diff --git a/github-actions/data.table/performance-tests.yml b/github-actions/data.table/performance-tests.yml index 0326789..e1b9a54 100644 --- 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 index 982cb7c..79fcd6f 100644 --- 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 index 8fff40b..5f3b7bb 100644 --- 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 index 2543b00..9963367 100644 --- 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: @@ -24,9 +24,9 @@ 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 @@ -34,7 +34,7 @@ jobs: - 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 index fc956af..469b5dc 100644 --- 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 index ed7650c..388830f 100644 --- 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 index 88996f3..b4e0b4f 100644 --- 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 index 577fbcd..e0cdc2e 100644 --- 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 index 4a9f403..553d638 100644 --- 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