Merge pull request #355 from NIEHS/pipeline-compact

0.4.0

.Rbuildignore

@@ -1,4 +1,3 @@
-^vignettes/
 ^tests/
 ^input/
 ^tools/
@@ -18,10 +17,16 @@ input/*
 inst/targets-wide
 ^.future/
 ^_targets/
+_targets.R
+_targets.yaml
+\*.Rproj
 \.out$
 \.err$
 \.sif$
 \.log$
 \.vscode
 \.qmd$
 \.sh$
+R/reserved.R
+^doc$
+^Meta$

.gitattributes

@@ -1,4 +1,4 @@
 *.csv filter=lfs diff=lfs merge=lfs -text
 *.nc filter=lfs diff=lfs merge=lfs -text
-
 input/** linguist-generated
+inst/extdata/aqs_88101_2022.qs filter=lfs diff=lfs merge=lfs -text

.github/workflows/check-standard.yaml

@@ -23,9 +23,19 @@ 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 dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
       - name: install remote packages
         run: |
           Rscript -e 'remotes::install_github(sprintf("NIEHS/%s", c("amadeus", "chopin")), upgrade = FALSE)'

.github/workflows/pkgdown.yaml

@@ -32,9 +32,16 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::pkgdown,
+            local::.
           needs: website
 
+      - name: install remote packages
+        run: |
+          Rscript -e 'remotes::install_github(sprintf("NIEHS/%s", c("amadeus", "chopin")), upgrade = FALSE)'
+        shell: bash
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

.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 }}/beethoven-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 }} 

.gitignore

@@ -102,3 +102,5 @@ slurm_error.log
 
 # Apptainer images
 **/*.sif
+/Meta/
+/doc/

.lintr

@@ -2,7 +2,7 @@ linters: linters_with_defaults(
     commented_code_linter = NULL
   )
 exclusions: list(
-    "tests/testthat/test-download_functions.R",
+    "tests",
     "inst",
     "_targets.R"
   )

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: beethoven
 Title: Building an Extensible, rEproducible, Test-driven, Harmonized, Open-source, Versioned, ENsemble model for air quality
-Version: 0.3.5
+Version: 0.4.0
 Authors@R: c(
     person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623")),
     person("Insang", "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
@@ -16,24 +16,23 @@ Authors@R: c(
 Description: Near Real Time air pollution model results and code produced by the SET group. It is fully tested, versioned, and open source and open access.
 Depends: R (>= 4.1.0)
 Imports:
+  amadeus,
   dplyr,
   sf,
   stats,
   terra,
   methods,
-  BART,
   data.table,
   future,
   targets,
   tune (>= 1.2.1),
   rlang,
   rsample,
+  spatialsample,
   tidyr,
   tidyselect,
   yardstick,
-  bonsai,
-  lightgbm,
-  vetiver,
+  torch,
   workflows,
   recipes,
   missRanger,
@@ -43,19 +42,25 @@ Imports:
   anticlust,
   qs,
   stringi,
+  tibble,
   collapse,
   tigris,
-  graphics
+  graphics,
+  scatterplot3d
 Suggests:
   testthat (>= 3.0.0),
   covr,
   withr,
-  tarchetypes,
-  tidymodels,
-  xgboost,
-  torch,
+  bonsai,
   brulee,
   glmnet,
+  lightgbm,
+  scoringRules,
+  future.mirai,
+  xgboost (<= 2.0.3.1),
+  vetiver,
+  tarchetypes,
+  tidymodels,
   knitr,
   rmarkdown,
   stars,
@@ -64,10 +69,10 @@ Suggests:
   FNN,
   ggplot2,
   doRNG,
-  scatterplot3d,
   furrr,
   quarto
 Remotes: NIEHS/amadeus, NIEHS/chopin
+SystemRequirements: NetCDF4, CUDA (>= 10.0)
 Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown
 Roxygen: list(markdown = TRUE)