Installation
============

GlyApp on your Web Browser
--------------------------

On your favorite browser (I recommend Firefox), go to https://jupyter.org/try-jupyter/lab/

Start a new notebook by clicking on *Python Pyodide*

.. image:: pyodide.png

.. |run| image:: run.png
Copy the following code in the first section. Run the section with Shift+Enter keys or clicking on the button |run|
::
	import sys, os, re, pyodide, numpy as np, pandas as pd, scipy.ndimage
	from datetime import date,time,timedelta,datetime
	import matplotlib.pyplot as plt, matplotlib.dates as mdates
	url='https://raw.githubusercontent.com/jorishey1234/glyapp/refs/heads/main/gly_toolbox_dev.py'
	exec(pyodide.http.open_url(url).read())

After GlyApp is loaded (it can take some time depending on your computer and connection), you should get the answer :
::
	Loading GlyApp dev version
	GlyApp successfully loaded !

.. hint:: You can create as much notebook as you want, for instance one per patient or by study if necessary. Copy the header code all the time to initialize the notebook. When the browser is closed, the notebook is saved automatically in the Browser history. To avoid loosing data, it can be good to externaly save notebooks on a local disk from time to time (Right click on the notebook, then *Download*). 

.. |add| image:: add.png

Start a new section in the notebook, clicking on |add|. 

If running for the first time, prepare the local environment folder structure and files with the command :

>>> init_environment()

Then you should be able to run glycemic statistics

>>> calc_glu('XX')

or get a plot on weekly intervals

>>> plot_patient('XX')

.. hint:: Any other patient data can now be added in try-jupyter by drag/drop a **patient** folder containing sensor data in the **DATA_DIR**, which is by default *./Data/patient/*. As for the notebooks, the data is saved automatically when closing the browser, until you clear the history. To avoid loosing data, keep a local version of your **DATA_DIR** folder, and regularly download the results in the **RESULTS_DIR** folder (right click on the result file, then *Download*).  
 


With python (v3.12) installed locally
-------------------------------------

Make sure you have the following packages installed. For instance with pip
::
	pip install sys, os, re, pyodide, numpy, pandas, scipy, datetime, matplotlib

then, in python run 

>>> from glyapp import *
>>> init_environment()
>>> calc_glu('XX')
>>> plot_patient('XX')


GlyApp File Structure
----------------------

Default Environment Variables
^^^^^^^^^^^^^^^^^^^^^^
   
.. autodata:: gly_toolbox_dev.DATA_DIR
.. autodata:: gly_toolbox_dev.RESULT_DIR

Setting Environment Folders and Files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. autofunction:: gly_toolbox_dev.init_environment

.. autofunction:: gly_toolbox_dev.make_synthetic_gly_data