New data collected at 2024-07-29_00-02-29

MichaelChirico · Jul 29, 2024 · 1d223ae · 1d223ae
1 parent fbc7ff3
commit 1d223ae
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Showing 17 changed files with 286 additions and 113 deletions.
diff --git a/github-actions/ggstatsplot/lint-changed-files.yaml b/github-actions/ggstatsplot/lint-changed-files.yaml
@@ -22,12 +22,12 @@ jobs:
         with:
           pak-version: devel
           upgrade: 'TRUE'
+          needs: check
           extra-packages: |
             any::gh
+            any::purrr
             r-lib/lintr
-
-      - name: Install package
-        run: R CMD INSTALL .
+            local::.
 
       - name: Extract and lint files changed by this PR
         run: |
@@ -37,30 +37,8 @@ jobs:
           changed_files <- purrr::map_chr(files, "filename")
           all_files <- list.files(recursive = TRUE)
           exclusions_list <- as.list(setdiff(all_files, changed_files))
-          lint_package(linters = linters_with_defaults(
-            absolute_path_linter = NULL,
-            assignment_linter = NULL,
-            commented_code_linter = NULL,
-            cyclocomp_linter(25L),
-            extraction_operator_linter = NULL,
-            if_not_else_linter(exceptions = character(0L)),
-            implicit_integer_linter = NULL,
-            library_call_linter = NULL,
-            line_length_linter(120L),
-            namespace_linter = NULL,
-            nonportable_path_linter = NULL,
-            object_name_linter = NULL,
-            object_length_linter(50L),
-            object_usage_linter = NULL,
-            string_boundary_linter = NULL,
-            strings_as_factors_linter = NULL,
-            todo_comment_linter = NULL,
-            undesirable_function_linter = NULL,
-            undesirable_operator_linter = NULL,
-            unnecessary_concatenation_linter(allow_single_expression = FALSE),
-            unused_import_linter = NULL,
-            defaults = linters_with_tags(tags = NULL)
-          ), exclusions = exclusions_list)
+          # lintr config in `.lintr` file
+          lint_package(exclusions = exclusions_list)
         shell: Rscript {0}
-        # env:
-        #   LINTR_ERROR_ON_LINT: true
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/github-actions/ggstatsplot/lint.yaml b/github-actions/ggstatsplot/lint.yaml
@@ -27,40 +27,18 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             r-lib/lintr
             local::.
           needs: lint
 
-      # TODO: Revisit to remove some of these allowances after more important lints
-      # have been removed.
       - name: Lint
         run: |
           options(crayon.enabled = TRUE)
           library(lintr)
-          lint_package(linters = linters_with_defaults(
-            absolute_path_linter = NULL,
-            assignment_linter = NULL,
-            commented_code_linter = NULL,
-            cyclocomp_linter(25L),
-            extraction_operator_linter = NULL,
-            if_not_else_linter(exceptions = character(0L)),
-            implicit_integer_linter = NULL,
-            library_call_linter = NULL,
-            line_length_linter(120L),
-            namespace_linter = NULL,
-            nonportable_path_linter = NULL,
-            object_name_linter = NULL,
-            object_length_linter(50L),
-            object_usage_linter = NULL,
-            string_boundary_linter = NULL,
-            strings_as_factors_linter = NULL,
-            todo_comment_linter = NULL,
-            undesirable_function_linter = NULL,
-            undesirable_operator_linter = NULL,
-            unnecessary_concatenation_linter(allow_single_expression = FALSE),
-            unused_import_linter = NULL,
-            defaults = linters_with_tags(tags = NULL)
-          ))
+          # lintr config in `.lintr` file
+          lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/github-actions/googlesheets4/R-CMD-check.yaml b/github-actions/googlesheets4/R-CMD-check.yaml
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -25,24 +27,22 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -60,3 +60,4 @@ jobs:
       - 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-actions/googlesheets4/pkgdown.yaml b/github-actions/googlesheets4/pkgdown.yaml
@@ -14,6 +14,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -28,8 +30,10 @@ jobs:
     env:
       GOOGLESHEETS4_KEY: ${{ secrets.GOOGLESHEETS4_KEY }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -48,7 +52,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/github-actions/googlesheets4/pr-commands.yaml b/github-actions/googlesheets4/pr-commands.yaml
@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/github-actions/googlesheets4/test-coverage.yaml b/github-actions/googlesheets4/test-coverage.yaml
@@ -13,6 +13,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -23,36 +25,45 @@ jobs:
       GOOGLESHEETS4_KEY: ${{ secrets.GOOGLESHEETS4_KEY }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/github-actions/googlesheets4/with-auth.yml b/github-actions/googlesheets4/with-auth.yml
@@ -5,6 +5,7 @@ on:
     branches: [main, master]
 
 name: with-auth
+permissions: read-all
 
 jobs:
   with-auth:

diff --git a/github-actions/mlflow/protos.yml b/github-actions/mlflow/protos.yml
@@ -11,7 +11,7 @@ on:
       - .github/workflows/protos.yml
       - mlflow/protos/**
       - mlflow/java/client/src/main/java/com/databricks/api/proto/**
-      - mlflow/server/graphql/graphql_schema_extensions.py # schema extension changes could trigger changes in the autogenerated schema
+      - mlflow/server/graphql/** # graphql related code changes could trigger changes in the autogenerated schema
       - requirements/skinny-requirements.txt
       - requirements/core-requirements.txt
 

diff --git a/github-actions/plotly/R-CMD-check.yaml b/github-actions/plotly/R-CMD-check.yaml
@@ -47,6 +47,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
+        with:
+          persist-credentials: false
 
       - uses: r-lib/actions/setup-r@v2
         id: install-r
@@ -81,7 +83,9 @@ jobs:
         uses: actions/upload-artifact@master
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: ./
+          path: |
+            ./
+            !./.git/
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2