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A tutorial book of workflows for research using NASA EarthData in the Cloud created by the NASA-Openscapes team

Home Page: https://nasa-openscapes.github.io/earthdata-cloud-cookbook

License: Other

JavaScript 0.12% Python 0.01% Lua 0.01% CSS 0.01% Jupyter Notebook 99.85% SCSS 0.01% Dockerfile 0.01% R 0.01% Shell 0.01%

earthdata-cloud-cookbook's Introduction

E. Eli Holmes Github

Research Fisheries Biologist, Northwest Fisheries Science Center, NOAA Fisheries
Affiliate faculty, SAFS, University of Washington, Seattle

My eeholmes account has mostly sandboxy repos. To find my code and teaching products, look in the GH orgs that I contribute to (table below). For time series stuff: ATSA book, ATSA course, MARSS, MARSS with Stan.

org
links status
Applied Time
Series Analysis		 GitHub org issues
NWFSC
Time Series		 GitHub org issues
NWFSC
Math Bio
Fish Forecast
Rverse
Tutorials
Ocean
Satellite Tools
Upwelling project GitHub org issues

I am also a contributor to NMFS OpenSci, Openscapes, NMFS Openscapes, NMFS R User Group and R-Govys.

Finding my stuff: You can try searching by topic: https://github.com/search?q=topic:<TOPIC>+user:eeholmes&type=Repositories. Topics: R, MARSS, jupyter, earthdata, remote-sensing, upwelling, teaching.

The repositories in my eeholmes GitHub account are scientific products and are not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. The scientific results and conclusions, as well as any views or opinions expressed herein, are mine and do not necessarily reflect the views of NOAA or the Department of Commerce. In addition, this account may have forked repositories that are not my work.

earthdata-cloud-cookbook's People

Contributors

abarciauskas-bgse avatar alexishunzinger avatar amfriesz avatar andypbarrett avatar asteiker avatar battistowx avatar betolink avatar briannalind avatar cassienickles avatar cboettig avatar cgangoda avatar christine-e-smit avatar cpkrehbiel avatar cscheid avatar cwannaz avatar eeholmes avatar erinmr avatar gokulprathin8 avatar jessnicwelch avatar jjallaire avatar jules32 avatar mjami00 avatar owenlittlejohns avatar pommevilla avatar rsignell-usgs avatar sciencecat18 avatar stefaniebutland avatar virdi avatar zihengsun avatar zmoon avatar

Stargazers

avatar

earthdata-cloud-cookbook's Issues

problem with raster, terra etc when using the devcontainer base image

@cboettig

In an image with

FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3

as the base image. We were unable to load spatial packages (installed via install.r).
https://github.com/nmfs-opensci/container-images/blob/main/images/coastwatch/Dockerfile
https://github.com/nmfs-opensci/container-images/blob/main/images/coastwatch/install.R

error

> library(raster)
Error: package or namespace load failed for ‘raster’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/terra/libs/terra.so':
  libproj.so.22: cannot open shared object file: No such file or directory

The file that it cannot open changes. terra.so and ncdf4.so were common.

fix

Switched to

FROM rocker/geospatial:4.2

to get it to work. Note install.R has rgdal which is deprecated. Maybe that is the issue? Need to test wo that.

to test

Use ghcr.io/rocker-org/devcontainer/tidyverse:4.3 in 'bring your image' and then install some spatial packages and see if problem persists. Or slowly add packages to install.R and see when the problem appears.

conda.Dockerfile

@cboettig

I separated the GA workflows into a conda and venv one so each was only triggered when needed.

Probably would be good to change the Quarto workflows so they are not triggered whenever there is a change to the image building.

The image builds are taking 45 minutes. Ouch.

The conda image still won't spin up on Openscapes but I think something is up and since the tag is not changing, the hub is not using the new image? Something is up. I am trying a new tag.

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