Merge pull request #6 from psysciacc/check-folder

Check folder

inst/03_Materials/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

inst/04_Procedure/lab_notebook.csv

@@ -0,0 +1 @@
+here,is,a,lab,notebook

notes/setup.R

@@ -6,4 +6,4 @@ roxygenize()
 
 devtools::check()
 
-devtools::install_github("psysciacc/psaverse")
+devtools::install_github("psysciacc/psaverse@check-folder")

tests/testthat/test-psa_check_folder.R

@@ -0,0 +1,52 @@
+# setup
+tdir <- file.path(tempdir(), "PSA")
+if (dir.exists(tdir)) unlink(tdir, recursive = TRUE)
+dir.create(tdir, showWarnings = FALSE)
+
+
+# Create model folder to check on
+test_path <- system.file("tests", "testthat", package = "psaverse")
+file.copy(test_path, tdir, recursive = TRUE)
+test_pkg <- file.path(tdir, "testthat", "testCheckFolder")
+
+# Activate dummy package to use the function on it
+usethis::proj_activate(test_pkg)
+
+test_that("ethics", {
+  expect_no_error(psa_check_folder(folder = "ethics"))
+})
+
+test_that("power", {
+  expect_no_error(psa_check_folder(folder = "power"))
+})
+
+test_that("materials", {
+  expect_no_error(psa_check_folder(folder = "materials"))
+})
+
+test_that("procedure", {
+  expect_no_error(psa_check_folder(folder = "procedure"))
+})
+
+test_that("data", {
+  expect_no_error(psa_check_folder(folder = "data"))
+})
+
+test_that("analysis", {
+  expect_no_error(psa_check_folder(folder = "analysis"))
+})
+
+test_that("communication", {
+  expect_no_error(psa_check_folder(folder = "communication"))
+})
+
+test_that("other", {
+  expect_no_error(psa_check_folder(folder = "other"))
+})
+
+test_that("all", {
+  expect_no_error(psa_check_folder(folder = "all"))
+})
+
+# clean up
+unlink(tdir, recursive = TRUE)

tests/testthat/testCheckFolder/.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

tests/testthat/testCheckFolder/DESCRIPTION

@@ -0,0 +1,11 @@
+Package: testCheckFolder
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <[email protected]>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true

tests/testthat/testCheckFolder/NAMESPACE

@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")

tests/testthat/testCheckFolder/R/hello.R

@@ -0,0 +1,18 @@
+# Hello, world!
+#
+# This is an example function named 'hello' 
+# which prints 'Hello, world!'.
+#
+# You can learn more about package authoring with RStudio at:
+#
+#   https://r-pkgs.org
+#
+# Some useful keyboard shortcuts for package authoring:
+#
+#   Install Package:           'Ctrl + Shift + B'
+#   Check Package:             'Ctrl + Shift + E'
+#   Test Package:              'Ctrl + Shift + T'
+
+hello <- function() {
+  print("Hello, world!")
+}

tests/testthat/testCheckFolder/inst/01_Ethics/README.md

@@ -0,0 +1 @@
+Test

tests/testthat/testCheckFolder/inst/01_Ethics/lab_ethics_summary.csv

@@ -0,0 +1 @@
+Test

tests/testthat/testCheckFolder/inst/02_Power/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/02_Power/power-analysis.R

@@ -0,0 +1 @@
+Some sort of power analysis should exist. 

tests/testthat/testCheckFolder/inst/02_Power/power-analysis.Rmd

@@ -0,0 +1 @@
+Some sort of power analysis should exist. 

tests/testthat/testCheckFolder/inst/03_Materials/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/03_Materials/Text/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/03_Materials/Translation/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/04_Procedure/English/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/04_Procedure/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/04_Procedure/Translation/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/04_Procedure/Video/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/04_Procedure/lab_notebook.csv

@@ -0,0 +1 @@
+here,is,a,lab,notebook

tests/testthat/testCheckFolder/inst/05_Data/Processed Data/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/05_Data/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/05_Data/Raw Data/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/05_Data/Scripts/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/06_Analysis/Images/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/06_Analysis/Includes/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/06_Analysis/Outputs/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/06_Analysis/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/06_Analysis/Supplemental/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/07_Communication/Manuscript/tenzing.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/07_Communication/Pre-Registration/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/07_Communication/Presentations/stimuli.txt

@@ -0,0 +1 @@
+A file here to ensure the folder syncs to github.

tests/testthat/testCheckFolder/inst/07_Communication/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/inst/08_Other/README.md

@@ -0,0 +1 @@
+A readme file should exist in this folder.

tests/testthat/testCheckFolder/man/hello.Rd

@@ -0,0 +1,12 @@
+\name{hello}
+\alias{hello}
+\title{Hello, World!}
+\usage{
+hello()
+}
+\description{
+Prints 'Hello, world!'.
+}
+\examples{
+hello()
+}

tests/testthat/testCheckFolder/testCheckFolder.Rproj

@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

vignettes/psaverse.Rmd

@@ -35,18 +35,73 @@ You can update the description of the package using the `psa_update_description(
 
 ```{r eval = F}
 psa_update_description(
-    package_title = NULL,
+    package_title = "SPAML IS GREAT",
     description = NULL,
     version = NULL,
     license = NULL
 )
+
+# make sure default to null 
+
+# make sure this updates on the current project 
+# seems to update the original folder 
+# function to make sure you are in the right project 
+# make sure we aren't reloading each time 
+```
+
+You can add authors to the package for other project monitors or the lead author of the paper. 
+
+```{r eval = F}
+psa_add_author(
+   given = "Lucy",
+   family = "van Pelt",
+   role = c("aut", "cre"),
+   email = "[email protected]",
+   comment = c(ORCID = "LUCY-ORCID-ID"))
+
+# why isn't comment working 
+```
+
+## Create Folder Structure
+
+`psa_create_folder("all")` will create the entire folder structure for the package, while you can also add one at a time. 
+
+Other options: 
+
+- "ethics": creates the "01_Ethics" folder.
+- "power": creates the "02_Power" folder.
+- "materials": creates the "03_Materials" folder.
+- "procedure": creates the "04_Procedure" folder.
+- "data": creates the "05_Data" folder.
+- "analysis": creates the "06_Analysis" folder.
+- "communication": creates the "07_Communication folder.
+- "all": creates all eight main folders.
+- Any other parameter option will be added into the 08_Other folder.
+
+```{r eval = F}
+# will create all folders 
+psa_create_folder("all")
+
+# also allow people to use the "real" folder names like 01_Ethics
+psa_create_folder("cheese")
 ```
 
-## Add Dataset
+## Add Documents
+
+You can then manually move the files you need into the folder structure or use the `psa_add_documents()` function to add individual files or entire folders. 
 
 ```{r eval = F}
-psa_data(
+psa_add_documents(
+  folder = "ethics", # where should it go
+  path = "~/Downloads", # to a single file or directory
+  should_replace = FALSE, # overwrite existing files?
+  recursive = FALSE # better explain this in docs 
 )
+
+# recheck copying individual files 
+# path should allow vector of file paths like a list of PDFs
+# or a directory 
+# or single file 
 ```
 
 ## Add R Package Dependencies
@@ -58,9 +113,12 @@ psa_dependencies(
     scan_folder = "inst",
     add_package = NULL # has to be one at a time
     )
+
+# add qmd files 
+# allow for vector of packages to be added 
 ```
 
-## Add R Package to PSA GitHub
+## Add this Package to PSA GitHub
 
 First, you should confirm you have the ability to push to the PsySciAcc github organization at https://github.com/psysciacc. Please ask to be added to the team. 
 
@@ -69,3 +127,27 @@ Second, you can use the `psa_git()` function to initialize your new project as a
 ```{r eval = F}
 psa_git()
 ```
+
+## Check Package Folders
+
+This function will check that you meet the minimum requires for documentation and files for the PSA folder structure. You will receive information on what you are missing. 
+
+Options: "ethics", "power", "materials", "procedure", "data", "analysis", "communication", "all". 
+
+```{r eval = F}
+psa_check_folder(folder = "ethics")
+
+# be sure to set working directory to the project so make it a global function 
+```
+
+working folder should not be empty if so make it "."
+
+can't write the testthat (or subfolders) for CRAN, so make sure it's writing to a temp directory
+(check scienceverse)
+
+https://scienceverse.github.io/scienceverse/index.html
+https://github.com/scienceverse/scienceverse/
+
+https://github.com/debruine/booktem/blob/master/tests/testthat/test-create_book.R
+- preclean up
+- and then if stops be sure to clean up as well