
index e69de29..5519020 100644
--- a/syncropatch_export/__init__.py
+++ b/syncropatch_export/__init__.py
@@ -0,0 +1,5 @@
+#
+# Syncropatch, main module
+#
+from ._version import __version__
+
diff --git a/syncropatch_export/_version.py b/syncropatch_export/_version.py
new file mode 100644
index 0000000..106c18b
--- /dev/null
+++ b/syncropatch_export/_version.py
@@ -0,0 +1,4 @@
+#
+# Syncropatch_export version number
+#
+__version__ = '0.0.1'
diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index 380c8e9..936ee0a 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -9,11 +9,14 @@
 
 
 class Trace:
-    """ Defines a Trace object from the output of a Nanion experiment.
+    """
+    Defines a Trace object from the output of a Nanion experiment.
 
-    @params
-    filepath: path pointing to folder containing .json and .dat files (str)
-    json_file: specific filename of json file (str)
+    Args:
+        filepath (str): A path pointing to folder containing both ``.json`` and
+            ``.dat`` files.
+        json_file (str): The name of a JSON file within ``path``, from which
+            meta data will be read.
     """
 
     def __init__(self, filepath, json_file: str):
@@ -22,7 +25,7 @@ def __init__(self, filepath, json_file: str):
         if json_file[-5:] == '.json':
             self.json_file = json_file
         else:
-            self.json_file = json_file + ".json"
+            self.json_file = json_file + '.json'
 
         # load json file
         with open(os.path.join(self.filepath, self.json_file)) as f:
@@ -59,64 +62,65 @@ def __init__(self, filepath, json_file: str):
 
         self.voltage_protocol = self.get_voltage_protocol()
 
-    def get_voltage_protocol(self, holding_potential=-80.0):
-        """Extract information about the voltage protocol from the json file
-
-        returns: a VoltageProtocol object
-
+    def get_voltage_protocol(self):
         """
+        Extract information about the voltage protocol from the JSON file.
 
-        voltage_protocol = VoltageProtocol.from_json(
+        Returns:
+            VoltageProtocol: A voltage protocol object.
+        """
+        return VoltageProtocol.from_json(
             self.meta['ExperimentConditions']['VoltageProtocol'],
             self.meta['ExperimentConditions']['VMembrane_mV']
         )
 
-        return voltage_protocol
-
     def get_voltage_protocol_json(self):
         """
-        Returns the voltage protocol as a JSON object
+        Returns unparsed JSON object representing the voltage protocol.
         """
+        #TODO Why only the first row?
         return self.meta['ExperimentConditions']['VoltageProtocol'][0]
 
     def get_protocol_description(self, holding_potential=-80.0):
-        """Get the protocol as a numpy array describing the voltages and
-        durations for each section
+        """
+        Returns the protocol as an ``np.numpy`` with an entry for each segment.
 
-        returns: np.array where each row contains the start time, end time,
-        initial voltage, and final voltage
+        Returns:
+            np.array: An array where each row contains the start time,
+                end time, initial voltage, and final voltage of a ramp or step
+                segment.
 
         """
         return self.get_voltage_protocol().get_all_sections()
 
     def get_voltage(self):
-        '''
+        """
         Returns the voltage stimulus from Nanion .json file
-        '''
-        return np.array(self.TimeScaling['Stimulus']).astype(np.float64)\
-            * 1e3
+        """
+        return np.array(self.TimeScaling['Stimulus']).astype(np.float64) * 1e3
 
     def get_times(self):
-        '''
+        """
         Returns the time steps from Nanion .json file
-        '''
+        """
         return np.array(self.TimeScaling['TR_Time']) * 1e3
 
     def get_all_traces(self, leakcorrect=False):
-        '''
+        """
 
-        Params:
-        leakcorrect: Bool. Set to true if using onboard leak correction
+        Args:
+            leakcorrect (bool): Set to true if using onboard leak correction
 
-        Returns: all raw current traces from .dat files
+        Returns:
+            All raw current traces from .dat files
 
-        '''
+        """
         return self.get_trace_sweeps(leakcorrect=leakcorrect)
 
     def get_trace_file(self, sweeps):
-        '''
+        """
         Returns the trace file index of the file for a given set of sweeps
-        '''
+        """
         OUT_file_idx = []
         OUT_idx_i = []
         for actSweep in sweeps:
@@ -133,9 +137,9 @@ def get_trace_file(self, sweeps):
         return OUT_file_idx, OUT_idx_i
 
     def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
-        '''
-        Returns a subset of sweeps defined by the input 'sweeps'
-        '''
+        """
+        Returns a subset of sweeps defined by the input ``sweeps``.
+        """
 
         # initialise output
         out_dict = {}
@@ -221,13 +225,13 @@ def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
         return out_dict
 
     def get_onboard_QC_values(self, sweeps=None):
-        '''Read quality control values Rseal, Cslow (Cm), and Rseries from a Nanion .json file
+        """
+        Return the quality control values Rseal, Cslow (Cm), and Rseries.
 
         returns: A dictionary where the keys are the well e.g. 'A01' and the
         values are the values used for onboard QC i.e., the seal resistance,
         cell capacitance and the series resistance.
-
-        '''
+        """
 
         # load QC values
         RSeal = np.array(self.meta['QCData']['RSeal'])
@@ -262,11 +266,13 @@ def get_onboard_QC_values(self, sweeps=None):
         return out_dict
 
     def get_onboard_QC_df(self, sweeps=None):
-        """Create a Pandas DataFrame which lists the Rseries, memebrane
+        """
+        Create a Pandas DataFrame which lists the Rseries, memebrane
         capacitance and Rseries for each well and sweep.
 
-        @Returns A pandas.DataFrame describing the onboard QC estimates for
-        each well, sweep
+        Returns:
+            pandas.DataFrame: A data frame describing the onboard QC estimates
+                for each well, sweep
 
         """
 
@@ -288,3 +294,4 @@ def get_onboard_QC_df(self, sweeps=None):
                 df_rows.append(df_row)
 
         return pd.DataFrame.from_records(df_rows)
+
diff --git a/syncropatch_export/voltage_protocols.py b/syncropatch_export/voltage_protocols.py
index bdb0265..b2b9e52 100644
--- a/syncropatch_export/voltage_protocols.py
+++ b/syncropatch_export/voltage_protocols.py
@@ -1,26 +1,46 @@
 import numpy as np
 
 
-class VoltageProtocol():
-    def from_json(json_protocol, holding_potential):
-        """ Converts a protocol (from the json file) into a np.array
+class VoltageProtocol:
+    """
+    Represent a voltage step (and ramp) protocol.
 
+    Each protocol is represented as
+
+    1. A list of segment starts, ends, initial voltages, and final voltages
+    2. A holding potential
+
+    To create a :class:`VoltageProtocol`, use either
+    :meth:`VoltageProtocol.from_json` or
+    `meth:`VoltageProtocol.from_voltage_trace`.
+    """
+
+    @classmethod
+    def from_json(cls, json_protocol, holding_potential):
         """
+        Reads a protocol from a JSON file.
 
+        Args:
+            json_protocol (list): A list or other sequence containing the
+                ``VoltageProtocol`` section from the JSON file.
+            holding_potential (float): The holding potential
+
+        """
         output_sections = []
         for section in json_protocol:
             tstart = float(section['SegmentStart_ms'])
             tdur = float(section['Duration ms'])
             vstart = float(section['VoltageStart'])
             vend = float(section['VoltageEnd'])
+            output_sections.append((tstart, tstart + tdur, vstart, vend))
+        return cls(np.array(output_sections), holding_potential)
 
-            output_sections.append(np.array((tstart, tstart + tdur,
-                                             vstart, vend)))
-
-        return VoltageProtocol(np.array(output_sections),
-                               holding_potential=holding_potential)
-
-    def from_voltage_trace(voltage_trace, times, holding_potential=-80.0):
+    @classmethod
+    def from_voltage_trace(cls, voltage_trace, times, holding_potential=-80.0):
+        """
+        Creates an approximate voltage protocol from a time series ``(times,
+        voltage_trace)``.
+        """
         threshold = 1e-3
 
         # Find gradient changes
@@ -28,11 +48,11 @@ def from_voltage_trace(voltage_trace, times, holding_potential=-80.0):
 
         windows = np.argwhere(diff2 > threshold).flatten()
         window_locs = np.unique(windows)
-        window_locs = np.array([val for val in window_locs if val + 1
-                                not in window_locs]) + 1
+        window_locs = 1 + np.array([
+            val for val in window_locs if val + 1 not in window_locs])
 
-        windows = zip([0] + list(window_locs), list(window_locs)
-                      + [len(voltage_trace) - 1])
+        windows = zip([0] + list(window_locs),
+                      list(window_locs) + [len(voltage_trace) - 1])
 
         lst = []
         for start, end in windows:
@@ -53,31 +73,46 @@ def from_voltage_trace(voltage_trace, times, holding_potential=-80.0):
             lst.append(np.array([start_t, end_t, v_start, v_end]))
 
         desc = np.vstack(lst)
-        return VoltageProtocol(desc, holding_potential)
+        return cls(desc, holding_potential)
 
     def __init__(self, desc, holding_potential):
         self._desc = desc
         self.holding_potential = holding_potential
 
     def get_holding_potential(self):
+        """ Returns this protocol's holding potential. """
         return self.holding_potential
 
     def get_step_start_times(self):
+        """ Returns a list of all segment start times. """
         return [line[0] for line in self._desc]
 
     def get_ramps(self):
+        """
+        Returns all segments that are ramps.
+
+        Each segment is represented as ``(start time, end time, start voltage,
+        end voltage)``.
+        """
         return [line for line in self._desc if line[2] != line[3]]
 
     def get_all_sections(self):
-        """ Return a np.array describing the protocol.
-
-        returns: an np.array where the ith row is the start-time,
-        end-time, start-voltage and end-voltage for the ith section of the protocol
-
+        """
+        Return an ``np.array`` describing the protocol, where each row in the
+        array contains the the start time, end time, initial voltage and final
+        voltage for a segment of the protocol.
         """
         return np.array(self._desc)
 
     def export_txt(self, fname):
+        """
+        Writes a partial textual representation of this protocol to a file.
+
+        The created file will have a header line, followed by one line per
+        segment. Segments are represented as "Type" (Set or Ramp), "Voltage"
+        (the final voltage of a segment), and "Duration".
+        """
+
         output_lines = ['Type \t Voltage \t Duration']
 
         desc = self.get_all_sections()
@@ -93,7 +128,7 @@ def export_txt(self, fname):
             if round:
                 vend = np.round(vend)
 
-            output_lines.append(f"{_type}\t{vend}\t{dur}")
+            output_lines.append(f'{_type}\t{vend}\t{dur}')
 
         with open(fname, 'w') as fout:
             for line in output_lines:

From 2a1326dacccfa4f24450313576487e4a875d7022 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:22:01 +0100
Subject: [PATCH 02/19] Update flake8 ignore rules

---
 .flake8                        | 5 ++---
 docs/source/conf.py            | 6 +++---
 syncropatch_export/__init__.py | 2 +-
 syncropatch_export/trace.py    | 2 +-
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.flake8 b/.flake8
index ab31112..4585697 100644
--- a/.flake8
+++ b/.flake8
@@ -9,10 +9,9 @@ ignore =
     W504,
     # missing whitespace around arithmetic operator
     E226,
-    # Import sorting
-    I201
-    I100
 
 exclude=
     .git,
+    .github,
     venv,
+    tests/test_data,
diff --git a/docs/source/conf.py b/docs/source/conf.py
index c5c072f..d1a2f70 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -19,7 +19,7 @@
 # -- General configuration ----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# 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.
@@ -33,7 +33,7 @@
 # Autodoc defaults
 autodoc_default_options = {
     'members': None,
-    #'inherited-members': None,
+    # 'inherited-members': None,
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -50,7 +50,7 @@
 
 # General information about the project.
 project = u'Syncropatch export'
-#copyright = datkit.COPYRIGHT
+# copyright = datkit.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
diff --git a/syncropatch_export/__init__.py b/syncropatch_export/__init__.py
index 5519020..53ae12e 100644
--- a/syncropatch_export/__init__.py
+++ b/syncropatch_export/__init__.py
@@ -1,5 +1,5 @@
 #
 # Syncropatch, main module
 #
-from ._version import __version__
+from ._version import __version__  # noqa
 
diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index 936ee0a..0e26536 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -78,7 +78,7 @@ def get_voltage_protocol_json(self):
         """
         Returns unparsed JSON object representing the voltage protocol.
         """
-        #TODO Why only the first row?
+        # TODO Why only the first row?
         return self.meta['ExperimentConditions']['VoltageProtocol'][0]
 
     def get_protocol_description(self, holding_potential=-80.0):

From 882e39beff2373955b3616ad661d388e7ec1697c Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:26:39 +0100
Subject: [PATCH 03/19] Added #noqa to unusual import

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index bdb0b74..14aac91 100644
--- a/setup.py
+++ b/setup.py
@@ -6,8 +6,8 @@
 
 
 # Load version number
-import os
-import sys
+import os   # noqa
+import sys  # noqa
 sys.path.append(os.path.abspath('syncropatch_export'))
 from _version import __version__ as version  # noqa
 sys.path.pop()

From 0e0c1de2b375983013e1785329e6042220b53ceb Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:28:56 +0100
Subject: [PATCH 04/19] Added # isort:skip for unusual import

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 14aac91..2a53965 100644
--- a/setup.py
+++ b/setup.py
@@ -6,8 +6,8 @@
 
 
 # Load version number
-import os   # noqa
-import sys  # noqa
+import os   # isort:skip
+import sys  # isort:skip
 sys.path.append(os.path.abspath('syncropatch_export'))
 from _version import __version__ as version  # noqa
 sys.path.pop()

From ba2c0e8f344127bd71f08f3be0b776caef968635 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:30:00 +0100
Subject: [PATCH 05/19] Added # isort:skip for unusual import

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2a53965..af05e42 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@
 import os   # isort:skip
 import sys  # isort:skip
 sys.path.append(os.path.abspath('syncropatch_export'))
-from _version import __version__ as version  # noqa
+from _version import __version__ as version  # noqa isort:skip
 sys.path.pop()
 del os, sys
 

From 9fcd993841f927e255283a675823167cd34c569a Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 15:33:06 +0100
Subject: [PATCH 06/19] Added style and isort instructions to readme

---
 README.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/README.md b/README.md
index ce1208d..3d66263 100644
--- a/README.md
+++ b/README.md
@@ -57,6 +57,15 @@ Tests are written using the standard [unittest](https://docs.python.org/3.13/lib
 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
 ```

From 8d386fcc65b43932552ed43416cbbd63b9f94bd9 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 16:41:35 +0100
Subject: [PATCH 07/19] Removed unused holding_potential argument

---
 syncropatch_export/trace.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index 0e26536..18cb570 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -81,7 +81,7 @@ def get_voltage_protocol_json(self):
         # TODO Why only the first row?
         return self.meta['ExperimentConditions']['VoltageProtocol'][0]
 
-    def get_protocol_description(self, holding_potential=-80.0):
+    def get_protocol_description(self):
         """
         Returns the protocol as an ``np.numpy`` with an entry for each segment.
 
@@ -119,7 +119,8 @@ def get_all_traces(self, leakcorrect=False):
 
     def get_trace_file(self, sweeps):
         """
-        Returns the trace file index of the file for a given set of sweeps
+        Returns the trace file index
+         of the file for a given set of sweeps
         """
         OUT_file_idx = []
         OUT_idx_i = []

From 92707e95f78bc837ff5473bec2f0b88d4bb4fe90 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 16:45:39 +0100
Subject: [PATCH 08/19] Tidied up docs config

---
 docs/Makefile                   |   2 +-
 docs/make.bat                   |   2 +-
 docs/source/_static/bg.png      | Bin 11174 -> 0 bytes
 docs/source/_static/placeholder |   1 +
 docs/source/conf.py             |   2 +-
 5 files changed, 4 insertions(+), 3 deletions(-)
 delete mode 100644 docs/source/_static/bg.png
 create mode 100644 docs/source/_static/placeholder

diff --git a/docs/Makefile b/docs/Makefile
index ad732be..0a6e431 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = SyncropatchExport
+SPHINXPROJ    = syncropath_export
 SOURCEDIR     = source
 BUILDDIR      = build
 
diff --git a/docs/make.bat b/docs/make.bat
index 16faa53..a56a7d5 100644
--- a/docs/make.bat
+++ b/docs/make.bat
@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=source
 set BUILDDIR=build
-set SPHINXPROJ=Myokit
+set SPHINXPROJ=syncropath_export
 
 if "%1" == "" goto help
 
diff --git a/docs/source/_static/bg.png b/docs/source/_static/bg.png
deleted file mode 100644
index 96009e79a27bc3cd666481b1bbca37334b4bc7ef..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/docs/source/_static/placeholder b/docs/source/_static/placeholder
new file mode 100644
index 0000000..8566aa9
--- /dev/null
+++ b/docs/source/_static/placeholder
@@ -0,0 +1 @@
+Images etc. can be placed here
diff --git a/docs/source/conf.py b/docs/source/conf.py
index d1a2f70..456da49 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -50,7 +50,7 @@
 
 # General information about the project.
 project = u'Syncropatch export'
-# copyright = datkit.COPYRIGHT
+# copyright = syncropath_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

From a35da7ab4a87eff7d787b8e5a922ee16f0dae292 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 16:46:46 +0100
Subject: [PATCH 09/19] Fixed typo

---
 docs/Makefile       | 2 +-
 docs/make.bat       | 2 +-
 docs/source/conf.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/Makefile b/docs/Makefile
index 0a6e431..e9bd66d 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = syncropath_export
+SPHINXPROJ    = syncropatch_export
 SOURCEDIR     = source
 BUILDDIR      = build
 
diff --git a/docs/make.bat b/docs/make.bat
index a56a7d5..481a7ec 100644
--- a/docs/make.bat
+++ b/docs/make.bat
@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=source
 set BUILDDIR=build
-set SPHINXPROJ=syncropath_export
+set SPHINXPROJ=syncropatch_export
 
 if "%1" == "" goto help
 
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 456da49..d708f16 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -50,7 +50,7 @@
 
 # General information about the project.
 project = u'Syncropatch export'
-# copyright = syncropath_export.COPYRIGHT
+# 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

From 893b79917b64fa4a08af259742eefbe082f2df45 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 17:56:46 +0100
Subject: [PATCH 10/19] Improved docstrings in Trace class

---
 syncropatch_export/trace.py | 91 +++++++++++++++++++++++++++----------
 1 file changed, 67 insertions(+), 24 deletions(-)

diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index 18cb570..3c1a26e 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -10,7 +10,18 @@
 
 class Trace:
     """
-    Defines a Trace object from the output of a Nanion experiment.
+    Reads a Nanion experiment and provides access to the data and meta data it
+    contains.
+
+    To create a :class:`Trace`, a directory name should be passed in, along
+    with the name of a JSON file within that directory containing the meta
+    data. Data can then be accessed using :meth:`get_all_traces` (to obtain a
+    ``dict`` mapping well names onto a 2-d numpy array containing the sampled
+    currents (in pA) for all sweeps.
+
+    Well are
+
+
 
     Args:
         filepath (str): A path pointing to folder containing both ``.json`` and
@@ -44,6 +55,13 @@ def __init__(self, filepath, json_file: str):
         self.MeasurementLayout = TraceHeader['MeasurementLayout']
         self.FileInformation = TraceHeader['FileInformation']
 
+        # Create (hardcoded) list-of-list of well names:
+        #  [['A01', 'B01', ..., 'P01'],
+        #   ['A02', 'B02', ..., 'P02'],
+        #   ...
+        #   ['A24', 'B24', ..., 'P24']]
+        # So a list of 24 lists with 16 entries each
+        #
         self.WELL_ID = np.array([
             [lab + str(i).zfill(2) for lab in string.ascii_uppercase[:16]]
             for i in range(1, 25)])
@@ -67,7 +85,7 @@ def get_voltage_protocol(self):
         Extract information about the voltage protocol from the JSON file.
 
         Returns:
-            VoltageProtocol: A voltage protocol object.
+            The :class:`VoltageProtocol` used in this experiment.
         """
         return VoltageProtocol.from_json(
             self.meta['ExperimentConditions']['VoltageProtocol'],
@@ -76,7 +94,8 @@ def get_voltage_protocol(self):
 
     def get_voltage_protocol_json(self):
         """
-        Returns unparsed JSON object representing the voltage protocol.
+        Returns an unparsed JSON object representing the first segment of the
+        voltage protocol.
         """
         # TODO Why only the first row?
         return self.meta['ExperimentConditions']['VoltageProtocol'][0]
@@ -86,33 +105,43 @@ def get_protocol_description(self):
         Returns the protocol as an ``np.numpy`` with an entry for each segment.
 
         Returns:
-            np.array: An array where each row contains the start time,
-                end time, initial voltage, and final voltage of a ramp or step
-                segment.
+            A numpy ``array`` where each row contains the start time, end time,
+            initial voltage, and final voltage of a ramp or step segment.
 
         """
         return self.get_voltage_protocol().get_all_sections()
 
     def get_voltage(self):
         """
-        Returns the voltage stimulus from Nanion .json file
+        Returns an array containing voltages (in mV) for each sampled point in
+        the traces.
         """
         return np.array(self.TimeScaling['Stimulus']).astype(np.float64) * 1e3
 
     def get_times(self):
         """
-        Returns the time steps from Nanion .json file
+        Returns the sampled times (in ms).
         """
         return np.array(self.TimeScaling['TR_Time']) * 1e3
 
     def get_all_traces(self, leakcorrect=False):
         """
+        Returns data for all wells and all sweeps (equivalent to calling
+        :meth:`get_trace_sweeps()` without any arguments).
+
+        Current is returned in pA.
+
+        By default, the data is returned without leak correction, but the leak
+        corrected data can be obtained by setting ``leakcorrect=True``.
 
         Args:
-            leakcorrect (bool): Set to true if using onboard leak correction
+            sweeps (int): The number of sweeps to return.
+            leakcorrect (bool): Used to choose corrected or uncorrected data.
 
         Returns:
-            All raw current traces from .dat files
+            A dictionary mapping well names (e.g. "A01") onto 2-d numpy arrays
+            of shape ``n_sweeps, n_times`` where ``n_sweeps`` is the number of
+            sweeps and ``n_times`` is the number of sampled points.
 
         """
         return self.get_trace_sweeps(leakcorrect=leakcorrect)
@@ -139,7 +168,22 @@ def get_trace_file(self, sweeps):
 
     def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
         """
-        Returns a subset of sweeps defined by the input ``sweeps``.
+        Returns the first ``sweeps`` sweeps, for all wells.
+
+        Current is returned in pA.
+
+        By default, the data is returned without leak correction, but the leak
+        corrected data can be obtained by setting ``leakcorrect=True``.
+
+        Args:
+            sweeps (int): The number of sweeps to return.
+            leakcorrect (bool): Used to choose corrected or uncorrected data.
+
+        Returns:
+            A dictionary mapping well names (e.g. "A01") onto 2-d numpy arrays
+            of shape ``n_sweeps, n_times`` where ``n_sweeps`` is the number of
+            sweeps and ``n_times`` is the number of sampled points.
+
         """
 
         # initialise output
@@ -149,11 +193,11 @@ def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
                 out_dict[ijWell] = []
 
         if sweeps is None:
-            #  Sometimes NofSweeps seems to be incorrect
+            # Sometimes NofSweeps seems to be incorrect
             sweeps = list(range(self.NofSweeps))
 
-        # check `getsweep` input is something sensible
-        if len(sweeps) > self.NofSweeps:
+        # Check `sweeps` is something sensible
+        elif len(sweeps) > self.NofSweeps:
             raise ValueError('Required #sweeps > total #sweeps.')
 
         # convert negative values to positive
@@ -193,9 +237,7 @@ def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
 
                 # convert to double in pA
                 iColTraces = trace[idx_i:idx_f] * self.I2DScale[i] * 1e12
-                iColWells = self.WELL_ID[i]
-
-                for j, ijWell in enumerate(iColWells):
+                for j, ijWell in enumerate(self.WELL_ID[i]):
                     if leakcorrect:
                         leakoffset = 1
                     else:
@@ -229,9 +271,11 @@ def get_onboard_QC_values(self, sweeps=None):
         """
         Return the quality control values Rseal, Cslow (Cm), and Rseries.
 
-        returns: A dictionary where the keys are the well e.g. 'A01' and the
-        values are the values used for onboard QC i.e., the seal resistance,
-        cell capacitance and the series resistance.
+        Returns:
+            A dict mapping well names ('A01' up to 'P24') to tuples
+            ``(R_seal, Cm, R_series)`` containing the seal resistance, membrane
+            capacitance, and series resistance.
+
         """
 
         # load QC values
@@ -268,12 +312,11 @@ def get_onboard_QC_values(self, sweeps=None):
 
     def get_onboard_QC_df(self, sweeps=None):
         """
-        Create a Pandas DataFrame which lists the Rseries, memebrane
-        capacitance and Rseries for each well and sweep.
+        Create a Pandas DataFrame containing the seal resistance, membrane
+        capacitance, and series resistance for each well and sweep.
 
         Returns:
-            pandas.DataFrame: A data frame describing the onboard QC estimates
-                for each well, sweep
+            A ``pandas.DataFrame`` with the onboard QC estimates.
 
         """
 

From 635bc3d7853f5f5d82ca7e23efbf9c97c02324f7 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 21:48:01 +0100
Subject: [PATCH 11/19] Made default VoltageTrace constructor copy mutable
 list/array data

---
 syncropatch_export/voltage_protocols.py | 28 ++++++++++---------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/syncropatch_export/voltage_protocols.py b/syncropatch_export/voltage_protocols.py
index b2b9e52..fe6c59f 100644
--- a/syncropatch_export/voltage_protocols.py
+++ b/syncropatch_export/voltage_protocols.py
@@ -3,7 +3,7 @@
 
 class VoltageProtocol:
     """
-    Represent a voltage step (and ramp) protocol.
+    Represent a voltage step and ramp protocol.
 
     Each protocol is represented as
 
@@ -15,6 +15,10 @@ class VoltageProtocol:
     `meth:`VoltageProtocol.from_voltage_trace`.
     """
 
+    def __init__(self, desc, holding_potential, copy_data=True):
+        self._desc = np.copy(desc) if copy_data else desc
+        self.holding_potential = holding_potential
+
     @classmethod
     def from_json(cls, json_protocol, holding_potential):
         """
@@ -33,7 +37,7 @@ def from_json(cls, json_protocol, holding_potential):
             vstart = float(section['VoltageStart'])
             vend = float(section['VoltageEnd'])
             output_sections.append((tstart, tstart + tdur, vstart, vend))
-        return cls(np.array(output_sections), holding_potential)
+        return cls(np.array(output_sections), holding_potential, False)
 
     @classmethod
     def from_voltage_trace(cls, voltage_trace, times, holding_potential=-80.0):
@@ -45,12 +49,9 @@ def from_voltage_trace(cls, voltage_trace, times, holding_potential=-80.0):
 
         # Find gradient changes
         diff2 = np.abs(np.diff(voltage_trace, n=2))
-
-        windows = np.argwhere(diff2 > threshold).flatten()
-        window_locs = np.unique(windows)
+        window_locs = np.unique(np.argwhere(diff2 > threshold).flatten())
         window_locs = 1 + np.array([
             val for val in window_locs if val + 1 not in window_locs])
-
         windows = zip([0] + list(window_locs),
                       list(window_locs) + [len(voltage_trace) - 1])
 
@@ -58,26 +59,19 @@ def from_voltage_trace(cls, voltage_trace, times, holding_potential=-80.0):
         for start, end in windows:
             start_t = times[start]
             end_t = times[end]
-
-            ramp = voltage_trace[end - 1] != voltage_trace[start]
-
             v_start = voltage_trace[start]
-
-            if ramp:
+            if voltage_trace[end - 1] != voltage_trace[start]:
+                # Ramp
                 grad = (voltage_trace[end - 1] - voltage_trace[start]) / \
                     (times[end - 1] - times[start])
                 v_end = v_start + grad * (end_t - start_t)
             else:
+                # Step
                 v_end = voltage_trace[end - 1]
 
             lst.append(np.array([start_t, end_t, v_start, v_end]))
 
-        desc = np.vstack(lst)
-        return cls(desc, holding_potential)
-
-    def __init__(self, desc, holding_potential):
-        self._desc = desc
-        self.holding_potential = holding_potential
+        return cls(np.vstack(lst), holding_potential, False)
 
     def get_holding_potential(self):
         """ Returns this protocol's holding potential. """

From ea24c57791b88d5c138c4d31472c55001fbc99e6 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 21:52:02 +0100
Subject: [PATCH 12/19] Added cover pragma to tests themselves

---
 tests/test_trace_class.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index 0b4901b..7d8ab8a 100644
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -19,7 +19,7 @@ def setUp(self):
         self.output_dir = os.path.join('test_output', 'test_trace_class')
 
         if not os.path.exists(self.output_dir):
-            os.makedirs(self.output_dir)
+            os.makedirs(self.output_dir)    # pragma: no-cover
         self.test_trace = tr(filepath, json_file)
 
     def test_protocol_descriptions(self):
@@ -60,11 +60,10 @@ def voltage_func(t):
             for tstart, tend, vstart, vend in voltage_protocol.get_all_sections():
                 if t >= tstart and t < tend:
                     if vstart != vend:
-                        return vstart + (vend - vstart) * (t - tstart)/(tend - tstart)
+                        return vstart + (vend - vstart) * (t - tstart) / (tend - tstart)
                     else:
                         return vstart
-
-            return voltage_protocol.get_holding_potential()
+            return voltage_protocol.get_holding_potential()  # pragma: no-cover
 
         for t, v in zip(times, voltages):
             self.assertLess(voltage_func(t) - v, 1e-3)

From 7061902838aa77c622d2f15c89f78acdc3ecdeec Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:22:02 +0100
Subject: [PATCH 13/19] Made tests use temporary directory. Added missing unit
 tests.

---
 tests/test_trace_class.py | 86 +++++++++++++++++++++++----------------
 1 file changed, 51 insertions(+), 35 deletions(-)
 mode change 100644 => 100755 tests/test_trace_class.py

diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
old mode 100644
new mode 100755
index 7d8ab8a..7038ba2
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -1,32 +1,33 @@
+#!/usr/bin/env python
 import json
 import os
+import tempfile
 import unittest
 
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 
-from syncropatch_export.trace import Trace as tr
+from syncropatch_export.trace import Trace
 from syncropatch_export.voltage_protocols import VoltageProtocol
 
 
 class TestTraceClass(unittest.TestCase):
-    def setUp(self):
-        filepath = os.path.join('tests', 'test_data', '13112023_MW2_FF',
-                                'staircaseramp (2)_2kHz_15.01.07')
-        json_file = "staircaseramp (2)_2kHz_15.01.07"
+    """
+    Tests both the Trace and VoltageProtocol classes.
+    """
 
-        self.output_dir = os.path.join('test_output', 'test_trace_class')
 
-        if not os.path.exists(self.output_dir):
-            os.makedirs(self.output_dir)    # pragma: no-cover
-        self.test_trace = tr(filepath, json_file)
+    def setUp(self):
+        f = 'staircaseramp (2)_2kHz_15.01.07'
+        self.trace = Trace(
+            os.path.join('tests', 'test_data', '13112023_MW2_FF', f), f)
 
     def test_protocol_descriptions(self):
-        voltages = self.test_trace.get_voltage()
-        times = self.test_trace.get_times()
+        voltages = self.trace.get_voltage()
+        times = self.trace.get_times()
 
-        protocol_from_json = self.test_trace.get_voltage_protocol()
+        protocol_from_json = self.trace.get_voltage_protocol()
         holding_potential = protocol_from_json.get_holding_potential()
         protocol_desc = VoltageProtocol.from_voltage_trace(voltages, times,
                                                            holding_potential)
@@ -43,18 +44,17 @@ def test_protocol_descriptions(self):
         self.assertLess(v_error, 1e-4)
 
     def test_protocol_export(self):
-        protocol = self.test_trace.get_voltage_protocol()
-        protocol.export_txt(os.path.join(self.output_dir, 'protocol.txt'))
-        json_protocol = self.test_trace.get_voltage_protocol_json()
-
-        with open(os.path.join(self.output_dir, 'protocol.json'), 'w') as fin:
-            json.dump(json_protocol, fin)
+        with tempfile.TemporaryDirectory() as d:
+            protocol = self.trace.get_voltage_protocol()
+            protocol.export_txt(os.path.join(d, 'protocol.txt'))
+            json_protocol = self.trace.get_voltage_protocol_json()
+            with open(os.path.join(d, 'protocol.json'), 'w') as fin:
+                json.dump(json_protocol, fin)
 
     def test_protocol_timeseries(self):
-        voltages = self.test_trace.get_voltage()
-        times = self.test_trace.get_times()
-
-        voltage_protocol = self.test_trace.get_voltage_protocol()
+        voltages = self.trace.get_voltage()
+        times = self.trace.get_times()
+        voltage_protocol = self.trace.get_voltage_protocol()
 
         def voltage_func(t):
             for tstart, tend, vstart, vend in voltage_protocol.get_all_sections():
@@ -68,21 +68,33 @@ def voltage_func(t):
         for t, v in zip(times, voltages):
             self.assertLess(voltage_func(t) - v, 1e-3)
 
+    def test_protocol_get_step_start_times(self):
+        a = list(self.trace.get_voltage_protocol().get_step_start_times())
+        b = [0, 250, 300, 696, 896, 1896, 2396, 3396, 3896, 4396, 4896, 5396,
+             5896, 6396, 6896, 7396, 7896, 8396, 8896, 9396, 9896, 10396,
+             10896, 11396, 11896, 12396, 12896, 13896, 14396, 14406, 14502,
+             14892]
+        self.assertEqual(a, b)
+
+    def test_protocol_get_ramps(self):
+        a = np.array(self.trace.get_voltage_protocol().get_ramps())
+        b = np.array([[300, 696, -120, -80], [14406, 14502, -70, -110]])
+        self.assertEqual(a.shape, b.shape)
+        self.assertTrue(np.all(a == b))
+
     def test_get_QC(self):
-        tr = self.test_trace
-        QC_values = tr.get_onboard_QC_values()
+        QC_values = self.trace.get_onboard_QC_values()
         self.assertGreater(len(QC_values), 0)
-        df = tr.get_onboard_QC_df()
+        df = self.trace.get_onboard_QC_df()
 
         self.assertGreater(df.shape[0], 0)
         self.assertGreater(df.shape[1], 0)
 
     def test_get_traces(self):
-        tr = self.test_trace
-        v = tr.get_voltage()
-        ts = tr.get_times()
-        all_traces = tr.get_all_traces(leakcorrect=True)
-        all_traces = tr.get_all_traces()
+        v = self.trace.get_voltage()
+        ts = self.trace.get_times()
+        all_traces = self.trace.get_all_traces(leakcorrect=True)
+        all_traces = self.trace.get_all_traces()
 
         self.assertTrue(np.all(np.isfinite(v)))
         self.assertTrue(np.all(np.isfinite(ts)))
@@ -90,11 +102,12 @@ def test_get_traces(self):
         for well, trace in all_traces.items():
             self.assertTrue(np.all(np.isfinite(trace)))
 
+        '''
         if self.output_dir:
             # plot test output
             fig, (ax1, ax2) = plt.subplots(2, 1)
             ax1.set_title("Example Sweeps")
-            some_sweeps = tr.get_trace_sweeps([0])['A01']
+            some_sweeps = self.trace.get_trace_sweeps([0])['A01']
 
             ax1.plot(ts, np.transpose(some_sweeps), color='grey', alpha=0.5)
             ax1.set_ylabel('Current')
@@ -104,13 +117,13 @@ def test_get_traces(self):
             ax2.set_ylabel('Voltage')
             ax2.set_xlabel('Time')
             plt.tight_layout()
-            plt.savefig(os.path.join(self.output_dir,
-                                     'example_trace'))
+            plt.savefig(os.path.join(self.output_dir, 'example_trace'))
             plt.close(fig)
+        '''
 
     def test_qc_df(self):
-        dfs = [self.test_trace.get_onboard_QC_df(sweeps=[0]),
-               self.test_trace.get_onboard_QC_df(sweeps=None)]
+        dfs = [self.trace.get_onboard_QC_df(sweeps=[0]),
+               self.trace.get_onboard_QC_df(sweeps=None)]
         for res in dfs:
             # Check res is a pd.DataFrame
             self.assertIsInstance(res, pd.DataFrame)
@@ -125,3 +138,6 @@ def test_qc_df(self):
         # Check restricting number of sweeps returns less data
         self.assertLess(dfs[0].shape[0], dfs[1].shape[0])
 
+
+if __name__ == '__main__':
+    unittest.main()

From c3263f7de3618300703feee6ba5c3b40c5109b2f Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:25:17 +0100
Subject: [PATCH 14/19] Style fix

---
 tests/test_trace_class.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index 7038ba2..10a435a 100755
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -4,7 +4,6 @@
 import tempfile
 import unittest
 
-import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 
@@ -17,7 +16,6 @@ class TestTraceClass(unittest.TestCase):
     Tests both the Trace and VoltageProtocol classes.
     """
 
-
     def setUp(self):
         f = 'staircaseramp (2)_2kHz_15.01.07'
         self.trace = Trace(
@@ -103,21 +101,26 @@ def test_get_traces(self):
             self.assertTrue(np.all(np.isfinite(trace)))
 
         '''
-        if self.output_dir:
-            # plot test output
+        # plot test output
+        if False:
+            d = 'test_output'
+            if not os.path.exists(d):
+                os.makedirs(d)
+
+            import matplotlib.pyplot as plt
             fig, (ax1, ax2) = plt.subplots(2, 1)
-            ax1.set_title("Example Sweeps")
+            ax1.set_title('Example Sweeps')
             some_sweeps = self.trace.get_trace_sweeps([0])['A01']
 
             ax1.plot(ts, np.transpose(some_sweeps), color='grey', alpha=0.5)
             ax1.set_ylabel('Current')
             ax1.set_xlabel('Time')
-            ax2.set_title("Voltage Protocol")
+            ax2.set_title('Voltage Protocol')
             ax2.plot(ts, v)
             ax2.set_ylabel('Voltage')
             ax2.set_xlabel('Time')
             plt.tight_layout()
-            plt.savefig(os.path.join(self.output_dir, 'example_trace'))
+            plt.savefig(os.path.join(d, 'example_trace'))
             plt.close(fig)
         '''
 

From fc7d1d2ee51f5b1da90dda3ae0547172dc83aa51 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:33:41 +0100
Subject: [PATCH 15/19] Added missing unit tests

---
 syncropatch_export/trace.py | 7 +++----
 tests/test_trace_class.py   | 6 ++++++
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index 3c1a26e..d3c5725 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -33,10 +33,9 @@ class Trace:
     def __init__(self, filepath, json_file: str):
         # store file paths
         self.filepath = filepath
-        if json_file[-5:] == '.json':
-            self.json_file = json_file
-        else:
-            self.json_file = json_file + '.json'
+        self.json_file = json_file
+        if not json_file.endswith('.json'):
+            self.json_file += '.json'
 
         # load json file
         with open(os.path.join(self.filepath, self.json_file)) as f:
diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index 10a435a..7cb9c6f 100755
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -41,6 +41,12 @@ def test_protocol_descriptions(self):
         self.assertLess(t_error, 1e-2)
         self.assertLess(v_error, 1e-4)
 
+    def test_get_protocol_description(self):
+        a = np.array(self.trace.get_protocol_description())
+        b = np.array(self.trace.get_voltage_protocol().get_all_sections())
+        self.assertEqual(a.shape, b.shape)
+        self.assertTrue(np.all(a == b))
+
     def test_protocol_export(self):
         with tempfile.TemporaryDirectory() as d:
             protocol = self.trace.get_voltage_protocol()

From ab5772409da1208a3d2fb95c228c4afa046c6975 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:46:54 +0100
Subject: [PATCH 16/19] Added missing unit tests

---
 syncropatch_export/trace.py | 26 +++++++++++++++-----------
 tests/test_trace_class.py   | 13 +++++++++++++
 2 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/syncropatch_export/trace.py b/syncropatch_export/trace.py
index d3c5725..cb144a6 100644
--- a/syncropatch_export/trace.py
+++ b/syncropatch_export/trace.py
@@ -175,7 +175,7 @@ def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
         corrected data can be obtained by setting ``leakcorrect=True``.
 
         Args:
-            sweeps (int): The number of sweeps to return.
+            sweeps (list): A list of sweep indexes to return, e.g. ``[0, 1, 2]``.
             leakcorrect (bool): Used to choose corrected or uncorrected data.
 
         Returns:
@@ -191,18 +191,22 @@ def get_trace_sweeps(self, sweeps=None, leakcorrect=False):
             for ijWell in iCol:
                 out_dict[ijWell] = []
 
+        # No sweeps selected? Then return full set
         if sweeps is None:
-            # Sometimes NofSweeps seems to be incorrect
             sweeps = list(range(self.NofSweeps))
-
-        # Check `sweeps` is something sensible
-        elif len(sweeps) > self.NofSweeps:
-            raise ValueError('Required #sweeps > total #sweeps.')
-
-        # convert negative values to positive
-        for i, sweep in enumerate(sweeps):
-            if sweep < 0:
-                sweeps[i] = self.NofSweeps + sweep
+        else:
+            # Allow negative values to index later sweeps
+            sweeps = [self.NofSweeps + x if x < 0 else x for x in sweeps]
+            # Check all sweeps exist
+            if max(sweeps) >= self.NofSweeps:
+                raise ValueError(
+                    f'Invalid sweep selection: sweep {max(sweeps)} requested,'
+                    f' but only {self.NofSweeps} available.')
+            if min(sweeps) < 0:
+                raise ValueError(
+                    f'Invalid sweep selection: sweep'
+                    f' {min(sweeps) - self.NofSweeps} requested, but only'
+                    f' {self.NofSweeps} available.')
 
         trace_file_idxs, idx_is = self.get_trace_file(sweeps)
 
diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index 7cb9c6f..5bb0676 100755
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -99,6 +99,7 @@ def test_get_traces(self):
         ts = self.trace.get_times()
         all_traces = self.trace.get_all_traces(leakcorrect=True)
         all_traces = self.trace.get_all_traces()
+        # TODO: Check the output, numerically, by comparing a few points
 
         self.assertTrue(np.all(np.isfinite(v)))
         self.assertTrue(np.all(np.isfinite(ts)))
@@ -106,6 +107,18 @@ def test_get_traces(self):
         for well, trace in all_traces.items():
             self.assertTrue(np.all(np.isfinite(trace)))
 
+        # Test complex sweep selection
+        a = self.trace.get_trace_sweeps([-1, -2])
+        b = self.trace.get_trace_sweeps([1, 0])
+        self.assertEqual(len(a), len(b))
+        self.assertTrue(np.all(a['A01'] == b['A01']))
+
+        # Test asking for non-existent sweeps
+        self.assertRaisesRegex(ValueError, 'Invalid sweep selection',
+                               self.trace.get_trace_sweeps, [2])
+        self.assertRaisesRegex(ValueError, 'Invalid sweep selection',
+                               self.trace.get_trace_sweeps, [-3])
+
         '''
         # plot test output
         if False:

From 14a279be31949fe99889defb129047ebf9868afd Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:49:40 +0100
Subject: [PATCH 17/19] Fixed cover pragma

---
 tests/test_trace_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index 5bb0676..a51295a 100755
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -67,7 +67,7 @@ def voltage_func(t):
                         return vstart + (vend - vstart) * (t - tstart) / (tend - tstart)
                     else:
                         return vstart
-            return voltage_protocol.get_holding_potential()  # pragma: no-cover
+            return voltage_protocol.get_holding_potential()  # pragma: no cover
 
         for t, v in zip(times, voltages):
             self.assertLess(voltage_func(t) - v, 1e-3)

From 1ae5d98f0c245e766814441f2fe2779b33a21d53 Mon Sep 17 00:00:00 2001
From: Michael Clerx <michael.clerx@nottingham.ac.uk>
Date: Tue, 15 Jul 2025 22:50:36 +0100
Subject: [PATCH 18/19] Added cover pragma

---
 tests/test_trace_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_trace_class.py b/tests/test_trace_class.py
index a51295a..bee8289 100755
--- a/tests/test_trace_class.py
+++ b/tests/test_trace_class.py
@@ -162,4 +162,4 @@ def test_qc_df(self):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()  # pragma: no cover

From 41b8d357bcab3b98c32fbb7722c27d74028d53dc Mon Sep 17 00:00:00 2001
From: Michael Clerx <MichaelClerx@users.noreply.github.com>
Date: Wed, 16 Jul 2025 11:51:08 +0100
Subject: [PATCH 19/19] Update .flake8

Co-authored-by: Kwabena Amponsah <kwabenantim@yahoo.com>
---
 .flake8 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.flake8 b/.flake8
index 4585697..8f9ea55 100644
--- a/.flake8
+++ b/.flake8
@@ -13,5 +13,6 @@ ignore =
 exclude=
     .git,
     .github,
+    .venv,
     venv,
     tests/test_data,