add pkg-dn, codecov

.Rbuildignore

@@ -1,2 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^codecov\.yml$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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
+
+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@v3
+
+      - 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

.gitignore

@@ -44,3 +44,4 @@ doc
 
 # Rproj
 hoodscanR.Rproj
+docs

DESCRIPTION

@@ -20,7 +20,7 @@ Description: hoodscanR is an user-friendly R package providing functions to assi
     perform neighborhood colocalization analysis and neighborhood-based cell clustering.
 biocViews: Spatial, Transcriptomics, SingleCell, Clustering
 License: GPL-3 + file LICENSE
-URL: https://github.com/DavisLaboratory/hoodscanR
+URL: https://github.com/DavisLaboratory/hoodscanR, https://davislaboratory.github.io/hoodscanR/
 BugReports: https://github.com/DavisLaboratory/hoodscanR/issues
 Encoding: UTF-8
 LazyData: false

README.md

@@ -1,6 +1,7 @@
 # hoodscanR: Cellular neighborhoods scanning from spatial transcriptomics data in R <img src="man/figures/hoodscanR_sticker.png" align="right" alt="" width="120" />
 
 [![R-CMD-check](https://github.com/DavisLaboratory/hoodscanR/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/DavisLaboratory/hoodscanR/actions)
+[![Coverage status](https://codecov.io/gh/DavisLaboratory/hoodscanR/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/DavisLaboratory/hoodscanR?branch=devel)
 
 
 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://davislaboratory.github.io/hoodscanR/
+template:
+  bootstrap: 5
+

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true