Merge branch 'master' into compathelper/new_version/2024-10-07-00-11-…

…36-542-01562492202

.github/workflows/CI.yml

@@ -30,8 +30,7 @@ jobs:
           - "part2"
           - "part3"
         julia-version:
-          - "1.6"
-          - "1.8"
+          - "1.10"
           - "1"
         os:
           - ubuntu-latest
@@ -54,15 +53,6 @@ jobs:
           - os: macOS-latest
             julia-version: "1"
             test: "part3"
-          - os: ubuntu-latest
-            julia-version: "~1.11.0-0"
-            test: "part1"
-          - os: ubuntu-latest
-            julia-version: "~1.11.0-0"
-            test: "part2"
-          - os: ubuntu-latest
-            julia-version: "~1.11.0-0"
-            test: "part3"
 
     steps:
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -4,14 +4,14 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
   - repo: https://github.com/domluna/JuliaFormatter.jl
-    rev: v1.0.56
+    rev: v1.0.61
     hooks:
       - id: julia-formatter
   - repo: https://github.com/pre-commit/mirrors-prettier

Project.toml

@@ -1,7 +1,7 @@
 name = "SymbolicRegression"
 uuid = "8254be44-1295-4e6a-a16d-46603ac705cb"
 authors = ["MilesCranmer <[email protected]>"]
-version = "0.25.0"
+version = "1.0.0-beta1"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -18,7 +18,6 @@ LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
 MLJModelInterface = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
-PackageExtensionCompat = "65ce6f38-6b18-4e1d-a461-8949797d7930"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
@@ -44,7 +43,7 @@ ADTypes = "^1.4.0"
 Compat = "^4.2"
 ConstructionBase = "<1.5.7"
 Dates = "1"
-DifferentiationInterface = "0.5"
+DifferentiationInterface = "0.5, 0.6"
 DispatchDoctor = "0.4"
 Distributed = "<0.0.1, 1"
 DynamicExpressions = "1"
@@ -56,7 +55,6 @@ LossFunctions = "0.10, 0.11"
 MLJModelInterface = "~1.5, ~1.6, ~1.7, ~1.8, ~1.9, ~1.10, ~1.11"
 MacroTools = "0.4, 0.5"
 Optim = "~1.8, ~1.9"
-PackageExtensionCompat = "1"
 Pkg = "<0.0.1, 1"
 PrecompileTools = "1"
 Printf = "<0.0.1, 1"
@@ -67,7 +65,7 @@ SpecialFunctions = "0.10.1, 1, 2"
 StatsBase = "0.33, 0.34"
 SymbolicUtils = "0.19, ^1.0.5, 2, 3"
 TOML = "<0.0.1, 1"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"

README.md

@@ -230,7 +230,7 @@ with the following function:
 ```julia
 import SymbolicRegression: node_to_symbolic
 
-eqn = node_to_symbolic(dominating[end].tree, options)
+eqn = node_to_symbolic(dominating[end].tree)
 println(simplify(eqn*5 + 3))
 ```
 
@@ -358,27 +358,35 @@ stateDiagram-v2
     AdaptiveParsimony --> Mutate
     AdaptiveParsimony --> Population
     AdaptiveParsimony --> RegularizedEvolution
+    AdaptiveParsimony --> SearchUtils
     AdaptiveParsimony --> SingleIteration
     AdaptiveParsimony --> SymbolicRegression
     CheckConstraints --> Mutate
     CheckConstraints --> SymbolicRegression
     Complexity --> CheckConstraints
     Complexity --> HallOfFame
     Complexity --> LossFunctions
+    Complexity --> MLJInterface
     Complexity --> Mutate
+    Complexity --> PopMember
     Complexity --> Population
     Complexity --> SearchUtils
     Complexity --> SingleIteration
     Complexity --> SymbolicRegression
+    ConstantOptimization --> ExpressionBuilder
     ConstantOptimization --> Mutate
     ConstantOptimization --> SingleIteration
     Core --> AdaptiveParsimony
     Core --> CheckConstraints
     Core --> Complexity
     Core --> ConstantOptimization
+    Core --> DimensionalAnalysis
+    Core --> ExpressionBuilder
+    Core --> ExpressionBuilder
     Core --> HallOfFame
     Core --> InterfaceDynamicExpressions
     Core --> LossFunctions
+    Core --> MLJInterface
     Core --> Migration
     Core --> Mutate
     Core --> MutationFunctions
@@ -390,42 +398,63 @@ stateDiagram-v2
     Core --> SingleIteration
     Core --> SymbolicRegression
     Dataset --> Core
+    DimensionalAnalysis --> LossFunctions
+    ExpressionBuilder --> SymbolicRegression
+    HallOfFame --> ExpressionBuilder
+    HallOfFame --> MLJInterface
     HallOfFame --> SearchUtils
     HallOfFame --> SingleIteration
     HallOfFame --> SymbolicRegression
+    HallOfFame --> deprecates
+    InterfaceDynamicExpressions --> ExpressionBuilder
+    InterfaceDynamicExpressions --> HallOfFame
     InterfaceDynamicExpressions --> LossFunctions
     InterfaceDynamicExpressions --> SymbolicRegression
+    InterfaceDynamicQuantities --> Dataset
+    InterfaceDynamicQuantities --> MLJInterface
     LossFunctions --> ConstantOptimization
-    LossFunctions --> HallOfFame
+    LossFunctions --> ExpressionBuilder
+    LossFunctions --> ExpressionBuilder
     LossFunctions --> Mutate
     LossFunctions --> PopMember
     LossFunctions --> Population
+    LossFunctions --> SingleIteration
     LossFunctions --> SymbolicRegression
+    MLJInterface --> SymbolicRegression
     Migration --> SymbolicRegression
     Mutate --> RegularizedEvolution
+    MutationFunctions --> ExpressionBuilder
     MutationFunctions --> Mutate
     MutationFunctions --> Population
     MutationFunctions --> SymbolicRegression
+    MutationFunctions --> deprecates
+    MutationWeights --> Core
+    MutationWeights --> Options
+    MutationWeights --> OptionsStruct
     Operators --> Core
     Operators --> Options
     Options --> Core
     OptionsStruct --> Core
     OptionsStruct --> Options
+    OptionsStruct --> Options
     PopMember --> ConstantOptimization
+    PopMember --> ExpressionBuilder
     PopMember --> HallOfFame
     PopMember --> Migration
     PopMember --> Mutate
     PopMember --> Population
-    PopMember --> RegularizedEvolution
+    PopMember --> SearchUtils
     PopMember --> SingleIteration
     PopMember --> SymbolicRegression
+    Population --> ExpressionBuilder
     Population --> Migration
     Population --> RegularizedEvolution
     Population --> SearchUtils
     Population --> SingleIteration
     Population --> SymbolicRegression
     ProgramConstants --> Core
     ProgramConstants --> Dataset
+    ProgramConstants --> Operators
     ProgressBars --> SearchUtils
     ProgressBars --> SymbolicRegression
     Recorder --> Mutate
@@ -435,10 +464,19 @@ stateDiagram-v2
     RegularizedEvolution --> SingleIteration
     SearchUtils --> SymbolicRegression
     SingleIteration --> SymbolicRegression
-    Utils --> CheckConstraints
     Utils --> ConstantOptimization
+    Utils --> Dataset
+    Utils --> DimensionalAnalysis
+    Utils --> HallOfFame
+    Utils --> InterfaceDynamicExpressions
+    Utils --> MLJInterface
+    Utils --> Migration
+    Utils --> Operators
     Utils --> Options
     Utils --> PopMember
+    Utils --> Population
+    Utils --> RegularizedEvolution
+    Utils --> SearchUtils
     Utils --> SingleIteration
     Utils --> SymbolicRegression
 ```
@@ -449,7 +487,7 @@ Bash command to generate dependency structure from `src` directory (requires `vi
 echo 'stateDiagram-v2'
 IFS=$'\n'
 for f in *.jl; do
-    for line in $(cat $f | grep -e 'import \.\.' -e 'import \.'); do
+    for line in $(cat $f | grep -e 'import \.\.' -e 'import \.' -e 'using \.' -e 'using \.\.'); do
         echo $(echo $line | vims -s 'dwf:d$' -t '%s/^\.*//g' '%s/Module//g') $(basename "$f" .jl);
     done;
 done | vims -l 'f a--> ' | sort

benchmark/benchmarks.jl

@@ -1,6 +1,8 @@
 using BenchmarkTools
 using SymbolicRegression, BenchmarkTools, Random
 using SymbolicRegression.AdaptiveParsimonyModule: RunningSearchStatistics
+using SymbolicRegression.MutateModule: next_generation
+using SymbolicRegression.RecorderModule: RecordType
 using SymbolicRegression.PopulationModule: best_of_sample
 using SymbolicRegression.ConstantOptimizationModule: optimize_constants
 using SymbolicRegression.CheckConstraintsModule: check_constraints
@@ -93,6 +95,57 @@ function create_utils_benchmark()
         )
     )
 
+    suite["next_generation_x100"] = @benchmarkable(
+        let
+            for member in members
+                next_generation(
+                    dataset,
+                    member,
+                    temperature,
+                    curmaxsize,
+                    rss,
+                    options;
+                    tmp_recorder=recorder,
+                )
+            end
+        end,
+        setup = (
+            nfeatures = 1;
+            dataset = Dataset(randn(nfeatures, 32), randn(32));
+            mutation_weights = MutationWeights(;
+                mutate_constant=1.0,
+                mutate_operator=1.0,
+                swap_operands=1.0,
+                rotate_tree=1.0,
+                add_node=1.0,
+                insert_node=1.0,
+                simplify=0.0,
+                randomize=0.0,
+                do_nothing=0.0,
+                form_connection=0.0,
+                break_connection=0.0,
+            );
+            options = Options(;
+                unary_operators=[sin, cos], binary_operators=[+, -, *, /], mutation_weights
+            );
+            recorder = RecordType();
+            temperature = 1.0;
+            curmaxsize = 20;
+            rss = RunningSearchStatistics(; options);
+            trees = [
+                gen_random_tree_fixed_size(15, options, nfeatures, Float64) for _ in 1:100
+            ];
+            expressions = [
+                Expression(tree; operators=options.operators, variable_names=["x1"]) for
+                tree in trees
+            ];
+            members = [
+                PopMember(dataset, expression, options; deterministic=false) for
+                expression in expressions
+            ]
+        )
+    )
+
     ntrees = 10
     suite["optimize_constants_x10"] = @benchmarkable(
         foreach(members) do member

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DynamicExpressions = "a40a106e-89c9-4ca8-8020-a735e8728b6b"
 Gumbo = "708ec375-b3d6-5a57-a7ce-8257bf98657a"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 

docs/make.jl

@@ -1,7 +1,21 @@
 using Documenter
 using SymbolicUtils
 using SymbolicRegression
-using SymbolicRegression: Dataset, update_baseline_loss!
+using SymbolicRegression:
+    AbstractExpression,
+    ExpressionInterface,
+    Dataset,
+    update_baseline_loss!,
+    AbstractMutationWeights,
+    AbstractOptions,
+    mutate!,
+    condition_mutation_weights!,
+    sample_mutation,
+    MutationResult,
+    AbstractRuntimeOptions,
+    AbstractSearchState,
+    @extend_operators
+using DynamicExpressions
 
 DocMeta.setdocmeta!(
     SymbolicRegression, :DocTestSetup, :(using LossFunctions); recursive=true
@@ -40,14 +54,8 @@ readme = replace(
 
 # We prepend the `<table>` with a ```@raw html
 # and append the `</table>` with a ```:
-readme = replace(
-    readme,
-    r"<table>" => s"```@raw html\n<table>",
-)
-readme = replace(
-    readme,
-    r"</table>" => s"</table>\n```",
-)
+readme = replace(readme, r"<table>" => s"```@raw html\n<table>")
+readme = replace(readme, r"</table>" => s"</table>\n```")
 
 # Then, we surround ```mermaid\n...\n``` snippets
 # with ```@raw html\n<div class="mermaid">\n...\n</div>```:
@@ -96,6 +104,7 @@ makedocs(;
         "API" => "api.md",
         "Losses" => "losses.md",
         "Types" => "types.md",
+        "Customization" => "customization.md",
     ],
 )
 

docs/src/api.md

@@ -7,7 +7,7 @@ SRRegressor
 MultitargetSRRegressor
 ```
 
-## equation_search
+## Low-Level API
 
 ```@docs
 equation_search