csdms / reccs

An interactive workshop on programming in the geosciences for the CU Boulder RECCS program

Python Programming in the Geosciences

This is a two-part (morning and afternoon) interactive workshop on using the Python programming language to perform data ingest, analysis, and visualization. The workshop is a part of the RECCS program at CU Boulder.

The workshop will not teach the details of Python--others have done this (see "Resources" below), and it takes more time than we have. The goal of this workshop is to show how a working geoscientist might use some of the plentiful scientific libraries available in Python.

Instructor

• Mark Piper

Requirements

• Computer
• Web browser
• Internet access
• Coffee (optional, but recommended)

Agenda

The workshop is divided into morning and afternoon sessions.

Morning

The morning session runs from 9 am until noon, with a break around the midpoint. It covers more basic concepts, but people with experience using Python can help those with less experience.

Topics:

• Introductions
• Why Python?
• Logging in to EarthscapeHub
• Using Jupyter Notebook
• Python fundamentals
• Importing Python libraries
• Reading data from a csv file with pandas
• Exercises and discussion

▶️ Run the workshop material on EarthscapeHub

Afternoon

The afternoon session runs from 1 pm until 4 pm, with a break around the midpoint. It covers more advanced topics.

Topics:

• Loops, conditionals, try statement, functions
• Reading data from a NetCDF file with scipy
• Analyzing and visualizing data with Basemap and matplotlib
• Exercises and discussion

▶️ Run the workshop material on the EarthscapeHub

Extra

Given time, some additional topics that can be covered.

Topics:

• Exporting a notebook to a PDF file
• Using shell commands in a terminal
• Anaconda and conda
• Using Python modules

Resources

Python:

• Software Carpentry, especially the Programming with Python lesson
• Data Carpentry
• The official Python tutorial is somewhat advanced, but has a lot of information
• The TutorialsPoint Python tutorial is also well done, and perhaps easier to follow
• When I have a Python question, usually someone on Stack Overflow has an answer
• The Matplotlib Gallery
• The CSDMS Ivy course material

CU Boulder:

• Community Surface Dynamics Modeling System (CSDMS)
• Cooperative Institute for Research in Environmental Sciences (CIRES)
• Institute for Arctic and Alpine Research (INSTAAR)

Acknowledgments

CSDMS is supported by the National Science Foundation under Award No. 1831623, Community Facility Support: The Community Surface Dynamics Modeling System (CSDMS).

Portions of the Python language fundamentals section were derived from material that is copyright Software Carpentry and remixed under their license.

NEON (National Ecological Observatory Network). 2D wind speed and direction (DP1.00001.001). https://data.neonscience.org (accessed May 26, 2021)

20th Century Reanalysis V2 data provided by the NOAA/OAR/ESRL PSL, Boulder, Colorado, USA, from their website at https://psl.noaa.gov/data/gridded/data.20thC_ReanV2.html.

reccs's Issues

Update 20thC Reanalysis example to use xarray

This example currently uses scipy.io.netcdf, which is sufficient, but the modern way to access netCDF is through xarray. The example should be updated to use xarray.

Planning the workshops

Python Programming in the Geosciences I, II

Thursday, 2021 June 3

Workshop I (introductory): 9 am -- 12 noon
Workshop II (advanced): 1 pm -- 4 pm

Approximately 18 students from the RECCS program.

Tasks

• Make syllabi for workshops I and II
• Use GitHub repo as workshop website
• Get data for examples
• Compile a list of online resources for further study through the summer (e.g., Software and Data Carpentry lessons)
• Make logins for students on CSDMS JupyterHub
• Set up Zoom links for workshops

Planning

• Use Excel or CSV as data format (data from NEON?)
• Use netCDF as a data format (use my example from Level Up! webinars)
• Review and use Software Carpentry Python material
• Record meeting for students to review (don't forget to pause recording at lunch)

Workshop I

Goal: Use Python to read data from a file and make a plot in a Jupyter Notebook.

Topics:

• Introductions
  • name, have you used Python, something about yourself
  • start with me
• Why Python?
• Logging on to the CSDMS JupyterHub
• Using a Jupyter Notebook
• (intro Python material from Software Carpentry)
• Python libraries (pandas, matplotlib)
• Read data from Excel with pandas
• Plot data with matplotlib
• Save notebook to a PDF file
• Go over resources for further study

Workshop II

Goal: Read data from a file, analyze data, make a Jupyter Notebook with graphics as a report.

Topics:

• Read data from a netCDF file with xarray
• Creating a Jupyter Notebook
• Loops, conditionals, try-except block, functions
• (Use my example from Level Up! webinar)
• (Analysis?)
• Go over resources for further study