Lint + importFrom fix

.github/workflows/check-standard.yaml

@@ -23,7 +23,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::remotes, any::units, any::rmarkdown
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::units
+            any::rmarkdown
           needs: check
 
       - name: install remote packages

.github/workflows/test-coverage.yaml

@@ -24,16 +24,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, any::remotes
+          extra-packages: any::covr, any::DT, any::htmltools
           needs: coverage
 
-      - name: install remote packages
-        run: |
-          Rscript -e 'remotes::install_github(sprintf("NIEHS/%s", c("amadeus", "chopin")), upgrade = FALSE)'
-        shell: bash
-
       - name: Cache C++ and R dependencies
-        uses: actions/cache@v4
+        uses: actions/cache@v2
         with:
           path: |
             ~/.cache/R
@@ -43,66 +38,51 @@ jobs:
             dependencies-${{ runner.os }}-
 
       - name: Test coverage
-        run: >
-          Rscript -e
-          "covd<-covr::coverage_to_list()$totalcoverage;
+        run: |
+          Rscript -e "covpack<-covr::package_coverage(install_path='${{ github.workspace }}/cov', clean=FALSE); \
+          covr::report(covpack, file = file.path('${{ github.workspace }}', 'chopin-coverage-report.html')); \
+          covd<-covr::coverage_to_list(covpack)$totalcoverage; \
           write.table(covd[length(covd)], file = '${{ github.workspace }}/local_cov.Rout', row.names = F, col.names = F)"
         shell: bash
 
+      - name: Upload covr report as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: covr-report
+          path: ${{ github.workspace }}/chopin-coverage-report.html
+
+      - name: Upload workspace dump as artifact if the test fails
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-outputs
+          path: ${{ github.workspace }}/**
+
       - name: Get Values
         id: get-values
         shell: bash
         run: |
           COV=$(cat ${{ github.workspace }}/local_cov.Rout)
-          echo "Patch coverage read from local_cov.Rout: $COV"
           echo "coverage=$COV" >> $GITHUB_OUTPUT
 
       - name: Checkout gh-pages
         uses: actions/checkout@v4
         with:
           ref: gh-pages
-
-      - name: Patch comparison
-        id: patch-comparison
-        shell: bash
-        run: |
-          cov_patch="${{ steps.get-values.outputs.coverage }}"
-          if [[ ! -f cov_current.Rout ]]; then
-            cov_current=0
-          else
-            cov_current=$(cat cov_current.Rout)
-          fi
-          echo "Current coverage: $cov_current"
-
-          if (( $(echo "$cov_patch >= $cov_current" | bc -l) )); then
-            echo "Patch coverage ($cov_patch) is greater than or equal to current coverage ($cov_current)."
-            echo "cov_update=$cov_patch" >> $GITHUB_OUTPUT
-           else
-            echo "Patch coverage ($cov_patch) is less than current coverage ($cov_current)."
-            exit 1
-          fi
-
-      - name: Overwrite cov_current.Rout
-        if: ${{ github.event_name == 'push' }}
-        shell: bash
-        run: |
-          cov_update="${{ steps.patch-comparison.outputs.cov_update }}"
-          touch cov_current.Rout
-          echo "$cov_update" > cov_current.Rout
-
+
       - name: Create Badges
         shell: bash
         run: |
           npm i -g badgen-cli
           export COV=${{ steps.get-values.outputs.coverage }}
-          COLOR=$(node -p '+process.env.COV >= 95 ? `green` : `yellow`')
+          COLOR=$(node -p '+process.env.COV >= 95 ? `green` : `orange`')
           mkdir -p badges
           badgen -j coverage -s $COV% -c $COLOR > badges/coverage.svg
   
       - name: Deploy Badges
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
-          commit_message: "Update badges [skip ci] & cov_current.Rout"
+          commit_message: "Update badges [skip ci]"
           branch: gh-pages
           skip_fetch: true
           skip_checkout: true
@@ -113,4 +93,4 @@ jobs:
       - name: Checkout Back
         uses: actions/checkout@v4
         with:
-          ref: ${{ github.ref }}  
+          ref: ${{ github.ref }} 

NAMESPACE

@@ -44,6 +44,17 @@ export(switch_generate_cv_rset)
 export(switch_model)
 export(unmarshal_function)
 export(vis_spt_rset)
+importFrom(amadeus,calc_covariates)
+importFrom(amadeus,calc_prepare_locs)
+importFrom(amadeus,calc_temporal_dummies)
+importFrom(amadeus,calc_worker)
+importFrom(amadeus,check_for_null_parameters)
+importFrom(amadeus,download_data)
+importFrom(amadeus,download_sanitize_path)
+importFrom(amadeus,generate_date_sequence)
+importFrom(amadeus,process_aqs)
+importFrom(amadeus,process_covariates)
+importFrom(amadeus,process_gmted_codes)
 importFrom(anticlust,balanced_clustering)
 importFrom(collapse,fnth)
 importFrom(collapse,fvar)
@@ -62,6 +73,7 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,`%>%`)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
+importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,slice_sample)
 importFrom(dplyr,summarize)
@@ -101,11 +113,15 @@ importFrom(stringi,stri_replace_all_regex)
 importFrom(targets,tar_resources)
 importFrom(targets,tar_resources_future)
 importFrom(terra,crs)
+importFrom(terra,describe)
 importFrom(terra,extract)
 importFrom(terra,rast)
+importFrom(terra,sds)
 importFrom(terra,subset)
 importFrom(terra,time)
 importFrom(terra,varnames)
+importFrom(terra,vect)
+importFrom(tibble,tribble)
 importFrom(tidyselect,all_of)
 importFrom(tigris,counties)
 importFrom(tune,control_bayes)

R/base_learner.R

@@ -875,7 +875,7 @@ generate_cv_index_sp <-
       }
     }
 
-    return(newcv)
+  return(newcv)
 }
 
 

R/calc_postprocessing.R

@@ -284,6 +284,7 @@ post_calc_join_yeardate <-
 #' @note This version assumes the time_id contains Date-like strings.
 #' @return data.frame
 #' @importFrom data.table merge.data.table
+#' @importFrom amadeus calc_temporal_dummies
 #' @export
 post_calc_merge_all <-
   function(
@@ -750,20 +751,4 @@ append_predecessors <-
   }
 
 
-# nested parallelization
-# IN PROGRESS
-# TODO: identify bottleneck
-#' @noRd
-par_nest <-
-  function(
-    path,
-    ...
-  ) {
-    chopin::par_grid(
-      path,
-      fun_dist = calculate,
-      ...
-    )
-  }
-
 # nocov end

R/calculate.R

@@ -20,14 +20,13 @@
 #' hard-coded subsets for subdataset selection
 #' @author Mitchell Manware, Insang Song
 #' @return a `SpatRaster` object;
-#' @importFrom terra rast
-#' @importFrom terra time
-#' @importFrom terra varnames
-#' @importFrom terra crs
-#' @importFrom terra subset
 #' @importFrom sf st_as_sf
 #' @importFrom future.apply future_lapply
 #' @importFrom data.table rbindlist
+#' @importFrom future plan multicore sequential
+#' @importFrom amadeus generate_date_sequence
+#' @importFrom terra describe rast time subset crs varnames vect sds extract
+#' @importFrom dplyr full_join
 #' @export
 calc_geos_strict <-
   function(path = NULL,
@@ -223,9 +222,9 @@ calc_geos_strict <-
 #' @param fun character(1). Function to apply.
 #' @param ... Additional parameters to be passed to other functions.
 #' @return A data.frame containing the extracted GMTED data.
-#' @importFrom terra rast
-#' @importFrom terra varnames
-#' @importFrom terra extract
+#' @importFrom terra rast varnames extract
+#' @importFrom amadeus process_gmted_codes calc_prepare_locs calc_worker
+#' @importFrom amadeus download_sanitize_path
 #' @export
 calc_gmted_direct <- function(
     variable = NULL,

R/init_arguments.R

@@ -85,6 +85,7 @@
 #' * nthreads_impute: Number of threads for imputing data.
 #' @author Insang Song
 #' @importFrom qs qsave
+#' @importFrom tibble tribble
 #' @export
 # nolint start
 set_args_calc <-

R/injection.R

@@ -6,6 +6,8 @@
 #'   dataset.
 #' @param dataset_name character(1). Dataset name.
 #' @param ... Arguments passed to `amadeus::download_data`
+#' @importFrom amadeus download_data
+#' @importFrom rlang inject
 #' @return logical(1).
 #' @export
 feature_raw_download <-
@@ -96,6 +98,8 @@ set_target_years <-
 #' @return A data.table object.
 #' @importFrom data.table rbindlist
 #' @importFrom rlang inject
+#' @importFrom amadeus process_covariates calc_covariates
+#' @importFrom future plan sequential multicore
 #' @export
 calculate <-
   function(

R/load.R

@@ -108,6 +108,7 @@ load_modis_files <- function(path, pattern = "hdf$", date = character(2)) {
 #' @param ... Passed arguments to `fun_aqs`
 #' @return Depending on `fun_aqs` specification.
 #' @importFrom qs qsave
+#' @importFrom amadeus process_aqs
 #' @export
 read_locs <-
   function(

R/processing.R

@@ -185,7 +185,9 @@ process_geos_bulk <-
 #'     path = "/path/to/data"
 #'   )
 #' }
-#'
+#' @importFrom amadeus download_sanitize_path check_for_null_parameters
+#' @importFrom amadeus generate_date_sequence
+#' @importFrom terra rast time subset
 #' @export
 process_narr2 <- function(
     date = c("2023-09-01", "2023-09-01"),

README.md

@@ -4,7 +4,7 @@
 <p>
 
 [![R-CMD-check](https://github.com/NIEHS/beethoven/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/NIEHS/beethoven/actions/workflows/check-standard.yaml)
-[![cov](https://NIEHS.github.io/beethoven/badges/coverage.svg)](https://github.com/NIEHS/beethoven/actions)
+[![cov](https://NIEHS.github.io/beethoven/badges/coverage.svg)](https://github.com/NIEHS/beethoven/actions/workflows/test-coverage.yaml)
 [![lint](https://github.com/NIEHS/beethoven/actions/workflows/lint.yaml/badge.svg)](https://github.com/NIEHS/beethoven/actions/workflows/lint.yaml)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
@@ -705,6 +705,7 @@ append_predecessors(
 The calculated features contain a fair amount of `NA` or `NaN`s depending on the raw dataset. We distinguish these into "true zeros" and "true missing" for the subsequent imputation process. For imputation, `missRanger` is used. The `missRanger` arguments can be adjusted in the `impute_all()` function.
 
 - True zeros: TRI features include many `NA`s as the raw data is a long `data.frame` with source location-chemicals pair keys. This structure requires long-to-wide pivoting, resulting in a sparse `data.frame` with `NA`s where no chemicals were reported in certain locations. Therefore, these `NA`s are considered true zeros.
+
 - Missing: daily satellite-derived features except for the 16-day NDVI are considered to include missing values. Such missing values are mainly coming from intermittent data transmission disruption or planned maintenance. `NA`s in the 16-day NDVI field are filled by the "last observation carried forward" principle. `NaN` values in others are replaced with `NA` and put into the imputation function.
 
 
@@ -713,7 +714,7 @@ The calculated features contain a fair amount of `NA` or `NaN`s depending on the
 
 For efficiency, GPU-enabled version is recommended for `xgboost`/`lightgbm` and `brulee`. These packages need to be installed manually with modifications of system environment variables. Developers should consult `lightgbm` official documentation for building the package by hand, `xgboost` GitHub repository release page for installing the CUDA version manually and `brulee` GitHub repository (i.e., in `gpu` branch) to install the proper version of each package with careful consideration on the computing infrastructure. "GPU" here refers to CUDA-enabled devices produced by NVIDIA corporation. This does not necessarily mean that this package as a part of U.S. government work endorses NVIDIA corporation and its products in any sort.
 
-[!WARNING]
+> [!WARNING]
 > As of version 0.3.10, `xgboost` < v2.1.0 should be used due to breaking changes in v2.1.0 in handling additional arguments in `xgb.DMatrix` (cf. [xgboost pull record](https://github.com/dmlc/xgboost/pull/9862)), which leads to break `parsnip::boost_tree()` function call.