refresh package; fix #24; fix #25; fix #26; fix #28

rapidsurveys · Jan 5, 2025 · 798fb16 · 798fb16
1 parent 8ba38cb
commit 798fb16
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,5 @@
 ^codecov\.yml$
 ^pkgdown$
 ^CRAN-SUBMISSION$
+^README\.html$
+^CODE_OF_CONDUCT\.md$
diff --git a/.github/CONTRIBUTING.MD b/.github/CONTRIBUTING.MD
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -0,0 +1,32 @@
+# Contributing
+
+## Bugs
+
+* Submit an issue on the [issues page](https://github.com/rapidsurveys/bbw/issues)
+
+## Code contributions
+
+* Fork this repository to your Github account
+
+* Clone your version on your account down to your machine from your account
+
+```
+git clone https://github.com/<yourgithubusername>/bbw.git
+```
+
+* Make sure to track progress upstream i.e., on our version of `bbw`
+at `rapidsurveys/bbw`, by doing
+
+```
+git remote add upstream https://github.com/rapidsurveys/bbw.git
+```
+
+* Before making changes make sure to pull changes in from `upstream` by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
+
+* Make your changes on a new feature branch
+
+* Please write a test or tests for your changes if they affect code and not just documentation
+
+* Push up changes to your account
+
+* Submit a pull request at `rapidsurveys/bbw`
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
diff --git a/.github/workflows/check-standard.yaml → .github/workflows/R-CMD-check.yaml b/.github/workflows/check-standard.yaml → .github/workflows/R-CMD-check.yaml
@@ -1,12 +1,13 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +30,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/netlify.yaml b/.github/workflows/netlify.yaml
@@ -0,0 +1,53 @@
+on:
+  pull_request:
+    branches: [main, master]
+
+name: pkgdown-pr
+
+jobs:
+  netlify:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - 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: Install package
+        run: R CMD INSTALL .
+
+      - name: Create website
+        run: |
+          pkgdown::build_site()
+        shell: Rscript {0}
+
+      - name: Create index file
+        run: |
+          echo '<!DOCTYPE html><html><head><meta http-equiv="refresh" content="0;URL=/dev/index.html" />  <script language="javascript"> window.location.replace('/dev/index.html')</script></head></html>' > ./docs/index.html
+
+      - name: Deploy to Netlify
+        uses: nwtgck/[email protected]
+        with:
+          publish-dir: './docs'
+          production-branch: main
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
+          # these default to 'true'
+          enable-commit-comment: false
+          enable-github-deployment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ 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
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,12 +1,13 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,16 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,7 @@
 /revdep/data.sqlite
 /revdep/library
 /revdep/library.noindex
+
+README.html
+/docs/
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,12 @@
 Package: bbw
 Type: Package
 Title: Blocked Weighted Bootstrap
-Version: 0.2.0
+Version: 0.2.1.9000
 Authors@R: c(
-    person("Mark", "Myatt", email = "[email protected]", role = "aut"),
+    person("Mark", "Myatt", 
+           email = "[email protected]", role = c("aut", "cph")),
     person("Ernest", "Guevarra", comment = c(ORCID = "0000-0002-4887-4415"), 
-           email = "[email protected]", role = c("aut", "cre")))
+           email = "[email protected]", role = c("aut", "cre", "cph")))
 Description: The blocked weighted bootstrap (BBW) is an estimation technique 
     for use with data from two-stage cluster sampled surveys in which either 
     prior weighting (e.g. population-proportional sampling or PPS as used in 
@@ -17,22 +18,22 @@ Description: The blocked weighted bootstrap (BBW) is an estimation technique
     <doi:10.1371/journal.pone.0163176> and Aaron et al (2016) 
     <doi:10.1371/journal.pone.0162462> for application of the blocked weighted 
     bootstrap to estimate indicators from two-stage cluster sampled surveys.
+License: GPL-3
+Depends: R (>= 3.0.1)
 Imports: 
     car,
     withr
-Depends: R (>= 3.0.1)
 Suggests: 
     knitr,
     rmarkdown,
     testthat,
     spelling,
     covr
-License: GPL-3
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 URL: https://github.com/rapidsurveys/bbw, https://rapidsurveys.io/bbw/
 BugReports: https://github.com/rapidsurveys/bbw/issues
 VignetteBuilder: knitr