Skip to content

Commit

Permalink
Merge pull request #747 from njtierney/tweaks-for-0-5-0
Browse files Browse the repository at this point in the history
Tweaks for 0 5 0
  • Loading branch information
njtierney authored Nov 10, 2024
2 parents 1092a05 + ab25df3 commit 3797d53
Show file tree
Hide file tree
Showing 145 changed files with 3,265 additions and 3,581 deletions.
6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
114 changes: 98 additions & 16 deletions codemeta.json
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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"]
}
18 changes: 13 additions & 5 deletions cran-comments.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down
28 changes: 10 additions & 18 deletions inst/CITATION
Original file line number Diff line number Diff line change
@@ -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"
)
46 changes: 43 additions & 3 deletions revdep/checks.noindex/libraries.csv
Original file line number Diff line number Diff line change
@@ -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,
Loading

0 comments on commit 3797d53

Please sign in to comment.