Working With Jupyter Notebooks

Jupyter notebooks are a great way to work with Python code by allowing code editing and running directly in a web browser. Additionaly, it offers the inclusion of formatted text, images and interactive visualizations inside of the notebook. Thus it is a great tool for data analysis.

To create a new notebook, follow these steps:

Open the ‘Miniforge Prompt’ from the Start menu.
Activate the environment created in Environment Creation section by typing:
```
(base) $ mamba activate circadipy_env
```
Navigate to the directory where you want to create the notebook. For example, to create a notebook in the ‘my_name/Documents’ folder, you would type:
```
(circadipy_env) $ cd my_name/Documents
```
Start the Jupyter notebook server by typing:
```
(circadipy_env) $ jupyter notebook
```
This will open a new tab in your web browser with the Jupyter notebook interface. Click on the ‘New’ button at the top right corner and select ‘Python 3’ to create a new notebook. At this point, you can start writing and running Python code using the CircadiPy library.

You can also run the tutorial notebook provided in the CircadiPy package (../circadipy/src/circadipy/tutorial_pipeline.ipynb). To do this, follow these steps:

Using the tutorial notebook

Open the ‘Miniforge Prompt’ from the Start menu.
Activate the environment created in Environment Creation section by typing:
```
(base) $ mamba activate circadipy_env
```
Run Python and import the CircadiPy and pathlib modules. Then, use the pathlib module to find the path to the tutorial notebook typing the following commands:
```
(circadipy_env) $ python
>>> import circadipy
>>> from pathlib import Path
>>> Path(circadipy.__file__).parent / 'tutorial_pipeline.ipynb'
```
Get the path to the tutorial notebook and copy it without the quotes. You will use this path in the next step
Exit the Python interpreter by typing:
```
>>> exit()
```
Start the Jupyter notebook server by typing “jupyter notebook” + the copied path:
```
(circadipy_env) $ jupyter notebook copied_path_here
```