Merge pull request #32 from databio/dev

Release PR for v 0.4.0

Author: nsheff

.Rbuildignore

@@ -3,4 +3,6 @@
 ^\.travis\.yml$
 ^cran-comments.md$
 ^CONDUCT\.md$
-^paper$
+^paper$
+.github
+^_pkgdown\.yaml$

.github/CONTRIBUTING.md

@@ -0,0 +1,20 @@
+# CONTRIBUTING #
+
+### Please contribute!
+
+We love collaboration.
+
+### Bugs?
+
+* Submit an issue on the [Issues page](https://github.com/databio/simpleCache/issues)
+
+### Code contributions
+
+* Fork this repo to your Github account
+* Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/databio/simpleCache.git`
+* Make sure to track progress upstream (i.e., on our version of `simpleCache` at `databio/simpleCache`) by doing `git remote add upstream https://github.com/databio/simpleCache.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
+* Make your changes (bonus points for making changes on a new feature branch)
+* Push up to your account
+* Submit a pull request to home base (likely master branch, but check to make sure) at `databio/simpleCache`
+
+### Thanks for contributing!

.github/issue_template.md

@@ -0,0 +1,8 @@
+<!-- If this issue relates to usage of the package, whether a question, bug or similar, along with your query, please paste your devtools::session_info() or sessionInfo() into the code block below, AND include a reproducible example. If not, delete all this and proceed :) -->
+
+<details> <summary><strong>Session Info</strong></summary>
+
+```r
+
+```
+</details>

.github/pull_request_template.md

@@ -0,0 +1,16 @@
+<!--- Provide a general summary of your changes in the Title above -->
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- if this closes an issue make sure include e.g., "fix #4"
+or similar - or if just relates to an issue make sure to mention
+it like "#4" -->
+
+## Example
+<!--- if introducing a new feature or changing behavior of existing
+methods/functions, include an example if possible to do in brief form -->
+
+<!--- Did you remember to include tests? Unless you're just changing
+grammar, please include new tests for your change -->

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: simpleCache
-Version: 0.3.1
+Version: 0.4.0
 Date: 2017-08-21
 Title: Simply Caching R Objects
 Description: Provides intuitive functions for caching R objects, encouraging
@@ -13,14 +13,13 @@ Description: Provides intuitive functions for caching R objects, encouraging
 Authors@R: c(person("VP", "Nagraj", email = "[email protected]", role =
     c("aut")), person("Nathan", "Sheffield", email = "[email protected]",
     role = c("aut", "cre")))
-Maintainer: Nathan Sheffield <[email protected]>
 Suggests:
     knitr,
     testthat
 Enhances: batchtools
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 Encoding: UTF-8
-URL: http://www.github.com/databio/simpleCache
-BugReports: http://www.github.com/databio/simpleCache
+URL: https://www.github.com/databio/simpleCache
+BugReports: https://www.github.com/databio/simpleCache
 RoxygenNote: 6.0.1.9000

NAMESPACE

@@ -10,7 +10,7 @@ export(setCacheDir)
 export(setSharedCacheDir)
 export(simpleCache)
 export(simpleCacheGlobal)
+export(simpleCacheOptions)
 export(simpleCacheShared)
 export(simpleCacheSharedGlobal)
 export(storeCache)
-export(viewCacheDirs)

NEWS

@@ -1,17 +1,31 @@
 # Change log
 All notable changes to this project will be documented in this file.
 
+## [0.4.0] -- Unreleased
+
+	- adds a lifespan arg to simpleCache() to create auto-expiring caches
+	- remove unnecessary parse argument to simpleCache()
+	- viewCacheDirs() renamed to simpleCacheOptions()
+	
+## [0.3.1] -- 2017-08-21
+
+	- fixed a bug in unit tests that left behind a test cache in user home dir.
+	- changes cache building to happen in parent.frame()
+	- repaired vignette so R code is displayed properly
+	- added deleteCaches() function and docs
+	- reduced size of unit test cache for speed increase
+
 ## [0.3.0] -- 2017-08-21
 
-	- Switched default cache dir to tempdir()
+	- switched default cache dir to tempdir()
 	- changed availCaches() to listCaches()
-	- changes cache building to happen in parent.frame(), so that any loaded
+	- changes cache building to happen in globalenv(), so that any loaded
 	  packages are available for cache building
 
 
 ## [0.2.1] -- 2017-07-30
 
-	- Added examples
+	- added examples
 
 ## [0.2.0] -- 2017-07-30
 
@@ -20,4 +34,4 @@ All notable changes to this project will be documented in this file.
 
 ## [0.0.1]
 
-	- Long-term stable version
+	- long-term stable version

R/cacheDirectories.R

@@ -6,7 +6,7 @@
 # caches.
 
 #' Sets a global variable specifying the default cache directory for
-#' simpleCache() calls.
+#' \code{\link{simpleCache}} calls.
 #'
 #' @param cacheDir Directory where caches should be stored
 #' @export
@@ -19,7 +19,7 @@ setCacheDir = function(cacheDir) {
 #' Set shared cache directory
 #'
 #' Sets global variable specifying the default cache directory for
-#' simpleCacheShared() calls; this function is simply a helper alias for caching
+#' \code{\link{simpleCacheShared}} calls; this function is simply a helper alias for caching
 #' results that will be used across projects.
 #'
 #' @param sharedCacheDir Directory where shared caches should be stored
@@ -36,11 +36,11 @@ setCacheBuildDir = function(cacheBuildDir) {
 	options(RBUILD.DIR=cacheBuildDir)
 }
 
-#' View cache directories
+#' View simpleCache options
 #'
-#' Views cache directory global variables
+#' Views simpleCache global variables
 #' @export
-viewCacheDirs = function() {
+simpleCacheOptions = function() {
 	message("RESOURCES.RCACHE:\t", getOption("RESOURCES.RCACHE"))
 	message("RCACHE.DIR:\t", getOption("RCACHE.DIR"))
 	message("RBUILD.DIR:\t", getOption("RBUILD.DIR"))
@@ -59,7 +59,7 @@ addCacheSearchEnvironment = function(addEnv) {
 	options(SIMPLECACHE.ENV=append(addEnv, getOption("SIMPLECACHE.ENV")))
 }
 
-#' Sets global option of cache search environments to NULL.
+#' Sets global option of cache search environments to \code{NULL}.
 #' 
 #' @export
 resetCacheSearchEnvironment = function() {

R/loadCaches.R

@@ -4,15 +4,17 @@
 #' for stuff you already cached previously, so it won't build any caches.
 #'
 #' @param cacheNames Vector of caches to load.
+#' @param loadEnvir Environment into which to load each cache.
 #' @param ... Additional parameters passed to simpleCache.
 #' @export
 #' @example
 #' R/examples/example.R
-loadCaches = function(cacheNames, ...) {
+loadCaches = function(cacheNames, loadEnvir=NULL, ...) {
+  if (is.null(loadEnvir)) { loadEnvir = parent.frame(n=2) }
 	for (i in 1:length(cacheNames)) {
 		# By default, load these caches into the environment that
 		# calls loadCaches (which is the grandparent, n=2, of the call to	
 		# simpleCache.
-		simpleCache(cacheNames[i], loadEnvir=parent.frame(n=2), ...)
+		simpleCache(cacheNames[i], loadEnvir=loadEnvir, ...)
 	}
 }

R/sharedCaches.R

@@ -8,7 +8,7 @@
 #' (instead of the typical default PROJECT directory)
 
 #' 
-#' @param ... Parameters passed to simpleCache().
+#' @param ... Parameters passed to \code{\link{simpleCache}}.
 #' @export
 simpleCacheShared = function(...) {
 	# Since this is a function calling this, I have to set the loadEnvir here,
@@ -22,15 +22,15 @@ simpleCacheShared = function(...) {
 #' simpleCache normally loads variables into the calling environment; this
 #' ensures that the variables are loaded in the global environment.
 #'
-#' @param ... Parameters passed to simpleCache().
+#' @param ... Parameters passed to \code{\link{simpleCache}}.
 #' @export
 simpleCacheGlobal = function(...) {
 	simpleCache(..., loadEnvir=globalenv())
 }
 
 #' Helper alias for loading shared caches into the global environment.
 #' 
-#' @param ... Parameters passed to simpleCache().
+#' @param ... Parameters passed to \code{\link{simpleCache}}.
 #' @export
 simpleCacheSharedGlobal = function(...) {
 	simpleCache(..., cacheDir=getOption("RESOURCES.RCACHE"), loadEnvir=globalenv())