Merge pull request #83 from NIEHS/isong-hucvars

0.2.0 dev

.github/workflows/pkgdown.yaml

@@ -12,7 +12,47 @@ on:
 name: pkgdown
 
 jobs:
+  test-covr:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+            extra-packages: |
+              any::pak
+              any::covr
+              any::devtools
+              any::DT
+              any::htmltools
+            needs: coverage
+
+      - name: Cache C++ and R dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/R
+            ~/.local/share/R
+          key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }}
+          restore-keys: |
+            dependencies-${{ runner.os }}-
+
+      - name: Run tests and generate covr report
+        run: |
+          Rscript -e 'covr::report(file = "coverage_report.html")'
+
+      - name: Upload covr report as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: covr-report
+          path: coverage_report.html
+
   pkgdown:
+    needs: test-covr
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
@@ -24,6 +64,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Download covr report
+        uses: actions/download-artifact@v4
+        with:
+          name: covr-report
+          path: .
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -41,7 +87,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage-local.yaml

@@ -24,11 +24,13 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
-          needs: coverage
+            extra-packages: |
+              any::pak
+              any::covr
+            needs: coverage
 
       - name: Cache C++ and R dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/R
@@ -38,10 +40,15 @@ jobs:
             dependencies-${{ runner.os }}-
 
       - name: Test coverage
-        run: >
-          Rscript -e
-          "covd<-covr::coverage_to_list()$totalcoverage;
-          write.table(covd[length(covd)], file = '${{ github.workspace }}/local_cov.Rout', row.names = F, col.names = F)"
+        run: |
+          Rscript ${{ github.workspace }}/.github/workflows/test-coverage.R ${{ runner.temp }} ${{ github.workspace }}
+        shell: bash
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Get Values
@@ -61,6 +68,10 @@ jobs:
         id: patch-comparison
         shell: bash
         run: |
+          if ( ! test -f cov_current.Rout ); then
+            echo "0" >> cov_current.Rout
+          fi
+
           cov_patch="${{ steps.get-values.outputs.coverage }}"
           cov_current=$(cat cov_current.Rout)
           echo "Current coverage: $cov_current"
@@ -86,7 +97,7 @@ jobs:
         run: |
           npm i -g badgen-cli
           export COV=${{ steps.get-values.outputs.coverage }}
-          COLOR=$(node -p '+process.env.COV >= 95 ? `green` : `orange`')
+          COLOR=$(node -p '+process.env.COV >= 95 ? `green` : `yellow`')
           mkdir -p badges
           badgen -j coverage -s $COV% -c $COLOR > badges/coverage.svg
   

.github/workflows/test-coverage.R

@@ -0,0 +1,15 @@
+args <- commandArgs(trailingOnly = TRUE)
+runnertemp <- args[[1]]
+ghworkspace <- args[[2]]
+
+dir.create(file.path(runnertemp, "package"), showWarnings = FALSE, recursive = TRUE)
+sink(paste0(runnertemp, '/package/testthat.Rout.res'))
+cov <- covr::package_coverage()
+sink()
+covd <- covr::coverage_to_list(cov)$totalcoverage
+write.table(
+  covd[length(covd)],
+  file = file.path(ghworkspace, 'local_cov.Rout'),
+  row.names = FALSE,
+  col.names = FALSE
+)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: amadeus
 Title: AMADEUS: A Machine for Data, Environments, and User Setup for common environmental and climate health datasets 
-Version: 0.1.7
+Version: 0.2.0
 Authors@R: c(
     person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623")),
     person("Mitchell", "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),
@@ -12,7 +12,7 @@ Authors@R: c(
     )
 Description: A Mechanism/Machine for Data, Environments, and User Setup package for health and climate research. It is fully tested, versioned, and open source and open access.
 Depends: R (>= 4.1.0)
-Imports: dplyr, sf, sftime, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringi, testthat (>= 3.0.0), doParallel, parallelly, stars, foreach, future, tidyr, rlang, rstac, nhdplusTools, archive
+Imports: dplyr, sf, sftime, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringi, testthat (>= 3.0.0), parallelly, stars, future, future.apply, tidyr, rlang, rstac, nhdplusTools, archive, collapse, devtools
 Suggests: covr, withr, knitr, rmarkdown, lwgeom, FNN, doRNG
 Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(as_mysftime)
+export(calc_check_time)
 export(calc_covariates)
 export(calc_ecoregion)
 export(calc_geos)
@@ -31,36 +32,36 @@ export(check_mysf)
 export(check_mysftime)
 export(check_url_status)
 export(check_urls)
-export(download_aqs_data)
-export(download_cropscape_data)
+export(download_aqs)
+export(download_cropscape)
 export(download_data)
-export(download_ecoregion_data)
+export(download_ecoregion)
 export(download_epa_certificate)
-export(download_geos_data)
-export(download_gmted_data)
-export(download_gridmet_data)
-export(download_hms_data)
-export(download_huc_data)
-export(download_koppen_geiger_data)
-export(download_merra2_data)
-export(download_modis_data)
-export(download_narr_monolevel_data)
-export(download_narr_p_levels_data)
-export(download_nei_data)
-export(download_nlcd_data)
-export(download_olm_data)
+export(download_geos)
+export(download_gmted)
+export(download_gridmet)
+export(download_hms)
+export(download_huc)
+export(download_koppen_geiger)
+export(download_merra2)
+export(download_modis)
+export(download_narr_monolevel)
+export(download_narr_p_levels)
+export(download_nei)
+export(download_nlcd)
+export(download_olm)
 export(download_permit)
-export(download_prism_data)
+export(download_prism)
 export(download_remove_command)
 export(download_remove_zips)
 export(download_run)
 export(download_sanitize_path)
-export(download_sedac_groads_data)
-export(download_sedac_population_data)
+export(download_sedac_groads)
+export(download_sedac_population)
 export(download_setup_dir)
 export(download_sink)
-export(download_terraclimate_data)
-export(download_tri_data)
+export(download_terraclimate)
+export(download_tri)
 export(download_unzip)
 export(dt_as_mysftime)
 export(extract_urls)
@@ -122,30 +123,34 @@ import(sf)
 import(sftime)
 import(stars)
 importFrom(archive,archive_extract)
+importFrom(collapse,rowbind)
 importFrom(data.table,.SD)
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
 importFrom(data.table,month)
 importFrom(data.table,rbindlist)
 importFrom(data.table,year)
-importFrom(doParallel,registerDoParallel)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,distinct)
 importFrom(dplyr,ends_with)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,lag)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,select)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(exactextractr,exact_extract)
-importFrom(foreach,"%dopar%")
-importFrom(foreach,foreach)
 importFrom(future,cluster)
+importFrom(future,multicore)
 importFrom(future,plan)
+importFrom(future,sequential)
+importFrom(future.apply,future_Map)
+importFrom(future.apply,future_lapply)
 importFrom(httr,GET)
 importFrom(httr,HEAD)
 importFrom(methods,is)
@@ -159,10 +164,16 @@ importFrom(rstac,read_collections)
 importFrom(rstac,read_items)
 importFrom(rstac,read_stac)
 importFrom(sf,st_as_sf)
+importFrom(sf,st_as_sfc)
+importFrom(sf,st_crs)
 importFrom(sf,st_drop_geometry)
 importFrom(sf,st_geometry)
+importFrom(sf,st_intersects)
+importFrom(sf,st_read)
+importFrom(sf,st_transform)
 importFrom(sf,st_union)
 importFrom(stars,read_stars)
+importFrom(stars,st_mosaic)
 importFrom(stars,st_warp)
 importFrom(stats,aggregate)
 importFrom(stats,setNames)
@@ -190,8 +201,7 @@ importFrom(terra,nlyr)
 importFrom(terra,perim)
 importFrom(terra,project)
 importFrom(terra,rast)
-importFrom(terra,same.crs)
-importFrom(terra,snap)
+importFrom(terra,set.crs)
 importFrom(terra,sprc)
 importFrom(terra,subset)
 importFrom(terra,tapp)