Merge pull request #518 from natverse/fix/igraph200

igraph dfs may signal unreachable nodes with 0

.Rbuildignore

@@ -15,3 +15,5 @@ travisbuildchildren.sh
 ^\.github$
 ^depends.Rds$
 ^codecov\.yml$
+^CODE_OF_CONDUCT\.md$
+^CRAN-SUBMISSION$

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

@@ -1,15 +1,14 @@
-#on: push
+# 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
+    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -21,71 +20,42 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          #- {os: windows-latest, r: 'release', rglusenull: "true"}
-          - {os: macOS-latest, r: 'release', rglusenull: "true"}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", rglusenull: "true", codecov: "true"}
-          #- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macos-latest,    r: 'release'}
+          - {os: windows-latest,  r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release', codecov: 'true'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RGL_USE_NULL: ${{ matrix.config.rglusenull }}
+      R_KEEP_PKG_SOURCE: yes
+      RGL_USE_NULL: true
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - 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-pandoc@v2
-
-      - name: Query dependencies
-        run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: Install Covr
-        run: Rscript -e "remotes::install_github('r-lib/covr')"
+          extra-packages: any::rcmdcheck, natverse/natcpp
+          needs: check
 
       - name: Build CMTK
+        if: ${{matrix.config.os != 'windows-latest'}}
         run: sh ./build-cmtk.sh
         env:
+          CC: clang
+          CXX: clang++
           MAKEFLAGS: "-j2"
 
-      - name: Install dependencies
-        run: Rscript -e "library(remotes)" -e "update(readRDS('depends.Rds'))" -e "remotes::install_cran('rcmdcheck')"
-
-      - name: Install manual dependencies
-        run: Rscript -e "remotes::install_github('natverse/natcpp')"
-
-      - name: Check
-        run: Rscript -e "rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')"
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Test coverage
-        if: matrix.config.codecov
-        run: |
-          Rscript -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - 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")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -27,7 +27,7 @@ Depends:
     rgl (>= 0.98.1)
 Imports:
     nabor,
-    igraph (>= 0.7.1),
+    igraph (>= 1.0),
     methods,
     filehash (>= 2.3),
     digest,

NAMESPACE

@@ -114,6 +114,7 @@ S3method(ndigest,neuron)
 S3method(ndigest,neuronlistfh)
 S3method(nvertices,default)
 S3method(nvertices,dotprops)
+S3method(nvertices,igraph)
 S3method(nvertices,neuron)
 S3method(nvertices,neuronlist)
 S3method(nvertices,shapelist3d)
@@ -389,27 +390,26 @@ importFrom(digest,digest)
 importFrom(igraph,"V<-")
 importFrom(igraph,E)
 importFrom(igraph,V)
-importFrom(igraph,add.edges)
+importFrom(igraph,add_edges)
 importFrom(igraph,as.directed)
 importFrom(igraph,as.undirected)
 importFrom(igraph,as_edgelist)
-importFrom(igraph,decompose.graph)
+importFrom(igraph,bfs)
+importFrom(igraph,decompose)
 importFrom(igraph,degree)
 importFrom(igraph,delete.vertices)
+importFrom(igraph,dfs)
 importFrom(igraph,diameter)
 importFrom(igraph,distances)
 importFrom(igraph,get.diameter)
-importFrom(igraph,get.shortest.paths)
-importFrom(igraph,get.vertex.attribute)
-importFrom(igraph,graph.bfs)
-importFrom(igraph,graph.dfs)
-importFrom(igraph,is.connected)
-importFrom(igraph,is.directed)
+importFrom(igraph,is_connected)
+importFrom(igraph,is_directed)
 importFrom(igraph,make_empty_graph)
 importFrom(igraph,neighborhood)
 importFrom(igraph,set_edge_attr)
-importFrom(igraph,shortest.paths)
+importFrom(igraph,shortest_paths)
 importFrom(igraph,vcount)
+importFrom(igraph,vertex_attr)
 importFrom(methods,is)
 importFrom(nabor,knn)
 importFrom(nat.utils,RunCmdForNewerInput)

R/graph-nodes.R

@@ -13,7 +13,7 @@
 #'   available). Set to FALSE when this is not desired.
 #' @param exclude.isolated Do not count isolated vertices as root/end points
 #'   (default)
-#' @importFrom igraph V degree get.vertex.attribute
+#' @importFrom igraph V degree vertex_attr
 #' @export
 #' @seealso \code{\link{rootpoints}}, \code{\link{ngraph}}
 #' @examples
@@ -27,7 +27,7 @@
 graph.nodes<-function(x, type=c('root','end','branch'), original.ids='name',
                       exclude.isolated=TRUE){
   type=match.arg(type)
-  if(type=='root' && !is.directed(x))
+  if(type=='root' && !is_directed(x))
     stop("Cannot establish root points for undirected graph")
 
   # root points are those without incoming edges
@@ -42,7 +42,7 @@ graph.nodes<-function(x, type=c('root','end','branch'), original.ids='name',
   }
 
   if(is.character(original.ids))
-    vertex_names=get.vertex.attribute(x, original.ids, index=vertex_idxs)
+    vertex_names=vertex_attr(x, original.ids, index=vertex_idxs)
   if(!is.character(original.ids) || is.null(vertex_names))
     as.integer(vertex_idxs)
   else