Merge pull request #2 from BerriJ/dev

Release 1.0.0

.Rbuildignore

@@ -1,2 +1,15 @@
-^.*\.Rproj$
-^\.Rproj\.user$
+.vscode
+.devcontainer
+.dev
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^man-roxygen
+src/test.cpp
+cran-comments.md
+^CRAN-RELEASE$
+^LICENSE\.md$
+^CRAN-SUBMISSION$
+inst/include/cpptimer/.git
+^cran-comments\.md$

.devcontainer/devcontainer.json

@@ -0,0 +1,75 @@
+{
+    "name": "DevEnv",
+    "image": "ghcr.io/berrij/devenv:latest",
+    // Grant xhost access to root user in order to start x11 devices (r plots)
+    "initializeCommand": "docker pull ghcr.io/berrij/devenv:latest",
+    "customizations": {
+        "vscode": {
+            // Extensions will get installed automatically
+            "extensions": [
+                // C++
+                "ms-vscode.cpptools-extension-pack",
+                // Python
+                "ms-python.vscode-pylance",
+                "ms-python.python",
+                "ms-python.black-formatter",
+                "visualstudioexptteam.vscodeintellicode",
+                "ms-toolsai.jupyter",
+                // R
+                "REditorSupport.r",
+                "rdebugger.r-debugger",
+                // Latex
+                "james-yu.latex-workshop",
+                "znck.grammarly",
+                // Git
+                "mhutchie.git-graph",
+                "github.vscode-pull-request-github",
+                // Markdown
+                "yzhang.markdown-all-in-one",
+                // Preview HTML
+                "daiyy.quick-html-previewer",
+                // Make fancy screenshots
+                "jeffersonlicet.snipped",
+                // Live Share
+                "ms-vsliveshare.vsliveshare",
+                // Copilot
+                "GitHub.copilot"
+            ],
+            // Set *default* container specific settings
+            // Important for radian and latex
+            "settings": {
+                // C++
+                "C_Cpp.default.configurationProvider": "ms-vscode.cmake-tools",
+                "cmake.configureSettings": {
+                    "CMAKE_TOOLCHAIN_FILE": "/usr/vcpkg/scripts/buildsystems/vcpkg.cmake"
+                },
+                // Python
+                "jupyter.notebookFileRoot": "${workspaceFolder}",
+                "python.pythonPath": "/usr/bin/python3",
+                "python.dataScience.interactiveWindowMode": "perFile",
+                "python.dataScience.sendSelectionToInteractiveWindow": true,
+                // R
+                "r.rterm.linux": "/usr/local/bin/radian",
+                "r.bracketedPaste": true,
+                "r.sessionWatcher": true,
+                "r.plot.useHttpgd": true,
+                "r.plot.defaults.fullWindowMode": true,
+                // Latex
+                "latex-workshop.latex.recipe.default": "latexmk (lualatex)",
+                "latex-workshop.latex.autoBuild.run": "onFileChange",
+                "latex-workshop.view.pdf.viewer": "tab",
+                "latex-workshop.linting.chktex.enabled": true,
+                "latex-workshop.linting.run": "onType",
+                "latex-workshop.synctex.afterBuild.enabled": true,
+                "latex-workshop.view.pdf.internal.synctex.keybinding": "double-click",
+                "latex-workshop.intellisense.unimathsymbols.enabled": true,
+                // Format code as you type
+                "editor.formatOnPaste": true,
+                "editor.formatOnType": true,
+                "editor.formatOnSave": true,
+                // Hide .gitignore files
+                "explorer.excludeGitIgnore": true
+            }
+        }
+    }
+}

.github/.gitignore

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

.github/workflows/R-CMD-check-Dev.yaml

@@ -0,0 +1,55 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on: [push, pull_request]
+
+name: R-CMD-check-Dev
+
+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'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - 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
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

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

@@ -0,0 +1,56 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  pull_request
+
+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'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - 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
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,41 @@
+on: push
+
+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 }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -0,0 +1,8 @@
+.dev/*
+docs
+src/*.o
+src/*.so
+src/*.dll
+src/test.cpp
+.vscode/.*
+inst/doc

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "inst/include/cpptimer"]
+	path = inst/include/cpptimer
+	url = git@github.com:BerriJ/cpptimer.git

.vscode/c_cpp_properties.json

@@ -0,0 +1,22 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/usr/local/lib/R/site-library/Rcpp/include",
+                "/usr/local/lib/R/site-library/RcppArmadillo/include",
+                "/usr/local/lib/R/site-library/RcppProgress/include",
+                "/usr/local/lib/R/site-library/splines2/include",
+                "/usr/share/R/include"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "gnu17",
+            "cppStandard": "gnu++14",
+            "intelliSenseMode": "linux-gcc-x64",
+            "configurationProvider": "ms-vscode.cmake-tools"
+        }
+    ],
+    "version": 4
+}

.vscode/debug.R

@@ -0,0 +1,9 @@
+env <- Sys.getenv()
+envnames <- names(env)
+rnames <- envnames[startsWith(envnames, "R_")]
+cached_names <- rnames
+ld_lib_path <- Sys.getenv("LD_LIBRARY_PATH")
+if (ld_lib_path != "") {
+    cached_names <- c("LD_LIBRARY_PATH", rnames)
+}
+writeLines(paste0(cached_names, "=", env[cached_names]), ".vscode/.env")

.vscode/launch.json

@@ -0,0 +1,45 @@
+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Debug RCPP",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "/usr/lib/R/bin/exec/R",
+      "args": [
+        "--vanilla",
+        "-e",
+        "devtools::test()"
+      ],
+      "stopAtEntry": false,
+      "envFile": "${workspaceFolder}/.vscode/.env",
+      "cwd": "${workspaceFolder}",
+      "externalConsole": false,
+      "MIMode": "gdb",
+      "setupCommands": [
+        {
+          "description": "Enable pretty-printing for gdb",
+          "text": "-enable-pretty-printing",
+          "ignoreFailures": true
+        }
+      ],
+      "preLaunchTask": "debug",
+      "osx": {
+        "program": "/Library/Frameworks/R.framework/Resources/bin/exec/R",
+        "MIMode": "lldb"
+      }
+    },
+    {
+      "type": "R-Debugger",
+      "name": "Debug R-Package",
+      "request": "launch",
+      "debugMode": "workspace",
+      "workingDirectory": "${workspaceFolder}",
+      "loadPackages": [
+        "."
+      ],
+      "includePackageScopes": true,
+      "allowGlobalDebugging": true
+    }
+  ]
+}