Add pkgdown and more cleanup

.Rbuildignore

@@ -17,3 +17,5 @@
 ^cran-comments\.md$
 ^LICENSE\.md$
 ^README\.md$
+^docs$
+^_pkgdown\.yml$

.github/environment/pixi.toml

@@ -10,11 +10,14 @@ libc = { family="glibc", version="2.17" }
 devtools_document = "R -e 'devtools::document()'"
 devtools_test = "R -e 'devtools::test()'"
 codecov = "R -e 'covr::codecov(quiet = FALSE)'"
+# build = "R -e 'devtools::build(args = c(\"--no-build-vignettes\"))'"
 build = "R -e 'devtools::build()'"
+# rcmdcheck = "R -e 'pkg <- list.files(\"..\", pattern = \".tar.gz\", full.names = TRUE); rcmdcheck::rcmdcheck(path = pkg[1], args = c(\"--as-cran\", \"--no-manual\", \"--ignore-vignettes\"))'"
 rcmdcheck = "R -e 'pkg <- list.files(\"..\", pattern = \".tar.gz\", full.names = TRUE); rcmdcheck::rcmdcheck(path = pkg[1], args = c(\"--as-cran\", \"--no-manual\"))'"
 use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'"
 use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'"
 use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'"
+pkgdown_build = "R -e 'pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)'"
 
 [feature.r43]
 dependencies = {"r-base" = "4.3.*"}
@@ -33,3 +36,4 @@ r44 = {features = ["r44"]}
 "r-mass" = "*"
 "r-rcmdcheck" = "*"
 "r-tidyverse" = "*"
+"qpdf" = "*"

.github/workflows/merge.yml

@@ -29,5 +29,33 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.4
 
-      # - name: Check unit test code coverage
-      #   run: pixi run codecov
+      - name: Check unit test code coverage
+        run: pixi run codecov
+
+  update_website:
+    if: github.event.pull_request.merged == true
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Create TOML from recipe
+        run: .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE}
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.8.4
+
+      - name: Check unit test code coverage
+        run: pixi run pkgdown_build
+
+      - 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

DESCRIPTION

@@ -15,6 +15,7 @@ Authors@R: c(
 Maintainer: Xuewei Cao <xc2270@cumc.columbia.edu>
 Description: This R package implements ColocBoost --- motivated and designed for colocalization analysis of multiple genetic association studies --- as a multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects, based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero effects on which subsets of response variables.
 Encoding: UTF-8
+LazyDataCompression: xz
 LazyData: true
 RoxygenNote: 7.3.2
 URL: https://github.com/StatFunGen/colocboost

NAMESPACE

@@ -1,12 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(colocboost)
-export(colocboost_assemble)
-export(colocboost_check_update_jk)
-export(colocboost_inits)
 export(colocboost_plot)
-export(colocboost_update)
-export(colocboost_workhorse)
 export(get_cos_summary)
 export(get_strong_colocalization)
 importFrom(grDevices,adjustcolor)

R/colocboost_assemble.R

@@ -18,7 +18,7 @@
 #'
 #' Summary of the colocboost results and get the output of colocboost (TO-DO-LIST)
 #'
-#' @export
+#' @noRd
 colocboost_assemble <- function(cb_obj,
                                 coverage = 0.95,
                                 weight_fudge_factor = 1.5,

R/colocboost_check_update_jk.R

@@ -1,14 +1,10 @@
-
-
-
-
-#' Model selection scheme in ColocBoost
+#' @title Model selection scheme in ColocBoost
 #'
 #' @details
 #' Model selection scheme in proximity smoothed gradient boosting algorithm to select update traits and update variants at each iteration.
 #'
 #' @return update_status and real_update_jk for each trait
-#' @export
+#' @noRd
 colocboost_check_update_jk <- function(cb_model, cb_model_para, cb_data,
                                        prioritize_jkstar = TRUE,
                                        jk_equiv_corr = 0.8, ##### more than 2 traits

R/colocboost_init.R

@@ -1,5 +1,3 @@
-
-
 #' @title Set of Internal functions for initial colocboost objects
 #'
 #' @description
@@ -21,7 +19,7 @@
 #'
 #' @keywords cb_objects
 #' @rdname colocboost_objects
-#' @export
+#' @noRd
 colocboost_inits <- function() {
     message("This function initializes colocboost objects. See details for more information.")
 }

R/colocboost_plot.R

@@ -4,7 +4,7 @@
 #'
 #' @description `colocboost_plot` generates visualization plots for colocalization events from a ColocBoost analysis.
 #'
-#' @param Output object from `colocboost` analysis 
+#' @param cb_output Output object from `colocboost` analysis 
 #' @param y Specifies the y-axis values, default is "log10p" for -log10 transformed marginal association p-values. 
 #' @param pos Optional plotting range of x-axis to zoom in to a specific region.
 #' @param plot_target_only Logical, if TRUE only plots colocalization with target outcome, default is FALSE.

R/colocboost_update.R

@@ -1,13 +1,11 @@
-
-
 #' Joint boosting algorithm in ColocBoost
 #'
 #' @details
 #' The gradient boosting algorithm for multiple outcomes
 #'
 #' @importFrom utils head tail
 #' @return colocboost object after gradient boosting update
-#' @export
+#' @noRd
 colocboost_update <- function(cb_model, cb_model_para, cb_data,
                               tau = 0.01,
                               learning_rate_decay = 1,

R/colocboost_workhorse.R

@@ -12,7 +12,7 @@
 #' 
 #' There is a version for LD free version with one causal assumption, implemented in `colocboost_one_causal`.
 #'
-#' @export
+#' @noRd
 colocboost_workhorse <- function(cb_data,
                                  M=NULL,
                                  tau = 0.01,

_pkgdown.yml

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

vignettes/Install.Rmd

@@ -7,7 +7,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-To install Seurat, [R](https://www.r-project.org/) version 4.0 or greater is required. We also recommend installing [R Studio](https://www.rstudio.com/).
+To install Seurat, [R](https://www.r-project.org/) version 4.0 or greater is required. We also recommend installing [R Studio](https://posit.co/).
 
 
 Seurat is available on [CRAN](https://cran.r-project.org/package=colocboost)??? for all platforms. To install, run: 
@@ -33,7 +33,7 @@ BiocManager::install("qvalue")
 
 # Install the development version of ColocBoost from GitHub
 
-Install the development version of ColocBoost - directly from [GitHub](https://github.com/xueweic/colocboost).
+Install the development version of ColocBoost - directly from [GitHub](https://github.com/StatFunGen/colocboost).
 
 ```{r eval = FALSE}
 # Enter commands in R (or R studio, if installed)

vignettes/announcements.Rmd

@@ -1,9 +1,11 @@
 ---
 title: "News"
-output:
-  html_document:
-    theme: united
-    df_print: kable
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{News}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+
 ---
 
 ## **Initial release in ColocBoost**