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smap_python_notebooks

A collection of Jupyter notebooks demonstrating how to utilize Python for downloading and visualizing Soil Moisture Active Passive (SMAP) data.

These notebooks were originally provided to NSIDC by Adam Purdy.

Level of Support

  • This repository is fully supported by NSIDC. If you discover any problems or bugs, please submit an Issue. If you would like to contribute to this repository, you may fork the repository and submit a pull request.

See the LICENSE for details on permissions and warranties. Please contact [email protected] for more information.

Requirements

  • Docker or Miniconda
  • Python with Jupyter

Installation

Starting the Jupyter Lab server

With Docker [Preferred method]

  1. Install Docker and docker-compose

  2. Run the Jupyter lab server using docker-compose:

     docker-compose -f docker-compose.yml up

Note: Some notebooks have cells that create and interact with files. Sometimes, the full path to these files will be displayed in the notebook's outputs. When using Docker, files and directories reported to be within /opt/smap/notebooks/ can be accessed directly from the local ./notebooks/ directory.

Building a Docker image in dev

Note that the docker-compose.yml file pulls the latest built nsidc/smap_python_notebook image from Dockerhub. If you need to adjust the runtime environment (e.g., add new python dependencies), you may want to build your own version of the image with the included docker-compose-dev.yml instead. This is usually an option only for advanced users:

$ docker-compose -f docker-compose-dev.yml build
$ docker-compose -f docker-compose-dev.yml up

Without Docker

  1. Install the Miniconda python package manager.

  2. Create a conda environment with the required dependencies:

     conda env create -f environment.yml

  3. Activate the smap conda environment:

     source activate smap

  4. Run the notebook:

     ./start_jupyterlab.sh

Usage

Accessing the tutorial notebooks

After running docker-compose up or ./start_jupyterlab.sh depending on installation method above, logs should be printed to the console that look something like this:

smap_notebooks_1  | [I 16:11:34.878 LabApp] Writing notebook server cookie secret to /home/jupyter_user/.local/share/jupyter/runtime/notebook_cookie_secret
smap_notebooks_1  | [I 16:11:35.068 LabApp] JupyterLab extension loaded from /home/jupyter_user/.conda/envs/smap/lib/python3.8/site-packages/jupyterlab
smap_notebooks_1  | [I 16:11:35.068 LabApp] JupyterLab application directory is /home/jupyter_user/.conda/envs/smap/share/jupyter/lab
smap_notebooks_1  | [I 16:11:35.071 LabApp] Serving notebooks from local directory: /opt/smap/notebooks
smap_notebooks_1  | [I 16:11:35.071 LabApp] Jupyter Notebook 6.1.5 is running at:
smap_notebooks_1  | [I 16:11:35.071 LabApp] http://1dbc28078f4d:8888/?token=d794f99d8044b54158b8dd42a4d59a55e8f3becdd612f1dd
smap_notebooks_1  | [I 16:11:35.071 LabApp]  or http://127.0.0.1:8888/?token=d794f99d8044b54158b8dd42a4d59a55e8f3becdd612f1dd
smap_notebooks_1  | [I 16:11:35.071 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
smap_notebooks_1  | [C 16:11:35.075 LabApp]
smap_notebooks_1  |
smap_notebooks_1  |     To access the notebook, open this file in a browser:
smap_notebooks_1  |         file:///home/jupyter_user/.local/share/jupyter/runtime/nbserver-46-open.html
smap_notebooks_1  |     Or copy and paste one of these URLs:
smap_notebooks_1  |         http://1dbc28078f4d:8888/?token=d794f99d8044b54158b8dd42a4d59a55e8f3becdd612f1dd
smap_notebooks_1  |      or http://127.0.0.1:8888/?token=d794f99d8044b54158b8dd42a4d59a55e8f3becdd612f1dd

Use the link that starts with http://127.0.0.1:8888/. In this case:

http://127.0.0.1:8888/?token=d794f99d8044b54158b8dd42a4d59a55e8f3becdd612f1dd

Note that the token associated with this URL is unique, and may change each time you run the software.

If the http://127.0.0.1:8888/ link does not work, try navigating to localhost:8888 and manually entring the token to login.

Once logged-in, navigate to one of the tutorials (one of the .ipynb files), and try it out!

License

See LICENSE.

Code of Conduct

See Code of Conduct.

Credit

This software was developed by the National Snow and Ice Data Center with funding from multiple sources.

DEV TODOs

  • Fix CircleCI config: why does the push to Dockerhub fail with denied: requested access to the resource is denied?? Login works.

  • Add versioning to this project and docker tag images with explicit versions instead of just latest.

  • Add and use an environment-lock.yml to fully pin dependencies