Merge branch 'release/v2.2.0'

ygeunkim · Feb 6, 2025 · c81790e · c81790e
2 parents 32ee857 + 4d93f1a
commit c81790e
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,4 +15,6 @@
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^revdep$
-^python$
+^python$
+inst/doxygen
+^logo$
diff --git a/.github/ISSUE_TEMPLATE/issue_template.md b/.github/ISSUE_TEMPLATE/issue_template.md
@@ -1,14 +1,20 @@
 ---
-name: Bug report or feature request
+name: Issue
 about: Describe a bug you've seen or make a case for a new feature
 ---
 
-Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://community.rstudio.com/>.
+## Type
 
-Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+- [ ] Bug report: write "[bug]" at the first of the title.
+- [ ] Feature request: write "[feature]" at the first of the title.
+- [ ] Documentation: write "[document]" at the first of the title.
+- [ ] Others
 
-Brief description of the problem
+## Languages
+<!-- Check every element related to your issue. -->
 
-```r
-# insert reprex here
-```
+- [ ] C++: Header files in `inst/include` directory
+- [ ] R: R package files (including C++ codes in `src` directory).
+- [ ] Python: Files in `python` directory.
+
+## Description
diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md
@@ -0,0 +1,25 @@
+---
+name: Pull request
+about: Fix a bug, add a new feature, etc
+---
+
+## Prerequisites
+
+- [ ] Ensure that this pull request targets the **develop** branch.
+- [ ] Aware that C++ header files are shared by both R and Python.
+- [ ] If the PR adds a new feature, write "[feature]" in the title. If it is a fix, write "[bugfix]".
+
+## Type
+
+- [ ] Bug fix: write "[bugfix]" at the first of the title.
+- [ ] New feature: write "[feature]" at the first of the title.
+- [ ] Documentation: write "[document]" at the first of the title.
+- [ ] Others
+
+## Languages
+
+- [ ] C++: Header files in `inst/include` directory
+- [ ] R: R package files (including C++ codes in `src` directory).
+- [ ] Python: Files in `python` directory.
+
+## Description
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, 'hotfix/*', 'release/*', develop]
+    branches: [main, master, 'hotfix/*', 'release/*', develop, 'feature/*-withci']
   pull_request:
     branches: [main, master, 'hotfix/*', 'release/*', develop]
 
@@ -21,14 +21,16 @@ jobs:
           - {os: macOS-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel-4'}
+          # rtools40's older compiler: R-4.0.0 to to R-4.1.3
+          - {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: '3.6'}
+          # add oldrel-4 in Spring 2025
+          # - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -44,35 +46,10 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
-      - name: Determine evaluate package version on Windows
-        if: runner.os == 'Windows'
-        run: |
-          if ($Env:MATRIX_CONFIG_R -lt "4.0.0") {
-            echo "[email protected]" >> $Env:GITHUB_ENV
-          } else {
-            echo "EVALUATE_PKG=evaluate" >> $Env:GITHUB_ENV
-           }
-        shell: pwsh
-
-      - name: Determine evaluate package version on non-Windows
-        if: runner.os != 'Windows'
-        run: |
-          if [ "${{ matrix.config.r }}" \< "4.0.0" ]; then
-            echo "[email protected]" >> $GITHUB_ENV
-          else
-            echo "EVALUATE_PKG=evaluate" >> $GITHUB_ENV
-          fi
-        shell: bash
-
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, ${{ env.EVALUATE_PKG }}
-          # extra-packages: >
-          #    any::rcmdcheck,
-          #    knitr=?ignore-before-r=4.0.0,
-          #    rmarkdown=?ignore-before-r=4.0.0,
-          #    testthat=?ignore-before-r=4.0.0
+          extra-packages: any::rcmdcheck
           needs: check
 
 # do not build vignettes in github actions check and ignore warnings
@@ -84,7 +61,7 @@ jobs:
           error-on: '"warning"'
           check-dir: '"check"'
           upload-snapshots: false
-          upload-results: false
+          upload-results: 'never'
 
       - name: Run check for CRAN
         uses: r-lib/actions/check-r-package@v2

diff --git a/.github/workflows/doxygen.yaml b/.github/workflows/doxygen.yaml
@@ -0,0 +1,47 @@
+# Render doxygen to github page repo
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+name: doxygen
+
+jobs:
+  doxygen:
+    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: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Doxygen
+        run: sudo apt-get install -y doxygen graphviz
+
+      - name: Extract version number from DESCRIPTION
+        run: |
+          VERSION=$(grep '^Version:' DESCRIPTION | cut -d ' ' -f 2)
+          sed -i "s|BVHAR_VERSION|${VERSION}|" inst/doxygen/Doxyfile
+    
+      - name: Render doxygen
+        run: doxygen inst/doxygen/Doxyfile
+
+      - name: Create .nojekyll
+        run: sudo touch inst/doxygen/html/.nojekyll
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          token: ${{ secrets.YGEUNKIM_PAGE_PAT }}
+          repository-name: ygeunkim/ygeunkim.github.io
+          clean: false
+          branch: master
+          folder: inst/doxygen/html
+          target-folder: package/bvhar/cpp
diff --git a/.github/workflows/py-conda-check.yaml b/.github/workflows/py-conda-check.yaml
@@ -1,6 +1,6 @@
 on:
   push:
-    branches: [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*']
+    branches: [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*', 'feature/*-withci']
   pull_request:
     branches: [main, master, 'hotfix/*', 'release/*', develop]
 

diff --git a/.github/workflows/py-github-check.yaml b/.github/workflows/py-github-check.yaml
@@ -1,6 +1,6 @@
 on:
   push:
-    branches: [main, master, 'hotfix/*', 'release/*', develop, 'feature/py-*']
+    branches: [main, master, 'hotfix/*', 'release/*', develop]
   pull_request:
     branches: [main, master, 'hotfix/*', 'release/*', develop]
 
@@ -32,22 +32,28 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y libboost-all-dev libeigen3-dev
+          sudo apt-get install -y libboost-all-dev libeigen3-dev libfmt-dev libspdlog-dev
           echo $(sudo apt list --installed)
           echo "EIGEN_INCLUDE_DIR=/usr/include/eigen3" >> $GITHUB_ENV
           echo "BOOST_INCLUDE_DIR=/usr/include/boost" >> $GITHUB_ENV
+          echo "SPDLOG_INCLUDE_DIR=/usr/include/spdlog" >> $GITHUB_ENV
+          echo "FMT_INCLUDE_DIR=/usr/include/fmt" >> $GITHUB_ENV
       
       - name: Set system dependencies on macOS
         if: runner.os == 'macOS'
         run: |
           brew update
-          brew install llvm libomp boost eigen
+          brew install llvm libomp boost eigen fmt spdlog
           EIGEN_LOC=$(brew --prefix eigen)
           BOOST_LOC=$(brew --prefix boost)
+          SPDLOG_LOC=$(brew --prefix spdlog)
+          FMT_LOC=$(brew --prefix fmt)
           LLVM_LOC=$(brew --prefix llvm)
           OMP_LOC=$(brew --prefix libomp)
           echo "EIGEN_INCLUDE_DIR=$EIGEN_LOC/include/eigen3" >> $GITHUB_ENV
           echo "BOOST_INCLUDE_DIR=$BOOST_LOC/include" >> $GITHUB_ENV
+          echo "SPDLOG_INCLUDE_DIR=$SPDLOG_LOC/include" >> $GITHUB_ENV
+          echo "FMT_INCLUDE_DIR=$FMT_LOC/include" >> $GITHUB_ENV
           echo "LLVM_LOC=$LLVM_LOC" >> $GITHUB_ENV
           echo "OMP_LOC=$OMP_LOC" >> $GITHUB_ENV
           echo "CC=$LLVM_LOC/bin/clang" >> $GITHUB_ENV
@@ -58,53 +64,61 @@ jobs:
       - name: Set system dependencies on Windows
         if: runner.os == 'Windows'
         run: |
-          choco install eigen -y --no-progress
-          choco install boost-msvc-14.3 -y --no-progress
-          $eigenPath = (
-            Get-ChildItem -Path "C:\ProgramData\chocolatey\lib\eigen" -Recurse -Filter "Eigen" |
-            Select-Object -First 1
-          ).Parent.FullName
-          if ($eigenPath) {
-            echo "eigen is installed in $eigenPath"
-          } else {
-            Write-Error "Wrong eigen path"
-            exit 1
-          }
-          $boostPath = $null
-          $boostCand = @("C:\local", "C:\ProgramData\chocolatey\lib")
-          foreach ($cand in $boostCand) {
-            $isPath = (
-                Get-ChildItem -Path $cand -Directory |
-                Where-Object { $_.Name -match  "boost" } |
-                Sort-Object LastWriteTime -Descending |
-                Select-Object -First 1
-            ).FullName
-            if ($isPath) {
-                $boostPath = $isPath
-                break
+          $vcpkgRoot = $Env:VCPKG_INSTALLATION_ROOT
+          vcpkg install eigen3 | Out-Null
+          vcpkg install boost | Out-Null
+          vcpkg install fmt | Out-Null
+          vcpkg install spdlog | Out-Null
+          $installPath = $null
+          $tripletCand = @(
+            "$vcpkgRoot\installed\x64-windows",
+            "$vcpkgRoot\installed\x86-windows",
+            "$vcpkgRoot\installed\arm64-windows"
+          )
+          foreach ($cand in $tripletCand) {
+            Write-Host "Checking triplet path: $cand"
+            if (Test-Path "$cand\include") {
+              $installPath = "$cand"
+              Write-Host "Valid installation: $installPath"
+              break
             }
           }
-          if ($boostPath) {
-            echo "boost is installed in $boostPath"
-          } else {
-            Write-Error "Wrong boost path"
+          if (-not $installPath) {
+            Write-Error "No valid installation path"
             exit 1
           }
-          echo "EIGEN_INCLUDE_DIR=$eigenPath" >> $Env:GITHUB_ENV
-          echo "BOOST_INCLUDE_DIR=$boostPath" >> $Env:GITHUB_ENV
+          $libPath = @{
+            "eigen" = "$installPath\include\eigen3"
+            "boost" = "$installPath\include"
+            "spdlog" = "$installPath\include"
+            "fmt" = "$installPath\include"
+          }
+          foreach ($lib in $libPath.Keys) {
+            if (Test-Path $libPath[$lib]) {
+              Write-Host "$lib is installed in $($libPath[$lib])"
+              echo "$($lib.ToUpper())_INCLUDE_DIR=$($libPath[$lib])" >> $Env:GITHUB_ENV
+            } else {
+              Write-Error "Wrong $lib path: $($libPath[$lib])"
+              exit 1
+            }
+          }
 
-      - name: Verify Eigen and boost on non-Windows
+      - name: Verify C++ libraries on non-Windows
         if: runner.os != 'Windows'
         run: |
           ls ${{ env.EIGEN_INCLUDE_DIR }}
           ls ${{ env.BOOST_INCLUDE_DIR }}
+          ls ${{ env.SPDLOG_INCLUDE_DIR }}
+          ls ${{ env.FMT_INCLUDE_DIR }}
           mkdir temp-dir
       
-      - name: Verify Eigen and boost on Windows
+      - name: Verify C++ libraries on Windows
         if: runner.os == 'Windows'
         run: |
           dir ${{ env.EIGEN_INCLUDE_DIR }}
           dir ${{ env.BOOST_INCLUDE_DIR }}
+          dir ${{ env.SPDLOG_INCLUDE_DIR }}
+          dir ${{ env.FMT_INCLUDE_DIR }}
           New-Item -ItemType Directory -Force -Path temp-dir
 
       - name: Install package from github