Merge pull request #163 from ANTsX/gha-workflows

DRAFT: get R CMD check workflow running (+ passing?) via GHA

.github/ISSUE_TEMPLATE/bug_report.md

@@ -24,7 +24,6 @@ A clear and concise description of what you expected to happen.
 
 Please include output from `R` of:
 ```r
-ANTsRCore::antsVersions
 sessioninfo::session_info("ANTsRCore")
 ````
 

.github/workflows/package-build.yml

@@ -1,48 +1,51 @@
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
+# 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
 #
-# See https://github.com/r-lib/actions/tree/master/examples#readme for
-# additional example workflows available for the R community.
-
-name: Package Build
-
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches: [ "master" ]
+    branches: [main, master]
   pull_request:
-    branches: [ "master" ]
+    branches: [main, master]
 
-permissions:
-  contents: read
+name: R-CMD-check
 
-env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE: Release
-
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
+      fail-fast: true
       matrix:
-        r-version: ['4.1.1']
+        config:
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Configure CMake
-        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-        run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
-      - name: Set up R ${{ matrix.r-version }}
-        uses: r-lib/actions/setup-r@f57f1301a053485946083d7a45022b278929a78a
+      - uses: actions/checkout@v2
+
+      - 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:
-          r-version: ${{ matrix.r-version }}
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

.gitignore

@@ -1,6 +1,34 @@
 *.tgz
 ..Rcheck/
 
+docs
+/src/*.o
+/src/*.o-*
+/src/*.d
+/src/*.so
+*.dll
+.RData
+.Rproj.user
+.Rhistory
+inst/doc
+.httr-oauth
+vignettes/*.R
+.DS_Store
+/clion-test.R
+/BROWSE
+/GPATH
+/GRTAGS
+/GTAGS
+/TAGS
+/.dir-locals.el
+/issues
+/.drake
+bench-libs
+doc
+Meta
+
+*.tar.gz
+*.Rcheck/
 # ignore all the backup files created by editors
 *~
 *.so

DESCRIPTION

@@ -14,11 +14,11 @@ LazyLoad: yes
 LazyData: true
 Depends: methods, R (>= 2.10)
 LinkingTo: Rcpp, ITKR
-Imports: Rcpp (>= 1.0.12), ITKR (>= 0.5.0), RcppEigen, tools, magrittr, stats, utils
-Suggests: abind, covr, knitr, rmarkdown, testthat
+Imports: Rcpp (>= 1.0.12), ITKR (>= 0.5.0), RcppEigen
+Suggests: covr, knitr, rmarkdown, testthat
 SystemRequirements: cmake, git, clang, GNU make, v8
 NeedsCompilation: yes
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
 Remotes: stnava/ITKR

R/RcppExports.R

@@ -1,6 +1,15 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#' ANTSIntegrateVectorField
+#'
+#' @param r_refimg value
+#' @param r_velocity value
+#' @param r_deformation value
+#' @param r_t0 value
+#' @param r_t1 value
+#' @param r_dt value
+#' @return ANTSIntegrateVectorField
 ANTSIntegrateVectorField <- function(r_refimg, r_velocity, r_deformation, r_t0, r_t1, r_dt) {
     .Call(`_ANTsRCore_ANTSIntegrateVectorField`, r_refimg, r_velocity, r_deformation, r_t0, r_t1, r_dt)
 }