fastcpd 0.17.0__tar.gz

fastcpd-0.17.0/.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.vscode$
+^cran-comments\.md$
+^LICENSE\.md$
+^\.github$
+^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^.lintr$
+^\.covrignore$
+^man/figures/cheatsheets\.pdf$
+^data-raw$
+^shiny$
+^CRAN-SUBMISSION$
+^vignettes/.*\.original$
+^vignettes/comparison-packages-results\.RData$
+
+# Bazel files.
+^bazel$
+^\.bazeliskrc$
+^\.bazelrc$
+^\.bazelversion$
+^WORKSPACE$
+^BUILD\.bazel$
+
+# Python files.
+^tests/.*\.py$
+^tests/BUILD\.bazel$
+^fastcpd$
+^\.clang-format$
+^bazelisk\.py$
+^Makefile$
+^MANIFEST\.in$
+^mypy\.ini$
+^pyproject\.toml$
+^pytest\.ini$
+^requirements\.in$
+^requirements_lock\.txt$
+^setup\.py$

fastcpd-0.17.0/.bazeliskrc

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+7.6.1

fastcpd-0.17.0/.bazelrc

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+common --enable_bzlmod=false
+common --enable_workspace=true
+common --repositories_without_autoloads=bazel_features_version,bazel_features_globals
+common --incompatible_python_disallow_native_rules

fastcpd-0.17.0/.bazelversion

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+7.6.1

fastcpd-0.17.0/.clang-format

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+# Copy from https://github.com/googleapis/google-cloud-cpp-bigquery/tree/main.
+
+# Use the Google style in this project.
+BasedOnStyle: Google
+
+# Some folks prefer to write "int& foo" while others prefer "int &foo".  The
+# Google Style Guide only asks for consistency within a project, we chose
+# "int& foo" for this project:
+DerivePointerAlignment: false
+PointerAlignment: Left
+
+# The Google Style Guide only asks for consistency w.r.t. "east const" vs.
+# "const west" alignment of cv-qualifiers. In this project we use "east const".
+QualifierAlignment: Right
+
+IncludeBlocks: Merge
+IncludeCategories:
+- Regex: '^\"google/cloud/internal/disable_deprecation_warnings.inc\"$'
+  Priority: -1
+# System and C-language headers should go last. These expressions may miss a few
+# cases, we can always add more.  Or we can conservative
+- Regex: '^<[A-Za-z0-9_]*\.h>$'
+  Priority: 10000
+- Regex: '^<sys/[A-Za-z0-9_]*\.h>$'
+  Priority: 10000
+# Matches common headers first, but sorts them after project includes
+- Regex: '^\"google/cloud/(internal/|grpc_utils/|testing_util/|[^/]+\.h)'
+  Priority: 1000
+- Regex: '^\"google/cloud/'  # project includes should sort first
+  Priority: 500
+- Regex: '^\"generator/'     # project includes should sort first
+  Priority: 500
+- Regex: '^\"generator/internal/' # project internals second
+  Priority: 1000
+- Regex: '^\"generator/testing/'  # testing helpers third
+  Priority: 1100
+- Regex: '^\"'         # And then includes from other projects or the system
+  Priority: 1500
+- Regex: '^<grpc/'
+  Priority: 2000
+- Regex: '^<google/*'
+  Priority: 3000
+- Regex: '^<.*/.*'
+  Priority: 4000
+- Regex: '^<.*.hpp>'
+  Priority: 4000
+- Regex: '^<[^/]*>'
+  Priority: 5000
+
+# Format raw string literals with a `pb` or `proto` tag as proto.
+RawStringFormats:
+- Language: TextProto
+  Delimiters:
+  - 'pb'
+  - 'proto'
+  BasedOnStyle: Google
+
+CommentPragmas: '(@copydoc|@copybrief|@see|@overload|@snippet)'

fastcpd-0.17.0/.covrignore

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+R/ref*
+src/ref*
+inst/include/ref*

fastcpd-0.17.0/.github/.gitignore

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+*.html

fastcpd-0.17.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Submit a bug report to help us improve fastcpd
+---
+
+### Tips for a helpful bug report:
+
+* Please include a **minimal reproducible example** to demonstrate the bug.
+  A reprex can be helpful. See
+  [make a reprex](https://www.tidyverse.org/help/#reprex).
+  Do not include session info unless it is explicitly asked for.
+
+* If you can, use a small toy dataset that exposes the bug. If for some reason,
+  the bug only occurs on your original data, try to limit the number of rows that
+  are necessary to expose the bug. Share such data by copying `dput()` output
+  rather than an external file.
+
+* Unless the bug is about the theme, labels, scales or other plot decoration:
+  please omit these from the code.
+
+* Please check whether somebody has reported the same problem in the
+  [issues](https://github.com/doccstat/fastcpd/issues).
+
+Delete these instructions once you have read them.
+
+---
+
+I found a problem with ...
+
+I expected ...
+
+Here is the code to reproduce the bug:
+
+```r
+# copy your code to the clipboard and run:
+reprex::reprex()
+```
+
+<!-- Copy and modified based on https://github.com/tidyverse/ggplot2/tree/main/.github/ISSUE_TEMPLATE -->

fastcpd-0.17.0/.github/ISSUE_TEMPLATE/config.yml

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+contact_links:
+  - name: Contact the maintainer
+    url: https://xingchi.li/
+    about: "Seek help from the maintainer instead."

fastcpd-0.17.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "Feature Request"
+about: Suggest a change or new feature in fastcpd
+---
+
+### Tips for a helpful feature request:
+
+* fastcpd is still under active development. Improvements to its current
+  functionality or to infrastructure are more than welcome.
+
+* Please motivate the need for change, if applicable with a
+  **minimal reproducible** example (reprex). If you've never heard of a reprex,
+  please read [make a reprex](https://www.tidyverse.org/help/#reprex). Do not
+  include session info unless it is explicitly asked for.
+
+Delete this instructions once you've read them.
+
+---
+
+In situations when ...
+
+I would like to be able to ...
+
+```r
+# copy your code to the clipboard and run:
+reprex::reprex()
+```
+
+<!-- Copy and modified based on https://github.com/tidyverse/ggplot2/tree/main/.github/ISSUE_TEMPLATE -->

fastcpd-0.17.0/.github/workflows/bazel_build_linux.yml

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+name: bazel_build_linux.yml
+
+on: ['push']
+
+jobs:
+  test_linux:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Update system
+        run: sudo apt update
+
+      - name: Install Dev Dependencies
+        run: sudo apt install python3-dev
+
+      - name: Build the code
+        run: bazel build //... --subcommands
+
+      - name: Setup venv
+        run: make venv
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements_lock.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install requirements
+        run: make install
+
+      - uses: actions/cache/save@v3
+        id: cache-pip-linux
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements_lock.txt') }}
+
+      - name: Install pip wheel
+        run: make install_fastcpd
+
+      - name: make sdist
+        run: make sdist
+
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --exclude venv/,env/,.venv/ --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --exclude venv/,env/,.venv/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Install `twine` to publish to PyPI.
+        run: python -m pip install twine
+
+      - name: Publish to PyPI test
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }}
+        run: |
+          make upload
+
+      - name: Publish to PyPI
+        if: github.ref == 'refs/heads/main'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          make upload_prod

fastcpd-0.17.0/.github/workflows/bazel_test_mac.yml

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+name: bazel_test_mac.yml
+
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - 'paper/**'
+      - 'tests/**'
+      - 'mkdocs.yml'
+
+jobs:
+  test_macos_bazel:
+    runs-on: macos-13
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, which is the CWD for
+      # the rest of the steps
+      - uses: actions/checkout@v4
+
+        # test
+      - name: Build the code
+        run: bazel build //...
+
+      - name: Run bazel tests
+        run: bazel test --test_output=errors //... --test_size_filters=medium
+
+
+  test_macos_python:
+    needs: test_macos_bazel
+
+    # virtual environments: https://github.com/actions/virtual-environments
+    runs-on: macos-13
+
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: [ "3.10", "3.11", "3.12", ]
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, which is the CWD for
+      # the rest of the steps
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Python version check
+        run: PYTHON=python3 python --version
+
+      - name: Install dependencies
+        run: PYTHON=python3 make install
+
+      - name: Build wheel
+        run: PYTHON=python3 make wheel
+
+      - name: install wheel in dist folder
+        run: PYTHON=python3 python -m pip install dist/fastcpd-*.whl
+
+      - name: Run python tests
+        run: |
+          mkdir -p tmp && \
+          cd tmp && \
+          cp -R ../tests  . && \
+          python3 -m pytest tests -m "not long"
+
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --exclude venv/,env/,.venv/ --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --exclude venv/,env/,.venv/ --count --exit-zero --max-complexity=15 --max-line-length=127 --statistics
+
+      - name: Install `twine` to publish to PyPI.
+        run: python -m pip install twine
+
+      - name: Publish to PyPI test
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }}
+        run: |
+          PYTHON=python3 make upload
+
+      - name: Publish to PyPI
+        if: github.ref == 'refs/heads/main'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          PYTHON=python3 make upload_prod

fastcpd-0.17.0/.github/workflows/check-standard.yaml

@@ -0,0 +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: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Install XQuartz on macOS
+        if: runner.os == 'macOS'
+        run: brew install xquartz --cask
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

fastcpd-0.17.0/.github/workflows/dependency-review.yml

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+# Dependency Review Action
+#
+# This Action will scan dependency manifest files that change as part of a Pull Request, surfacing known-vulnerable versions of the packages declared or updated in the PR. Once installed, if the workflow run is marked as required, PRs introducing known-vulnerable packages will be blocked from merging.
+#
+# Source repository: https://github.com/actions/dependency-review-action
+# Public documentation: https://docs.github.com/en/code-security/supply-chain-security/understanding-your-software-supply-chain/about-dependency-review#dependency-review-enforcement
+name: 'Dependency Review'
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout Repository'
+        uses: actions/checkout@v4
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@v3

fastcpd-0.17.0/.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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

fastcpd-0.17.0/.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          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