update to v2.5.0

mingdeyu · Dec 14, 2024 · e214c25 · e214c25
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dgpsi
 Type: Package
 Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations 
-Version: 2.4.0-9000
+Version: 2.5.0
 Authors@R: c(
   person('Deyu', 'Ming', role = c('aut', 'cre', 'cph'),
          email = 'deyu.ming.16@ucl.ac.uk'),
@@ -13,7 +13,7 @@ Description: Interface to the 'python' package 'dgpsi' for Gaussian process, dee
              and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). 
              The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and 
              Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and 
-             Ming & Williamson (2023) <arXiv:2306.01212>. To get started with the package, 
+             Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package, 
              see <https://mingdeyu.github.io/dgpsi-R/>.
 License: MIT + file LICENSE
 URL: https://github.com/mingdeyu/dgpsi-R, https://mingdeyu.github.io/dgpsi-R/

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# dgpsi 2.4.0-9000 (development version)
+# dgpsi 2.5.0
 - Training times for DGP emulators are now approximately 30%-40% faster.
 - The computation of (D)GP predictions and Leave-One-Out (LOO) evaluations is now 6-7 times faster.
 - The `nb_parallel` argument has been removed from relevant functions, as multi-threading is now integrated by default.

diff --git a/R/initi_py.R b/R/initi_py.R
@@ -43,13 +43,13 @@ 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', 'faiss-cpu >=1.7.4')
-    env_name <- 'dgp_si_R_2_4_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', 'faiss-cpu >=1.7.4')
+    #env_name <- 'dgp_si_R_2_4_0_9000'
     ##For release version
-    #dgpsi_ver <- 'dgpsi==2.4.0'
-    #env_name <- 'dgp_si_R_2_4_0'
+    dgpsi_ver <- 'dgpsi==2.5.0'
+    env_name <- 'dgp_si_R_2_5_0'
   } else {
     env_name <- paste('dgp_si_R_', gsub(".", "_", dgpsi_ver,fixed=TRUE), sep = "")
     dgpsi_ver <- paste('dgpsi==', dgpsi_ver, sep = "")

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 [![Download](https://cranlogs.r-pkg.org/badges/grand-total/dgpsi?color=brightgreen)](https://CRAN.R-project.org/package=dgpsi)
 [![R-CMD-check](https://github.com/mingdeyu/dgpsi_R/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mingdeyu/dgpsi-R/actions/workflows/R-CMD-check.yaml)
 [![DOC](https://img.shields.io/badge/DOC-release-brightgreen)](https://mingdeyu.github.io/dgpsi-R/)
-[![python](https://img.shields.io/badge/Python-dgpsi%20v2.4.0-informational)](https://github.com/mingdeyu/DGP)
+[![python](https://img.shields.io/badge/Python-dgpsi%20v2.5.0-informational)](https://github.com/mingdeyu/DGP)
 <!-- badges: end -->
 
 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). 
@@ -29,8 +29,9 @@ The R package `dgpsi` provides R interface to Python package [`dgpsi`](https://g
 * Multi-core predictions and validations for GP, DGP, and Linked (D)GP emulators.
 * Sequential designs for (D)GP emulators and bundles of (D)GP emulators.
 * Automatic pruning of DGP emulators, both statically and dynamically.
-* [![Feature Badge](https://img.shields.io/badge/New-In%20Dev%20Version-orange)](https://mingdeyu.github.io/dgpsi-R/dev/) [Large-scale GP, DGP, and Linked (D)GP emulations](https://mingdeyu.github.io/dgpsi-R/dev/articles/large_scale_emulation.html).
-* [![Feature Badge](https://img.shields.io/badge/New-In%20Dev%20Version-orange)](https://mingdeyu.github.io/dgpsi-R/dev/) [Scalable DGP classification using Stochastic Imputation](https://mingdeyu.github.io/dgpsi-R/dev/articles/classification.html).
+* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Large-scale GP, DGP, and Linked (D)GP emulations](https://mingdeyu.github.io/dgpsi-R/articles/large_scale_emulation.html).
+* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Scalable DGP classification using Stochastic Imputation](https://mingdeyu.github.io/dgpsi-R/articles/classification.html).
+* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Bayesian optimization](https://mingdeyu.github.io/dgpsi-R/articles/bayes_opt.html).
 
 ## Getting started
 * Check [A Quick Guide to dgpsi](https://mingdeyu.github.io/dgpsi-R/articles/dgpsi.html) to get started with the package.
@@ -55,7 +56,7 @@ After the installation, run
 library(dgpsi)
 ```
 
-to load the package. To install or activate the required Python environment automatically, simply run a function from the package. That's it, the package is now ready to use!
+to load the package. To install or activate the required Python environment automatically, you can either run `dgpsi::init_py()` explicitly or simply call any function from the package. That's it - the package is ready to use!
 
 > **Note**  
 > After loading `dgpsi`, the package may take some time to compile and initiate the underlying Python environment the first

diff --git a/man/alm.Rd b/man/alm.Rd
diff --git a/man/combine.Rd b/man/combine.Rd
diff --git a/man/continue.Rd b/man/continue.Rd
diff --git a/man/deserialize.Rd b/man/deserialize.Rd
diff --git a/man/design.Rd b/man/design.Rd
diff --git a/man/dgp.Rd b/man/dgp.Rd
diff --git a/man/dgpsi-package.Rd b/man/dgpsi-package.Rd
diff --git a/man/draw.Rd b/man/draw.Rd
diff --git a/man/get_thread_num.Rd b/man/get_thread_num.Rd
diff --git a/man/gp.Rd b/man/gp.Rd
diff --git a/man/init_py.Rd b/man/init_py.Rd
diff --git a/man/lgp.Rd b/man/lgp.Rd
diff --git a/man/mice.Rd b/man/mice.Rd
diff --git a/man/nllik.Rd b/man/nllik.Rd
diff --git a/man/pack.Rd b/man/pack.Rd
diff --git a/man/plot.Rd b/man/plot.Rd
diff --git a/man/predict.Rd b/man/predict.Rd
diff --git a/man/prune.Rd b/man/prune.Rd
diff --git a/man/read.Rd b/man/read.Rd
diff --git a/man/serialize.Rd b/man/serialize.Rd
diff --git a/man/set_id.Rd b/man/set_id.Rd
diff --git a/man/set_imp.Rd b/man/set_imp.Rd
diff --git a/man/set_linked_idx.Rd b/man/set_linked_idx.Rd
diff --git a/man/set_seed.Rd b/man/set_seed.Rd
diff --git a/man/set_thread_num.Rd b/man/set_thread_num.Rd
diff --git a/man/set_vecchia.Rd b/man/set_vecchia.Rd
diff --git a/man/summary.Rd b/man/summary.Rd
diff --git a/man/trace_plot.Rd b/man/trace_plot.Rd
diff --git a/man/unpack.Rd b/man/unpack.Rd
diff --git a/man/update.Rd b/man/update.Rd
diff --git a/man/validate.Rd b/man/validate.Rd
diff --git a/man/vigf.Rd b/man/vigf.Rd
diff --git a/man/window.Rd b/man/window.Rd
diff --git a/man/write.Rd b/man/write.Rd