Merge pull request #18 from pythonhealthdatascience/dev

Dev

Author: amyheather

.github/workflows/lint.yaml

@@ -23,12 +23,6 @@ jobs:
             cache: 'pip'
         - run: pip install -r requirements.txt
 
-        - name: Lint model code
+        - name: Lint
           run: |
-            flake8 ./simulation
-            pylint ./simulation
-
-        - name: Lint tests
-          run: |
-            flake8 ./tests
-            pylint ./tests
+            bash lint.sh

README.md

@@ -55,7 +55,7 @@ This repository provides a template for building discrete-event simulation (DES)
 
 For clarity, changes from the DES book in this template are explained in `docs/hsma_changes.md`.
 
-✨ **Style:** The coding style is based on the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). Linting is implemented using `flake8` and `pylint` for `.py` files, and `pycodestyle` for `.ipynb` files.
+✨ **Style:** The coding style is based on the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). Linting is implemented using `pylint` (with `nbqa` to enable it to run on jupyter notebooks).
 
 🧱 **Package structure:** In Python, a package can simply be defined as a directory with an `__init__.py` file in it. In this repository, the scripts for model (within `simulation/`) are treated as a little local package. This keeps the code model code isolated from our experiments and analysis. It is installed as an editable (`-e`) local import - with `-e` meaning it will update with changes to the local files in `simulation/`. As it is installed in our environment, it can then easily be used anywhere else in the directory - here, in `notebooks/` and `tests/` - without needing any additional code (e.g. no need to modify `sys.path`, or have additional `__init__.py` files).
 
@@ -162,18 +162,22 @@ If you have changed the model behaviour, you may wish to amend, remove or write
 
 🔎 **Linting**
 
-You can lint the `.py` files by running either of this commands from the terminal:
+You can lint the `.py` files by running:
 
 ```
-flake8 simulation/model.py
 pylint simulation/model.py
 ```
 
-The first commands in the `.ipynb` files will lint the notebooks using `pycodestyle` when executed:
+You can lint the `.ipynb` by adding `nbqa` to the start of the command - e.g.:
 
 ```
-%load_ext pycodestyle_magic
-%pycodestyle_on
+nbqa pylint notebooks/analysis.ipynb
+```
+
+A bash script has been provided which can be used to lint all files in succession by running:
+
+```
+bash lint.sh
 ```
 
 <br>
@@ -225,6 +229,7 @@ repo/
 ├── CONTRIBUTING.md       # Contribution instructions
 ├── environment.yaml      # Conda environment (includes Python version)
 ├── LICENSE               # Licence file
+├── lint.sh               # Bash script to lint all .py and .ipynb files at once
 ├── pyproject.toml        # Metadata for local `simulation/` package
 ├── README.md             # This file! Describes the repository
 └── requirements.txt      # Virtual environment (used by GitHub actions)

docs/time_weighted_averages.ipynb

@@ -2,24 +2,20 @@ name: template-des
 channels:
   - conda-forge
 dependencies:
-  - black
-  - flake8=7.1.1
   - ipykernel=6.29.5
   - jinja2=3.1.5
   - joblib=1.4.2
   - nbformat=5.10.4
-  - nbqa
-  - numpy=2.1.3
+  - nbqa=1.9.0
+  - numpy=2.2.2
   - pandas=2.2.3
-  - pip=24.3.1
+  - pip=25.0
   - plotly_express=0.4.1
-  - pycodestyle=2.12.1
-  - pylint=3.3.3
+  - pylint=3.3.4
   - pytest=8.3.4
   - pytest-xdist=3.6.1
-  - python=3.13.0
+  - python=3.13.1
   - simpy=4.1.1
   - pip:
     - kaleido==0.2.1
-    - pycodestyle_magic==0.5
     - -e .[dev]

environment.yaml

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+echo "Linting model code..."
+pylint ./simulation
+
+echo "Linting tests..."
+pylint ./tests
+
+echo "Linting notebooks..."
+nbqa pylint ./notebooks
+
+echo "Linting time-weighted averages notebook..."
+nbqa pylint ./docs/time_weighted_averages.ipynb