Add initial documentation

.github/workflows/check-standard.yaml

@@ -20,9 +20,7 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -22,6 +22,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 17
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2

.github/workflows/test-coverage.yaml

@@ -10,7 +10,7 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macos-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

.gitignore

@@ -1,3 +1,13 @@
+## General ----
+*.swp
+*.swo
+*.html
+*.pdf
+.DS_Store
+.httr-oauth
+vignettes/*.log
+vignettes/figure/
+
 .Rproj.user
 .Rhistory
 .RData

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.3
+Version: 0.3.1
 Authors@R:
     person(
         given = "Brandon",
@@ -20,6 +20,9 @@ Description:
     from unphased species characterized by low genetic diversity and
     high-density genotyping.
 License: Apache License (>= 2) | file LICENSE
+URL:
+    https://github.com/maize-genetics/rPHG2,
+    https://rphg2.maizegenetics.net/
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
@@ -35,6 +38,9 @@ Imports:
     methods,
     rJava,
     tibble
-Suggests: 
+VignetteBuilder: knitr
+Suggests:
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,10 @@
+## rPHG2 0.4
+* Added vignettes and README updates
+  + `vignette("rPHG2")`
+* Created build system for website generation
+  + [rphg2.maizegenetics.net](https://rphg2.maizegenetics.net)
+
+
 ## rPHG2 0.3
 * Added new class, `PHGDataSet`
   + In memory representation of hVCF data sets

README.md

@@ -2,6 +2,8 @@
 
 <!-- badges: start -->
 [![Life Cycle Status](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![R-CMD-check](https://github.com/maize-genetics/rPHG2/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/maize-genetics/rPHG2/actions/workflows/check-standard.yaml)
+[![codecov](https://codecov.io/gh/maize-genetics/rPHG2/graph/badge.svg?token=BEEI8KZ96H)](https://codecov.io/gh/maize-genetics/rPHG2)
 <!-- badges: end -->
 
 `rPHG2` is a system to interact with and retrieve information from **version 2** 
@@ -15,19 +17,69 @@ framework for genotype inference. This is accomplished by leveraging the
 You can install the development version of rphg2 from [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("maize-genetics/rPHG2")
+# install.packages("pak")
+pak::pak("maize-genetics/rPHG2")
 ```
 
-## Example
 
-This is a basic example which shows you how to solve a common problem:
+## Usage
 
+### Initialize with PHGv2 JARs
 ``` r
-library(rphg2)
+initPhg("my/phg/jar/path")
+```
+
+### Create a connection
+``` r
+locCon <- list.files("my/hvcf/dir") |>
+    PHGLocalCon()
+```
+
+### Build a graph
+``` r
+graph <- locCon |> buildHaplotypeGraph()
+```
+
+### Read data into R
+``` r
+phgDs <- graph |> readPhgDataSet()
+```
+
+### Identify areas of interest
+``` r
+gr <- GRanges(
+    seqnames = c("1", "2"),
+    ranges = IRanges(
+        c(100, 800),
+        c(400, 900)
+    )
+)
+
+phgDs |> 
+    filterSamples(c("B73", "Ky21", "Mo17")) |> 
+    filterRefRanges(gr)
+```
+
+
+## Lifecycle
+[![Life Cycle Status](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 
-phgCon <- PHGServerCon("localhost", 8080, "http")
+`rPHG2` is a relatively new R package and may be subject to changes in
+workflow and function definitions. If you would like to see anything added
+or run into problems, please feel free to contact the team using the 
+[issues page](https://github.com/maize-genetics/rPHG2/issues).
 
-phgCon |> readSamples()
+
+## Learning rPHG2
+If installed locally, you can read the "Introduction to rPHG2" vignette by
+using:
+
+``` r
+vignette("rPHG2")
 ```
 
+Alternatively, the package's [website](https://rphg2.maizegenetics.net) is
+another great place to read up on function usage, code changes, and
+workflows.
+
+

pkgdown/_pkgdown.yml

@@ -0,0 +1,33 @@
+url: https://rphg2.maizegenetics.net
+
+template:
+  theme: breeze-light
+  bootstrap: 5
+  bslib:
+    base_font: {google: "Barlow"}
+    heading_font: {google: "Oswald"}
+    code_font: {google: "Roboto Mono"}
+  extra_css: pkgdown/extra.css
+
+navbar:
+  structure:
+    left:  [intro, articles, reference, news]
+    right: [search, github, phg]
+  components:
+    phg:
+      icon: fa-dna
+      href: https://github.com/maize-genetics/phg_v2
+      aria-label: PHG Source
+
+footer:
+  structure:
+    left: acknowledgment
+  components:
+    acknowledgment: <b>rPHG2</b> is an R package developed by <a href="https://www.maizegenetics.net/">The Buckler Lab</a>
+
+home:
+  links:
+  - text: Report a bug
+    href: https://github.com/maize-genetics/rPHG2/issues
+
+

pkgdown/extra.css

@@ -0,0 +1,6 @@
+.navbar-brand {
+  font-family: 'Oswald', sans-serif; /* Change font family */
+  font-size: 20px; /* Change font size */
+  font-weight: bold; /* Make font bold */
+  color: #363636; /* Change font color to red */
+}

rphg2.Rproj

@@ -19,4 +19,4 @@ LineEndingConversion: Posix
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

tests/testthat/setup.R

@@ -18,6 +18,12 @@ getLatestReleaseUrl <- function(repo) {
 
     response <- httr::GET(apiUrl)
 
+    message("  * API total rate...............: ", response$headers$`x-ratelimit-limit`)
+    message("  * API rate limit (remaining)...: ", response$headers$`x-ratelimit-remaining`)
+    message("  * API rate limit (used)........: ", response$headers$`x-ratelimit-used`)
+    message("  * UTC Epoch time to reset......: ", response$headers$`x-ratelimit-reset`)
+
+
     # Check if the request was successful
     if (httr::http_status(response)$category != "Success") {
         stop(