New data collected at 2024-09-30_00-02-17

MichaelChirico · Sep 30, 2024 · 7a96613 · 7a96613
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commit 7a96613
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Showing 9 changed files with 69 additions and 71 deletions.
diff --git a/github-actions/data.table/performance-tests.yml b/github-actions/data.table/performance-tests.yml
@@ -1,4 +1,4 @@
-name: Autocomment atime-based performance regression analysis on PRs
+name: atime performance tests
 
 on:
   pull_request:
@@ -22,4 +22,4 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       repo_token: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: Anirban166/Autocomment-atime-results@v1.2.1
+      - uses: Anirban166/Autocomment-atime-results@v1.3.1
diff --git a/github-actions/data.table/test-coverage.yaml b/github-actions/data.table/test-coverage.yaml
@@ -1,44 +1,55 @@
+# 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:
-      - master
+    branches: [master]
   pull_request:
+    branches: [master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          r-version: '4.3' # TODO(r-lib/covr#567): Go back to using r-devel
 
-      - 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)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Install dependencies
+      - name: Test coverage
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
+          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}
 
-      - name: Test coverage
-        run: covr::codecov()
-        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: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/github-actions/mlflow/autoformat.yml b/github-actions/mlflow/autoformat.yml
@@ -16,7 +16,7 @@ jobs:
   check-comment:
     runs-on: ubuntu-latest
     timeout-minutes: 10
-    if: ${{ github.event.issue.pull_request && contains(github.event.comment.body, '@mlflow-automation') && contains(github.event.comment.body, 'autoformat') }}
+    if: ${{ github.event.issue.pull_request && contains(github.event.comment.body, 'autoformat') }}
     permissions:
       statuses: write # autoformat.createStatus
       pull-requests: write # autoformat.createReaction on PRs

diff --git a/github-actions/prophet/build-and-test.yml b/github-actions/prophet/build-and-test.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.10"]
-        os: ["macos-latest", "ubuntu-latest", "windows-latest", "macos-latest-xlarge"]
+        os: ["macos-13", "ubuntu-latest", "windows-latest", "macos-latest-xlarge"]
       fail-fast: false
 
     steps:
@@ -24,17 +24,17 @@ jobs:
         (Get-ItemProperty "HKLM:System\CurrentControlSet\Control\FileSystem").LongPathsEnabled
         $os_version = (Get-CimInstance Win32_OperatingSystem).version
         Echo "OS_VERSION=$os_version" >> $env:GITHUB_ENV
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
         cache-dependency-path: "**/python/pyproject.toml"
     - name: "Restore RTools40"
       if: startsWith(runner.os, 'Windows')
       id: cache-rtools
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: C:/rtools40
         key: ${{ runner.os }}-${{ env.OS_VERSION }}-rtools-v1
@@ -58,7 +58,7 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: r-lib/actions/setup-pandoc@v2
     - name: Set up R
       uses: r-lib/actions/setup-r@v2
@@ -75,7 +75,7 @@ jobs:
       shell: Rscript {0}
     - name: Restore R package cache
       if: runner.os != 'Windows'
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

diff --git a/github-actions/prophet/wheel.yml b/github-actions/prophet/wheel.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest", "ubuntu-latest", "windows-latest", "macos-latest-xlarge"]
+        os: ["macos-13", "ubuntu-latest", "windows-latest", "macos-latest-xlarge"]
         cibw_arch: ["native"]
         # Build one wheel (ABI = none) using first build spec, then test on all python versions.
         cibw_build: ["cp39-* cp310-* cp311-*"]
@@ -38,34 +38,28 @@ jobs:
       - name: "Checkout repo"
         uses: actions/checkout@v4
 
-      # Temporary, until pipx is added to the macOS large runner image
-      - name: "Install pipx"
-        if: matrix.os == 'macos-latest-xlarge'
-        run: |
-          brew install pipx
-          pipx ensurepath
-
       - name: "Restore RTools40"
         if: startsWith(runner.os, 'Windows')
         id: cache-rtools
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: C:/rtools40
           key: ${{ runner.os }}-${{ env.OS_VERSION }}-rtools-v1
 
       - name: Set up QEMU
         if: matrix.cibw_arch == 'aarch64'
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
         with:
           platforms: arm64
 
       - name: "Build wheels"
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.21.1
         with:
           package-dir: python
         env:
           CIBW_ENVIRONMENT: >
             STAN_BACKEND="${{ env.STAN_BACKEND }}"
+            MACOSX_DEPLOYMENT_TARGET="${{ matrix.os == 'macos-13' && 10.11 || 11.0 }}"
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_SKIP: "*musllinux*"
@@ -75,7 +69,7 @@ jobs:
           CIBW_TEST_COMMAND: pytest --pyargs prophet
 
       - name: "Upload wheel as artifact"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: artifact-${{ matrix.os }}-${{ matrix.cibw_arch }}-wheel
           path: "./**/*.whl"
@@ -84,12 +78,12 @@ jobs:
     name: Make source distribution
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - run: pipx run build --sdist
       working-directory: python
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: artifact-source-dist
         path: "./**/dist/*.tar.gz"
@@ -101,7 +95,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
     - name: Download all artifacts
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
 
     - name: Copy artifacts to dist/ folder
       run: |
@@ -111,7 +105,7 @@ jobs:
         find . -name '*.whl' -exec mv '{}' dist/ \;
 
     - name: Upload
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1.10.2
       with:
         user: ${{ secrets.PYPI_USERNAME }}
         password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/github-actions/rio/pkgdown.yml b/github-actions/rio/pkgdown.yml
@@ -3,8 +3,8 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
-    branches: [main, master]
+  # pull_request:
+  #   branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:

diff --git a/gitignore/xgboost.gitignore b/gitignore/xgboost.gitignore
@@ -27,7 +27,7 @@
 *vali
 *sdf
 Release
-*exe*
+*exe
 *exp
 ipch
 *.filters

diff --git a/gitlab-ci/data.table.gitlab-ci.yml b/gitlab-ci/data.table.gitlab-ci.yml
@@ -9,20 +9,21 @@ variables:
   _R_CHECK_FORCE_SUGGESTS_: "false"
   _R_CHECK_NO_STOP_ON_TEST_ERROR_: "true"
   _R_CHECK_SYSTEM_CLOCK_: "false"  ## https://stackoverflow.com/questions/63613301/r-cmd-check-note-unable-to-verify-current-time
+  _R_CHECK_TESTS_NLINES_: "0"
   TZ: "UTC"  ## to avoid 'Failed to create bus connection' from timedatectl via Sys.timezone() on Docker with R 3.4.
              ## Setting TZ for all GLCI jobs to isolate them from timezone. We could have a new GLCI job to test under
              ## a non-UTC timezone, although, that's what we do routinely in dev.
-  R_REL_VERSION:  "4.3"
-  R_REL_WIN_BIN:  "https://cloud.r-project.org/bin/windows/base/old/4.3.2/R-4.3.2-win.exe"
-  RTOOLS_REL_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools43/files/rtools43-5958-5975.exe"
+  R_REL_VERSION:  "4.4"
+  R_REL_WIN_BIN:  "https://cloud.r-project.org/bin/windows/base/old/4.4.1/R-4.4.1-win.exe"
+  RTOOLS_REL_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools44/files/rtools44-6104-6039.exe"
   RTOOLS43_HOME:  "/c/rtools"
-  R_DEV_VERSION:  "4.4"
+  R_DEV_VERSION:  "4.5"
   R_DEV_WIN_BIN:  "https://cloud.r-project.org/bin/windows/base/R-devel-win.exe"
-  RTOOLS_DEV_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools43/files/rtools43-5958-5975.exe"
-  RTOOLS44_HOME:  "" ## in case R-devel will use new Rtools toolchain, now it uses 4.3 env var
-  R_OLD_VERSION:  "4.2"
-  R_OLD_WIN_BIN:  "https://cloud.r-project.org/bin/windows/base/old/4.2.3/R-4.2.3-win.exe"
-  RTOOLS_OLD_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools42/files/rtools42-5355-5357.exe"
+  RTOOLS_DEV_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools44/files/rtools44-6104-6039.exe"
+  RTOOLS44_HOME:  "" ## in case R-devel will use new Rtools toolchain, now it uses 4.4 env var
+  R_OLD_VERSION:  "4.3"
+  R_OLD_WIN_BIN:  "https://cloud.r-project.org/bin/windows/base/old/4.3.3/R-4.3.3-win.exe"
+  RTOOLS_OLD_BIN: "https://cloud.r-project.org/bin/windows/Rtools/rtools43/files/rtools43-5958-5975.exe"
   RTOOLS42_HOME:  "/c/rtools"
 
 stages:
@@ -114,7 +115,6 @@ test-lin-rel:
     _R_CHECK_CRAN_INCOMING_: "FALSE"
     _R_CHECK_CRAN_INCOMING_REMOTE_: "FALSE"
     _R_CHECK_FORCE_SUGGESTS_: "TRUE"
-    _R_CHECK_TESTS_NLINES_: "0"
     OPENBLAS_MAIN_FREE: "1"
   script:
     - *install-deps

diff --git a/pkgdown/targets_pkgdown.yml b/pkgdown/targets_pkgdown.yml
@@ -25,7 +25,6 @@ reference:
   - 'tar_edit'
   - 'tar_github_actions'
   - 'tar_helper'
-  - 'tar_helper_raw'
   - 'tar_renv'
   - 'tar_script'
 - title: Configuration
@@ -43,7 +42,6 @@ reference:
   contents:
   - 'tar_cue'
   - 'tar_target'
-  - 'tar_target_raw'
 - title: Pipeline
   contents:
   - 'tar_make'
@@ -59,11 +57,9 @@ reference:
   contents:
   - 'tar_format'
   - 'tar_load'
-  - 'tar_load_raw'
   - 'tar_load_everything'
   - 'tar_objects'
   - 'tar_read'
-  - 'tar_read_raw'
 - title: Content-addressable storage
   contents:
   - 'tar_repository_cas'
@@ -82,7 +78,6 @@ reference:
 - title: Inspect
   contents:
   - 'tar_deps'
-  - 'tar_deps_raw'
   - 'tar_manifest'
   - 'tar_outdated'
   - 'tar_sitrep'
@@ -121,7 +116,6 @@ reference:
   - 'tar_newer'
   - 'tar_older'
   - 'tar_timestamp'
-  - 'tar_timestamp_raw'
 - title: Existence
   contents:
   - 'tar_exist_meta'
@@ -133,7 +127,6 @@ reference:
   contents:
   - 'tar_branch_index'
   - 'tar_branch_names'
-  - 'tar_branch_names_raw'
   - 'tar_branches'
   - 'tar_pattern'
 - title: Resources
-Original file line number
+Diff line change
@@ Expand Up / @@ -27,7 +27,7 @@ @@
     *vali
     *sdf
     Release
-    *exe*
+    *exe
     *exp
     ipch
     *.filters
@@ Expand Down @@