Devel

.github/workflows/test-coverage.yaml

@@ -1,62 +1,50 @@
-# 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
+name: test-coverage
+
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-
-name: test-coverage.yaml
-
-permissions: read-all
+    branches: [main]
 
 jobs:
-  test-coverage:
+  coverage:
     runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    permissions:
+      contents: write
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr, any::xml2
-          needs: coverage
+      - name: Install system dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
 
-      - 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@v4
-        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 }}
-          file: ./cobertura.xml
-          plugin: noop
-          disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Show testthat output
-        if: always()
+      - name: Install dependencies
         run: |
-          ## --------------------------------------------------------------------
-          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          Rscript -e 'install.packages(c("remotes", "covr", " testthat", "DT", "htmltools"))'
+          Rscript -e 'remotes::install_deps(dependencies = TRUE)'
 
-      - name: Upload test results
-        if: failure()
-        uses: actions/upload-artifact@v4
+
+      - name: Run coverage and generate badge
+        run: |
+          mkdir -p coverage
+          Rscript -e '
+            cov <- covr::package_coverage(type = "tests")
+            covr::to_cobertura(cov, "coverage/cobertura.xml")
+            covr::report(cov, file = "coverage/coverage.html")
+            pct <- round(covr::percent_coverage(cov))
+            col <- if (pct >= 90) "brightgreen" else if (pct >= 75) "orange" else "red"
+            url <- sprintf("https://img.shields.io/badge/coverage-%s%%25-%s.svg", pct, col)
+            download.file(url, "coverage/badge.svg", quiet = TRUE)
+          '
+
+      - name: Deploy badge and reports to gh-pages
+        uses: peaceiris/actions-gh-pages@v3
         with:
-          name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./coverage
+          publish_branch: gh-pages
+          destination_dir: _xml_coverage_reports/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: envsetup
 Title: Support the Setup of the R Environment for Clinical Trial Programming Workflows
-Version: 0.2.1
+Version: 0.3.0
 Authors@R: c(
     person("Nicholas", "Masel", email = "nmasel@its.jnj.com", role = c("aut", "cre")),
     person("Mike", "Stackhouse", email = "mike.stackhouse@atorusresearch.com", role = c("aut"), comment = c(ORCID = "0000-0001-6030-723X")),
@@ -24,7 +24,8 @@ Imports:
     purrr,
     rlang,
     usethis,
-    roxygen2
+    envnames,
+    utils
 Suggests: 
     rmarkdown,
     testthat,

NAMESPACE

@@ -2,13 +2,15 @@
 
 export(build_from_config)
 export(detach_autos)
+export(envsetup_environment)
+export(get_path)
 export(init)
-export(library)
 export(read_path)
 export(rprofile)
 export(validate_config)
 export(write_path)
 importFrom(config,get)
+importFrom(envnames,environment_name)
 importFrom(fs,dir_tree)
 importFrom(purrr,walk)
 importFrom(purrr,walk2)
@@ -20,4 +22,6 @@ importFrom(usethis,ui_done)
 importFrom(usethis,ui_field)
 importFrom(usethis,ui_info)
 importFrom(usethis,ui_oops)
+importFrom(usethis,ui_value)
 importFrom(usethis,ui_yeah)
+importFrom(utils,getFromNamespace)

NEWS.md

@@ -1,3 +1,14 @@
+# envsetup 0.3.0
+
+- `paths` no are no longer attached to the search path (#80)
+- `paths` objects default to the global environment now, but they can be changed using the `envsetup.path.environment` option (#80)
+- `get_path()` was added to help you retrieve a path with changing the storage environment using the `envsetup.path.environment` option (#80)
+- `autos` are no longer attached to the search path, and are sourced to global (#81)
+- `rprofile` lets you specify if sourcing of autos should overwrite an object in global if it already exists (#81)
+- extensive messaging added to make users aware of autos being attached and conflicts (#81)
+- object metadata storage is added to track what functions were sourced from where, see `envsetup_environment$object_metadata` (#81)
+- vignettes updated to divide content into smaller chunks (#82)
+
 # envsetup 0.2.1
 
 - `set_autos()` will now handle NULL hierarchical paths (#66)