Merge pull request #11 from pepkit/dev

Release 0.0.4

Author: nsheff

.Rbuildignore

@@ -1,4 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
-^_pkgdown\.yml$
+^_pkgdown\.yml$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.0.3
+Version: 0.0.4
 Date: 2017-08-09
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cre")),person("Michal","Stolarczyk",email="mjs5kd@virginia.edu",role=c("ctb")))
@@ -17,5 +17,6 @@ Suggests:
     testthat,
     rmarkdown
 VignetteBuilder: knitr
-License: GPL-3
+License: BSD_2_clause + file LICENSE
+BugReports: https://github.com/pepkit/pepr
 RoxygenNote: 6.1.0

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2018
+COPYRIGHT HOLDER: Nathan Sheffield

NAMESPACE

@@ -1,19 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.expandPath)
+export(.printNestedList)
+export(.strformat)
 export(Project)
-export(activateSubproject)
-export(assemblyByOrganism)
-export(expandPath)
+export(config)
+export(getSample)
+export(getSubsample)
 export(listSubprojects)
-export(listifyDF)
-export(loadConfig)
-export(printNestedList)
-export(strformat)
+export(samples)
 exportClasses(Config)
 exportClasses(Project)
-exportMethods(config)
-exportMethods(getSubsample)
-exportMethods(samples)
 import(pryr)
 import(stringr)
 import(yaml)

NEWS.md

@@ -0,0 +1,44 @@
+# pepr 0.0.4
+
+## TBA
+
+## New Functionalites
+
+## Changes
+
+* change the `Project` object construction, the subproject can be activated at construction time
+* change `implied/derived_columns` to `implied/derived_attributes`. Backwards compatible
+* change `constants` to `constantAttributes`. Backwards compatible
+	
+## Bug Fixes
+
+* fix `expandPath()` function, add error when environment variable not found
+
+
+# pepr 0.0.3
+
+## 2018-09-12
+
+## New Functionalities
+
+* add `derived_columns` functionality
+* add `implied_columns` functionality
+* add `subannotation` functionality
+	
+## Changes
+
+## Bug Fixes
+
+
+# pepr 0.0.2 
+
+## 2018-09-06
+
+## New Functionalites
+
+* first release, includes basic [PEP](https://pepkit.github.io/) reading functions
+
+## Changes
+
+## Bug Fixes
+