From 90be3de7ebf142cb4065c797f56cc2ea437409a6 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Sat, 13 Jul 2024 18:34:13 +0100
Subject: [PATCH 1/2] roxygenise

---
 man/geom_neuron.Rd | 6 +++---
 man/ggneuron.Rd    | 4 ++++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/man/geom_neuron.Rd b/man/geom_neuron.Rd
index 2fd4fa1..391e3b7 100644
--- a/man/geom_neuron.Rd
+++ b/man/geom_neuron.Rd
@@ -127,9 +127,9 @@ It supports 'neuron', 'neuronlist', and 'mesh3d' objects.
 \examples{
 \dontrun{
 library(ggplot2)
-ggplot() + geom_neuron(my_neuron)
-ggplot() + geom_neuron(my_neuronlist)
-ggplot() + geom_neuron(my_mesh)
+ggplot() + geom_neuron(nat::Cell07PNs[[1]], root = 10)
+ggplot() + geom_neuron(nat::Cell07PNs)
+ggplot() + geom_neuron(nat::MBL.surf)
 }
 
 }
diff --git a/man/ggneuron.Rd b/man/ggneuron.Rd
index e616742..24c16d2 100644
--- a/man/ggneuron.Rd
+++ b/man/ggneuron.Rd
@@ -57,6 +57,10 @@ ggneuron(banc_neuropil.surf, banc.surf)
 # Visualize the banc brain neuropil
 ggneuron(banc_neuropil.surf,
 rotation_matrix = bancr:::banc_rotation_matrices[["front"]])
+
+# See constituents of a neuronlist
+ggneuron(nat::Cell07PNs, volume = nat::MBL.surf,
+root = 10, high = "red", low = "black")
 }
 
 }

From e503d4911abed94e03d58383d40c075b84d79e14 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Sat, 13 Jul 2024 18:37:22 +0100
Subject: [PATCH 2/2] implement pkgdown

---
 .github/workflows/pkgdown.yaml | 67 ++++++++++++++++++++++++++++++++++
 DESCRIPTION                    |  5 +--
 _pkgdown.yml                   |  2 +
 3 files changed, 71 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..d25f876
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,67 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    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 }}
+      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
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::., catmaid=natverse/rcatmaid
+          needs: website
+
+      - name: Install fafbseg + python
+        run: |
+          pak::local_install()
+          library(fafbseg)
+          simple_python()
+          dr_fafbseg()
+        shell: Rscript {0}
+
+      - name: writetoken
+        run: fafbseg::flywire_set_token(token=Sys.getenv("CHUNKEDGRAPH_SECRET"))
+        shell: Rscript {0}
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 04c41f6..0dc9863 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,7 @@ Description: Access to the BANC 'righty' EM dataset, focussing on support for
     BANC autosegmentation. Organised as a wrapper around the fafbseg
     package.
 License: GPL-3
-URL: https://github.com/flyconnectome/bancr
+URL: https://github.com/flyconnectome/bancr, https://flyconnectome.github.io/bancr/
 BugReports: https://github.com/flyconnectome/bancr/issues
 Depends: 
     R (>= 3.5.0),
@@ -70,10 +70,9 @@ Remotes:
     tidyverse/ggplot2,
     eliocamp/ggnewscale
 Config/testthat/edition: 3
-LazyDataCompression:xz
+LazyDataCompression: xz
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-
diff --git a/_pkgdown.yml b/_pkgdown.yml
index cb24c84..95edf9d 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,6 @@
 url: https://flyconnectome.github.io/bancr
+template:
+  bootstrap: 5
 navbar:
   structure:
     left: