preparing DESCRIPTION and NEWS for release

.Rbuildignore

@@ -13,6 +13,7 @@
 ^LICENSE\.md$
 LICENSE
 ^cran-comments\.md$
+^revdep$
 
 ^logos$
 ^paper$

.gitignore

@@ -13,3 +13,6 @@ docs/*.Rmd
 docs/examples
 paper/paper.html
 inst/doc
+
+revdep/checks.noindex
+revdep/library.noindex

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: greta
 Title: Simple and Scalable Statistical Modelling in R
-Version: 0.4.3.9000
+Version: 0.4.4
 Authors@R: c(
     person("Nick", "Golding", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0001-8916-5570")),
@@ -51,6 +51,7 @@ Suggests:
     covr,
     cramer,
     DiagrammeR,
+    DiagrammeRsvg,
     extraDistr,
     fields,
     ggplot2,
@@ -62,6 +63,7 @@ Suggests:
     mvtnorm,
     rmarkdown,
     rmutil,
+    rsvg,
     spelling,
     testthat (>= 3.1.0),
     tidyverse,
@@ -73,7 +75,7 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 SystemRequirements: Python (>= 2.7.0) with header files and shared
     library; TensorFlow (v1.14; https://www.tensorflow.org/); TensorFlow
     Probability (v0.7.0; https://www.tensorflow.org/probability/)

NEWS.md

@@ -1,4 +1,8 @@
-# greta (development version)
+# greta 0.4.4
+
+## Bug fixes
+
+- Some small documentation bugs were fixed, namely the sentinel "_PACKAGE" documentation, and various small changes to correctly export S3 methods.
 
 # greta 0.4.3
 

R/inference.R

@@ -847,16 +847,16 @@ print.initials <- function(x, ...) {
 
 #' @return `opt` - a list containing the following named elements:
 #'   \itemize{
-#'    \item{`par`} {a named list of the optimal values for the greta arrays
-#'     specified in `model`}
-#'    \item{`value`} {the (unadjusted) negative log joint density of the
-#'     model at the parameters 'par'}
-#'    \item{`iterations`} {the number of iterations taken by the optimiser}
-#'    \item{`convergence`} {an integer code, 0 indicates successful
+#'    \item `par` a named list of the optimal values for the greta arrays
+#'     specified in `model`
+#'    \item `value` the (unadjusted) negative log joint density of the
+#'     model at the parameters 'par'
+#'    \item `iterations` the number of iterations taken by the optimiser
+#'    \item `convergence` an integer code, 0 indicates successful
 #'     completion, 1 indicates the iteration limit `max_iterations` had
-#'     been reached}
-#'   \item{`hessian`} {(if `hessian = TRUE`) a named list of hessian
-#'     matrices/arrays for the parameters (w.r.t. `value`)}
+#'     been reached
+#'   \item `hessian` (if `hessian = TRUE`) a named list of hessian
+#'     matrices/arrays for the parameters (w.r.t. `value`)
 #'  }
 #'
 opt <- function(model,

README.md

@@ -15,7 +15,7 @@ CRAN:
 install.packages("greta")
 ```
 
-Or install the development version of `greta` from [r-universe](https://greta-dev.r-universe.dev/ui#builds):
+Or install the development version of `greta` from [r-universe](http://greta-dev.r-universe.dev/ui/):
 
 ```r
 # Enable this universe
@@ -51,7 +51,7 @@ If these python modules aren't yet installed, when `greta` is used, it provides
 [![R-CMD-check](https://github.com/greta-dev/greta/workflows/R-CMD-check/badge.svg)](https://github.com/greta-dev/greta/actions)
 [![cran
 version](http://www.r-pkg.org/badges/version/greta)](https://CRAN.R-project.org/package=greta)
-[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/license/apache-2-0/)
 [![doi](https://zenodo.org/badge/73758247.svg)](https://zenodo.org/badge/latestdoi/73758247)
 [![joss](https://joss.theoj.org/papers/10.21105/joss.01601/status.svg)](https://joss.theoj.org/papers/10.21105/joss.01601)
 ![](logos/bottom_banner.png)

codemeta.json

@@ -7,13 +7,13 @@
   "codeRepository": "https://github.com/njtierney/greta",
   "issueTracker": "https://github.com/greta-dev/greta/issues",
   "license": "https://spdx.org/licenses/Apache-2.0",
-  "version": "0.4.3",
+  "version": "0.4.4",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.2.1 (2022-06-23)",
+  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -156,6 +156,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=DiagrammeR"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "DiagrammeRsvg",
+      "name": "DiagrammeRsvg",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=DiagrammeRsvg"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "extraDistr",
@@ -288,6 +300,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rmutil"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "rsvg",
+      "name": "rsvg",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=rsvg"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "spelling",
@@ -515,7 +539,7 @@
     },
     "SystemRequirements": "Python (>= 2.7.0) with header files and shared\n    library; TensorFlow (v1.14; https://www.tensorflow.org/); TensorFlow\n    Probability (v0.7.0; https://www.tensorflow.org/probability/)"
   },
-  "fileSize": "1313.486KB",
+  "fileSize": "2098.014KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -1,13 +1,12 @@
 ## Test environments
-* local R installation, R 4.2.1
-* ubuntu 18.04 (on github actions), R 4.2.1
+* local R installation, R 4.3.2
 * win-builder (devel)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
 
-* Days since last update: 170
+* Days since last update: 510
 
 ## revdepcheck results
 

inst/CITATION

@@ -1,8 +1,8 @@
 citHeader("To cite greta in publications use:")
 
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
   title        = "{greta}: simple and scalable statistical modelling in R",
-  author       = personList(as.person("Nick Golding")),
+  author       = c(person(given = "Nick", family = "Golding", email = "[email protected]")),
   journal      = "Journal of Open Source Software",
   year         = "2019",
   volume       = "4",

inst/WORDLIST

@@ -15,10 +15,10 @@ Inf
 Jupyter
 Lmax
 Lmin
-Maëlle
 Miniconda
 Nesterov
 NumPy
+ORCID
 OpenBUGS
 PSAT
 Poisson
@@ -31,7 +31,6 @@ TensorFlow
 TensorFlow's
 Tensorflow
 WinBUGS
-Wujciak
 XLA
 bayesplot
 cholesky
@@ -63,7 +62,6 @@ pkgdown
 poisson
 polygamma
 schoolers
-snapshotting
 softmax
 speedup
 st

revdep/README.md

@@ -0,0 +1,26 @@
+# Platform
+
+|field    |value                                                                                      |
+|:--------|:------------------------------------------------------------------------------------------|
+|version  |R version 4.3.2 (2023-10-31)                                                               |
+|os       |macOS Sonoma 14.0                                                                          |
+|system   |aarch64, darwin20                                                                          |
+|ui       |RStudio                                                                                    |
+|language |(EN)                                                                                       |
+|collate  |en_US.UTF-8                                                                                |
+|ctype    |en_US.UTF-8                                                                                |
+|tz       |Australia/Hobart                                                                           |
+|date     |2024-01-16                                                                                 |
+|rstudio  |2023.12.0+369 Ocean Storm (desktop)                                                        |
+|pandoc   |3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) |
+
+# Dependencies
+
+|package |old   |new    |Δ  |
+|:-------|:-----|:------|:--|
+|greta   |0.4.3 |0.4.4  |*  |
+|future  |NA    |1.33.1 |*  |
+|Rcpp    |NA    |1.0.12 |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

revdep/problems.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

tests/testthat/_snaps/check-m1.md

@@ -2,7 +2,7 @@
 
     Code
       check_tf_version("error")
-    Message <simpleMessage>
+    Message
       greta does not currently work with Apple Silicon (M1)
       We are working on getting this resolved ASAP, see <https://github.com/greta-dev/greta/issues/458> for current progress.FALSE