diff --git a/DESCRIPTION b/DESCRIPTION index 8ae59f4..76370d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: greta.gp Title: Gaussian Process Modelling in 'greta' -Version: 0.2.2.9000 +Version: 0.2.3 Authors@R: c( person( given = "Nick", @@ -23,16 +23,18 @@ Authors@R: c( comment = c(ORCID = "https://orcid.org/0000-0003-1460-8722") ) ) -Description: Provides a syntax to create and combine Gaussian process kernels - in 'greta'. You can then them to define either full rank or sparse Gaussian - processes. This is an extension to the 'greta' software, Golding (2019) - . +Description: Provides a syntax to create and combine Gaussian process kernels + in 'greta'. You can then use these kernels to define either full rank or + sparse Gaussian processes, and project a fitted process to new coordinates. + This lets you include Gaussian process components in the statistical models + you write with 'greta'. This is an extension to the 'greta' software, Golding + (2019) . License: Apache License (>= 2) URL: https://github.com/greta-dev/greta.gp, https://greta-dev.github.io/greta.gp/ BugReports: https://github.com/greta-dev/greta.gp/issues Depends: - greta (>= 0.5.0), + greta (>= 0.6.0), R (>= 4.1.0) Imports: cli, @@ -48,11 +50,11 @@ Suggests: VignetteBuilder: knitr Config/testthat/edition: 3 +Config/Needs/website: greta-dev/greta.pkgdown Encoding: UTF-8 Language: en-GB -LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 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/) +Config/roxygen2/version: 8.0.0 diff --git a/NEWS.md b/NEWS.md index 02f166d..9b78be2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,15 @@ # greta.gp (development version) +# greta.gp 0.2.3 + +* Resubmission to CRAN. `greta.gp` was archived in September 2025 as a + consequence of its dependency, `greta`, being archived. `greta` returned to + CRAN as version 0.6.0, and this release restores `greta.gp`. +* Now depends on `greta` version 0.6.0 or above. +* Fixed a grammatical error in the package `Description`. +* Fixed the r-universe installation instructions in the README, which referred + to the wrong package. + # greta.gp 0.2.2 * Add "rlang" to package imports. diff --git a/R/gp.R b/R/gp.R index 0fddc0a..6c4bf50 100644 --- a/R/gp.R +++ b/R/gp.R @@ -21,9 +21,9 @@ #' one or more Gaussian processes #' #' @details `gp()` returns a greta array representing the values of the -#' Gaussian process(es) evaluated at `x`. This Gaussian process can be -#' made sparse (via a reduced-rank representation of the covariance) by -#' providing an additional set of inducing point coordinates `inducing`. +#' Gaussian process (or processes) evaluated at `x`. This Gaussian process +#' can be made sparse (via a reduced-rank representation of the covariance) +#' by providing an additional set of inducing point coordinates `inducing`. #' `project()` evaluates the values of an existing Gaussian process #' (created with `gp()`) to new data. #' diff --git a/README.Rmd b/README.Rmd index 34e4c09..badad3f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,7 @@ set.seed(1) [![R-CMD-check](https://github.com/greta-dev/greta.gp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/greta-dev/greta.gp/actions/workflows/R-CMD-check.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/greta.gp)](https://CRAN.R-project.org/package=greta.gp) -[![codecov](https://codecov.io/gh/greta-dev/greta.gp/graph/badge.svg?token=sDr01k2p2r)](https://codecov.io/gh/greta-dev/greta.gp) +[![Codecov test coverage](https://codecov.io/gh/greta-dev/greta.gp/graph/badge.svg?token=sDr01k2p2r)](https://app.codecov.io/gh/greta-dev/greta.gp) `greta.gp` extends greta to let you define Gaussian processes as part of your model. It provides a syntax to create and combine GP kernels, and use them to define either full rank or sparse Gaussian processes. @@ -33,7 +33,7 @@ You can install the current release version of `greta.gp` from CRAN: install.packages("greta.gp") ``` -Or install the development version of `greta.dynamics` from [r-universe](http://greta-dev.r-universe.dev/): +Or install the development version of `greta.gp` from [r-universe](https://greta-dev.r-universe.dev/): ```r install.packages("greta.gp", repos = "https://greta-dev.r-universe.dev") diff --git a/README.md b/README.md index 0b95094..005c9ca 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,8 @@ [![R-CMD-check](https://github.com/greta-dev/greta.gp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/greta-dev/greta.gp/actions/workflows/R-CMD-check.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/greta.gp)](https://CRAN.R-project.org/package=greta.gp) -[![codecov](https://codecov.io/gh/greta-dev/greta.gp/graph/badge.svg?token=sDr01k2p2r)](https://codecov.io/gh/greta-dev/greta.gp) +[![Codecov test +coverage](https://codecov.io/gh/greta-dev/greta.gp/graph/badge.svg?token=sDr01k2p2r)](https://app.codecov.io/gh/greta-dev/greta.gp) `greta.gp` extends greta to let you define Gaussian processes as part of @@ -23,8 +24,8 @@ You can install the current release version of `greta.gp` from CRAN: install.packages("greta.gp") ``` -Or install the development version of `greta.dynamics` from -[r-universe](http://greta-dev.r-universe.dev/): +Or install the development version of `greta.gp` from +[r-universe](https://greta-dev.r-universe.dev/): ``` r install.packages("greta.gp", repos = "https://greta-dev.r-universe.dev") @@ -91,7 +92,7 @@ for (i in 1:200) { } ``` - + ## Code of Conduct diff --git a/_pkgdown.yml b/_pkgdown.yml index 4b72d47..31ae55a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,58 @@ url: https://greta-dev.github.io/greta.gp/ + +development: + mode: auto + template: + package: greta.pkgdown bootstrap: 5 + # The shared template defaults to `man/figures/name_icon_on_purple.png`, + # which greta.gp does not ship. The image is served from pkgdown/assets/ + # instead, so it is not added to the package tarball. + opengraph: + image: + src: name_icon_on_purple.png + alt: "greta.gp" + +home: + sidebar: false + title: greta.gp — Gaussian process modelling in greta + description: > + greta.gp extends greta to let you define Gaussian processes as part of + your model, with a syntax to create and combine GP kernels. + +navbar: + structure: + left: [get-started, reference, news] + components: + get-started: + text: get started + href: articles/getting-started.html + reference: + text: docs + href: reference/index.html + +reference: + - title: Gaussian process kernels + desc: > + Create and combine covariance functions (kernels) to describe the + structure of a Gaussian process. + contents: + - kernels + + - title: Gaussian processes + desc: > + Define full rank or sparse Gaussian processes from kernels, and project + a fitted process to new coordinates. + contents: + - gp + - project + + - title: Package + contents: + - greta.gp-package +articles: + - title: Get started + contents: + - getting-started diff --git a/cran-comments.md b/cran-comments.md index 1c6d92c..ec2240e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,12 +1,47 @@ ## Test environments -* local R installation, R 4.4.2 +* local macOS install, R 4.6.1 * win-builder (devel) ## R CMD check results -0 errors | 0 warnings | 0 notes +0 errors | 0 warnings | 1 note + +The one NOTE is the expected archival notice: + +``` +* checking CRAN incoming feasibility ... NOTE +Maintainer: 'Nicholas Tierney ' +New submission +Package was archived on CRAN +CRAN repository db overrides: + X-CRAN-Comment: Archived on 2025-09-20 as requires archived package + 'greta'. +``` ## Submission notes -* Submitted this release to address rlang import issue +This is a resubmission of a previously archived package. + +`greta.gp` was archived from CRAN on 2025-09-20 as a consequence of its +dependency, `greta`, being archived. `greta` has since been fixed and returned +to CRAN as version 0.6.0. This release of `greta.gp` depends on +`greta` (>= 0.6.0) and has been checked against it, so the reason for the +archival no longer applies. + +The tests and examples require Python, TensorFlow and TensorFlow Probability, +which are not available on CRAN's check machines. As with the `greta` package +itself, examples are wrapped in `\dontrun{}` and the tests skip themselves when +those dependencies are absent, so the checks remain fast and self-contained on +CRAN. The full test suite and all examples have been run locally against +`greta` 0.6.0 and pass. + +## revdepcheck results + +As the package was archived, there are no reverse dependencies to check. + +## Method references + +The methods implemented in this package are described in the reference already +given in the `Description` field, Golding (2019) , +which describes the `greta` software that this package extends. diff --git a/man/figures/README-plotting-1.png b/man/figures/README-plotting-1.png index 71b8673..9e65ea7 100644 Binary files a/man/figures/README-plotting-1.png and b/man/figures/README-plotting-1.png differ diff --git a/man/gp.Rd b/man/gp.Rd index 643cdae..b5bfc64 100644 --- a/man/gp.Rd +++ b/man/gp.Rd @@ -38,9 +38,9 @@ Define Gaussian processes, and project them to new coordinates. } \details{ \code{gp()} returns a greta array representing the values of the -Gaussian process(es) evaluated at \code{x}. This Gaussian process can be -made sparse (via a reduced-rank representation of the covariance) by -providing an additional set of inducing point coordinates \code{inducing}. +Gaussian process (or processes) evaluated at \code{x}. This Gaussian process +can be made sparse (via a reduced-rank representation of the covariance) +by providing an additional set of inducing point coordinates \code{inducing}. \code{project()} evaluates the values of an existing Gaussian process (created with \code{gp()}) to new data. } diff --git a/man/greta.gp.Rd b/man/greta.gp.Rd index c452f33..465a367 100644 --- a/man/greta.gp.Rd +++ b/man/greta.gp.Rd @@ -24,6 +24,7 @@ Useful links: Authors: \itemize{ + \item Nicholas Tierney \email{nicholas.tierney@gmail.com} (\href{https://orcid.org/0000-0003-1460-8722}{ORCID}) \item Nick Golding \email{nick.golding.research@gmail.com} (\href{https://orcid.org/0000-0001-8916-5570}{ORCID}) [copyright holder] } diff --git a/pkgdown/assets/name_icon_on_purple.png b/pkgdown/assets/name_icon_on_purple.png new file mode 100644 index 0000000..d2c0c0f Binary files /dev/null and b/pkgdown/assets/name_icon_on_purple.png differ diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png new file mode 100644 index 0000000..be18b25 Binary files /dev/null and b/pkgdown/favicon/apple-touch-icon.png differ diff --git a/pkgdown/favicon/favicon-96x96.png b/pkgdown/favicon/favicon-96x96.png new file mode 100644 index 0000000..5f22d5c Binary files /dev/null and b/pkgdown/favicon/favicon-96x96.png differ diff --git a/pkgdown/favicon/favicon.ico b/pkgdown/favicon/favicon.ico new file mode 100644 index 0000000..4435acf Binary files /dev/null and b/pkgdown/favicon/favicon.ico differ diff --git a/pkgdown/favicon/favicon.svg b/pkgdown/favicon/favicon.svg new file mode 100644 index 0000000..2d41240 --- /dev/null +++ b/pkgdown/favicon/favicon.svg @@ -0,0 +1 @@ +RealFaviconGeneratorhttps://realfavicongenerator.net \ No newline at end of file diff --git a/pkgdown/favicon/site.webmanifest b/pkgdown/favicon/site.webmanifest new file mode 100644 index 0000000..4ebda26 --- /dev/null +++ b/pkgdown/favicon/site.webmanifest @@ -0,0 +1,21 @@ +{ + "name": "", + "short_name": "", + "icons": [ + { + "src": "/web-app-manifest-192x192.png", + "sizes": "192x192", + "type": "image/png", + "purpose": "maskable" + }, + { + "src": "/web-app-manifest-512x512.png", + "sizes": "512x512", + "type": "image/png", + "purpose": "maskable" + } + ], + "theme_color": "#ffffff", + "background_color": "#ffffff", + "display": "standalone" +} \ No newline at end of file diff --git a/pkgdown/favicon/web-app-manifest-192x192.png b/pkgdown/favicon/web-app-manifest-192x192.png new file mode 100644 index 0000000..6a757d7 Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-192x192.png differ diff --git a/pkgdown/favicon/web-app-manifest-512x512.png b/pkgdown/favicon/web-app-manifest-512x512.png new file mode 100644 index 0000000..cfd8487 Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-512x512.png differ