Merge pull request #97 from FredHutch/release-1.0.0

Release 1.0.0

.Rbuildignore

@@ -6,3 +6,4 @@
 ^Meta$
 CONDUCT.md
 CONTRIBUTING.md
+^\.github$

.github/.gitignore

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

.github/workflows/check-standard.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1

.gitignore

@@ -3,3 +3,4 @@
 .Rproj.user
 doc
 Meta
+inst/doc

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: VISCtemplates
 Title: Tools for writing reproducible reports at VISC
-Version: 0.3.4
+Version: 1.0.0
 Authors@R: 
     person(given = "Jimmy",
            family = "Fulp",
@@ -18,11 +18,13 @@ Description: The goal of VISCtemplates is to automate project setup provide a co
 License: GPL-3 + file LICENSE
 Depends: R (>= 3.0)
 Imports:
+    fs,
     bookdown,
     here,
     rmarkdown,
     stringr,
-    usethis
+    usethis,
+    glue
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/FredHutch/VISCtemplates

NAMESPACE

@@ -10,7 +10,9 @@ export(set_kable_warnings)
 export(set_pandoc_markup)
 export(use_visc_docs)
 export(use_visc_gitignore)
+export(use_visc_methods)
 export(use_visc_pr_template)
 export(use_visc_readme)
+export(use_visc_report)
 export(visc_pdf_document)
 export(visc_word_document)

NEWS.md

@@ -1,4 +1,19 @@
 
+# VISCtemplates 1.0.0
+
+The new release number is bumped to 1.0.0 because this version implements the structure needed for assay-specific templates.
+
+* New feature: `use_visc_report()` creates a VISC report template with assay-specific R Markdown files.
+* New vignette: a new vignette outlines how to set up a VISC analysis project (`vignette("create_a_visc_analysis_project")`).
+* Changes to the PT report README to make it easier to use.
+* Minor changes:
+    + "*.zip" added to the .gitignore template
+    + *.R template files created with `create_visc_project()` are saved to R/ in the analysis project template. 
+    + The study schema template is an R function.
+    + New prompt with `create_visc_project()` asks about the project name.
+    + Added \sloppy to .tex template to help with antigen name formatting.
+* Minor edits to template language and documentation throughout. 
+
 # VISCtemplates 0.3.4
 
 * Bug fix: updated `bibliography.bib` file to fix citation format for R Core Team citation.

R/create_visc_project.R

@@ -6,8 +6,11 @@
 #' @export
 create_visc_project <- function(path){
 
+  challenge_directory(path)
+
   # top level folder should follow VDCNNNAnalysis format
   repo_name <- basename(path)
+  challenge_visc_name(repo_name)
 
   # get "VDCNNN" if it exists
   # this is a variable that is inserted into templates
@@ -20,7 +23,7 @@ create_visc_project <- function(path){
   # create package
   usethis::create_package(
     path = path
-  ) # add check for existing package
+  )
 
   # must set active project otherwise it is <no active project>
   usethis::proj_set(path = path)
@@ -48,6 +51,41 @@ create_visc_project <- function(path){
 }
 
 
+challenge_directory <- function(path) {
+
+  path <- fs::path_expand(path)
+
+  dir_exists <- dir.exists(path)
+
+  if (dir_exists) {
+
+    continue <- usethis::ui_yeah("
+      The directory {path} already exists.
+      Would you like to continue?")
+
+    if (!continue) {
+      usethis::ui_stop("Stopping `create_visc_project()`")
+    } else if (continue) {
+      usethis::ui_warn("
+        Creating new VISC project in {path}, which already exists.
+        Be sure to check the directory for unexpected files.")
+    }
+  }
+}
+
+
+challenge_visc_name <- function(repo_name) {
+
+  continue <- usethis::ui_yeah("
+    Creating a new VISC project called {repo_name}.
+    At VISC, we use a naming convention for analysis projects, VDCnnnAnalysis,
+    where 'VDC' is the CAVD PI name, and 'nnn' is the CAVD project number.
+    Would you like to continue?")
+
+  if (!continue) {
+    usethis::ui_stop("Stopping `create_visc_project()`")
+    }
+}
 
 # Set up project with RStudio GUI ----------------------------------------------
 

R/template.R

@@ -74,17 +74,17 @@ use_project_objectives <- function(study_name) {
 
 use_group_colors <- function(study_name) {
   usethis::use_template(
-    template = "group-colors.R",
-    save_as = "docs/group-colors.R",
+    template = "group_colors.R",
+    save_as = "R/group_colors.R",
     data = list(study_name = study_name),
     package = "VISCtemplates"
   )
 }
 
 use_study_schema <- function(study_name) {
   usethis::use_template(
-    template = "study-schema.R",
-    save_as = "docs/study-schema.R",
+    template = "study_schema.R",
+    save_as = "R/study_schema.R",
     data = list(study_name = study_name),
     package = "VISCtemplates"
   )
@@ -99,6 +99,105 @@ use_bib <- function(study_name) {
   )
 }
 
+#' Use a VISC Report Template
+#'
+#' @param report_name name of the file (character)
+#' @param path path of the file within the active project
+#' @param report_type "empty", "generic", or "bama"
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' use_visc_report(report_name = "BAMA-PT-Report", path = "bama", report_type = "bama")
+#' }
+use_visc_report <- function(report_name = "PT-Report",
+                            path = ".",
+                            report_type = c("empty", "generic", "bama")) {
+
+  stopifnot(report_type %in% c("empty", "generic", "bama"))
+
+  if (report_type == "empty") {
+    rmarkdown::draft(
+      file = file.path(path, report_name),
+      template = "visc_empty",
+      package = "VISCtemplates",
+      create_dir = TRUE,
+      edit = FALSE
+      )
+    usethis::ui_done(
+      glue::glue("Creating an empty VISC report at '{{file.path(path, report_name)}}'")
+      )
+
+  } else {
+    rmarkdown::draft(
+      file = file.path(path, report_name),
+      template = "visc_report",
+      package = "VISCtemplates",
+      create_dir = TRUE,
+      edit = FALSE
+    )
+    usethis::ui_done(
+      glue::glue("Creating a VISC report at '{{file.path(path, report_name)}}'")
+    )
+    use_visc_methods(path = file.path(path, report_name), assay = report_type)
+  }
+
+
+}
+
+#' Use template files for methods sections in PT reports
+#'
+#' Creates a "methods" directory that contains 3 "child" R Markdown documents
+#'  used in PT reports: statistical-methods.Rmd, lab-methods.Rmd,
+#'  and biological-endpoints.Rmd
+#'
+#' @param assay "bama" or "generic"
+#' @param path path within the active project
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' use_visc_methods(path = "bama/BAMA-PT-Report", assay = "bama")
+#' }
+use_visc_methods <- function(path = ".", assay = c("generic", "bama")) {
+
+  pkg_ver <- utils::packageVersion("VISCtemplates")
+
+  usethis::use_directory(file.path(path, "methods"))
+
+  usethis::use_template(
+    template = file.path(
+      paste0("methods-", assay),
+      paste0(assay, "-statistical-methods.Rmd")
+      ),
+    data = list(pkg_ver = pkg_ver),
+    save_as = file.path(path, "methods", "statistical-methods.Rmd"),
+    package = "VISCtemplates"
+  )
+
+  usethis::use_template(
+    template = file.path(
+      paste0("methods-", assay),
+      paste0(assay, "-lab-methods.Rmd")
+      ),
+    data = list(pkg_ver = pkg_ver),
+    save_as = file.path(path, "methods", "lab-methods.Rmd"),
+    package = "VISCtemplates"
+  )
+
+  usethis::use_template(
+    template = file.path(
+      paste0("methods-", assay),
+      paste0(assay, "-biological-endpoints.Rmd")
+      ),
+    data = list(pkg_ver = pkg_ver),
+    save_as = file.path(path, "methods", "biological-endpoints.Rmd"),
+    package = "VISCtemplates"
+  )
+
+}
 
 #' Convert to a VISC Report PDF/LaTeX document
 #'

R/use_visc_gitignore.R

@@ -37,7 +37,8 @@ use_visc_gitignore <- function(directory = ".") {
       # files from Latex
       "*.log",
       "**/figure-latex/*.pdf",
-      "**/figure-docx/*.pdf"
+      "**/figure-docx/*.pdf",
+      "*.zip"
     ),
     directory = directory
   )