fix: building vignettes and testthat

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @novica

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/R-CMD-check.yml

@@ -0,0 +1,59 @@
+name: R CMD Check
+
+on:
+  pull_request:
+    paths-ignore:
+      - "*.md"
+      - ".github/**"
+      - "*.json "
+      - "*.toml "
+  workflow_dispatch:
+
+permissions: read-all
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}
+  cancel-in-progress: true
+
+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@v7
+
+      - 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:
+          error-on: '"error"'
+          upload-snapshots: true
+          build_args: 'c("--no-build-vignettes")'
+          args: 'c("--no-manual", "--as-cran")'

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  pull_request:
+    branches: [master]
+    paths:
+      - "R/**"
+      - "inst/**"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Install
+      uses: posit-dev/setup-air@v1
+
+    - name: Check
+      run: air format . --check
+
+    - name: Setup jarl
+      uses: etiennebacher/setup-jarl@v0.1.1
+
+    - name: Run jarl lint
+      run: jarl check .

.github/workflows/pkgdown.yml

@@ -0,0 +1,73 @@
+name: Build pkgdown site
+
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - "*.md"
+      - ".github/**"
+      - "*.json "
+      - "*.toml "
+  release:
+    types:
+      - published
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v7
+
+      - 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 release site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+        env:
+          PKGDOWN_DEV_MODE: release
+
+      - name: Build dev site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+        env:
+          PKGDOWN_DEV_MODE: devel
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v5
+        with:
+          path: "./docs/"
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: pkgdown
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v6
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

.github/workflows/release-please.yml

@@ -0,0 +1,75 @@
+name: Release Please
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      - uses: googleapis/release-please-action@v5
+        id: release
+        with:
+          config-file: release-please-config.json
+          manifest-file: .release-please-manifest.json
+
+      - uses: actions/checkout@v7
+        if: ${{ steps.release.outputs.pr }}
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Update NEWS.md from CHANGELOG.md
+        if: ${{ steps.release.outputs.pr }}
+        env:
+          PR_JSON: ${{ steps.release.outputs.pr }}
+        run: |
+          PR_BRANCH=$(echo "$PR_JSON" | jq -r '.headBranchName')
+          git fetch origin "$PR_BRANCH"
+          git checkout "$PR_BRANCH"
+
+          python3 - <<'EOF'
+          import re, sys
+          from pathlib import Path
+
+          pkg = Path("DESCRIPTION").read_text()
+          pkg = re.search(r"^Package:\s*(\S+)", pkg, re.MULTILINE).group(1)
+
+          changelog = Path("CHANGELOG.md").read_text()
+
+          # Extract the latest entry (first ## [...] block)
+          m = re.search(
+              r"^## \[([^\]]+)\][^\n]*\n(.*?)(?=^## \[|\Z)",
+              changelog, re.MULTILINE | re.DOTALL
+          )
+          if not m:
+              sys.exit(0)
+
+          version, body = m.group(1), m.group(2).strip()
+
+          # ### Section  →  ## Section
+          body = re.sub(r"^### ", "## ", body, flags=re.MULTILINE)
+
+          new_entry = f"# {pkg} {version}\n\n{body}\n"
+
+          news = Path("NEWS.md")
+          existing = news.read_text() if news.exists() else ""
+
+          if f"# {pkg} {version}" in existing:
+              sys.exit(0)
+
+          news.write_text(new_entry + "\n" + existing)
+          EOF
+
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add NEWS.md
+          git diff --staged --quiet || \
+            git commit -m "style: update NEWS.md from CHANGELOG.md"
+          git push origin "$PR_BRANCH"

.github/workflows/test-coverage.yml

@@ -0,0 +1,58 @@
+name: Test Coverage
+
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - "*.md"
+      - ".github/**"
+      - "*.json "
+      - "*.toml "
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -4,3 +4,4 @@ README.Rmd
 CRAN-RELEASE
 .Rproj.user
 Support
+docs

.release-please-manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.2.5"
+}

DESCRIPTION

@@ -1,7 +1,9 @@
 Package: ParBayesianOptimization
 Title: Parallel Bayesian Optimization of Hyperparameters
 Version: 1.2.5
-Authors@R: person("Samuel", "Wilson", email = "samwilson303@gmail.com", role = c("aut", "cre"))
+Authors@R: c(
+    person("Novica", "Nakov", email = "nnovica@gmail.com", role = "cre"),
+    person("Samuel", "Wilson", email = "samwilson303@gmail.com", role = "aut"))
 Description: Fast, flexible framework for implementing Bayesian optimization of model 
 	hyperparameters according to the methods described in Snoek et al. <arXiv:1206.2944>.
 	The package allows the user to run scoring function in parallel, save intermediary 
@@ -11,9 +13,8 @@ URL: https://github.com/AnotherSamWilson/ParBayesianOptimization
 BugReports: https://github.com/AnotherSamWilson/ParBayesianOptimization/issues
 Depends: R (>= 3.4)
 Imports: data.table (>= 1.11.8), DiceKriging, stats, foreach, dbscan, lhs, crayon, ggplot2, ggpubr (>= 0.2.4)
-Suggests: knitr, rmarkdown, xgboost, doParallel, testthat
+Suggests: knitr, xgboost, doParallel, testthat, quarto
 License: GPL-2
 Encoding: UTF-8
 RoxygenNote: 7.2.1
-VignetteBuilder: knitr
-Maintainer: Samuel Wilson <samwilson303@gmail.com>
+VignetteBuilder: quarto