More sophisticated checks in restoreoptsum.

NEWS.md

@@ -1,3 +1,7 @@
+MixedModels v4.25.1 Release Notes
+==============================
+- Use more sophisticated checks on property names in `restoreoptsum` to allow for optsums saved by pre-v4.25 versions to be used with this version and later. [#775] 
+
 MixedModels v4.25 Release Notes
 ==============================
 - Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
@@ -538,3 +542,4 @@ Package dependencies
 [#769]: https://github.com/JuliaStats/MixedModels.jl/issues/769
 [#772]: https://github.com/JuliaStats/MixedModels.jl/issues/772
 [#773]: https://github.com/JuliaStats/MixedModels.jl/issues/773
+[#775]: https://github.com/JuliaStats/MixedModels.jl/issues/775

Project.toml

@@ -1,7 +1,7 @@
 name = "MixedModels"
 uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 author = ["Phillip Alday <[email protected]>", "Douglas Bates <[email protected]>", "Jose Bayoan Santiago Calderon <[email protected]>"]
-version = "4.25.0"
+version = "4.25.1"
 
 [deps]
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"

src/serialization.jl

@@ -10,11 +10,24 @@ function restoreoptsum!(
 ) where {T}
     dict = JSON3.read(io)
     ops = m.optsum
-    okay =
-        (setdiff(propertynames(ops), keys(dict)) == [:lowerbd]) &&
-        all(ops.lowerbd .≤ dict.initial) &&
-        all(ops.lowerbd .≤ dict.final)
-    if !okay
+    allowed_missing = (
+        :lowerbd,       # never saved, -Inf not allowed in JSON
+        :xtol_zero_abs, # added in v4.25.0
+        :ftol_zero_abs, # added in v4.25.0
+        :sigma,         # added in v4.1.0
+        :fitlog,        # added in v4.1.0
+    )
+    nmdiff = setdiff(
+        propertynames(ops),  # names in freshly created optsum
+        union!(Set(keys(dict)), allowed_missing), # names in saved optsum plus those we allow to be missing
+    )
+    if !isempty(nmdiff)
+        throw(ArgumentError(string("optsum names: ", nmdiff, " not found in io")))
+    end
+    if length(setdiff(allowed_missing, keys(dict))) > 1 # 1 because :lowerbd
+        @warn "optsum was saved with an older version of MixedModels.jl: consider resaving."
+    end
+    if any(ops.lowerbd .> dict.initial) || any(ops.lowerbd .> dict.final)
         throw(ArgumentError("initial or final parameters in io do not satisfy lowerbd"))
     end
     for fld in (:feval, :finitial, :fmin, :ftol_rel, :ftol_abs, :maxfeval, :nAGQ, :REML)
@@ -33,12 +46,16 @@ function restoreoptsum!(
     end
     ops.optimizer = Symbol(dict.optimizer)
     ops.returnvalue = Symbol(dict.returnvalue)
-    # provides compatibility with fits saved before the introduction of fixed sigma
+    # compatibility with fits saved before the introduction of various extensions
+    for prop in [:xtol_zero_abs, :ftol_zero_abs]
+        fallback = getproperty(ops, prop)
+        setproperty!(ops, prop, get(dict, prop, fallback))
+    end
     ops.sigma = get(dict, :sigma, nothing)
     fitlog = get(dict, :fitlog, nothing)
     ops.fitlog = if isnothing(fitlog)
         # compat with fits saved before fitlog
-        [(ops.initial, ops.finitial, ops.final, ops.fmin)]
+        [(ops.initial, ops.finitial), (ops.final, ops.fmin)]
     else
         [(convert(Vector{T}, first(entry)), T(last(entry))) for entry in fitlog]
     end

test/pls.jl

@@ -543,6 +543,106 @@ end
         @test loglikelihood(fm) ≈ loglikelihood(m)
         @test bic(fm) ≈ bic(m)
         @test coef(fm) ≈ coef(m)
+
+        # check restoreoptsum from older versions
+        m = LinearMixedModel(
+            @formula(reaction ~ 1 + days + (1 + days | subj)),
+            MixedModels.dataset(:sleepstudy),
+        )
+        iob = IOBuffer(
+"""
+{
+    "initial":[1.0,0.0,1.0],
+    "finitial":1784.642296192436,
+    "ftol_rel":1.0e-12,
+    "ftol_abs":1.0e-8,
+    "xtol_rel":0.0,
+    "xtol_abs":[1.0e-10,1.0e-10,1.0e-10],
+    "initial_step":[0.75,1.0,0.75],
+    "maxfeval":-1,
+    "maxtime":-1.0,
+    "feval":57,
+    "final":[0.9292213195402981,0.01816837807519162,0.22264487477788353],
+    "fmin":1751.9393444646712,
+    "optimizer":"LN_BOBYQA",
+    "returnvalue":"FTOL_REACHED",
+    "nAGQ":1,
+    "REML":false
+}
+"""
+        )
+        @test_logs((:warn,
+                    r"optsum was saved with an older version of MixedModels.jl: consider resaving"),
+                    restoreoptsum!(m, seekstart(iob)))
+        @test loglikelihood(fm) ≈ loglikelihood(m)
+        @test bic(fm) ≈ bic(m)
+        @test coef(fm) ≈ coef(m)
+        iob = IOBuffer(
+"""
+{
+    "initial":[1.0,0.0,1.0],
+    "finitial":1784.642296192436,
+    "ftol_rel":1.0e-12,
+    "xtol_rel":0.0,
+    "xtol_abs":[1.0e-10,1.0e-10,1.0e-10],
+    "initial_step":[0.75,1.0,0.75],
+    "maxfeval":-1,
+    "maxtime":-1.0,
+    "feval":57,
+    "final":[0.9292213195402981,0.01816837807519162,0.22264487477788353],
+    "fmin":1751.9393444646712,
+    "optimizer":"LN_BOBYQA",
+    "returnvalue":"FTOL_REACHED",
+    "nAGQ":1,
+    "REML":false,
+    "sigma":null,
+    "fitlog":[[[1.0,0.0,1.0],1784.642296192436]]
+}
+"""
+        )
+        @test_throws(ArgumentError("optsum names: [:ftol_abs] not found in io"),
+                     restoreoptsum!(m, seekstart(iob)))
+
+        iob = IOBuffer(
+"""
+{
+    "initial":[1.0,0.0,1.0],
+    "finitial":1784.642296192436,
+    "ftol_rel":1.0e-12,
+    "ftol_abs":1.0e-8,
+    "xtol_rel":0.0,
+    "xtol_abs":[1.0e-10,1.0e-10,1.0e-10],
+    "initial_step":[0.75,1.0,0.75],
+    "maxfeval":-1,
+    "maxtime":-1.0,
+    "feval":57,
+    "final":[-0.9292213195402981,0.01816837807519162,0.22264487477788353],
+    "fmin":1751.9393444646712,
+    "optimizer":"LN_BOBYQA",
+    "returnvalue":"FTOL_REACHED",
+    "nAGQ":1,
+    "REML":false,
+    "sigma":null,
+    "fitlog":[[[1.0,0.0,1.0],1784.642296192436]]
+}
+"""
+        )
+        @test_throws(ArgumentError("initial or final parameters in io do not satisfy lowerbd"),
+                     restoreoptsum!(m, seekstart(iob)))
+
+        # make sure new fields are correctly restored
+        mktemp() do path, io
+            m = deepcopy(last(models(:sleepstudy)))
+            m.optsum.xtol_zero_abs = 0.5
+            m.optsum.ftol_zero_abs = 0.5
+            saveoptsum(io, m)
+            m.optsum.xtol_zero_abs = 1.0
+            m.optsum.ftol_zero_abs = 1.0
+            restoreoptsum!(m, seekstart(io))
+            @test m.optsum.xtol_zero_abs == 0.5
+            @test m.optsum.ftol_zero_abs == 0.5
+        end
+
     end
 
     @testset "profile" begin