Merge pull request #51 from pepkit/dev

Release 0.5.1

Author: nsheff

.Rbuildignore

@@ -10,4 +10,5 @@
 
 CNAME
 test.sh
-.github
+.github
+^cran-comments\.md$

.github/workflows/R-CMD-check.yml

@@ -22,7 +22,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest, r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

.gitignore

@@ -14,4 +14,5 @@ docs
 doc
 Meta
 pepr.Rcheck/
-pepr_*.tar.gz
+pepr_*.tar.gz
+cran-comments.md

DESCRIPTION

@@ -1,31 +1,31 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.5.0
-Date: 2023-11-16
+Version: 0.6.0
+Date: 2026-02-27
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cph","cre")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut")))
 Maintainer: Nathan Sheffield <nathan@code.databio.org>
-Description: A PEP, or Portable Encapsulated Project, is a dataset that 
+Description: A PEP, or Portable Encapsulated Project, is a dataset that
     subscribes to the PEP structure for organizing metadata. It is written using
-    a simple YAML + CSV format, it is your one-stop solution to metadata 
-    management across data analysis environments. This package reads this 
-    standardized project configuration structure into R. 
+    a simple YAML + CSV format, it is your one-stop solution to metadata
+    management across data analysis environments. This package reads this
+    standardized project configuration structure into R.
     Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.
 Imports:
     yaml,
     stringr,
-    pryr,
     data.table,
     methods,
-    RCurl
+    RCurl,
+    httr2
 Suggests:
     knitr,
-    testthat,
+    testthat (>= 3.1.2),
     rmarkdown,
     curl
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
-BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 7.2.3
+BugReports: https://github.com/pepkit/pepr/issues
+RoxygenNote: 7.3.3
 Encoding: UTF-8

NAMESPACE

@@ -18,14 +18,17 @@ export(getSample)
 export(getSubsample)
 export(listAmendments)
 export(makeSectionsAbsolute)
+export(pullProject)
 export(sampleTable)
+export(saveJWT)
+export(saveProject)
 exportClasses(Config)
 exportClasses(Project)
 exportMethods("$")
 exportMethods("[")
 exportMethods("[[")
 import(RCurl)
-import(pryr)
+import(httr2)
 import(stringr)
 import(yaml)
 importFrom(methods,as)

NEWS.md

@@ -1,3 +1,28 @@
+# pepr 0.6.0 - 2026-02-27
+
+## Added
+
+* `pullProject()` to fetch PEPs from PEPhub API via registry paths (e.g., `databio/example:default`)
+* `saveProject()` to write a Project object to local files (config YAML + sample CSVs)
+* `saveJWT()` to store an authentication token for private PEPs
+* PEPhub integration vignette examples in Getting Started guide
+
+## Changed
+
+* Replaced `httr` with `httr2` for PEPhub API calls
+* Replaced `tidyr` dependency with base R for subsample unnesting
+* Added mocked tests for PEPhub API (CRAN-compatible)
+* Graceful error handling when PEPhub API is unreachable
+
+# pepr 0.5.1 - 2026-02-27
+
+## Changed
+
+* Removed dependency on archived `pryr` package; replaced `pryr::partial()` with base R anonymous functions
+* Fixed BugReports URL in DESCRIPTION
+* Updated all pep.databio.org URLs to current paths
+* Removed codecov badge from README
+
 # pepr 0.5.0 - 2023-11-16
 
 ## Fixed
@@ -55,7 +80,7 @@
 
 ## Changed
 
-* **project configuration file to follow [PEP2.0.0 specification](http://pep.databio.org/en/2.0.0/specification/).** Browse the specification for changes related to config format
+* **project configuration file to follow [PEP2.0.0 specification](https://pep.databio.org/spec/specification/).** Browse the specification for changes related to config format
 
 
 # pepr 0.2.2 - 2020-01-09

R/config.R

@@ -26,6 +26,11 @@ setMethod("initialize", "Config", function(.Object, data) {
 #' @export
 #' @rdname Config-class
 Config = function(file, amendments = NULL) {
+  ### if the config from the Project constructor is a list and not a filepath, it is from a PEP fetched from PEPhub
+  if (typeof(file) == 'list') {
+    config = methods::new("Config", data = file)
+    return(config)
+  }
   message("Loading config file: ", file)
   cfg_data = .loadConfig(filename = file, amendments = amendments)
   config = methods::new("Config", data = cfg_data)
@@ -58,7 +63,7 @@ setMethod(
 #' .expandList(x)
 #' @export
 #' @keywords internal
-.expandList <- function(x) {
+.expandList = function(x) {
   if (is.list(x))
     return(lapply(x, .expandList))
   if (length(x) > 1)
@@ -81,7 +86,7 @@ setMethod(
 #' .getSubscript(l, 1) == .getSubscript(l, "a")
 #' @export
 #' @keywords internal
-.getSubscript <- function(lst, i) {
+.getSubscript = function(lst, i) {
   if (is.character(i))
     return(grep(paste0("^", i, "$"), names(lst)))
   return(i)
@@ -135,7 +140,7 @@ setMethod("[[", "Config", function(x, i) {
 })
 
 
-.DollarNames.Config <- function(x, pattern = "")
+.DollarNames.Config = function(x, pattern = "")
   grep(paste0("^", pattern), grep(names(x), value = TRUE))
 
 #' @rdname select-config
@@ -170,7 +175,7 @@ setMethod(
   ),
   definition = function(object, sections, cfgPath) {
     # Enable creation of absolute path using given parent folder path.
-    absViaParent = pryr::partial(.makeAbsPath, parent = dirname(cfgPath))
+    absViaParent = function(x) .makeAbsPath(x, parent = dirname(cfgPath))
     for (section in sections) {
       if (section %in% names(object))
         object[[section]] = absViaParent(object[[section]])
@@ -297,7 +302,7 @@ setMethod(
   # or for user information when the Project is created, where message
   # is preferred
   if (!style == "message") {
-    printFun = pryr::partial(cat, fill = T)
+    printFun = function(...) cat(..., fill = TRUE)
   } else{
     printFun = message
   }

R/constants.R

@@ -20,4 +20,5 @@ CFG_DUPLICATE_KEY = "duplicate"
 CFG_REMOVE_KEY = "remove"
 CFG_LOOPER_KEY = "looper"
 SAMPLE_NAME_ATTR = "sample_name"
-SUBSAMPLE_NAME_ATTR = "subsample_name"
+SUBSAMPLE_NAME_ATTR = "subsample_name"
+BASE_URL = "https://pephub-api.databio.org/api/v1/"

R/pepr.R

@@ -7,7 +7,7 @@
 #' @author Michal Stolarczyk, Nathan Sheffield
 #' @import yaml
 #' @import stringr
-#' @import pryr
+#' @import httr2
 #'
 #' @references 
 #' GitHub: \url{https://github.com/pepkit/pepr}, Documentation: \url{https://code.databio.org/pepr/}