From 8394bce6d52d757dfd477d6e3d1cd05c7e0ad7bf Mon Sep 17 00:00:00 2001
From: Collin Erickson <collinberickson@gmail.com>
Date: Thu, 15 Feb 2024 23:38:05 -0500
Subject: [PATCH] Added deprecation to old model

---
 R/GauPro_Gauss.R         | 33 ++++++++-------------------------
 scratch/ToDo.md          |  8 +-------
 tests/testthat/test_1D.R |  7 +++++++
 3 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/R/GauPro_Gauss.R b/R/GauPro_Gauss.R
index fa4383d..046ffb3 100644
--- a/R/GauPro_Gauss.R
+++ b/R/GauPro_Gauss.R
@@ -1,22 +1,3 @@
-# correlation function should implement:
-# corr: name of correlation
-# corr_func
-# update_params
-# get_optim_functions: return optim.func, optim.grad, optim.fngr
-# param_optim_lower - lower bound of params
-# param_optim_upper - upper
-# param_optim_start - current param values
-# param_optim_start0 - some central param values that can be used for optimization restarts
-# param_optim_jitter - how to jitter params in optimization
-
-# Suggested
-# deviance
-# deviance_grad
-# deviance_fngr
-# grad
-
-
-
 #' Corr Gauss GP using inherited optim
 #'
 #' @docType class
@@ -75,12 +56,14 @@ GauPro_Gauss <- R6::R6Class(
                           theta = NULL, theta_short = NULL, theta_map = NULL,
                           ...) {
       # This doesn't work inside R6 init as of now.
-      # # Deprecating, haven't used in years. Use kernel model instead.
-      # lifecycle::deprecate_soft(
-      #   when = "0.2.7",
-      #   what = "GauPro_Gauss$new()",
-      #   details = paste0("Please use GauPro::GauPro_kernel_model instead")
-      # )
+      # Deprecating, haven't used in years. Use kernel model instead.
+      # Can't use deprecate_soft:
+      #   https://github.com/r-lib/lifecycle/issues/149#issuecomment-1790953600
+      lifecycle::deprecate_warn(
+        when = "0.2.12",
+        what = "GauPro_Gauss$new()",
+        details = paste0("Please use GauPro::GauPro_kernel_model instead")
+      )
 
       super$initialize(X=X,Z=Z,verbose=verbose,useC=useC,useGrad=useGrad,
                        parallel=parallel,
diff --git a/scratch/ToDo.md b/scratch/ToDo.md
index 06c6065..fd15060 100644
--- a/scratch/ToDo.md
+++ b/scratch/ToDo.md
@@ -11,19 +11,13 @@
 
 * Knowledge gradient: multiple starts for optim
 
-* When giving in formula/data
-  * add to doc
-  * message what chosen kernel is
-
 * Large Z variance is bad. Extend range of s2. Warning to rescale. Tell kernel
 that initial optim values should be large.
 
 * Plot2D:
-  add axis names, either X1/X2 or colnames
+  add axis names, either X1/X2 or colnames (need to add option to CF::gcf_grid)
   fix for factors
 
-* Add deprecated for old model: lifecycle::
-
 * Check kernel start par outside of bounds set by user. Test if it gives all errors.
 
 * Make gpkm doc look good. Look into R7.
diff --git a/tests/testthat/test_1D.R b/tests/testthat/test_1D.R
index d0d7fa0..f3a4240 100644
--- a/tests/testthat/test_1D.R
+++ b/tests/testthat/test_1D.R
@@ -1,3 +1,10 @@
+test_that("GauPro_Gauss will give deprecation warning on first time", {
+  n <- 12
+  x <- matrix(seq(0,1,length.out = n), ncol=1)
+  y <- sin(2*pi*x) + rnorm(n,0,1e-1)
+  expect_no_error({expect_warning({gp <- GauPro_Gauss$new(X=x, Z=y, parallel=FALSE)})})
+})
+
 test_that("1D data works", {
 
   n <- 12