Jupyter

.binder/requirements.txt

@@ -0,0 +1 @@
+e .[notebook]

.github/workflows/python-publish.yml

@@ -12,26 +12,39 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
-      - name: Install dependencies
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml', 'requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install build & test dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip install build twine
+          # Install test/dev dependencies (pytest etc.)
           pip install -r requirements.txt
+          # Install the project (will pull runtime deps from pyproject)
+          pip install .
+
       - name: Run pytest
-        run: |
-          pytest
+        run: pytest -q
+
+      - name: Build (sdist & wheel)
+        run: python -m build
 
-      - name: Build and publish
+      - name: Publish to PyPI
+        if: startsWith(github.ref, 'refs/tags/')
         env:
           TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+        run: twine upload dist/*

.github/workflows/run-pytest-on-push-and-all-prs.yml

@@ -12,30 +12,33 @@ on:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
     # Runs tests on multiple python versions across the range we support
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v4 # latest as at March 2024
-
-    - name: Set up Python version ${{ matrix.python-version }}
-      uses: actions/setup-python@v5 # latest as at March 2024
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Display Python version
-      run: python -c "import sys; print(sys.version)"
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel
-        pip install -r requirements.txt
-
-    - name: Run pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[notebook]  # ensure optional extras still work
+          pip install -r requirements.txt
+
+      - name: Run pytest
+        run: pytest -q

Dockerfile

@@ -1,20 +1,47 @@
-FROM python:3.12
+FROM python:3.12-slim
+
+# Environment hygiene
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    DEBIAN_FRONTEND=noninteractive
 
-# Set the working directory in the container
 WORKDIR /app
 
-# Copy the requirements file into the container
-COPY requirements.txt .
+# System deps (slim image minimal; add build-essential if future compiled deps needed)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    curl \
+    build-essential \
+    gfortran \
+    libopenblas-dev \
+    pkg-config \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy metadata first for build cache
+COPY pyproject.toml README.md ./
+COPY requirements.txt ./
+
+# Copy the full source (needed for editable install)
+COPY rcpchgrowth rcpchgrowth
+
+# Upgrade pip/setuptools/wheel first
+RUN pip install --upgrade pip setuptools wheel
+
+# Install runtime + notebook deps first (ensures wheels pulled before editable wiring)
+RUN pip install python-dateutil scipy pandas matplotlib jupyterlab ipykernel
+
+# Install dev/test tools
+RUN pip install -r requirements.txt
 
-# Create a virtual environment
-RUN python -m venv /app/venv
+# Finally perform editable install (should be fast now; minimal build isolation work)
+RUN pip install -e . || (echo '--- Editable install failed; running pip debug ---' && python -m pip debug && exit 1)
 
-# Upgrade pip and install the dependencies in the virtual environment
-RUN /app/venv/bin/pip install --upgrade pip
-RUN /app/venv/bin/pip install -r requirements.txt
+# Bring in notebooks only after package install so they are never considered for package discovery
+COPY notebooks notebooks
 
-# Copy the rest of the application code
-COPY . .
+# Expose Jupyter port
+EXPOSE 8888
 
-# Set the entrypoint to use the virtual environment's Python interpreter
-CMD ["python3"]
+# Helpful default: open bash; docker-compose can override with jupyter lab
+CMD ["bash"]

README.md

@@ -1,5 +1,90 @@
-# RCPCH Digital Growth Python library
+# RCPCHGrowth Python library
 
-Please go to <https://growth.rcpch.ac.uk/products/python-library/> for all documentation
+## Calculations for children's measurements against UK and international growth references.
+
+[![PyPI version](https://img.shields.io/pypi/v/rcpchgrowth.svg?style=flat-square&labelColor=%2311a7f2&color=%230d0d58)](https://pypi.org/project/rcpchgrowth/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg?style=flat-square&labelColor=%2311a7f2&color=%230d0d58)](https://www.gnu.org/licenses/agpl-3.0)
+[![Binder](https://img.shields.io/badge/Binder-Launch?style=flat-square&labelColor=%2311a7f2&color=%230d0d58&logo=binder&logoColor=white)](https://mybinder.org/v2/gh/rcpch/rcpchgrowth-python/live?labpath=notebooks%2FQuickstart.ipynb)
+[![Codespaces](https://img.shields.io/badge/Codespaces-Open_in_Cloud?style=flat-square&labelColor=%2311a7f2&color=%230d0d58&logo=github&logoColor=white)](https://codespaces.new/rcpch/rcpchgrowth-python?quickstart=1)
+
+Please go to <https://growth.rcpch.ac.uk/products/python-library/> for full documentation.
 
 Issues can be raised here <https://github.com/rcpch/rcpchgrowth-python/issues>
+
+---
+
+## Installation
+
+### Docker
+
+If you want to avoid setting up docker environments, there are shortcut scripts the create a dockerized environment with RCPCHGrowth already installed.
+
+First ensure the folders have the correct permissions:
+
+```bash
+chmod +x s/dev
+```
+
+To generate a container which will launch the notebooks in a browser and allow local dev ( with hot reload)
+
+```bash
+s/dev
+```
+
+### Minimal installation (assuming you have a python virtual env setup)
+
+```bash
+pip install rcpchgrowth
+```
+
+With notebook & package dependencies:
+
+```bash
+pip install "rcpchgrowth[notebook]"
+```
+
+The `notebook` extra currently pulls in: `pandas`, `matplotlib`, `jupyterlab`, `ipykernel`.
+
+To verify versions inside a Jupyter session:
+
+```python
+import rcpchgrowth, pandas as pd, sys
+print(rcpchgrowth.__version__, pd.__version__, sys.version)
+```
+
+## Example notebooks
+
+Example notebooks live in `notebooks/`:
+
+- `Quickstart.ipynb` – single measurement, small batch, simple plot.
+- `ResearchTemplate.ipynb` – structured workflow for batch CSV processing (ages, SDS, centiles, quality flags, export).
+- `AdditionalFunctions.ipynb` - exposes some of the date and calculation functions for more in-depth exploration
+- `ExperimentalFunctions.ipynb` - exposes functions that are in development and more experimental
+
+## Data handling / privacy
+
+<table>
+<tr>
+  <td width="6" style="background:#2311a7f2;"></td>
+  <td>
+    <strong>Data handling & privacy</strong><br>
+    <strong>Never commit identifiable patient data.</strong><br>
+    • Keep raw identifiable data outside version control (secure, access‑controlled).<br>
+    • De‑identify before analysis (remove names, NHS numbers, full DOB; date‑shift if required).<br>
+    • Do not push raw exports to forks, PRs or gists.<br>
+    • Use <code>ResearchTemplate.ipynb</code> for generating de‑identified derived outputs.<br>
+    <em>If in doubt, stop and seek local information governance guidance.</em>
+  </td>
+</tr>
+</table>
+
+
+---
+
+## Contributing
+
+See issues list and please open discussions before large changes.
+
+---
+
+Copyright © Royal College of Paediatrics and Child Health

docker-compose.yml

@@ -1,11 +1,27 @@
-version: "3.12"
-
+version: "3.9"
 services:
-  rcpchgrowth-python:
+  dev:
     build: .
+    container_name: rcpchgrowth-dev
     volumes:
       - .:/app
     working_dir: /app
-    tty: true # Allocate a pseudo-TTY
-    stdin_open: true # Keep stdin open
-    container_name: rcpchgrowth-python
+    environment:
+      - PYTHONPATH=/app
+    ports:
+      - "8888:8888"
+    command:
+      - bash
+      - -lc
+      - |
+        set -e
+        mkdir -p /app/notebooks
+        echo '[DEV] Editable install'
+        pip install -e /app[notebook]
+        echo '[DEV] Sanity import'
+        echo '[DEV] Register kernel'
+        python -m ipykernel install --name rcpchgrowth --display-name 'rcpchgrowth' --sys-prefix
+        echo '[DEV] Launching JupyterLab'
+        exec jupyter lab --ip=0.0.0.0 --no-browser --allow-root \
+          --NotebookApp.token='' --NotebookApp.password='' \
+          --notebook-dir=/app/notebooks