pkgdown

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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

@@ -3,3 +3,5 @@
 .Rdata
 .httr-oauth
 .DS_Store
+inst/doc
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.3.4
+Version: 0.4.0
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
@@ -10,6 +10,8 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Imports: 
@@ -18,5 +20,10 @@ Imports:
     ggplot2,
     glue,
     S7
-URL: https://github.com/jeffkimbrel/qSIP2
+URL: https://github.com/jeffkimbrel/qSIP2,
+    https://jeffkimbrel.github.io/qSIP2/
 BugReports: https://github.com/jeffkimbrel/qSIP2/issues
+VignetteBuilder: knitr
+Depends: 
+    R (>= 2.10)
+LazyData: true

R/qsip_sample_object.R

@@ -15,20 +15,20 @@
 qsip_sample_object <- S7::new_class("qsip_sample_object",
                                 properties = list(
                                   data = S7::class_data.frame,
-                                  isotope = S7::class_character,
-                                  isotopolog = S7::class_character,
+                                  isotope = S7::new_property(S7::class_character, default = "isotope"),
+                                  #isotopolog = S7::class_character,
                                   isotopolog_label = S7::class_character,
-                                  isotopolog_approach = S7::class_character,
+                                  #isotopolog_approach = S7::class_character,
                                   gradient_position = S7::new_property(S7::class_character, default = "gradient_position"),
                                   gradient_pos_density = S7::new_property(S7::class_character, default = "gradient_pos_density"),
                                   gradient_pos_amt = S7::new_property(S7::class_character, default = "gradient_pos_amt"),
                                   gradient_pos_rel_amt = S7::new_property(S7::class_character, default = "gradient_pos_rel_amt"),
                                   source_mat_id = S7::new_property(S7::class_character, default = "source_mat_id")
                                 ),
                                 validator = function(self) {
-                                  qSIP2::isotope_validation(self@data %>% pull(self@isotope))
-                                  qSIP2::gradient_pos_density_validation(self@data %>% pull(self@gradient_pos_density))
-                                  qSIP2::gradient_position_validation(self@data %>% pull(self@gradient_position))
+                                  qSIP2::isotope_validation(self@data |> dplyr::pull(self@isotope))
+                                  qSIP2::gradient_pos_density_validation(self@data |> dplyr::pull(self@gradient_pos_density))
+                                  qSIP2::gradient_position_validation(self@data |> dplyr::pull(self@gradient_position))
                                 }
 )
 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://jeffkimbrel.github.io/qSIP2/
+template:
+  bootstrap: 5
+

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/sample_data.Rmd

@@ -0,0 +1,37 @@
+---
+title: "sample_data"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{sample_data}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(qSIP2)
+```
+
+# Sample Data 
+
+The `qSIP2` package comes with a basic example tibble called `sample_data_MISIP`, and some of the columns are already formatted with proper MISIP headers. 
+
+# Make a qSIP sample data object
+
+The `qsip_sample_object` constructor builds a sample data object from a dataframe. 
+
+```{r}
+qdf = qsip_sample_object(sample_data_MISIP)
+```
+
+And that's that, for now.
+
+