RCPCH Digital Growth Charts

https://growth.rcpch.ac.uk/
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An expert-built child growth API providing accurate centile and SDS calculations for child...
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### Start API server on Mac/Linux

Source: https://growth.rcpch.ac.uk/developer/api-python

Starts the API server using the 'uvicorn-start' script on macOS or Linux systems.

```bash
s/uvicorn-start
```

--------------------------------

### Start API server on Windows

Source: https://growth.rcpch.ac.uk/developer/api-python

Starts the API server using uvicorn with hot-reloading enabled on Windows systems.

```bash
uvicorn main:app --reload
```

--------------------------------

### Start the Zensical development server with Docker Compose

Source: https://growth.rcpch.ac.uk/developer/writing-documentation

Use Docker Compose to run the Zensical site in a container, allowing local preview without installing Python or Zensical. Ensure Docker and Docker Compose are installed and running.

```bash
docker compose up

```

--------------------------------

### Start Development Server without Docker

Source: https://growth.rcpch.ac.uk/developer/react-client

Run the React client development server directly from the command line without using Docker. This requires Node.js and npm to be installed.

```bash
npm run dev
```

--------------------------------

### Install common requirements on Windows

Source: https://growth.rcpch.ac.uk/developer/api-python

Installs dependencies from the common-requirements.txt file using pip within the activated virtual environment.

```bash
pip install -r requirements/common-requirements.txt
```

--------------------------------

### Install RCPCHgrowth Directly

Source: https://growth.rcpch.ac.uk/researchers/introduction

Install the core RCPCHgrowth package without additional notebook dependencies. Use this if you already have the necessary notebook tools installed.

```bash
pip install rcpchgrowth
```

--------------------------------

### Install React Chart Component

Source: https://growth.rcpch.ac.uk/developer/react-component

Install the RCPCH Digital Growth Charts React Component Library using npm.

```bash
npm i --save @rcpch/digital-growth-charts-react-component-library
```

--------------------------------

### Verify CLI Installation

Source: https://growth.rcpch.ac.uk/products/command-line-client%28deprecated%29

Check if the rcpchgrowth-cli was installed correctly by running the help command. This should display available options and usage instructions.

```bash
rcpchgrowth --help

```

--------------------------------

### Install dependencies with pip

Source: https://growth.rcpch.ac.uk/developer/api-python

Installs project dependencies listed in requirements.txt using pip within the activated virtual environment.

```bash
pip install -r requirements.txt
```

--------------------------------

### Install RCPCHGrowth CLI Tool

Source: https://growth.rcpch.ac.uk/products/command-line-client%28deprecated%29

Install the command-line interface tool using pip. This command ensures you have the necessary package for terminal-based growth calculations.

```bash
pip install rcpchgrowth-python-cli

```

--------------------------------

### Uvicorn development server output

Source: https://growth.rcpch.ac.uk/developer/api-python

Example output messages from the uvicorn development server indicating it is running, reloading, and the application has started.

```text
INFO:     Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
INFO:     Started reloader process [61645] using watchgod
INFO:     Started server process [61647]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
```

--------------------------------

### Example MkDocs Navigation Configuration

Source: https://growth.rcpch.ac.uk/developer/writing-documentation

This excerpt from 'mkdocs.yml' demonstrates how to define the site's navigation structure, including top-level headings and nested sub-pages.

```yaml
nav:
  - Home: "index.md"
  - About:
      - "about/about.md"
      - "about/overview.md"

```

--------------------------------

### Start Docker Container

Source: https://growth.rcpch.ac.uk/developer/react-client

Start the Docker container for the React client. This command launches the application within the Docker environment.

```bash
s/docker-start
```

--------------------------------

### Start Docker Container for RCPCHgrowth

Source: https://growth.rcpch.ac.uk/researchers/introduction

Initiate the Docker container to set up the RCPCHgrowth development environment. This command builds the package and makes Jupyter notebooks accessible via a provided link.

```bash
s/up
```

--------------------------------

### Local Development Setup for Charts Package

Source: https://growth.rcpch.ac.uk/developer/react-component

Steps to link the local chart library with a React client for development. Ensure consistent Node.js versions and manage potential dependency conflicts.

```bash
npm link
npm link @rcpch/digital-growth-charts-react-component-library
npm run build
```

--------------------------------

### Upgrade pip and install virtualenv

Source: https://growth.rcpch.ac.uk/developer/api-python

Upgrades the pip package installer to the latest version and then installs the virtualenv package.

```bash
python.exe -m pip install --upgrade pip

pip install virtualenv
```

--------------------------------

### Install RCPCHGrowth Package

Source: https://growth.rcpch.ac.uk/products/python-library

Install the rcpchgrowth package into your Python project using pip.

```bash
pip install rcpchgrowth

```

--------------------------------

### Install development packages on Ubuntu/Linux Mint

Source: https://growth.rcpch.ac.uk/developer/api-python

Installs essential development header packages required for compiling Python from source with pyenv on Ubuntu/Linux Mint.

```bash
sudo apt-get install liblzma-dev libbz2-dev zlib1g-dev
```

--------------------------------

### Install RCPCHgrowth with Notebook Dependencies

Source: https://growth.rcpch.ac.uk/researchers/introduction

Install the RCPCHgrowth package along with optional notebook-related dependencies. This is recommended if you plan to use the provided Jupyter notebooks.

```bash
pip install rcpchgrowth['notebook']
```

--------------------------------

### Example of Truncated API Response

Source: https://growth.rcpch.ac.uk/integrator/making-api-calls

This is an example of a truncated JSON response from the API, showing the structure of the returned data.

```json
{"birth_data":{"birth_date":"2020-04-12", ... :{"events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"]}}
```

--------------------------------

### Run Docker Container with Local Package Installation

Source: https://growth.rcpch.ac.uk/developer/api-docker

Use the 's/dev' script to create a Docker container that installs a local version of RCPCHGrowth as an editable package, useful for testing local modifications without PyPi deployment. Ensure the RCPCHGrowth package folder is parallel to the server folder.

```bash
s/dev

```

--------------------------------

### Clone the documentation repository

Source: https://growth.rcpch.ac.uk/developer/writing-documentation

Clone the repository to your local machine to begin editing documentation offline. Ensure Git is installed.

```bash
git clone https://github.com/rcpch/digital-growth-charts-documentation.git

```

--------------------------------

### Install Development Version Locally

Source: https://growth.rcpch.ac.uk/developer/rcpchgrowth-cli

Install the development version of the library locally using pip for testing changes. This allows immediate reflection of local code modifications in the CLI tool.

```bash
pip install -e .

```

--------------------------------

### Install Python Version with pyenv

Source: https://growth.rcpch.ac.uk/developer/api-python

Install Python version 3.12.0 using pyenv. This ensures the correct version of Python is available for the project.

```bash
pyenv install 3.12.0

```

--------------------------------

### Install Python with Big Sur patch

Source: https://growth.rcpch.ac.uk/developer/api-python

Installs a specific Python version (3.8.0) using pyenv with a patch from a GitHub commit, intended for Big Sur compatibility.

```bash
pyenv install --patch 3.8.0 < <(curl -sSL https://github.com/python/cpython/commit/8ea6353.patch\?full_index\=1)
```

--------------------------------

### Render Chart Without React

Source: https://growth.rcpch.ac.uk/integrator/using-the-chart-component

This example demonstrates how to use the RCPCH Growth Charts component without a React framework. It shows how to import the library via CDN and render a chart by providing configuration options to the `RCPCHGrowthCharts.render` function.

```html
<!doctype html>
<html>
    <head>
        <title>Growth Chart Example</title>
        <!-- React dependencies. Must come first -->
        <script crossorigin src="https://unpkg.com/react@18/umd/react.production.min.js" defer></script>
        <script crossorigin src="https://unpkg.com/react-dom@18/umd/react-dom.production.min.js" defer></script>
        <!-- RCPCH Growth Charts library -->
        <!-- You must use the integrity check to ensure you are using the expected code as this component   -->
        <!-- can render patient data. You can get the value from this file, adjusting the version as needed -->
        <!-- https://cdn.jsdelivr.net/npm/@rcpch/digital-growth-charts-react-component-library@7.5.0/build/sri-hash.txt -->
        <script 
            src="https://cdn.jsdelivr.net/npm/@rcpch/digital-growth-charts-react-component-library@7.5.0/build/rcpch-digital-growth-charts.umd.min.js" 
            integrity="sha384-yu1MIbRclkM3UCyciRAULihnERx26NqFKjP/EuddYVumiom3Oy5p9KBGSUHABc8g"
            crossorigin="anonymous"
            defer>
        </script>
        <script defer>
            document.addEventListener('DOMContentLoaded', function () {
                const demoMeasurements = [ /* RCPCH digital growth charts API response goes here */ ];
                window.RCPCHGrowthCharts.render({
                    targetElementId: 'growth-chart-container',
                    title: 'Demo UK-WHO Growth Chart for Children',
                    measurementMethod: 'height',
                    reference: 'uk-who',
                    sex: 'female',
                    measurements: { height: demoMeasurements },
                    midParentalHeightData: {},
                    enableZoom: false,
                    chartType: 'centile',
                    enableExport: false,
                    clinicianFocus: false,
                    theme: 'tanner3',
                    height: 800,
                    width: 800,
                });
            });
        </script>
    </head>
    <body>
        <div id="growth-chart-container"></div> <!-- The charts will appear here -->
    </body>
</html>

```

--------------------------------

### Formatted JSON Response Example

Source: https://growth.rcpch.ac.uk/integrator/making-api-calls

A nicely formatted JSON response object after processing with `jq`, illustrating the structured data returned by the API.

```json
{
  "birth_data": {
    "birth_date": "2020-04-12",
    "gestation_weeks": 40,
... # truncated
    "events_text": [
        "Growth hormone start",
        "Growth Hormone Deficiency diagnosis"
    ]
  }
}
```

--------------------------------

### Set environment variable for pip requirements installation on Big Sur

Source: https://growth.rcpch.ac.uk/developer/api-python

Sets the SYSTEM_VERSION_COMPAT environment variable to 1, which may be required for pip to correctly install requirements on Big Sur.

```bash
export SYSTEM_VERSION_COMPAT=1
```

--------------------------------

### Linear Interpolation using SciPy

Source: https://growth.rcpch.ac.uk/clinician/how-the-api-works

This example shows the use of SciPy's `interp1d` function for linear interpolation. It's employed when a child's measurement is close to a reference threshold and only one age point is available above or below.

```python
from scipy.interpolate import interp1d

# Example usage:
# f = interp1d([x0, x1], [y0, y1])
# f(x)
```

--------------------------------

### Run Storybook for Charts Package

Source: https://growth.rcpch.ac.uk/developer/react-component

Launch Storybook to develop and preview the chart components locally.

```bash
npm run storybook
```

--------------------------------

### Navigate to the cloned directory

Source: https://growth.rcpch.ac.uk/developer/writing-documentation

Change into the newly cloned directory to access the documentation project files. This is a necessary step after cloning.

```bash
cd digital-growth-charts-documentation

```

--------------------------------

### Navigate to the Project Directory

Source: https://growth.rcpch.ac.uk/developer/api-python

Change your current directory to the root of the cloned repository. This is necessary for subsequent commands to work correctly.

```bash
cd digital-growth-charts-server

```

--------------------------------

### Build and Run Docker Container for Development

Source: https://growth.rcpch.ac.uk/developer/api-docker

Use the 's/up' script to build the Docker image with dependencies and run it in a container for rapid development. The server will be available at https://localhost:8000.

```bash
s/up

```

--------------------------------

### Navigate to Code Projects Directory

Source: https://growth.rcpch.ac.uk/developer/react-client

Change the current directory to your code projects folder. This is the first step before cloning the repository.

```bash
cd YourCodeProjects
```

--------------------------------

### Clone the Server Repository

Source: https://growth.rcpch.ac.uk/developer/api-docker

Clone the digital growth charts server repository to your local machine to begin local development.

```bash
git clone https://github.com/rcpch/digital-growth-charts-server.git

```

--------------------------------

### Change directory

Source: https://growth.rcpch.ac.uk/developer/api-python

Navigates into the cloned digital-growth-charts-server directory.

```bash
cd digital-growth-charts-server
```

--------------------------------

### Navigate back to root directory

Source: https://growth.rcpch.ac.uk/developer/api-python

Navigates from the 'Scripts' directory back to the root directory of the project.

```bash
cd ..
cd ..
```

--------------------------------

### Set environment variables for macOS Big Sur Python 3.12.0 installation

Source: https://growth.rcpch.ac.uk/developer/api-python

Sets CFLAGS and LDFLAGS environment variables to include necessary paths for libraries like openssl, bzip2, readline, and zlib when installing Python 3.12.0 on macOS Big Sur via pyenv.

```bash
export CFLAGS="-I$(brew --prefix openssl)/include -I$(brew --prefix bzip2)/include -I$(brew --prefix readline)/include -I$(xcrun --show-sdk-path)/usr/include"
export LDFLAGS="-L$(brew --prefix openssl)/lib -L$(brew --prefix readline)/lib -L$(brew --prefix zlib)/lib -L$(brew --prefix bzip2)/lib"
```

--------------------------------

### Recompile Python with pyenv

Source: https://growth.rcpch.ac.uk/developer/api-python

Recompiles a specific Python version using pyenv, typically after installing development header packages.

```bash
pyenv install 3.8.3
```

--------------------------------

### Build Docker Image

Source: https://growth.rcpch.ac.uk/developer/react-client

Build the Docker image for the React client. This command is used to create the container environment.

```bash
s/docker-rebuild
```

--------------------------------

### Navigate to Scripts directory

Source: https://growth.rcpch.ac.uk/developer/api-python

Changes the current directory to the 'Scripts' folder within the virtual environment, where activation scripts are located.

```bash
cd env/Scripts
```

--------------------------------

### Activate virtual environment on Windows

Source: https://growth.rcpch.ac.uk/developer/api-python

Runs the activate.bat script to activate the virtual environment. The command prompt should prepend '(env)' upon successful activation.

```batch
activate.bat
```

--------------------------------

### Make Scripts Executable

Source: https://growth.rcpch.ac.uk/developer/api-docker

Ensure development scripts are executable. Use 'chmod +x <filename>' for *nix environments or WSL.

```bash
chmod +x <filename>

```

--------------------------------

### Create a virtual environment on Windows

Source: https://growth.rcpch.ac.uk/developer/api-python

Creates a new virtual environment named 'env' using the 'venv' module. Ensure 'env' is used consistently in subsequent commands.

```bash
py -m venv env
```

--------------------------------

### Create a Virtual Environment with pyenv

Source: https://growth.rcpch.ac.uk/developer/api-python

Create a virtual environment named 'dgc-server' using Python 3.12.0. This isolates project dependencies.

```bash
pyenv virtualenv 3.12.0 dgc-server

```

--------------------------------

### Enable Git Committers and PDF Export for Local Development

Source: https://growth.rcpch.ac.uk/developer/writing-documentation

Use these environment variables to enable specific plugins during local development. This helps in testing plugin functionality before pushing changes.

```bash
export ENABLE_GIT_COMMITTERS=true; zensical serve
export ENABLE_PDF_EXPORT=true; zensical serve

```

--------------------------------

### Open React Client in Browser

Source: https://growth.rcpch.ac.uk/developer/react-client

Access the React client application by opening it in your web browser. The default address is http://localhost:3000.

```bash
open http://localhost:3000
```

--------------------------------

### Git Branch-based Code Promotion Strategy

Source: https://growth.rcpch.ac.uk/safety/csmf/clinical-risk-mgmt-plan

Describes the standard 'code promotion' process using a Git Branch-based strategy for deploying changes. New features are developed in separate branches, reviewed, and merged through stages like 'test' before reaching the 'live' branch.

```text
New features are developed in branches specific to that feature. Following successful testing, user acceptance, and automated tests, a successful feature can be merged into the next branch 'up' which may be a `test` branch or other nomenclature. The process of merging requires code review by nominated individuals and is a further opportunity for clinical safety review.
Code in the `live` branch is changed relatively infrequently (except for urgent security or safety updates) but the code which is promoted into `live` would have by then undergone several rounds of review as it progressed through our branch promotion strategy.
```

--------------------------------

### Create Pyenv Virtual Environment

Source: https://growth.rcpch.ac.uk/developer/rcpchgrowth-cli

Create a virtual environment named 'rcpchgrowth-python-cli' using Pyenv with Python 3.10.2.

```bash
pyenv virtualenv 3.10.2 rcpchgrowth-python-cli

```

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### Activate pyenv virtualenv

Source: https://growth.rcpch.ac.uk/developer/api-python

Activates a specific pyenv virtual environment. Ensure the virtualenv is created before activation.

```bash
pyenv activate dgc-server
```

--------------------------------

### API Credentials Configuration

Source: https://growth.rcpch.ac.uk/products/flutter-app

Store API base URL and key in a .env file at the project root. Ensure credentials are not committed to version control.

```dotenv
DGC_BASE_URL=https://api.rcpch.ac.uk/growth/v1
DGC_API_KEY="YOUR-API_KEY"
```

--------------------------------

### Clone React Client Repository

Source: https://growth.rcpch.ac.uk/developer/react-client

Clone the official dGC React Client repository from GitHub. This command downloads the project's source code.

```bash
git clone https://github.com/rcpch/digital-growth-charts-react-client.git
```

--------------------------------

### Generate and Store Chart Data with Overwrite

Source: https://growth.rcpch.ac.uk/developer/versioning

This Python snippet demonstrates how to call the `generate_and_store_chart_data` function with the `overwrite=True` argument to rebuild all centile data files, even if they already exist. This is useful for forcing a regeneration of reference data.

```python
from main import generate_and_store_chart_data
generate_and_store_chart_data(overwrite=True)
```

--------------------------------

### Measurement Class Optional Parameters

Source: https://growth.rcpch.ac.uk/developer/rcpchgrowth

These parameters can be optionally provided during Measurement class initialization. If not provided, they default to None. Bone age related parameters are optimized for chart plugins.

```python
bone_age: float

bone_age_centile: float

bone_age_sds: float

bone_age_text: str

bone_age_type ["greulich-pyle", 'tanner-whitehouse-ii', 'tanner-whitehouse-iii', 'fels']

events_text: list of str
```

--------------------------------

### Run Postman Collection with Newman

Source: https://growth.rcpch.ac.uk/developer/api-testing

Execute a Postman collection against a local API using Newman. This command specifies the collection URL and sets an environment variable for the base URL.

```bash
newman run https://www.getpostman.com/collections/e1ac5fe1fef92761c2ed --env-var "baseUrl=localhost:8000"
```

--------------------------------

### Import RCPCHgrowth Package

Source: https://growth.rcpch.ac.uk/researchers/introduction

Import the RCPCHgrowth package into your Python script or Jupyter notebook to access its calculation functions.

```python
import rcpchgrowth
```
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