first draft coordinate handling functions

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

@@ -1,16 +1,13 @@
-# 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
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,64 +19,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(c(remotes::system_requirements("ubuntu", "20.04"), remotes::system_requirements("ubuntu", "20.04", package="curl")))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,50 +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
-    tags:
-      -'*'
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: natcpp
 Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
-Version: 0.1.1
+Version: 0.1.1.9000
 Authors@R: 
     person(given = "Gregory",
            family = "Jefferis",
@@ -16,7 +16,7 @@ Description: Fast functions implemented in C++ via 'Rcpp' to support the
     package will automatically use routines from this package when it is
     available to enable large performance gains.
 License: GPL (>= 3)
-URL: https://github.com/natverse/natcpp
+URL: https://github.com/natverse/natcpp, https://natverse.org/natcpp/
 BugReports: https://github.com/natverse/natcpp/issues
 Imports: 
     Rcpp (>= 1.0.6)

NAMESPACE

@@ -2,8 +2,11 @@
 
 export(c_EdgeListFromSegList)
 export(c_ListofMatrixRows)
+export(c_coords21dindex)
+export(c_ijkpos)
 export(c_listlengths)
 export(c_seglengths)
+export(c_sub2ind)
 export(c_topntail)
 export(c_topntail_list)
 export(c_total_cable)

R/RcppExports.R

@@ -20,6 +20,43 @@ c_total_cable <- function(sl, x, y, z) {
     .Call(`_natcpp_c_total_cable`, sl, x, y, z)
 }
 
+#' Convert physical coordinates to pixel coordinates
+#'
+#' @param xyz Nx3 matrix of physical coordinates
+#' @param dims Integer dimensions of the 3d image array
+#' @param origin Numeric: 3d coordinates of the origin
+#' @param voxdims Numeric: 3 numbers describing the voxel dimensions
+#' @param clamp Logical: whether or not to clamp values within the pixel
+#'   boundaries of the image.
+#' @return Nx3 integer matrix of pixel coordinates
+#' @export
+c_ijkpos <- function(xyz, origin, voxdims, dims, clamp = FALSE) {
+    .Call(`_natcpp_c_ijkpos`, xyz, origin, voxdims, dims, clamp)
+}
+
+#' Find 1D index given n-dimensional indices
+#' @param dims Integer dimensions of the array (usually 3d)
+#' @param indices Nx3 integer matrix of pixel coordinates
+#' @return numeric vector of linear indices into the array
+#' @export
+c_sub2ind <- function(dims, indices) {
+    .Call(`_natcpp_c_sub2ind`, dims, indices)
+}
+
+#' Convert physical coordinates to 1d indices into image array
+#'
+#' @param xyz Nx3 matrix or data.frame of physical coordinates
+#' @param dims Integer dimensions of the 3d image array
+#' @param origin Numeric: 3d coordinates of the origin
+#' @param voxdims Numeric: 3 numbers describing the voxel dimensions
+#' @param clamp Logical: whether or not to clamp values within the pixel
+#'   boundaries of the image.
+#' @return Nx3 integer matrix of pixel coordinates
+#' @export
+c_coords21dindex <- function(xyz, origin, voxdims, dims, clamp = FALSE) {
+    .Call(`_natcpp_c_coords21dindex`, xyz, origin, voxdims, dims, clamp)
+}
+
 #' Convert a matrix into list of row vectors
 #'
 #' @details Typically this will be for 3D coordinates but there are no limits

README.md

@@ -7,6 +7,7 @@
 [![R-CMD-check](https://github.com/natverse/natcpp/workflows/R-CMD-check/badge.svg)](https://github.com/natverse/natcpp/actions)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/natcpp)](https://CRAN.R-project.org/package=natcpp)
+[![R-CMD-check](https://github.com/natverse/natcpp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/natverse/natcpp/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of *natcpp* is to provide accelerated routines through compiled C++ 

_pkgdown.yml

@@ -1,26 +1,33 @@
+url: https://natverse.org/natcpp/
+template:
+  bootstrap: 5
 navbar:
   structure:
     left:
-    - home
     - intro
     - reference
     - articles
     - tutorials
-    - news
     - help
+    - news
     right:
-    - natverse
+    - search
     - github
+    - natverse
+    - lightswitch
   components:
-    home:
-      icon: fas fa-home fa-lg
-      href: index.html
     reference:
       text: Reference
       href: reference/index.html
+    search:
+      search: []
+    news:
+      text: Changelog
+      href: news/index.html
     github:
       icon: fab fa-github fa-lg
       href: https://github.com/natverse/natcpp/
+      aria-label: GitHub
     natverse:
       text: natverse
       href: https://natverse.github.io