Merge pull request #36 from pepkit/dev

v0.3.0

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^_pkgdown\.yml$
+^doc$
+^Meta$

.gitignore

@@ -2,3 +2,14 @@
 .Rhistory
 .RData
 .Ruserdata
+*DS_Store
+*DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+pepr.Rproj
+docs
+doc
+Meta

.travis.yml

@@ -1,6 +1,6 @@
-language: R
+language: r
+os: "linux"
 warnings_are_errors: false
-sudo: false
 cache: packages
 r_packages: devtools
 r_github_packages: 

DESCRIPTION

@@ -1,22 +1,23 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.2.2
-Date: 2019-06-21
+Version: 0.3.0
+Date: 2020-05-26
 Authors@R: c(person("Nathan", "Sheffield", email = "[email protected]",
-    role = c("aut", "cre")),person("Michal","Stolarczyk",email="mjs5kd@virginia.edu",role=c("ctb")))
-Maintainer: Nathan Sheffield <[email protected]>
+    role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre")))
+Maintainer: Michal Stolarczyk <[email protected]>
 Description: Reads standardized project configuration files into R.
 Imports:
     yaml,
     stringr,
     pryr,
-    data.table
+    data.table,
+    methods
 Suggests:
     knitr,
     testthat,
     rmarkdown
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0

NAMESPACE

@@ -1,21 +1,32 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.checkSection)
+export(.expandList)
 export(.expandPath)
+export(.getSubscript)
 export(.listifyDF)
+export(.makeAbsPath)
 export(.printNestedList)
-export(.sanitizeConfig)
 export(.strformat)
+export(Config)
 export(Project)
-export(activateSubproject)
+export(activateAmendments)
+export(checkSection)
 export(config)
 export(fetchSamples)
 export(getSample)
 export(getSubsample)
-export(listSubprojects)
-export(samples)
+export(listAmendments)
+export(makeSectionsAbsolute)
+export(sampleTable)
 exportClasses(Config)
 exportClasses(Project)
-exportMethods(checkSection)
+exportMethods("$")
+exportMethods("[")
+exportMethods("[[")
 import(pryr)
 import(stringr)
 import(yaml)
+importFrom(methods,as)
+importFrom(methods,callNextMethod)
+importFrom(methods,is)

NEWS.md

@@ -1,3 +1,21 @@
+# pepr 0.3.0 - 2020-05-26
+
+**This version introduced backwards-incompatible changes.**
+
+## Added
+
+* auto path expansion in `Config` class
+* attribute duplication functionality
+* config importing functionality
+* attribute removal functionality
+* possibility to define multi-attribute rules in attribute implication
+
+
+## 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
+
+
 # pepr 0.2.2 - 2020-01-09
 
 ## Changed
@@ -59,4 +77,4 @@
 
 ## Added
 
-* first release, includes basic [PEP](https://pepkit.github.io/) reading functions
+* first release, includes basic [PEP](https://pepkit.github.io/) reading functions