Merge pull request #77 from biometryhub/dev

Merge dev to main for new release
biometryhub · May 31, 2024 · 3c88046 · 3c88046
2 parents 99fc341 + dc9577d
commit 3c88046
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,6 +12,8 @@ todo.md
 variogram_2d.R
 ^.*pdf$
 ^.*csv$
+^.*xls$
+^.*xlsx$
 ^.*docx$
 check_rhub.R
 cran-comments.md
@@ -25,3 +27,4 @@ sommer_vs_asreml.R
 Data2020.Rdata
 ^CRAN-SUBMISSION$
 .RDataTmp
+summary_graph
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -24,71 +24,63 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: 'oldrel'}
           # - {os: windows-latest, r: '4.0'}
-          - {os: ubuntu-22.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04,   r: 'release', rspm: "https://p3m.dev/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://p3m.dev/cran/__linux__/jammy/latest"}
 
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      # RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      vsni_LICENSE: ${{ secrets.vsni_LICENSE }}
+      # vsni_LICENSE: ${{ secrets.vsni_LICENSE }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Create and populate .Renviron file
-        run: echo vsni_LICENSE="vsni_LICENSE" >> ~/.Renviron
+      # - name: Create and populate .Renviron file
+      #   run: echo vsni_LICENSE="vsni_LICENSE" >> ~/.Renviron
 
 
-      - name: Install data.table dependencies
-        if: runner.os == 'Linux'
-        run: sudo -s apt-get install zlib1g-dev pkg-config
+      # - name: Install data.table dependencies
+      #   if: runner.os == 'Linux'
+      #   run: sudo -s apt-get install zlib1g-dev pkg-config
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
+          use-public-rspm: true
+
+      # - name: Query dependencies
+      #   run: |
+      #     install.packages('remotes')
+      #     saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+      #   shell: Rscript {0}
+
+      # - name: Cache R packages
+      #   if: runner.os != 'Windows'
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: ${{ env.R_LIBS_USER }}
+      #     key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
+      #     restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
+
+      # - name: Install system dependencies
+      #   if: runner.os == 'Linux'
+      #   env:
+      #     RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+      #   run: |
+      #     Rscript -e "remotes::install_github('r-hub/sysreqs')"
+      #     sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+      #     sudo -s eval "$sysreqs"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck, asreml=?ignore-before-r=5.0.0
+          needs: check
 
       - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+        uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -6,44 +6,37 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
 
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r@v2
-        id: install-r
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ubuntu-22.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ubuntu-22.04-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_dev("pkgdown")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Build and deploy pkgdown site
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -16,53 +16,28 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
-      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"
-      vsni_LICENSE: ${{ secrets.vsni_LICENSE }}
+      # RSPM: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      # vsni_LICENSE: ${{ secrets.vsni_LICENSE }}
 
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Set up RSPM
-        run: |
-          echo "options(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))" >> ~/.Rprofile.site
-          echo "options(HTTPUserAgent = sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version['platform'], R.version['arch'], R.version['os'])))" >> ~/.Rprofile.site
-        shell: bash
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Get R and OS version
-        id: get-version
-        run: |
-          cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
-          cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2, asreml=?ignore-before-r=5.0.0
+          needs: coverage
 
-      - name: Create and populate .Renviron file
-        run: echo vsni_LICENSE="vsni_LICENSE" >> ~/.Renviron
+      # - name: Create and populate .Renviron file
+      #   run: echo vsni_LICENSE="vsni_LICENSE" >> ~/.Renviron
 
       # - name: Licence ASreml
       #   run: |
@@ -71,5 +46,33 @@ jobs:
       #   shell: Rscript {0}
 
       - 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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.1.3
-Date: 2023-07-19 05:07:30 UTC
-SHA: 477c5510e61d94b013ee2be2c8105b428a116863
+Version: 1.2.0
+Date: 2024-05-31 09:46:32 UTC
+SHA: ebce045fe222badd826f94e2d7cabb4475a5f32d
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: biometryassist
 Title: Functions to Assist Design and Analysis of Agronomic Experiments
-Version: 1.1.3
+Version: 1.2.0
 Authors@R: 
     c(person(given = "Sharon",
              family = "Nielsen",
@@ -38,6 +38,7 @@ Depends:
     R (>= 4.0.0)
 Imports: 
     agricolae,
+    askpass,
     cowplot,
     curl,
     emmeans,
@@ -48,13 +49,12 @@ Imports:
     pracma,
     rlang (>= 1.0.0),
     scales, 
-    stringi
+    stringi,
+    xml2
 Suggests: 
     covr,
     crayon,
-    getPass,
     knitr,
-    mockery,
     rmarkdown,
     testthat,
     vdiffr,
@@ -69,5 +69,5 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr