add r-cmd-check and test-coverage

Author: sbidari

.Rbuildignore

@@ -0,0 +1 @@
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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: 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::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    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::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -379,3 +379,5 @@ docs/site/
 # such, it should not be committed for packages, but should be committed for
 # applications that require a static environment.
 #Manifest.toml
+
+/.quarto/

DESCRIPTION

@@ -10,3 +10,16 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Imports: 
+    dplyr,
+    forecasttools,
+    fs,
+    glue,
+    lubridate,
+    readr,
+    stringr
+Remotes:
+    forecasttools=github::cdcgov/forecasttools
+Suggests:
+    testthat,
+    tibble

R/update_hub_target_data.R

@@ -63,7 +63,7 @@ update_hub_target_data <- function(
       as_of = !!today,
       target = glue::glue("wk inc {disease} hosp")
     ) |>
-    dplyr::filter(!(location %in% !!excluded_locations))
+    dplyr::filter(!(.data$location %in% !!excluded_locations))
 
   hubverse_format_nhsn_data <- nhsn_data |> dplyr::select(-"jurisdiction")
 
@@ -99,7 +99,7 @@ update_hub_target_data <- function(
       as_of = !!today,
       target = glue::glue("wk inc {disease} prop ed visits")
     ) |>
-    dplyr::select(all_of(c(
+    dplyr::select(dplyr::all_of(c(
       "date",
       "observation",
       "location",

README.md

@@ -1,3 +1,7 @@
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/CDCgov/hubhelpr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CDCgov/hubhelpr/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 # hubhelpr
 
 ## Overview