Merge pull request #101 from CardiacModelling/coverage

Add scripts to coverage testing

Author: MichaelClerx

.github/workflows/pytest.yml

@@ -0,0 +1,72 @@
+name: Tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    branches:
+      - '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
+
+    env:
+        python-latest: 3.14
+    strategy:
+      matrix:
+        python-version: ['3.10', 3.11, 3.12, 3.13, 3.14]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e .[test]
+
+    - name: Check code style with flake8
+      if: ${{ matrix.python-version == env.python-latest }}
+      run: |
+        python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
+
+    - name: Check import ordering with isort
+      if: ${{ matrix.python-version == env.python-latest }}
+      run: |
+        python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
+
+    - name: Extract test data
+      run: |
+        wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
+        tar xvf tests/test_data.tar.xz -C tests/
+
+    - name: Run unit tests (without coverage testing)
+      if: ${{ success() && matrix.python-version != env.python-latest }}
+      run: python -m unittest
+
+    - name: Run unit tests (with coverage testing)
+      if: ${{ success() && matrix.python-version == env.python-latest }}
+      run: coverage run -m unittest
+
+    - name: Install TeX dependencies for run_herg_qc test
+      timeout-minutes: 15
+      run: sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
+
+    - name: Run `run_herg_qc` script
+      timeout-minutes: 15
+      run: pcpostprocess run_herg_qc tests/test_data/13112023_MW2_FF -w A01 A02 A03
+
+    - name: Report coverage to codecov
+      uses: codecov/codecov-action@v4
+      if: ${{ success() && matrix.python-version == env.python-latest }}
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+

.github/workflows/tests.yml

@@ -60,7 +60,7 @@ In addition to the rules checked by flake8, we try to use single quotes (`'`) fo
 
 ### Spelling
 
-**TODO WE SHOULD MAYBE DISCUSS WHICH ENGLISH TO USE? [#106](https://github.com/CardiacModelling/pcpostprocess/issues/106)**
+Class, method, and argument names are in UK english.
 
 ### Import ordering
 
@@ -95,6 +95,8 @@ make html
 [reStructuredText](http://docutils.sourceforge.net/docs/user/rst/quickref.html)
 [Sphinx](http://www.sphinx-doc.org/en/stable/)
 
+UK english
+
 ## Testing
 
 To run all unit tests, locally:

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-[![Unit tests](https://github.com/CardiacModelling/pcpostprocess/actions/workflows/pytest.yml/badge.svg)](https://github.com//CardiacModelling/pcpostprocess/actions/workflows/pytest.yml)
+[![Unit tests](https://github.com/CardiacModelling/pcpostprocess/actions/workflows/tests.yml/badge.svg)](https://github.com//CardiacModelling/pcpostprocess/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/CardiacModelling/pcpostprocess/graph/badge.svg?token=HOL0FrpGqs)](https://codecov.io/gh/CardiacModelling/pcpostprocess)
 
 This repository contains a python package and scripts for handling time-series data from patch-clamp experiments.
@@ -19,13 +19,15 @@ cd pcpostprocess
 Create and activate a virtual environment.
 
 ```sh
-python3 -m venv .venv && source .venv/bin/activate
+python3 -m venv .venv
+source .venv/bin/activate
 ```
 
 Then install the package with `pip`.
 
 ```sh
-python3 -m pip install --upgrade pip && python3 -m pip install -e .'[test]'
+python3 -m pip install --upgrade pip
+python3 -m pip install -e .'[test]'
 ```
 
 To run the tests you must first download some test data.

README.md

@@ -4,9 +4,6 @@
 
 # Copy this config file to the top-level data directory and modify fields.
 
-# Data output directory
-savedir = './data'
-
 # Save name for this set of data
 saveID = 'EXPERIMENT_NAME'
 

example_export_config.py

@@ -18,7 +18,7 @@ def main():
     sys.argv.pop(1)  # Subcommand's argparser shouldn't see this
 
     if args.subcommand == "run_herg_qc":
-        run_herg_qc.main()
+        run_herg_qc.run_from_command_line()
 
     elif args.subcommand == "summarise_herg_export":
         summarise_herg_export.main()