Test that everything works#
If you don’t have the Anaconda Prompt open, please open it. Anaconda Prompt can be found by clicking on the Windows start menu button and start typing Anaconda Prompt.
Also always make sure you have activated your biogeomon2022 environment.
(C:\dev\conda3) activate biogeomon2022
(biogeomon2022)
You can test that the installations have worked by running following commands in a Python console. At first start the Python console:
(biogeomon2022) python
Type "help", "copyright", "credits" or "license" for more information.
>>>
# Processing
import pandas as pd
import numpy as np
import xarray as xr
import rioxarray # for CRS management in Xarray
# Data loading
import intake
import intake_xarray # Xarray wrapper for Intake
import h5netcdf # for NetCDF reading
# Plotting
import matplotlib
import matplotlib.pyplot as plt
# Trend analysis
import pymannkendall as mk
If you don’t receive any errors, everything should be working!
In order to close the Python interpreter type exit() or press Ctrl+Z plus Return to exit.
(biogeomon2022) >>> exit()
Setting up Jupyter Notebook#
The Jupyter Notebook server is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. Jupyter Lab is an extended version that allows to have several notebooks open at the same time. We will be mostly working with Jupyter Lab.
Before we start Python coding we will make our newly created conda Python environment known to the Jupyter notebook system by installing the kernel, basically the execution engine link from Jupyter web notebook to our Python environment:
Make sure you are in your dedicated working directory, your “biogeomon2022” folder, on the Command line window (Anaconda prompt). And make sure the biogeomon2022 conda environment is activated:
(C:\dev\conda3) activate biogeomon2022
(biogeomon2022) python -m ipykernel install --user --name biogeomon2022
That should be it. You should now be able to start the Jupyter notebook server:
(biogeomon2022) jupyter lab
This should open a webpage in your default webbrowser.
Note
Don’t close the console window nor the browser window where the notebooks opened. Always use the “File” -> “Save and Checkpoint” and then -> “Close and Halt” menu options in the notebooks, and the “Quit” button on the main notebook server webpage.