geom_neuron, ggneuron and friends moved to natverse/nat.ggplot2

* moved to: https://github.com/natverse/nat.ggplot

Author: alexanderbates

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

@@ -1,83 +1,51 @@
-# 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:
-    runs-on: ubuntu-latest
+    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'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CHUNKEDGRAPH_SECRET: ${{ secrets.CHUNKEDGRAPH_SECRET }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      FLYTABLE_TOKEN: ${{ secrets.FLYTABLE_TOKEN }}
-      RETICULATE_MINICONDA_PYTHON_VERSION: 3.8
-      RGL_USE_NULL: TRUE
-      _R_CHECK_DONTTEST_EXAMPLES_: FALSE
-      _R_CHECK_TESTS_NLINES_: 0
-      _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - 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
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::pkgdown, catmaid=natverse/rcatmaid
+          extra-packages: any::rcmdcheck
           needs: check
 
-      - name: Fix Conda permissions on macOS
-        if: runner.os == 'macOS'
-        run: sudo chown -R $UID $CONDA
-
-      - name: Install fafbseg + python
-        run: |
-          pak::local_install()
-          pak::pak('natverse/coconatfly')
-          library(bancr)
-          library(fafbseg)
-          simple_python()
-          simple_python('none', pkgs='cloud-volume~=8.32.1')
-          dr_banc()
-        shell: Rscript {0}
-
-      - name: writetoken
-        run: fafbseg::flywire_set_token(token=Sys.getenv("CHUNKEDGRAPH_SECRET"))
-        shell: Rscript {0}
-
       - uses: r-lib/actions/check-r-package@v2
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v4
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Upload check log results
-        if: failure()
-        uses: actions/upload-artifact@v4
-        with:
-          name: ${{ matrix.config.tag }}-results
-          path: ${{ github.event.repository.name }}.Rcheck/00check.log
-
-      - name: Test coverage
-        # if: runner.os == 'macOS'
-        if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}}
-        run: covr::codecov(errorsAreFatal=FALSE)
-        shell: Rscript {0}
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: bancr
 Title: R Client Access to the Brain And Nerve Cord (BANC) Dataset
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: 
     c(person(given = "Alexander",
            family = "Bates",
@@ -37,7 +37,8 @@ Imports:
     dplyr,
     magrittr,
     utils,
-    reticulate
+    reticulate,
+    nat.ggplot
 Suggests: 
     testthat (>= 3.0.0),
     readobj,
@@ -81,7 +82,8 @@ Remotes:
     tidyverse/ggplot2,
     eliocamp/ggnewscale,
     natverse/coconat,
-    natverse/coconatfly
+    natverse/coconatfly,
+    natverse/nat.ggplot
 Config/testthat/edition: 3
 LazyDataCompression: xz
 Encoding: UTF-8

NAMESPACE

@@ -14,21 +14,6 @@ S3method(banc_decapitate,neuron)
 S3method(banc_decapitate,neuronlist)
 S3method(banc_reroot,neuron)
 S3method(banc_reroot,neuronlist)
-S3method(geom_neuron,"NULL")
-S3method(geom_neuron,data.frame)
-S3method(geom_neuron,dotprops)
-S3method(geom_neuron,hxsurf)
-S3method(geom_neuron,list)
-S3method(geom_neuron,matrix)
-S3method(geom_neuron,mesh3d)
-S3method(geom_neuron,neuron)
-S3method(geom_neuron,neuronlist)
-S3method(geom_neuron,splitneuron)
-S3method(geom_neuron,synapticneuron)
-S3method(ggplot2_neuron_path,"NULL")
-S3method(ggplot2_neuron_path,mesh3d)
-S3method(ggplot2_neuron_path,neuron)
-S3method(ggplot2_neuron_path,neuronlist)
 export(banc_add_synapses)
 export(banc_all_synapses)
 export(banc_annotate_backbone_proofread)
@@ -48,7 +33,6 @@ export(banc_codex_search)
 export(banc_decapitate)
 export(banc_edgelist)
 export(banc_front_view)
-export(banc_ggneuron)
 export(banc_ids)
 export(banc_islatest)
 export(banc_latestid)
@@ -99,9 +83,6 @@ export(choose_banc)
 export(dr_banc)
 export(elastix_xform)
 export(franken_meta)
-export(geom_neuron)
-export(ggneuron)
-export(ggplot2_neuron_path)
 export(navis_elastix_xform)
 export(register_banc_coconat)
 export(with_banc)
@@ -125,7 +106,6 @@ importFrom(reticulate,conda_list)
 importFrom(reticulate,import)
 importFrom(reticulate,py_install)
 importFrom(reticulate,use_condaenv)
-importFrom(rlang,.data)
 importFrom(stats,na.omit)
 importFrom(utils,browseURL)
 importFrom(utils,capture.output)

R/cave-tables.R

@@ -100,7 +100,9 @@ Please ask for help on #annotation_infrastructure https://flywire-forum.slack.co
 #' distributed neural control and behaviour-centric neural modules across the
 #' brain-VNC boundary.
 #' @export
-banc_edgelist <- function(edgelist_view = c("synapses_250226_backbone_proofread_and_peripheral_nerves_counts",
+banc_edgelist <- function(edgelist_view = c("synapses_v2_backbone_proofread_and_peripheral_nerves_counts",
+                                            "synapses_v2_backbone_proofread_counts",
+                                            "synapses_250226_backbone_proofread_and_peripheral_nerves_counts",
                                             "synapses_250226_backbone_proofread_counts",
                                             "synapses_v1_backbone_proofread_counts"),
                           ...){