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NIEHS / amadeus

https://niehs.github.io/amadeus/
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Reopen mm-copy-functions pull request with branch version 2 #19

Closed mitchellmanware closed 9 months ago

mitchellmanware commented 9 months ago
  1. Migrate NARR, GEOS-CF, HMS, GMTED, and SEDAC population functions and tests from beethoven
  2. Merge with current process.R and calculate_covariates.R files
  3. Add spatial subset test data sets
  4. Update README.md
  5. download_noaa_hms_smoke_data > download_hms_data (reflected in man/ and all tests)
  6. Utilize base R strsplit() in the extract_urls() download support function.
    • Replaced stringr dependency with stringi for stringi::stri_pad() in process_narr()
  7. Lighter and fewer geos/ test data
  8. testthat::test_path() in unit tests
  9. Added method = "SKIP" to check_urls() to skip HTTP status check in the MODIS download unit tests
mitchellmanware commented 9 months ago

Pull request checks continue to fail as a result of MODIS download function unit tests. I am very confused how previously passing tests are now failing without editing any of the unit tests or MODIS functions. I thought that the failures may be related to limits on GitHub runner API request or CRAN 60 second limit on HTTP requests, but utilizing a faster HTTP method with httr2 package increased the running time and still resulted in failures. Local R CMD build with devtools::check(), and running tests individually with testthat::test_file(), also fail due to the three MODIS unit tests.

Screenshot 2024-02-23 at 2 48 36 PM

@sigmafelix @eva0marques @Spatiotemporal-Exposures-and-Toxicology Any thoughts on causes or solutions?

sigmafelix commented 9 months ago

Related #20; I found that manual download using links from download_modis_data gives timeout error. NASA server might have issues or just blocked our office IPs at the moment. We might just remove url checks for MODIS data.

mitchellmanware commented 9 months ago

Implementing URL status skips for MODIS download tests after discussion https://github.com/Spatiotemporal-Exposures-and-Toxicology/amadeus/issues/20

codecov[bot] commented 9 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 95.76%. Comparing base (37ba1fe) to head (3cf2384).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #19 +/- ## ========================================== + Coverage 94.45% 95.76% +1.31% ========================================== Files 6 6 Lines 2182 2978 +796 ========================================== + Hits 2061 2852 +791 - Misses 121 126 +5 ```

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