update to v2.4.0

Author: mingdeyu

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dgpsi
 Type: Package
 Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations 
-Version: 2.3.0-9000
+Version: 2.4.0
 Authors@R: c(
   person('Deyu', 'Ming', role = c('aut', 'cre', 'cph'),
          email = 'deyu.ming.16@ucl.ac.uk'),

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2024
 COPYRIGHT HOLDER: Deyu Ming

NEWS.md

@@ -1,4 +1,4 @@
-# dgpsi 2.3.0-9000 (development version)
+# dgpsi 2.4.0
 - One can now use `design()` to implement sequential designs using `f` and a fixed candidate set passed to `x_cand` with `y_cand = NULL`.
 - The sizes of `.pkl` files written by `write()` are significantly reduced.
 - One can now set different kernel functions to nodes in different layers in a DGP emulator by passing a vector of kernel function names to `name` argument of `dgp()`.

R/initi_py.R

@@ -40,13 +40,13 @@ init_py <- function(py_ver = NULL, dgpsi_ver = NULL, reinstall = FALSE, uninstal
   if ( is.null(py_ver) ) py_ver <- '3.9.13'
   if ( is.null(dgpsi_ver) ) {
     ##For devel version
-    dgpsi_ver <- c('cython>=0.29.30', 'dill>=0.3.2, <=0.3.5.1', 'jupyter>=1.0.0', 'matplotlib-base>=3.2.1', 'numba >=0.51.2',
-                   'numpy >=1.18.2', 'pathos ==0.2.9', 'multiprocess ==0.70.13', 'psutil >=5.8.0', 'pybind11 >=2.10.0', 'pythran >=0.11.0',
-                   'scikit-build >=0.15.0', 'scikit-learn >=0.22.0', 'scipy >=1.4.1', 'tqdm >=4.50.2', 'tabulate >=0.8.7')
-    env_name <- 'dgp_si_R_2_3_0_9000'
+    #dgpsi_ver <- c('cython>=0.29.30', 'dill>=0.3.2, <=0.3.5.1', 'jupyter>=1.0.0', 'matplotlib-base>=3.2.1', 'numba >=0.51.2',
+    #               'numpy >=1.18.2', 'pathos ==0.2.9', 'multiprocess ==0.70.13', 'psutil >=5.8.0', 'pybind11 >=2.10.0', 'pythran >=0.11.0',
+    #               'scikit-build >=0.15.0', 'scikit-learn >=0.22.0', 'scipy >=1.4.1', 'tqdm >=4.50.2', 'tabulate >=0.8.7')
+    #env_name <- 'dgp_si_R_2_3_0_9000'
     ##For release version
-    #dgpsi_ver <- 'dgpsi==2.3.0'
-    #env_name <- 'dgp_si_R_2_3_0'
+    dgpsi_ver <- 'dgpsi==2.4.0'
+    env_name <- 'dgp_si_R_2_4_0'
   } else {
     env_name <- paste('dgp_si_R_', gsub(".", "_", dgpsi_ver,fixed=TRUE), sep = "")
     dgpsi_ver <- paste('dgpsi==', dgpsi_ver, sep = "")

README.md

@@ -6,7 +6,7 @@
   [![REF](https://img.shields.io/badge/REF-Linked%20GP-informational)](https://doi.org/10.1137/20M1323771)
   [![REF](https://img.shields.io/badge/REF-Deep%20GP-informational)](https://doi.org/10.1080/00401706.2022.2124311)
   [![REF](https://img.shields.io/badge/REF-Linked%20DGP-informational)](https://arxiv.org/abs/2306.01212)
-  [![python](https://img.shields.io/badge/Python-dgpsi%20v2.3.0-informational)](https://github.com/mingdeyu/DGP)
+  [![python](https://img.shields.io/badge/Python-dgpsi%20v2.4.0-informational)](https://github.com/mingdeyu/DGP)
   ![CRAN_License](https://img.shields.io/cran/l/dgpsi?color=green)
 
 The R package `dgpsi` provides R interface to Python package [`dgpsi`](https://github.com/mingdeyu/DGP) for deep and linked Gaussian process emulations using stochastic imputation (SI). 
@@ -79,7 +79,7 @@ to load the package. To install or activate the required Python environment auto
 > ```
 
 ## Research Notice
-This package is part of an ongoing research initiative. For detailed information about the research aspects and guidelines for use, please refer to our [Research Notice](./RESEARCH-NOTICE.md).
+This package is part of an ongoing research initiative. For detailed information about the research aspects and guidelines for use, please refer to our [Research Notice](https://github.com/mingdeyu/dgpsi-R/blob/master/RESEARCH-NOTICE.md).
 
 ## References
 > [Ming, D. and Williamson, D. (2023) Linked deep Gaussian process emulation for model networks. arXiv:2306.01212](https://arxiv.org/abs/2306.01212)

cran-comments.md

@@ -1,6 +1,6 @@
-This is the submission of 'dgpsi' 2.3.0.
+This is the submission of 'dgpsi' 2.4.0.
 
-Various updates have been made in this version. A detailed list of changes that have been made since the last version 2.2.0 is contained in NEWS.md.  
+Various updates have been made in this version. A detailed list of changes that have been made since the last version 2.3.0 is contained in NEWS.md.  
 
 ## Test environments
 

vignettes/dgpsi.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-`dgpsi` provides a flexible toolbox for Gaussian process (GP), deep Gaussian process (DGP) and linked (D)GP emulations. In this guide, we show how to use the package to emulate a step function with a three-layered DGP structure. There are other examples showing the functionality of the package in [`Articles`](https://mingdeyu.github.io/dgpsi-R/dev/articles/index.html) on the package website, and how to customize a DGP structure. A comprehensive reference of available functions is documented in [`Reference`](https://mingdeyu.github.io/dgpsi-R/dev/reference/index.html) section of the package website. 
+`dgpsi` provides a flexible toolbox for Gaussian process (GP), deep Gaussian process (DGP) and linked (D)GP emulations. In this guide, we show how to use the package to emulate a step function with a three-layered DGP structure. There are other examples showing the functionality of the package in [`Articles`](https://mingdeyu.github.io/dgpsi-R/articles/index.html) on the package website, and how to customize a DGP structure. A comprehensive reference of available functions is documented in [`Reference`](https://mingdeyu.github.io/dgpsi-R/reference/index.html) section of the package website. 
 
 ## Load the package
 

vignettes/seq_design.Rmd

@@ -277,7 +277,7 @@ It can be seen from the plot above that with static space-filling designs, the q
 
 ### See also
 
-See [`Sequential Design II`](https://mingdeyu.github.io/dgpsi-R/dev/articles/seq_design_2.html) for the sequential design of a bundle of DGP emulators with automatic terminations.
+See [`Sequential Design II`](https://mingdeyu.github.io/dgpsi-R/articles/seq_design_2.html) for the sequential design of a bundle of DGP emulators with automatic terminations.
 
 ### References
 

vignettes/seq_design_2.Rmd

@@ -317,4 +317,4 @@ It can be seen from the plot above that with the sequential design, emulators in
 
 ### See also
 
-See [`Sequential Design I`](https://mingdeyu.github.io/dgpsi-R/dev/articles/seq_design.html) for the sequential design and automatic structure simplification of a DGP emulator on a 2D simulator.
+See [`Sequential Design I`](https://mingdeyu.github.io/dgpsi-R/articles/seq_design.html) for the sequential design and automatic structure simplification of a DGP emulator on a 2D simulator.