nasa-openscapes / corn Goto Github PK

Following this work by the CryoCloud community -

https://blog.jupyter.org/desktop-gis-software-in-the-cloud-with-jupyterhub-ddced297019a

https://github.com/GenericMappingTools/gmt

The recent environment.yml update has caused the netCDF4 and netcdf-c libraries to be updated to their most recent packages. After some troubleshooting with Xiaohua Pan, we discovered that there are issues with the netcdf-c (libnetcdf) >=4.9.1 library and Cloud OPeNDAP links, where an "access denied" error is being triggered when both https and dap4 URLs are passed. This appears to be true for multiple granules from various collections, and only works with the granule from this OPeNDAP notebook: https://github.com/OPENDAP/notebooks/blob/master/tutorials/netCDF4_tutorial.ipynb

This issue proposes a fix by setting netcdf4==1.6.2 in environment.yml, which should also install netcdf-c 4.9.0 and should fix this issue.

I have also opened an issue in the netcdf-c Github relating to this: Unidata/netcdf-c#2704

I keep pointing people to the GItHub repo but then they cannot find the image.

Thanks!

Hi @betolink ,

I wanted to chat with you about the most up-to-date ways to update quarto in the Hub. I can update these instructions in the README after we finish (https://github.com/NASA-Openscapes/corn#updating-quarto).

Today, following those instructions (including stopping and restarting my server), asking quarto check in the Terminal still returns Version: 1.0.35 rather than 1.2.269 now in the Dockerfile.

When you are back and have time, could we cowork on this together? I'll detail them below. Thank you!

Purpose: I'm hoping this will solve some weird quarto behavior @asteiker and I have been seeing in the Hub, and I'll document them here:

1. R code

quarto preview fails when Amy has an empty R code cell, she gets this error with the following code:

ERROR: Error executing 'Rscript': No such file or directory (os error 2)

Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/

2. formatting

In my local RStudio (quarto 1.2.269), I'm able to add code chunk headers to indicate the language:

But in the Hub it is very grumpy about it: it doesn't handle bash well and then ignores the ones I have for python.

Documenting progress here and where I'm stuck - to discuss with @battistowx tomorrow
Our best corn update instructions is here: https://github.com/NASA-Openscapes/corn#overview

• Today I updated the quarto version here in corn to try to trigger a build and bring the newest earthaccess to 2i2c (commit)
• This should trigger a GitHub Action to Docker, but the GitHub Action is not triggered (from https://github.com/NASA-Openscapes/corn > https://hub.docker.com/r/openscapes/python).
  • See previous action logs and the action itself
• I also sleuthed Luis' communication with 2i2c, because we need to send them a PR to update in 2i2c (we no longer to this manually in the admin > configurator console). Some Issues:
  • Feb 2023 2i2c-org/infrastructure#2150
  • Dec 2022 2i2c-org/infrastructure#2011

(Screenshots of sleuthing) > I started with the Pull Requests results and then Issues

Hi Luis,

Is corn windows compatible?

We were looking at these lines with @andypbarrett @michele-personal

https://github.com/NASA-Openscapes/corn/blob/main/ci/environment.yml#L56-L58

Thanks!

Jupytext provides a jupyterlab extension that automates maintaining text versions of jupyter notebooks. Our Champions cohort group would benefit from having it installed.

I'm eager to understand how all our infrastructure works, and would like to submit the very simple PR this takes and follow it through to deployment. I'm sure I'll be pinging @betolink for better understanding the process. Thanks in advance.

Also, thank you @battistowx for the advice today.

Noting this here for us in the next corn iteration - @betolink @erinmr

Could we please add the python base image to both the Matlab and R images. Since Matlab and R will often act as wrappers or we're otherwise testing things in Python, this is a sticking point. It also came up with the NASA Mentors when the Matlab image didn't have earthaccess installed.

Also: the JupyterHub looks the same in all cases so it's confusing that python isn't there

Is there a reason holoviews is pinned to - holoviews=1.16.2? There was a invert y-axis bug that was fixed in v 1.17 in addition v 1.18 fixed compatibility issues with xarray 2023.12 (https://github.com/holoviz/holoviews/releases/tag/v1.18.2)

I was trying to run the tutorials from AGU workshop & 2021 Hackathon using mybinder.org yesterday.

This lead me to the corn repo which I think I was able to use on mybinder with these modifications. Could send as PR -- would that be of interest to you?

We need to elevate Julia to a first class citizen among the languages as is widely used in a lot of interesting projects.

Would be great to add the Quarto extension for JupyterLab to corn:

https://quarto.org/docs/tools/jupyter-lab-extension.html

"The Quarto JuptyerLab extension enables JupyterLab Notebooks which use Quarto markdown to properly display the contents of the markdown cells. For example, when the Quarto JupyterLab extension is installed, your Notebook will show rendered previews of elements like Callouts, Divs, Mermaid charts, as well as other Quarto elements (including the document front matter as a title block)."