deprecate transform_to_real

Author: odunbar

src/Emulator.jl

@@ -319,8 +319,10 @@ function predict(
     emulator::Emulator{FT},
     new_inputs::AM;
     encode=nothing, # maps decoded inputs to decoded outputs
+    add_obs_noise_cov=false,
     mlt_kwargs...,
 ) where {FT <: AbstractFloat, AM <: AbstractMatrix}
+                    
     # Check if the size of new_inputs is consistent with the training data input
     input_dim, output_dim = size(get_io_pairs(emulator), 1)
     encoded_input_dim, encoded_output_dim = size(get_encoded_io_pairs(emulator), 1)
@@ -443,6 +445,7 @@ function predict(
     fmw::FMW,
     new_inputs::AM;
     encode=nothing, # maps decoded inputs to decoded outputs
+    add_obs_noise_cov=false,
 ) where {FMW <: ForwardMapWrapper, AM <: AbstractMatrix}
     # Check if the size of new_inputs is consistent with the training input data
     input_dim, output_dim = size(get_io_pairs(fmw), 1)
@@ -514,4 +517,38 @@ function predict(
     end
 end
 
+
+### Deprecated keywords
+
+function predict(
+    em_or_fmw::EorFMW,
+    new_inputs::AM;
+    transform_to_real = nothing,
+    kwargs...,
+) where {AM <: AbstractMatrix,  EorFMW <: Union{Emulator, ForwardMapWrapper}}
+    
+    if !isnothing(transform_to_real)
+        Base.depwarn(
+            """`transform_to_real` keyword is deprecated. Please use the `encode` and `add_obs_noise_cov` keywords instead.
+
+Recommended usage for users is now set by default as:
+ - `encode=nothing`, `add_obs_noise_cov=false`
+This behaviour takes in non-encoded inputs, and returns non-encoded outputs. It gives only the uncertainty from the Machine Learning Tool (not inflated by observational noise)
+
+This simulation will continue with the old behavior:
+ - `transform_to_real=true` replaced with `encode=nothing, add_obs_noise_cov=true`
+ - `transform_to_real=false` replaced with `encode="out", add_obs_noise_cov=true`
+    """,
+            :predict,
+        )
+        
+        # modify kwargs
+        kw = Dict(kwargs)
+        kw[:add_obs_noise_cov] = true
+        kw[:encode] = transform_to_real ? nothing : "out"
+        predict(em_or_fmw, new_inputs; kw...)
+    end
+
+    return predict(em_or_fmw, new_inputs; kwargs...)
+
 end