Tweaks for 0 5 0

DESCRIPTION

@@ -84,9 +84,9 @@ Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-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/)
+SystemRequirements: Python (>= 3.7.0) with header files and shared
+    library; TensorFlow (>= v2.0.0; https://www.tensorflow.org/); TensorFlow
+    Probability (v0.8.0; https://www.tensorflow.org/probability/)
 Collate:
     'package.R'
     'utils.R'

codemeta.json

@@ -4,16 +4,17 @@
   "identifier": "greta",
   "description": "Write statistical models in R and fit them by MCMC and optimisation on CPUs and GPUs, using Google 'TensorFlow'. greta lets you write your own model like in BUGS, JAGS and Stan, except that you write models right in R, it scales well to massive datasets, and it’s easy to extend and build on. See the website for more information, including tutorials, examples, package documentation, and the greta forum.",
   "name": "greta: Simple and Scalable Statistical Modelling in R",
-  "codeRepository": "https://github.com/njtierney/greta",
+  "relatedLink": ["https://greta-stats.org", "https://CRAN.R-project.org/package=greta"],
+  "codeRepository": "https://github.com/greta-dev/greta",
   "issueTracker": "https://github.com/greta-dev/greta/issues",
   "license": "https://spdx.org/licenses/Apache-2.0",
-  "version": "0.4.4",
+  "version": "0.5.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -156,6 +157,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=DiagrammeR"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "dplyr",
+      "name": "dplyr",
+      "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=dplyr"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "DiagrammeRsvg",
@@ -276,6 +289,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=mvtnorm"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "purrr",
+      "name": "purrr",
+      "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=purrr"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -339,15 +364,27 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "tidyverse",
-      "name": "tidyverse",
+      "identifier": "tibble",
+      "name": "tibble",
+      "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=tibble"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "tidyr",
+      "name": "tidyr",
       "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=tidyverse"
+      "sameAs": "https://CRAN.R-project.org/package=tidyr"
     },
     {
       "@type": "SoftwareApplication",
@@ -372,14 +409,26 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=withr"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "rstudioapi",
+      "name": "rstudioapi",
+      "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=rstudioapi"
     }
   ],
   "softwareRequirements": {
     "1": {
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
-      "version": ">= 3.1.0"
+      "version": ">= 4.1.0"
     },
     "2": {
       "@type": "SoftwareApplication",
@@ -409,7 +458,7 @@
       "@type": "SoftwareApplication",
       "identifier": "cli",
       "name": "cli",
-      "version": ">= 3.0.0",
+      "version": ">= 3.4.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -513,10 +562,22 @@
       "sameAs": "https://CRAN.R-project.org/package=reticulate"
     },
     "13": {
+      "@type": "SoftwareApplication",
+      "identifier": "rlang",
+      "name": "rlang",
+      "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=rlang"
+    },
+    "14": {
       "@type": "SoftwareApplication",
       "identifier": "tensorflow",
       "name": "tensorflow",
-      "version": ">= 2.7.0",
+      "version": "== 2.16.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -525,7 +586,29 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tensorflow"
     },
-    "14": {
+    "15": {
+      "@type": "SoftwareApplication",
+      "identifier": "tools",
+      "name": "tools"
+    },
+    "16": {
+      "@type": "SoftwareApplication",
+      "identifier": "utils",
+      "name": "utils"
+    },
+    "17": {
+      "@type": "SoftwareApplication",
+      "identifier": "whisker",
+      "name": "whisker",
+      "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=whisker"
+    },
+    "18": {
       "@type": "SoftwareApplication",
       "identifier": "yesno",
       "name": "yesno",
@@ -537,9 +620,9 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=yesno"
     },
-    "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/)"
+    "SystemRequirements": "Python (>= 3.7.0) with header files and shared\n    library; TensorFlow (>= v2.0.0; https://www.tensorflow.org/); TensorFlow\n    Probability (v0.8.0; https://www.tensorflow.org/probability/)"
   },
-  "fileSize": "2098.014KB",
+  "fileSize": "1625.784KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -569,8 +652,7 @@
       }
     }
   ],
-  "relatedLink": "https://greta-stats.org",
-  "releaseNotes": "https://github.com/njtierney/greta/blob/master/NEWS.md",
-  "readme": "https://github.com/njtierney/greta/blob/master/README.md",
-  "contIntegration": ["https://app.codecov.io/gh/greta-dev/greta?branch=master", "https://github.com/greta-dev/greta/actions"]
+  "releaseNotes": "https://github.com/greta-dev/greta/blob/master/NEWS.md",
+  "readme": "https://github.com/greta-dev/greta/blob/master/README.md",
+  "contIntegration": ["https://github.com/greta-dev/greta/actions", "https://app.codecov.io/gh/greta-dev/greta?branch=master"]
 }

cran-comments.md

@@ -1,20 +1,28 @@
 ## Test environments
-* local R installation, R 4.3.3
+* local R installation, R 4.4.2
 * win-builder (devel)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 1 notes
 
-* Days since last update: 38
+> Found the following (possibly) invalid URLs:
+  URL: http://www.phidot.org/software/mark/docs/book/
+    From: inst/doc/example_models.html
+    Status: 403
+    Message: Forbidden
+
+We could not find an issue with this link, or an alternative link.
+
+* Days since last update: 244 days
 
 ## Submission notes
 
-This release is due to a bug we discovered with trailing commas from the `glue` package (https://github.com/tidyverse/glue/issues/320). It is a very small change, but it is very critical. We have also 
+This release is a substantial overhaul of the internals of greta to migrate the internals from tensorflow 1 to tensorflow 2.
 
 ## revdepcheck results
 
-We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 1 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

inst/CITATION

@@ -1,19 +1,11 @@
-citHeader("To cite greta in publications use:")
-
-citEntry(entry = "Article",
-  title        = "{greta}: simple and scalable statistical modelling in R",
-  author       = personList(as.person("Nick Golding")),
-  journal      = "Journal of Open Source Software",
-  year         = "2019",
-  volume       = "4",
-  number       = "40",
-  pages        = "1601",
-  url          = "http://dx.doi.org/10.21105/joss.01601",
-  doi          = "10.21105/joss.01601",
-
-  textVersion  =
-  paste("Nick Golding (2019).",
-        "greta: simple and scalable statistical modelling in R.",
-        "Journal of Open Source Software, 4(40), 1601.",
-        "URL http://dx.doi.org/10.21105/joss.01601.")
+bibentry(
+  bibtype  = "Article",
+  title    = "{greta}: simple and scalable statistical modelling in R",
+  author   = "Nick Golding",
+  journal  = "Journal of Open Source Software",
+  year     = 2019,
+  volume   = 4,
+  number   = 40,
+  pages    = 1601,
+  doi      = "10.21105/joss.01601"
 )

revdep/checks.noindex/libraries.csv

@@ -1,4 +1,44 @@
 package,old,new,delta
-greta,0.4.3,0.4.4,*
-future,NA,1.33.1,*
-Rcpp,NA,1.0.12,*
+greta,0.4.5,0.5.0,*
+abind,1.4-8,1.4-8,
+backports,1.5.0,1.5.0,
+base64enc,0.1-3,0.1-3,
+callr,3.7.6,3.7.6,
+cli,3.6.3,3.6.3,
+coda,0.19-4.1,0.19-4.1,
+config,0.3.2,0.3.2,
+crayon,1.5.3,1.5.3,
+digest,0.6.37,0.6.37,
+future,1.34.0,1.34.0,
+globals,0.16.3,0.16.3,
+glue,1.8.0,1.8.0,
+here,1.0.1,1.0.1,
+hms,1.1.3,1.1.3,
+jsonlite,1.8.9,1.8.9,
+lifecycle,1.0.4,1.0.4,
+listenv,0.9.1,0.9.1,
+magrittr,2.0.3,2.0.3,
+parallelly,1.38.0,1.38.0,
+pkgconfig,2.0.3,2.0.3,
+png,0.1-8,0.1-8,
+prettyunits,1.2.0,1.2.0,
+processx,3.8.4,3.8.4,
+progress,1.2.3,1.2.3,
+ps,1.8.1,1.8.1,
+R6,2.5.1,2.5.1,
+rappdirs,0.3.3,0.3.3,
+Rcpp,1.0.13-1,1.0.13-1,
+RcppTOML,0.2.2,0.2.2,
+reticulate,1.39.0,1.39.0,
+rlang,1.1.4,1.1.4,
+rprojroot,2.0.4,2.0.4,
+rstudioapi,0.17.1,0.17.1,
+tensorflow,2.16.0,2.16.0,
+tfautograph,0.3.2,0.3.2,
+tfruns,1.5.3,1.5.3,
+tidyselect,1.2.1,1.2.1,
+vctrs,0.6.5,0.6.5,
+whisker,0.4.1,0.4.1,
+withr,3.0.2,3.0.2,
+yaml,2.3.10,2.3.10,
+yesno,0.1.3,0.1.3,