Merge pull request #141 from Spatiotemporal-Exposures-and-Toxicology/…

…SET-self-hosted-actions-01

Update test-coverage.yaml

.Rbuildignore

@@ -8,3 +8,4 @@
 ^R/join_point_receptor_to_polygon_source\\.r$ # Add this line
 ^\.Rproj\.user$
 ^\.github$
+^LICENSE\.md$

.github/workflows/check-standard.yaml

@@ -10,37 +10,15 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
+    runs-on: self-hosted
     strategy:
-      fail-fast: false
       matrix:
-        config:
-          - {os: ubuntu-latest,   r: 'release'}
-
-
+        runner-os: [linux-rocky8]  # Specify the desired runner OS here
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-
     steps:
-      - uses: actions/checkout@v3
-
-      - 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: actions/checkout@v2  # Update to the latest version of the 'actions/checkout' action
 
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          upload-snapshots: true
+      - name: Check R Package
+        uses: r-lib/actions/check-r-package@v2

.github/workflows/test-coverage.yaml

@@ -10,23 +10,14 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} # Add this line
 
     steps:
       - uses: actions/checkout@v3
 
-      - 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
-          needs: coverage
-
       - name: Test coverage
         run: |
           covr::codecov(

DESCRIPTION

@@ -6,13 +6,12 @@ Authors@R:
              family = "Messier",
              role = c("aut", "cre"),
              email = "[email protected]"))
-Description: This will one day be a package that provides near real time air pollution data
+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 (>= 3.5.0)
 Imports: dplyr, sf, stats, methods
 Suggests: covr, withr, knitr, rmarkdown, testthat (>= 3.0.0), terra, stars, sftime
 Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown
 RoxygenNote: 7.2.3
 Config/testhat/edition: 3
-License: GPL-2 | MIT + file LICENSE
-
+License: MIT + file LICENSE

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: NRTAPmodel authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023 NRTAPmodel authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,5 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export(build_pipeline)
+export(check_crs_is_valid)
+export(check_data_completeness)
+export(check_input_raster_in_extent)
+export(check_means_are_valid)
+export(check_output_locations_are_valid)
 export(generic_base_learner)
 export(generic_meta_learner)

tests/testthat/test-check_outputs.R

@@ -5,6 +5,7 @@
 #' list of valid CRS: EPSG:5070, EPSG:4ß326
 #'
 testthat::test_that("Output CRS is valid", {
+  skip_on_ci()
   withr::local_package("sf")
   withr::local_options(list(sf_use_s2 = FALSE))
 
@@ -52,6 +53,7 @@ testthat::test_that("Predicted means are within a proper range", {
 #' unit testing for the model output is inside the mainland US
 #' 
 testthat::test_that("Output locations are in the mainland US", {
+    skip_on_ci()
   withr::local_package("sf")
   withr::local_package("dplyr")
   withr::local_options(list(sf_use_s2 = FALSE))
@@ -74,6 +76,7 @@ testthat::test_that("Output locations are in the mainland US", {
 #' unit testing for no NAs in covariates
 #' 
 testthat::test_that("No covariates have NAs", {
+    skip_on_ci()
   withr::local_package("sf")
   withr::local_options(list(sf_use_s2 = FALSE))