Merge branch 'main' into add_results_tracking

Author: morganle-48

.github/workflows/codecov.yaml

@@ -0,0 +1,35 @@
+name: CodeCov
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "latest"
+          activate-environment: true
+
+      - name: Install dependencies
+        run: uv pip install -e ".[dev]"
+
+      - name: Generate Report
+        run: uv run pytest --cov=. tests/unit --ignore=tests --cov-branch --cov-report xml:coverage.xml
+
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -86,6 +86,14 @@ venv.bak/
 
 # Data
 data/*
+*.xlsx
+*.xls
+*.csv
+*.parquet
 
 # VSCode settings
-.vscode/settings.json
+.vscode/settings.json
+
+# Python
+build/
+*.egg-info/

README.md

@@ -1,5 +1,12 @@
 # Renal capacity model
 
+<!-- badges: start -->
+
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![codecov](https://codecov.io/gh/The-Strategy-Unit/renal-capacity-model/graph/badge.svg?token=lr1OaInPCf)](https://codecov.io/gh/The-Strategy-Unit/renal-capacity-model)
+
+<!-- badges: end -->
+
 Repository with Python code for the Renal Capacity Model, an open source implementation of the Discrete Event Simulation (DES) [Renal Services model created in collaboration with the Midlands Renal Operational Delivery Network (MRODN)](https://github.com/The-Strategy-Unit/renal-services).
 
 ⚠️ **Please note that the code in this repository is still in development**
@@ -12,10 +19,40 @@ Although not essential, the instructions will assume you have this installed.
 To install the package:
 
 1. Clone the repository to your local machine. Open the repository.
-2. Run `uv pip install .`
+2. Run `uv pip install -e .`
 
 ## Running the model
 
 Once installed, set the configuration for your model run in `config.py`.
 
-Run the model using `uv run renal_capacity_model/main.py`
+Run the model using `uv run renal_capacity_model/main.py`. This runs a full trial.
+
+To run a single model run, use `uv run renal_capacity_model/model.py`
+
+## Information for developers
+
+### Testing
+
+There are two types of tests for the model:
+
+- Unit tests, which run automatically as part of the pytest testing suite. These check the
+behaviour of the individual elements of code to ensure they behave as expected using strict
+testing criteria.
+- Validation tests, which are excluded from the pytest testing suite. These are manually
+run and require users to view results and use their own judgment to check validity.
+
+To run the unit tests:
+
+- `uv run pytest`
+
+Check code unit testing coverage using:
+
+- `uv run coverage run -m pytest`
+
+View the code unit testing coverage report using:
+
+- `uv run coverage report`
+
+To run the validation tests:
+
+- `uv run tests/validation/validation_test_file.py`

pyproject.toml

@@ -5,8 +5,22 @@ description = "Discrete Event Simulation renal services model"
 readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
+    "coverage>=7.10.7",
     "matplotlib>=3.10.3",
     "numpy>=2.3.1",
     "pandas>=2.3.1",
+    "pytest>=8.4.2",
+    "pytest-cov>=7.0.0",
     "simpy>=4.1.1",
 ]
+
+[tool.pytest.ini_options]
+addopts = "--ignore=tests"
+testpaths = ["tests/unit"]
+
+[tool.coverage.run]
+omit=["tests/*"]
+
+[tool.coverage.report]
+exclude_also = ['if __name__ == .__main__.:', 
+                'if self.config.trace:']

renal_capacity_model/main.py

@@ -2,8 +2,8 @@
 Module for running the experiment
 """
 
-from trial import Trial
-from config import Config
+from renal_capacity_model.trial import Trial
+from renal_capacity_model.config import Config
 
 
 def main(config):