DO NOT MERGE: Compare speed improvement from initial release

.Rbuildignore

@@ -1,16 +1,25 @@
+^.*-in_tree$
 ^.*\.Rproj$
-^\.Rproj\.user$
 ^API$
-^README\.Rmd$
+^CONTRIBUTING\.md$
+^LICENSE\.md$
+^Meta$
 ^README-.*\.png$
-^.travis.yml
-^appveyor\.yml$
-^tic\.R$
-^\.travis\.yml$
-^docs$
-^_pkgdown\.yml$
-CONTRIBUTING.md
+^README\.Rmd$
+^\.Rproj\.user$
+^\.github$
 ^\.gitsum$
-^gitsum$
-
+^\.lintr$
+^\.pre-commit-config\.yaml$
+^_pkgdown\.yaml$
 ^cran-comments\.md$
+^doc$
+^docs$
+^gitsum$
+^inst/WORDLIST$
+^inst/hooks/.*$
+^revdep$
+^tests/testmanual$
+^tic\.R$
+^touchstone$
+^vignettes/gsoc_proposal$

.gitattributes

@@ -1 +1 @@
-tests/testthat/**/*_tree linguist-generated=true
+tests/testthat/**/*_tree linguist-generated=true

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/dependabot.yaml

@@ -0,0 +1,8 @@
+version: 2
+
+updates:
+  # Keep dependencies for GitHub Actions up-to-date
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/check-all-examples.yaml

@@ -0,0 +1,42 @@
+# Make sure all examples run successfully, even the ones that are not supposed
+# to be run or tested on CRAN machines by default.
+#
+# The examples that fail should use
+#  - `if (FALSE) { ... }` (if example is included only for illustrative purposes)
+#  - `try({ ... })` (if the intent is to show the error)
+#
+# This workflow helps find such failing examples that need to be modified.
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: check-all-examples
+
+jobs:
+  check-all-examples:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::devtools
+            local::.
+
+      - name: Run examples
+        run: |
+          options(crayon.enabled = TRUE)
+          devtools::run_examples(fresh = TRUE, run_dontrun = TRUE, run_donttest = TRUE)
+        shell: Rscript {0}

.github/workflows/check-full.yaml

@@ -0,0 +1,61 @@
+# 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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+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'}
+          # 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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: 'ifelse(getRversion() > 3.6, "warning", "note")'
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false

.github/workflows/check-link-rot.yaml

@@ -0,0 +1,43 @@
+on:
+  pull_request:
+    branches: [main, master]
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Trigger once a month at 00:00 on the 1st day of the month.
+    - cron: "0 0 1 * *"
+
+name: check-link-rot
+
+jobs:
+  check-link-rot:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "devel"
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::rcmdcheck
+            any::urlchecker
+
+      - name: Run URL checker
+        run: |
+          options(crayon.enabled = TRUE)
+          rotten_links <- urlchecker::url_check(progress = FALSE)
+          print(rotten_links)
+          if (length(rotten_links$URL) > 0L) {
+            stop("Some URLs are outdated and need to be updated.", call. = FALSE)
+          }
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# 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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pre-commit.yaml

@@ -0,0 +1,58 @@
+name: pre-commit
+on:
+  push:
+    branches-ignore:
+      - "master"
+      - "main"
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    if: >-
+      !contains(github.event.head_commit.message, 'ci skip') &&
+      (
+        startsWith(github.ref, 'refs/heads') ||
+        github.event.pull_request.draft == false
+      )
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          # your system installation code here
+          # sudo apt-get install -y libcurl4-openssl-dev
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+          architecture: "x64"
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]
+        env: 
+          SKIP: pkgdown
+      - name: Commit files
+        if: failure() && startsWith(github.ref, 'refs/heads')
+        run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git checkout -- .github/workflows
+            git commit -m "pre-commit" -a
+          fi
+      - name: Push changes
+        if: failure() && startsWith(github.ref, 'refs/heads')
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
+    env:
+      RENV_CONFIG_CACHE_ENABLED: FALSE
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,31 @@
+# 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:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

.github/workflows/touchstone-comment.yaml

@@ -0,0 +1,22 @@
+name: Continuous Benchmarks (Comment)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  workflow_run:
+    workflows: ["Continuous Benchmarks (Receive)"]
+    types:
+      - completed
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    if: >
+      ${{ github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - uses: lorenzwalthert/touchstone/actions/comment@main
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}