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479b072
playing with chelsa script
adammwilson Jan 11, 2022
ee67437
merge with main
adammwilson Jan 18, 2022
9f4cf32
udpate meta
adammwilson Jan 18, 2022
eb31274
update targets file
adammwilson Jan 26, 2022
e4707b8
add side script for bioscape domain definition
adammwilson Feb 7, 2022
48fea77
udpate readme
adammwilson Feb 14, 2022
5cd40b0
update gitignore
adammwilson Feb 14, 2022
7671914
update readme fig
adammwilson Feb 14, 2022
e981914
add Brian's files
adammwilson Feb 14, 2022
73c92e3
update targets
adammwilson Apr 10, 2025
80ba45d
start playing with appeears instead of earth engine
adammwilson Apr 29, 2025
f88236f
merge with dev-adam
adammwilson Apr 29, 2025
791fdfe
clean up merge
adammwilson May 5, 2025
d00f972
Update targets.yaml
adammwilson May 27, 2025
b7528af
Merge branch 'main' into dev-adam
adammwilson Dec 23, 2025
93cfcd2
- update appeears_auth file - works now locally
adammwilson Jan 5, 2026
6fe3870
Refactor domain and national boundary functions for improved clarity …
adammwilson Jan 5, 2026
edcd1f0
Add functions to download and process NDVI and NDWI layers from MODIS…
adammwilson Jan 8, 2026
08ba1d6
Add README and ccr_startup script for CCR job setup
adammwilson Jan 8, 2026
1595b5d
Merge branch 'dev-adam-appeears' of https://github.com/AdamWilsonLab/…
adammwilson Jan 8, 2026
913a557
Update DESCRIPTION and R scripts to include ncdf4 package and improve…
adammwilson Jan 8, 2026
2a488a3
Enhance domain definition by adding "Succulent Karoo" biome and updat…
adammwilson Jan 9, 2026
cbaba88
Update GitHub Actions workflow to include 'dev-adam-appeears' branch …
adammwilson Jan 9, 2026
2c14094
Remove deprecated secret decryption scripts and comment out unused st…
adammwilson Jan 9, 2026
daad59c
Update GitHub Actions workflow to use 'dev-adam-appeears' branch and …
adammwilson Jan 9, 2026
cab8ff0
Refactor library loading in _targets.R to streamline package options …
adammwilson Jan 9, 2026
af020fb
Refactor library loading in _targets.R to remove unnecessary lib.loc …
adammwilson Jan 9, 2026
e165243
Add environment variables for Earthdata credentials and R package sou…
adammwilson Jan 9, 2026
e2957b3
Add installation of system dependencies for keyring in GitHub Actions…
adammwilson Jan 9, 2026
01772e8
Comment out the closing parenthesis for the precipitation_chelsa targ…
adammwilson Jan 9, 2026
9053425
Update national_boundary function to download GeoJSON directly and re…
adammwilson Jan 9, 2026
8f3b145
Add shapefile and associated metadata for All_fires_23_24_gw dataset
adammwilson Jan 9, 2026
7b585ed
Add vegmap processing and enhance domain rasterization
adammwilson Jan 9, 2026
20b4f92
Fix gdal_vector_driver option and update domain_rasterize call in _ta…
adammwilson Jan 9, 2026
71f0c50
Refactor data processing functions: update vegmap handling in data_ve…
adammwilson Jan 9, 2026
68c361a
Fix domain parameter references in tar_terra_rast calls for correct d…
adammwilson Jan 9, 2026
8c00b71
Fix data reading in domain_define function by applying janitor::clean…
adammwilson Jan 9, 2026
1022235
Fix domain_define call in tar_terra_vect to use correct parameter for…
adammwilson Jan 9, 2026
d4ddac5
Fix st_intersection call in domain_define to use correct CRS from veg…
adammwilson Jan 9, 2026
9f1f674
Fix file path in tar_target for capenature_fires_shp to ensure correc…
adammwilson Jan 9, 2026
afb2d26
Refactor workflow and R scripts: update cron schedule, add get_countr…
adammwilson Jan 9, 2026
6fac51f
Update .gitignore with additional patterns and cleanup
adammwilson Jan 9, 2026
f55bf03
Add new spatial data layers and update functions
adammwilson Jan 9, 2026
f5835e9
update distance calculation
adammwilson Jan 9, 2026
b29b1ea
Enhance workflow: rename step and add error handling for targets pipe…
adammwilson Jan 12, 2026
ec8f446
Enhance data processing workflows: add error handling to targets pipe…
adammwilson Jan 12, 2026
24f166a
Add functions to download and process vegetation map, including metad…
adammwilson Jan 12, 2026
2c8398b
Update vegmap shapefile download and metadata; add new functions and …
adammwilson Jan 12, 2026
ac34e7d
Update GitHub Actions workflow: add permissions for contents, pull re…
adammwilson Jan 12, 2026
0d52ce5
Refactor vegetation map download function to check for shapefile in s…
adammwilson Jan 12, 2026
03ce2bc
Add debug message to list files in local directory after downloading …
adammwilson Jan 12, 2026
69d9a22
Enhance domain rasterization function: add domain indicator, update r…
adammwilson Jan 13, 2026
a9c1264
Update domain rasterization and targets: enhance remnant vegetation i…
adammwilson Jan 13, 2026
a124461
Enhance data processing functions: add output file parameter to data_…
adammwilson Jan 14, 2026
343513b
Add functions for downloading national boundaries and managing GitHub…
adammwilson Jan 14, 2026
2d7c42d
Refactor code structure for improved readability and maintainability
adammwilson Jan 15, 2026
fd0c800
Enhance domain bounding box function and GitHub release handling:
adammwilson Jan 15, 2026
f787953
Add logging for GITHUB_ACTIONS environment variable and improve run m…
adammwilson Jan 15, 2026
68473b6
Refactor code structure for improved readability and maintainability
adammwilson Jan 15, 2026
3da0dd2
Add GitHub CLI installation step and simplify run mode determination
adammwilson Jan 15, 2026
7d69749
Remove auto-generated label from PR closing message
adammwilson Jan 15, 2026
e780d6d
Add workflow failure log for review
github-actions[bot] Jan 15, 2026
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52 changes: 0 additions & 52 deletions .github/decrypt_secret.sh

This file was deleted.

19 changes: 0 additions & 19 deletions .github/decrypt_secret_gd.sh

This file was deleted.

171 changes: 171 additions & 0 deletions .github/workflow-logs/failure-20260115-033017.log
Original file line number Diff line number Diff line change
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Starting tar_make()
[1] "Starting tar_make() - print"
qs 0.27.3. Announcement: https://github.com/qsbase/qs/issues/103
Registered S3 method overwritten by 'httr':
method from
print.cache_info hoardr

Attaching package: ‘arrow’

The following object is masked from ‘package:utils’:

timestamp

System info: sysname=Linux; release=6.11.0-1018-azure; version=#18~24.04.1-Ubuntu SMP Sat Jun 28 04:46:03 UTC 2025; nodename=440c605558f8; machine=x86_64; login=unknown; user=root; effective_user=root
Run mode: update
[1] "R/appeears_auth.R"
Setting up NASA EarthData authentication (keyring file backend)
AppEEARS authentication configured
[1] "R/data_chelsa.R"
terra 1.8.86

Attaching package: ‘terra’

The following object is masked from ‘package:arrow’:

buffer

[1] "R/data_vegmap.R"
[1] "R/domain_bbox.R"
[1] "R/domain_define_bioscape.R"
[1] "R/domain_define.R"
[1] "R/domain_figures.R"
[1] "R/domain_rasterize.R"
[1] "R/download_vegmap_release.R"
[1] "R/functions.R"
[1] "R/get_country.R"
[1] "R/get_elevation.R"
[1] "R/get_release_alos.R"
[1] "R/get_release_climate_chelsa.R"
[1] "R/get_release_clouds_wilson.R"
[1] "R/get_release_fire_modis_appeears.R"
[1] "R/get_release_landcover_za.R"
[1] "R/get_release_ndvi_evi_modis_appeears.R"
[1] "R/get_release_ndvi_viirs_appeears.R"
[1] "R/get_release_precipitation_chelsa.R"
[1] "R/get_release_soil_gcfr.R"
[1] "R/get_release_template_raster.R"
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.1 ✔ stringr 1.6.0
✔ ggplot2 4.0.0 ✔ tibble 3.3.0
✔ lubridate 1.9.4 ✔ tidyr 1.3.1
✔ purrr 1.2.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ lubridate::duration() masks arrow::duration()
✖ tidyr::extract() masks terra::extract()
✖ dplyr::filter() masks stats::filter()
✖ readr::guess_encoding() masks rvest::guess_encoding()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
[1] "R/git_functions.R"
[1] "R/model_data.R"
[1] "R/process_dynamic_data.R"
[1] "R/process_fix_modis_NDVI_release_extent.R"
[1] "R/process_fix_modis_projection.R"
[1] "R/process_fix_modis_release_extent.R"
[1] "R/process_fix_modis_release_projection_and_extent.R"
[1] "R/process_fix_modis_release_projection.R"
[1] "R/process_release_alos.R"
[1] "R/process_release_burn_date_to_last_burned_date.R"
Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
[1] "R/process_release_climate_chelsa.R"
[1] "R/process_release_clouds_wilson.R"
[1] "R/process_release_dynamic_data_to_parquet.R"
[1] "R/process_release_elevation_nasadem.R"
[1] "R/process_release_fire_doy_to_unix_date.R"
[1] "R/process_release_landcover_za.R"
[1] "R/process_release_ndvi_relative_days_since_fire.R"
[1] "R/process_release_precipitation_chelsa.R"
[1] "R/process_release_protected_area_distance.R"
udunits database from /usr/share/xml/udunits/udunits2.xml
[1] "R/process_release_soil_gcfr.R"
[1] "R/process_release_stable_data.R"
[1] "R/process_stable_data.R"
[1] "R/release_data.R"
[1] "R/robust_download_file.R"
[1] "R/robust_pb_download.R"
[1] "R/robust_pb_upload.R"
[1] "R/tar_release_storage.R"
[1] "R/vegetation_map.R"
Objects: clean_data
Objects: data_vegmap
Objects: domain_define
Objects: domain_map
Objects: domain_rasterize
Objects: download_vegmap_release
Objects: earthdata_pass
Objects: earthdata_user
Objects: existing_kr
Objects: fit_model
Objects: get_alos_data
Objects: get_chelsa
Objects: get_country
Objects: get_elevation
Objects: get_model_data
Objects: get_release_alos
Objects: get_release_climate_chelsa
Objects: get_release_clouds_wilson
Objects: get_release_fire_modis_appeears
Objects: get_release_landcover_za
Objects: get_release_ndvi_evi_modis_appeears
Objects: get_release_ndvi_viirs_appeears
Objects: get_release_precipitation_chelsa
Objects: get_release_soil_gcfr
Objects: get_release_template_raster
Objects: get_vegmap
Objects: group_data_function
Objects: kr_name
Objects: kr_pwd
Objects: make_domain_bbox
Objects: max_layers
Objects: process_dynamic_data_to_parquet
Objects: process_fix_modis_NDVI_release_extent
Objects: process_fix_modis_projection
Objects: process_fix_modis_release_extent
Objects: process_fix_modis_release_projection
Objects: process_fix_modis_release_projection_and_extent
Objects: process_release_alos
Objects: process_release_burn_date_to_last_burned_date
Objects: process_release_climate_chelsa
Objects: process_release_clouds_wilson
Objects: process_release_dynamic_data_to_parquet
Objects: process_release_elevation_nasadem
Objects: process_release_fire_doy_to_unix_date
Objects: process_release_landcover_za
Objects: process_release_ndvi_relative_days_since_fire
Objects: process_release_precipitation_chelsa
Objects: process_release_protected_area_distance
Objects: process_release_soil_gcfr
Objects: process_release_stable_data
Objects: process_stable_data
Objects: release_data
Objects: robust_download_file
Objects: robust_max
Objects: robust_min
Objects: robust_pb_download
Objects: robust_pb_download_solo
Objects: robust_pb_upload
Objects: rstoken
Objects: run_mode
Objects: sleep_time
Objects: spatial_outputs
Objects: stan_data_function
Objects: summarize_posteriors
Objects: sys_info
Objects: tag
Objects: tar_github_release_repo
Objects: tar_github_release_resources
Objects: temp_directory
Objects: update_git
Objects: verbose
+ vegmap_shp dispatched
Downloading vegmap from GitHub release using piggyback...
Unzipping vegmap...
✖ vegmap_shp errored
✖ errored pipeline [12.3s, 0 completed, 1 skipped]
Error:
! Error in tar_make():
Error resolving output location: missing files: data/manual_download/NVM2024/shapefile/NVM2024Final_IEM5_12_07012025.shp
See https://books.ropensci.org/targets/debugging.html
Execution halted
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