Added type hints and updating contributing.md

Author: MichaelClerx

.flake8

@@ -14,3 +14,4 @@ exclude=
     .git,
     venv,
     test_data,
+    pcp1,

.github/workflows/tests.yml

@@ -14,10 +14,10 @@ jobs:
     if: github.event.pull_request.draft == false
 
     env:
-        python-latest: 3.14
+        python-latest: '3.14'
     strategy:
       matrix:
-        python-version: ['3.10', 3.11, 3.12, 3.13, 3.14]
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
     - name: Checkout repository
@@ -31,12 +31,17 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -e .[test]
+        python -m pip install -e .[dev]
 
     - name: Check code style with flake8
       if: ${{ matrix.python-version == env.python-latest }}
       run: |
-        python -m flake8 pcpostprocess
+        python -m flake8 -j4
+
+    - name: Check typing with mypy
+      if: ${{ matrix.python-version == env.python-latest }}
+      run: |
+        python -m mypy
 
     - name: Extract test data
       run: |

CONTRIBUTING.md

@@ -42,7 +42,7 @@ When making changes, we try to follow the procedure below.
 **TODO: Once there is a "user" way to install, move the git clone etc. information here [#105](https://github.com/CardiacModelling/pcpostprocess/issues/105).**
 
 ```
-pip install -e .[test]
+pip install -e .[dev]
 ```
 
 ## Style guidelines
@@ -62,6 +62,17 @@ In addition to the rules checked by flake8, we try to use single quotes (`'`) fo
 
 Class, method, and argument names are in UK english.
 
+### Type hints
+
+We'll try to use [type hints](https://docs.python.org/3/library/typing.html), checked with [mypy](https://www.mypy-lang.org/).
+
+To run locally, use
+```
+$ mypy
+```
+
+Mypy is configured in `pyproject.toml`.
+
 ## Documentation
 
 Every method and every class should have a [docstring](https://www.python.org/dev/peps/pep-0257/) that describes in plain terms what it does, and what the expected input and output is.

README.md

@@ -5,7 +5,7 @@ This repository contains a python package and scripts for handling time-series d
 The package has been tested with data from a SyncroPatch 384, but may be adapted to work with data in other formats.
 It can also be used to perform quality control (QC) as described in [Lei et al. (2019)](https://doi.org/10.1016%2Fj.bpj.2019.07.029).
 
-This package is tested on Ubuntu with Python 3.10, 3.11, 3.12, 3.13 and 3.14.
+This package is tested on Ubuntu with Python 3.10 to 3.14.
 
 ## Getting Started
 
@@ -27,7 +27,7 @@ Then install the package with `pip`.
 
 ```sh
 python3 -m pip install --upgrade pip
-python3 -m pip install -e .'[test]'
+python3 -m pip install -e .'[dev]'
 ```
 
 To run the tests you must first download some test data.

pcpostprocess/__init__.py

@@ -0,0 +1,14 @@
+#
+# This file is part of pcpostprocess.
+# See https://github.com/CardiacModelling/pcpostprocess for copyright, sharing,
+# and licensing details.
+#
+
+from ._trace import (
+    Trace,
+)
+
+from ._leak import (
+    estimate_gE_leak_ramp,
+    estimate_gE_leak_step,
+)

pcpostprocess/_leak.py

@@ -0,0 +1,65 @@
+#
+# Leak estimation and correction
+#
+# This file is part of pcpostprocess.
+# See https://github.com/CardiacModelling/pcpostprocess for copyright, sharing,
+# and licensing details.
+#
+from . import Trace
+
+
+def estimate_gE_leak_ramp(
+        trace : Trace, ramp: int | None = None, step: int | None = None):
+    """
+    Estimates ``g * (V - E)`` leak using a "leak ramp" in the voltage protocol.
+
+    Parameters
+    ----------
+    trace : Trace
+
+    ramp : int, optional
+        The index of the ramp in the voltage protocol: 0 for the first segment
+        that's a ramp, 1 for the second segment that's a ramp, etc. If neither
+        ``ramp_index`` or ``step_index`` is given, the first ramp will be used.
+    step : int, optional
+        An alternative way to specify the
+
+    Returns
+    -------
+
+    """
+    return 0
+
+
+def estimate_gE_leak_step(trace : Trace, step_1: int, step_2: int):
+    """
+    Estimates ``g * (V - E)`` leak using a "leak ramp" in the voltage protocol.
+
+
+
+
+
+
+    """
+    return 0
+
+
+def correct_gE_leak(trace : Trace, g : float, E : float):
+    """
+    """
+    pass
+
+
+# Alternative:
+class gELeak:
+
+    def __init__(self, g, E):
+        pass
+
+    @classmethod
+    def from_ramp(trace, ramp_index=None, step_index=None):
+        pass
+
+    def from_steps(trace, step_1, step_2):
+        pass
+

pcpostprocess/_protocol.py

@@ -0,0 +1,17 @@
+#
+# Voltage protocol
+#
+# This file is part of pcpostprocess.
+# See https://github.com/CardiacModelling/pcpostprocess for copyright, sharing,
+# and licensing details.
+#
+#import numpy as np
+
+
+class VoltageProtocol:
+    """
+    Represents a voltage protocol consisting of a sequence of steps and/or
+    ramps.
+    """
+    # Internal format: Sequence of (duration, v_start, v_end) objects.
+

pcpostprocess/_trace.py

@@ -0,0 +1,14 @@
+#
+# Trace class and implementations
+#
+# This file is part of pcpostprocess.
+# See https://github.com/CardiacModelling/pcpostprocess for copyright, sharing,
+# and licensing details.
+#
+#import numpy as np
+
+
+class Trace:
+
+    def __init__(self, time, current):
+        pass

pyproject.toml

@@ -1,12 +1,11 @@
 [build-system]
+build-backend = 'setuptools.build_meta'
 requires = [
     'setuptools>=80',
     'setuptools_scm>=8.0',
-    'wheel',
+    #'wheel',
 ]
 
-build-backend = 'setuptools.build_meta'
-
 [tool.setuptools_scm]
 local_scheme = 'dirty-tag'
 write_to = 'pcpostprocess/_version.py'
@@ -42,27 +41,33 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-test = [
+dev = [
     'coverage',             # For coverage testing
     'codecov>=2.1.3',       # To upload coverage reports
     'flake8>=3',            # For code style checking
+    'mypy>=1',              #
 ]
 
-[tools.setuptools.package-data]
-include_package_data = true
-
 [project.urls]
 Homepage = 'https://github.com/CardiacModelling/pcpostprocess'
 Source = 'https://github.com/CardiacModelling/pcpostprocess'
 
-[project.scripts]
-pcpostprocess = 'pcpostprocess.scripts.__main__:main'
+#[project.scripts]
+#pcpostprocess = 'pcpostprocess.scripts.__main__:main'
+
+[tools.setuptools.package-data]
+include_package_data = true
 
 [tool.setuptools.packages.find]
 include = [
     'pcpostprocess',
 ]
 
+[tool.mypy]
+modules = [
+    'pcpostprocess',
+]
+
 [tool.coverage.run]
 source = [
     'pcpostprocess',