Merge pull request #115 from uclahs-cds/stefaneng-vignette-pkgdown-fixes

Fix vignette/README/image file paths for pkgdown

Author: stefaneng

.github/workflows/pkgdown.yaml

@@ -25,9 +25,13 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, local::., any::roxygen2
           needs: website
 
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

.gitignore

@@ -2,7 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
-man/
 vignettes/HistogramZoo.html
 *.Rproj
 inst/setup.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: HistogramZoo
 Title: A Method for Peak Merging And Distribution Fitting Across Biological Replicates
-Version: 1.3.0
+Version: 1.3.1
 Authors@R:
     c(
     person(given = "Helen",

NEWS.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - S3 methods to allow numeric/Histogram/GenomicHistogram input in key segment_and_fit functions
 
 ### Fixed
+- Minor fixes to vignette file path locations for successful pkgdown build
 
 ## [1.3.0] - 2023-04-14
 

README.md

@@ -15,7 +15,7 @@ The characteristic function provided by HistogramZoo is `segment_and_fit` which
 
 Finally, HistogramZoo provides several convenient functions to summarize fits and visualize data.
 
-![overview plot](readme_imports/Overview.png)
+![overview plot](man/figures/Overview.png)
 
 ## Installation
 
@@ -65,7 +65,7 @@ create_coverageplot(results);
 | -21-102   |          1 |    19 |  79 |              1 | 61,            | 1,              |               9 |            20 | 0.9554924687 | consensus | norm | 33.03241096 | 14.88105209 | mean             | sd               |
 
 **Coverage plot**
-![coverage plot](readme_imports/hz_output.png)
+![coverage plot](man/figures/hz_output.png)
 
 ## Resources
 

_pkgdown.yml

@@ -1,4 +1,4 @@
 ---
-url: https://friendly-invention-3cb82740.pages.github.io/
+url: https://uclahs-cds.github.io/public-R-HistogramZoo/
 template:
   bootstrap: 5