Merge pull request #25 from pepkit/dev

v0.1.1

.Rbuildignore

@@ -1,3 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
+^_pkgdown.yaml
+^docs
+^update_examples.sh

.gitignore

@@ -1,4 +1,7 @@
+inst/doc
 .Rproj.user
 .Rhistory
 .RData
-.DS_Store
+.DS_Store
+docs
+*.RProj

.travis.yml

@@ -1,8 +1,12 @@
-# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
-
 language: R
 sudo: false
 cache: packages
 warnings_are_errors: false
-before_install:
- - Rscript -e "install.packages('devtools');devtools::install_github(repo = 'pepkit/pepr',ref = 'dev');source('https://bioconductor.org/biocLite.R');biocLite('GenomicRanges');biocLite('BiocFileCache');devtools::install_github(repo = 'databio/simpleCache')"
+r_packages: devtools
+r_github_packages: 
+  - pepkit/pepr
+  - databio/simpleCache
+bioc_packages: 
+  - GenomicRanges
+  - BiocStyle
+  - BiocFileCache

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.1
+Version: 0.1.1
 Authors@R: c(person("Michal", "Stolarczyk", email = "[email protected]",role = c("aut", "cre")), 
 	person("Nathan", "Sheffield", email = "[email protected]",role = c("aut")))
 Description: A Bioconductor-oriented project management class. It wraps the
@@ -9,11 +9,15 @@ Description: A Bioconductor-oriented project management class. It wraps the
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-Depends: S4Vectors, pepr
+Depends: S4Vectors, pepr, methods
 Suggests:
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat,
+    yaml
 Enhances: BiocFileCache, simpleCache, GenomicRanges
+biocViews: DataImport, DataRepresentation
 RoxygenNote: 6.1.1
+URL: https://github.com/pepkit/BiocProject
 BugReports: https://github.com/pepkit/BiocProject
 VignetteBuilder: knitr

NAMESPACE

@@ -1,7 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.insertPEP)
+export(.updateList)
 export(BiocProject)
 exportMethods(config)
 exportMethods(getProject)
 exportMethods(is)
 exportMethods(samples)
+import(S4Vectors)
+import(methods)
+import(pepr)

NEWS.md

@@ -1,58 +1,63 @@
-# BiocProject 0.1
+# BiocProject Changelog
 
-## 2019-01-28
+## [0.1.1] - 2019-02-15
 
-## Added
+### Added
 
-* methods: `is` (overwrites this method behavior just for the class `Annotated`), `.is.project`, `samples`, `config` for signiture `Annotated`
+* passes `BiocCheck`
+* added option to specify additional arguments in the config file using a `funcArgs` subsection within the `bioconductor` section of the PEP config `yaml` file.
+
+### Changed
+
+* now, any object can be returned by the data processing function, rather than requiring objects to inherit from `Annotated`
+* when errors are encountered, BiocProject now returns a PEP (`pepr::Project`) along with the error message in a `S4Vectors::List` object
+* the `bioconductor` section of the config file now follows the Bioconductor coding style (`camelCaps`)
+
+## [0.1] - 2019-01-28
+
+### Added
+
+* methods: `is` (overwrites this method behavior just for the class `Annotated`), `.is.project`, `samples`, `config` for signature `Annotated`
 * functions: `.insertPEP` and `BiocProject` (the workhorse of the package)
 
-## Changed
+### Changed
 
 * **complete concept redesign**: no `BiocProject` class. The objects returned by the custom data reading function have to be of class `Annotated` and the `PEP` is inserted as the first element of its `metadata()` list
 
-# BiocProject 0.0.4
+## [0.0.4] - 2019-01-25
 
-## 2019-01-25
-
-## Changed
+### Changed
 
 * better custom data loading function error/warning communication
 * all exceptions are caught with `BiocProject` constructor
 * fix `.updateSubconfig(.Object@config, sp) : Subproject not found:` warning in `toProject` method
 
-# BiocProject 0.0.3
-
-## 2018-12-21
+## [0.0.3] - 2018-12-21
 
-## Changed
+### Changed
 
 * the default values for all optional arguments are `NULL`
 * change `lambda function` to `anonymous function`
 
-# BiocProject 0.0.2
+## [0.0.2] - 2018-12-01
 
-## 2018-12-01
-
-## Changed
+### Changed
 
 * the object constructor does not fail if the `pepr::Project` object is provided in the `funcArgs` arguments list
 * if the user-supplied function errors or throws a warning, appropriate messages are nicely displayed
 * errors and warnings (if any) are returned instead of the data
 * if the object constructor can't find the function file, the message is more informative
 
-# BiocProject 0.0.1
-
-## 2018-11-20
+## [0.0.1] - 2018-11-20
 
-## Added
+### Added
 
 * add `BiocProject::BiocProject` constructor function
 * add `BiocProject::getData` method to extract the data from the object
 * allow for passing additional arguments for user-provided functions in `BiocProject::BiocProject`
 * allow to use lambda functions with `func` parameter
 
-## Changed
+### Changed
 
 * make `BiocProject` class inherit from `pepr::Project` and `base::list`
 * the `initialize` method can read in the data with the provided `func`

R/constants.R

@@ -0,0 +1,14 @@
+# config section names
+# 
+# The YAML file looks like this:
+# 
+# MAIN_SECTION:
+#   FUNCTION_NAME: <name>
+#   FUNCTION_PATH: <path>
+#   FUNCTION_ARGS:
+#       <arg1>: <val1>
+#       <arg2>: <val2>
+MAIN_SECTION = "bioconductor"
+FUNCTION_ARGS = "funcArgs"
+FUNCTION_PATH = "readFunPath"
+FUNCTION_NAME = "readFunName"