Pkgdown setup

Author: michaelhallquist

.Rbuildignore

@@ -1,3 +1,6 @@
 ^\.github$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# 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:
+  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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -51,3 +51,4 @@ site-library/
 
 # Local files for development
 local/
+docs

DESCRIPTION

@@ -30,3 +30,4 @@ Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 LinkingTo: Rcpp, RNifti, RcppArmadillo
+URL: https://uncdependlab.github.io/BrainGnomes/

_pkgdown.yml

@@ -0,0 +1,5 @@
+url: https://uncdependlab.github.io/BrainGnomes/
+template:
+  bootstrap: 5
+  bootswatch: spacelab
+

man/BrainGnomes-package.Rd

@@ -0,0 +1,72 @@
+---
+title: "BrainGnomes: Building Singularity Containers"
+author: "Michael Hallquist"
+date: "29 Jul 2025"
+output: 
+  rmarkdown::html_vignette:
+    toc: true
+vignette: >
+  %\VignetteIndexEntry{BrainGnomes Building Containers}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options:
+  chunk_output_type: console
+---
+
+# Running singularity
+
+On most HPC systems, Singularity is not available on login nodes. Thus, to build containers, you must enter an interactive compute session and build there. For example, on SLURM, for an 8-hour session with 32 GB RAM, use:
+
+```
+srun -t 8:00:00 --mem=32gb -p interact -N 1 -n 4  --pty /bin/bash
+```
+
+Now that you're in that session, you can proceed with building containers needed for BrainGnomes
+
+# Heudiconv
+
+```
+singularity pull docker://nipy/heudiconv:latest
+```
+
+More details here: https://heudiconv.readthedocs.io/en/latest/installation.html
+
+# fmriprep
+
+Fill in a version, such as 25.1.3
+
+```
+singularity build /proj/hng/software/containers/fmriprep-<version>.simg docker://nipreps/fmriprep:<version>
+```
+
+# MRIQC
+
+```
+singularity build /proj/mnhallqlab/mriqc-latest.simg docker://nipreps/mriqc:latest
+```
+
+# fmripost-aroma (ICA-AROMA)
+
+```
+singularity build /proj/hng/software/containers/aroma-latest.simg docker://nipreps/fmripost-aroma:main
+```
+
+Details: https://github.com/nipreps/fmripost-aroma?tab=readme-ov-file#installation
+
+# AFNI
+
+Not currently used, but if you want it!
+
+```
+singularity build /proj/hng/software/containers/afni-latest.simg  docker://afni/afni_make_build
+```
+
+# BIDS-validator
+
+Not quite as easy
+
+```
+module load node
+npm install -g deno
+deno compile -ERWN -o bids-validator jsr:@bids/validator
+```