Build website for the crantr package

flyconnectome · Oct 27, 2024 · 8c2d051 · 8c2d051
1 parent 1f5b590
commit 8c2d051
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Showing 81 changed files with 25,213 additions and 7 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,4 +2,6 @@
 ^\.Rproj\.user$
 ^_pkgdown\.yml$
 ^docs$
-^LICENSE\.md$
+^LICENSE\.md$
+^pkgdown$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,50 @@
+# 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.yaml
+
+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 }}
+    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::.
+          needs: website
+
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
-docs
-inst/doc
 data-raw/*
-data/banc_data.sqlite
+data/crant_data.sqlite
diff --git a/R/ant-table.R b/R/ant-table.R
@@ -318,7 +318,7 @@ crant_table_update_tracing <- function(table = "CRANTb_meta",
 
   # Only add ngl_link for a certain set of statuses
   cat('generating neuroglancer links ...\n')
-  n_rows <- nrow(ac %>% dplyr::filter(grepl("TRACING_ISSUE$|PROOFREADING_ISSUE$|PARTIALLY_PROOFREAD$", status)))
+  n_rows <- nrow(ac %>% dplyr::filter(grepl("TRACING_ISSUE$|TRACING_ISSUE,|PROOFREADING_ISSUE$|PROOFREADING_ISSUE,|PARTIALLY_PROOFREAD$|PARTIALLY_PROOFREAD,", status)))
   p <- dplyr::progress_estimated(n_rows)
   ac.new <- ac %>%
     dplyr::filter(grepl("TRACING_ISSUE$|PROOFREADING_ISSUE$|PARTIALLY_PROOFREAD$", !!rlang::sym("status"))) %>%

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: https://flyconnectome.github.io/bancr
+url: https://flyconnectome.github.io/crantr/
 template:
   bootstrap: 5
 navbar:
@@ -18,12 +18,13 @@ navbar:
     home:
       icon: fas fa-home fa-lg
       href: index.html
+      aria-label: Home
     reference:
       text: Reference
       href: reference/index.html
     github:
       icon: fab fa-github fa-lg
-      href: https://github.com/flyconnectome/bancr/
+      href: https://github.com/flyconnectome/crantr/
     natverse:
       text: natverse
       href: https://natverse.github.io

diff --git a/docs/404.html b/docs/404.html