Release 0.4.0 (#104)

* Update version number, update docs, add NEWS, retire version() * Use TileDB R consistently * Use packageVersion() for version tag * Simplified and tweaked .travis.yml * Export rendered notebook via docs/ * Add one more element to test matrix
TileDB-Inc · Mar 6, 2020 · 5ba4c66 · 5ba4c66
1 parent 54f531b
commit 5ba4c66
Show file tree

Hide file tree

Showing 115 changed files with 2,619 additions and 428 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -6,27 +6,25 @@ sudo: required
 services: docker
 
 env:
-  global:
-    - DOCKER_OPTS="--rm -ti -v $(pwd):/mnt -w /mnt"
-      R_BLD_OPTS="--no-build-vignettes --no-manual"
-      R_CHK_OPTS="--no-vignettes --no-manual"
   jobs:
+    - INFO="ci-r"
+      CONTAINER="tiledb/ci-r"
     - INFO="dev"
-      DOCKER_CNTR="tiledb/ci-r"
+      CONTAINER="eddelbuettel/rocker-tiledb:dev"
     - INFO="1.7.6"
-      DOCKER_CNTR="eddelbuettel/rocker-tiledb:1.7.6"
+      CONTAINER="eddelbuettel/rocker-tiledb:1.7.6"
     - INFO="1.7.5"
-      DOCKER_CNTR="eddelbuettel/rocker-tiledb:1.7.5"
+      CONTAINER="eddelbuettel/rocker-tiledb:1.7.5"
 
 before_install:
-  - docker pull ${DOCKER_CNTR}
-  - docker run ${DOCKER_OPTS} ${DOCKER_CNTR} r -p -e 'sessionInfo()'
+  - docker pull ${CONTAINER}
+  - docker run --rm -ti -v $(pwd):/mnt -w /mnt ${CONTAINER} r -p -e 'sessionInfo()'
 
 install:
-  - docker run ${DOCKER_OPTS} ${DOCKER_CNTR} R CMD build ${R_BLD_OPTS} .
+  - docker run --rm -ti -v $(pwd):/mnt -w /mnt ${CONTAINER} R CMD build --no-build-vignettes --no-manual .
 
 script:
-  - docker run ${DOCKER_OPTS} ${DOCKER_CNTR} R CMD check ${R_CHK_OPTS} tiledb_*.tar.gz
+  - docker run --rm -ti -v $(pwd):/mnt -w /mnt ${CONTAINER} R CMD check --no-vignettes --no-manual tiledb_*.tar.gz
 
 notifications:
   email:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tiledb
 Type: Package
 Title: Sparse and Dense Multidimensional Array Data Management
-Version: 0.3.1
+Version: 0.4.0
 Author: TileDB <[email protected]>
 Maintainer: TileDB <[email protected]>
 Description: The efficient multi-dimensional array management system 'TileDB' introduces a novel on-disk format that can effectively store dense and sparse array data with support for fast updates and reads. It features excellent compression, an efficient parallel I/O system which also scales well, and bindings to multiple languages.

diff --git a/NAMESPACE b/NAMESPACE
@@ -70,7 +70,6 @@ export(tiledb_stats_enable)
 export(tiledb_stats_print)
 export(tiledb_subarray)
 export(tiledb_version)
-export(version)
 exportClasses("tiledb_sparse")
 exportClasses(tiledb_array_schema)
 exportClasses(tiledb_attr)
@@ -107,5 +106,6 @@ importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,slot)
+importFrom(utils,packageVersion)
 importFrom(utils,tail)
 useDynLib(tiledb, .registration = TRUE)
diff --git a/R/Ctx.R b/R/Ctx.R
@@ -141,12 +141,12 @@ tiledb_ctx_set_tag <- function(object, key, value) {
 #' Sets default context tags
 #'
 #' @param object `tiledb_ctx` object
-#'
+#' @importFrom utils packageVersion
 tiledb_ctx_set_default_tags <- function(object) {
   stopifnot(is(object, "tiledb_ctx"))
 
   tiledb_ctx_set_tag(object, "x-tiledb-api-language", "r")
-  tiledb_ctx_set_tag(object, "x-tiledb-api-language-version", paste(version(), sep=".", collapse=""))
+  tiledb_ctx_set_tag(object, "x-tiledb-api-language-version", as.character(packageVersion("tiledb")))
   info <- Sys.info()
   tiledb_ctx_set_tag(object, "x-tiledb-api-sys-platform", paste(info["sysname"], info["release"], info["machine"], collapse=""))
 }
diff --git a/R/Version.R b/R/Version.R
@@ -1,19 +1,9 @@
 #' The version of the libtiledb library
 #'
-#' @return An named int vector c(major, minor, patch) 
+#' @return An named int vector c(major, minor, patch)
 #' @examples
 #' tiledb_version()
 #' @export
 tiledb_version <- function() {
-  libtiledb_version() 
+  libtiledb_version()
 }
-
-#' The version of the R library
-#'
-#' @return An named int vector c(major, minor, patch) 
-#' @examples
-#' version()
-#' @export
-version <- function() {
-  c(0,3,0) 
-}
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 # TileDB-R
 
-`TileDB-R` is a [R](https://www.r-project.org/) interface to the [storage engine](https://github.com/TileDB-Inc/TileDB) of [TileDB](https://tiledb.com/).
+The TileDB R package offers an [R](https://www.r-project.org/) interface to the [storage engine](https://github.com/TileDB-Inc/TileDB) of [TileDB](https://tiledb.com/).
 
 Note that the R interface to TileDB is under development, and the API is subject to change.
 
@@ -13,52 +13,47 @@ Note that the R interface to TileDB is under development, and the API is subject
 ## Quickstart
 
 TileDB needs to be installed first (from a package or from source)
-for the TileDB-R package to build and link correctly:
-  
+for the TileDB R package to build and link correctly:
+
     > install.packages("remotes")
     > library(remotes)
     > remotes::install_github("TileDB-Inc/TileDB-R")
     ...
     > library(tiledb)
     > tiledb_version()
     major minor patch
-    1     7     0 
+        1     7     6
     > help(package=tiledb)
 
 ## Installation
 
-As the `TileDB-R`package has not been published on [CRAN](https://cran.r-project.org/),
+As the TileDB R package has not been published on [CRAN](https://cran.r-project.org/),
 it must be installed from source.
 
 The most recent released version can be installed from [Github](https://github.com/TileDB-Inc/TileDB-R) using the package [remotes](https://cran.r-project.org/package=remotes).
-    
-    install.packages("remotes") 
+
+    install.packages("remotes")
     library(remotes)
     remotes::install_github("TileDB-Inc/TileDB-R")
 
 If the TileDB library is installed in a custom location, you need to pass the explicit path:
-  
+
     remotes::install_github("TileDB-Inc/TileDB-R",
         args="--configure-args='--with-tiledb=/path/to/tiledb'")
 
-Note that the TileDB-R package is developed against latest stable (`v1.7.x`) version of TileDB 
-
-Note that `install_github` will delete all temporary files upon failure. To debug build failures, clone this repository locally and run either `devtools::install("/path/to/TileDB-R")`, or create and install from a `tar.gz` as usual.
+Note that the TileDB R package is developed and tested against the latest stable (`v1.7.x`) version of TileDB, but should also build against the newest development version.
 
 ## Quick Links
 
 - [Installation](https://docs.tiledb.com/developer/installation)
 - [Quickstart](https://docs.tiledb.com/developer/quickstart)
 - [Reference Docs](https://tiledb-inc.github.io/TileDB-R/)
+- [Support](https://forum.tiledb.com/)
 
-## Compatibility
+## Copyright
 
-TileDB-R follows semantic versioning. Currently tiledb core library does not,
-so the table below references which versions are compatible.
+The TileDB R package is Copyright 2018-2020 TileDB, Inc
 
-| TileDB-R Version | TileDB Version |
-| ----------------- | -------------- |
-| 0.1.X             | 1.3.X          |
-| 0.2.X             | 1.6.X          |
-| 0.3.X             | 1.7.X          |
+## License
 
+MIT
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/documentation.html b/docs/documentation.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/reference/as.data.frame.tiledb_config.html b/docs/reference/as.data.frame.tiledb_config.html
diff --git a/docs/reference/as.vector.tiledb_config.html b/docs/reference/as.vector.tiledb_config.html
diff --git a/docs/reference/as_data_frame.html b/docs/reference/as_data_frame.html