1.8 (not for merge)

.Rbuildignore

@@ -9,3 +9,9 @@ travisbuildchildren.sh
 ^build-cmtk.sh$
 ^build_docs.r$
 ^vignettes/.*pdf$
+^\.httr-oauth$
+^spare$
+^CRAN-RELEASE$
+^.github$
+^codecov\.yml$
+^CRAN-SUBMISSION$

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

@@ -0,0 +1,91 @@
+#on: push
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+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: 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"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RGL_USE_NULL: ${{ matrix.config.rglusenull }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - 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
+        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')"
+
+      - name: Build CMTK
+        run: sh ./build-cmtk.sh
+        env:
+          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 = 'error', check_dir = 'check')"
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        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}}")'

.gitignore

@@ -4,3 +4,6 @@
 inst/doc
 *.Rout
 docs/figs/*.pdf
+tests/testthat/Rplots.pdf
+.httr-oauth
+spare

DESCRIPTION

@@ -1,13 +1,15 @@
 Package: nat
 Type: Package
 Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
-Version: 1.8.12
+Version: 1.8.24
 Authors@R: c(
-    person("Gregory", "Jefferis", , "[email protected]", role = c("aut", "cre")),
-    person("James", "Manton", role = c("aut"))
+    person("Gregory","Jefferis", email="[email protected]", 
+    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")),
+    person("James", "Manton", role = c("aut"), comment = c(ORCID = "0000-0001-9260-3156")),
+    person("Dominik", "Krzeminski", role = c("ctb"), comment = c(ORCID = "0000-0003-4568-0583"))
     )
-URL: https://github.com/jefferis/nat, http://jefferislab.org
-BugReports: https://github.com/jefferis/nat/issues
+URL: https://github.com/natverse/nat, https://natverse.org/
+BugReports: https://github.com/natverse/nat/issues
 Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
     biological image data, especially traced neurons. Reads and writes 3D images
     in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
@@ -24,9 +26,9 @@ Depends:
     rgl (>= 0.98.1)
 Imports:
     nabor,
-    igraph (>= 0.7.1),
+    igraph (>= 1.3.0),
     methods,
-    filehash,
+    filehash (>= 2.3),
     digest,
     nat.utils (>= 0.4.2),
     plyr,
@@ -38,8 +40,10 @@ Suggests:
     XML,
     knitr,
     rmarkdown,
+    markdown,
     MASS,
-    alphashape3d
+    alphashape3d,
+    webshot2
 License: GPL-3
 LazyData: yes
 Collate:
@@ -84,5 +88,6 @@ Collate:
     'xformimage.R'
     'xformpoints.R'
     'zzz.R'
-RoxygenNote: 6.0.1
+RoxygenNote: 7.2.3
+Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -42,13 +42,15 @@ S3method(as.mesh3d,hxsurf)
 S3method(as.neuron,data.frame)
 S3method(as.neuron,default)
 S3method(as.neuron,igraph)
+S3method(as.neuron,morphml_cell)
 S3method(as.neuron,neuron)
 S3method(as.neuron,ngraph)
 S3method(as.neuronlist,default)
 S3method(as.neuronlist,neuronlistfh)
 S3method(as.neuronlistfh,neuronlist)
 S3method(as.ngraph,data.frame)
 S3method(as.ngraph,igraph)
+S3method(as.ngraph,morphml_cell)
 S3method(as.ngraph,neuron)
 S3method(as.ngraph,ngraph)
 S3method(as.seglist,default)
@@ -67,6 +69,7 @@ S3method(branchpoints,igraph)
 S3method(branchpoints,neuron)
 S3method(c,neuronlist)
 S3method(c,reglist)
+S3method(cmtk.targetvolume,character)
 S3method(cmtk.targetvolume,default)
 S3method(cmtk.targetvolume,im3d)
 S3method(cmtk.targetvolume,list)
@@ -107,6 +110,7 @@ S3method(ndigest,neuron)
 S3method(ndigest,neuronlistfh)
 S3method(nvertices,default)
 S3method(nvertices,dotprops)
+S3method(nvertices,igraph)
 S3method(nvertices,neuron)
 S3method(nvertices,neuronlist)
 S3method(plot,neuron)
@@ -320,24 +324,24 @@ 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,decompose.graph)
+importFrom(igraph,bfs)
+importFrom(igraph,decompose)
 importFrom(igraph,degree)
-importFrom(igraph,delete.vertices)
+importFrom(igraph,delete_vertices)
+importFrom(igraph,dfs)
 importFrom(igraph,diameter)
-importFrom(igraph,get.diameter)
-importFrom(igraph,get.shortest.paths)
-importFrom(igraph,get.vertex.attribute)
-importFrom(igraph,graph.bfs)
-importFrom(igraph,graph.dfs)
-importFrom(igraph,graph.empty)
-importFrom(igraph,is.connected)
-importFrom(igraph,is.directed)
+importFrom(igraph,distances)
+importFrom(igraph,get_diameter)
+importFrom(igraph,is_connected)
+importFrom(igraph,is_directed)
+importFrom(igraph,make_empty_graph)
 importFrom(igraph,neighborhood)
-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)