Merge pull request #1 from Spatiotemporal-Exposures-and-Toxicology/in…

…it-spinoff

Initial migration

.Rbuildignore

@@ -0,0 +1,14 @@
+^vignettes/
+^input/
+^tools/
+^manuscript/
+^output/
+^\.github/workflows/
+^amadeus\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^.lintr

.github/workflows/check-standard.yaml

@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          #- {os: macos-13-xlarge,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::tictoc
+            any::units
+            any::rcmdcheck
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,59 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} # Add this line
+
+    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::tictoc
+            any::units
+            any::knitr
+            any::rmarkdown
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+      - name: Upload coverage to Codecov # Add this step
+        run: |
+          Rscript -e "covr::codecov(token = Sys.getenv('CODECOV_TOKEN'))"

.gitignore

@@ -47,3 +47,7 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+# DS_Store
+.DS_Store
+**/.DS_Store

.lintr

@@ -0,0 +1,6 @@
+linters: linters_with_defaults(
+    commented_code_linter = NULL
+  )
+exclusions: list(
+    "tests/testthat/test-download_functions.R"
+  )

DESCRIPTION

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+Package: amadeus
+Title: AMADEUS: A Mechanism/Machine for Data, Environments, and User Setup
+Version: 0.0.1
+Authors@R: c(
+    person("Kyle", "Messier", , "[email protected]", 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")),
+    person("Insang", "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
+    person("Eva", "Marques", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-9817-6546")),
+    person("Mariana", "Alifa Kassien", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-2295-406X")),
+    person("Ranadeep", "Daw", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-3590-909X")),	
+    person("Daniel", "Zilber", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-4387-0271"))
+    )
+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, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringr, testthat (>= 3.0.0), doParallel, parallelly, stars, foreach, future
+Suggests: covr, withr, knitr, rmarkdown, sftime, lwgeom, FNN, doRNG
+Encoding: UTF-8
+VignetteBuilder: knitr, rmarkdown
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.0
+Config/Needs/website: tidyverse/tidytemplate
+Config/testhat/edition: 3
+License: MIT + file LICENSE
+URL: https://github.com/Spatiotemporal-Exposures-and-Toxicology/amadeus, 
+https: //spatiotemporal-exposures-and-toxicology.github.io/amadeus/

NAMESPACE

@@ -0,0 +1,110 @@
+# Generated by roxygen2: do not edit by hand
+
+export(calc_covariates)
+export(calc_ecoregion)
+export(calc_koppen_geiger)
+export(calc_modis)
+export(calc_nei)
+export(calc_nlcd_ratio)
+export(calc_temporal_dummies)
+export(calc_tri)
+export(check_for_null_parameters)
+export(check_url_status)
+export(check_urls)
+export(convert_stdt)
+export(convert_stdt_sftime)
+export(convert_stdt_spatrastdataset)
+export(convert_stdt_spatvect)
+export(convert_stobj_to_stdt)
+export(download_aqs_data)
+export(download_data)
+export(download_ecoregion_data)
+export(download_epa_certificate)
+export(download_geos_cf_data)
+export(download_gmted_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_noaa_hms_smoke_data)
+export(download_permit)
+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_setup_dir)
+export(download_sink)
+export(download_tri_data)
+export(download_unzip)
+export(extract_urls)
+export(generate_date_sequence)
+export(is_stdt)
+export(modis_aggregate_sds)
+export(modis_get_vrt)
+export(modis_mosaic_mod06)
+export(modis_prefilter_sds)
+export(modis_preprocess_vnp46)
+export(modis_warp_stars)
+export(modis_worker)
+export(read_commands)
+export(test_download_functions)
+import(rvest)
+importFrom(data.table,.SD)
+importFrom(data.table,as.data.table)
+importFrom(data.table,fread)
+importFrom(data.table,melt)
+importFrom(data.table,merge.data.table)
+importFrom(data.table,month)
+importFrom(data.table,rbindlist)
+importFrom(data.table,year)
+importFrom(doParallel,registerDoParallel)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,left_join)
+importFrom(exactextractr,exact_extract)
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
+importFrom(future,cluster)
+importFrom(future,plan)
+importFrom(httr,GET)
+importFrom(httr,HEAD)
+importFrom(methods,is)
+importFrom(parallelly,availableWorkers)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_coordinates)
+importFrom(sf,st_crs)
+importFrom(sf,st_drop_geometry)
+importFrom(sf,st_geometry)
+importFrom(sf,st_transform)
+importFrom(sf,st_union)
+importFrom(stars,read_stars)
+importFrom(stars,st_warp)
+importFrom(stats,reshape)
+importFrom(stringr,str_split_i)
+importFrom(terra,buffer)
+importFrom(terra,coltab)
+importFrom(terra,crop)
+importFrom(terra,crs)
+importFrom(terra,describe)
+importFrom(terra,ext)
+importFrom(terra,extract)
+importFrom(terra,intersect)
+importFrom(terra,merge)
+importFrom(terra,mosaic)
+importFrom(terra,nlyr)
+importFrom(terra,project)
+importFrom(terra,rast)
+importFrom(terra,same.crs)
+importFrom(terra,sds)
+importFrom(terra,snap)
+importFrom(terra,tapp)
+importFrom(terra,vect)
+importFrom(testthat,expect_true)
+importFrom(utils,download.file)
+importFrom(utils,head)
+importFrom(utils,read.csv)
+importFrom(utils,tail)