Merge pull request #72 from SymbolicML/refactor-modules

MilesCranmer · web-flow · commit f68d92e44652 · 2024-04-28T21:29:56.000+01:00
refactor!: module names to match struct names
diff --git a/Project.toml b/Project.toml
@@ -52,9 +52,10 @@ Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Test", "SafeTestsets", "Aqua", "Bumper", "Enzyme", "ForwardDiff", "LinearAlgebra", "LoopVectorization", "Optim", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "Zygote"]
+test = ["Test", "SafeTestsets", "Aqua", "Bumper", "Enzyme", "ForwardDiff", "LinearAlgebra", "LoopVectorization", "Optim", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "Suppressor", "Zygote"]
diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ DynamicExpressions.jl is the backbone of [SymbolicRegression.jl](https://github.
 
 A dynamic expression is a snippet of code that can change throughout runtime - compilation is not possible! **DynamicExpressions.jl does the following:**
 1. Defines an enum over user-specified operators.
-2. Using this enum, it defines a [very lightweight and type-stable data structure](https://symbolicml.org/DynamicExpressions.jl/dev/types/#DynamicExpressions.EquationModule.Node) for arbitrary expressions.
+2. Using this enum, it defines a [very lightweight and type-stable data structure](https://symbolicml.org/DynamicExpressions.jl/dev/types/#DynamicExpressions.NodeModule.Node) for arbitrary expressions.
 3. It then generates specialized [evaluation kernels](https://github.com/SymbolicML/DynamicExpressions.jl/blob/fe8e6dfa160d12485fb77c226d22776dd6ed697a/src/EvaluateEquation.jl#L29-L66) for the space of potential operators.
 4. It also generates kernels for the [first-order derivatives](https://github.com/SymbolicML/DynamicExpressions.jl/blob/fe8e6dfa160d12485fb77c226d22776dd6ed697a/src/EvaluateEquationDerivative.jl#L139-L175), using [Zygote.jl](https://github.com/FluxML/Zygote.jl).
 5. DynamicExpressions.jl can also operate on arbitrary other types (vectors, tensors, symbols, strings, or even unions) - see last part below.
diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl
@@ -1,5 +1,4 @@
 using DynamicExpressions, BenchmarkTools, Random
-using DynamicExpressions.EquationUtilsModule: is_constant
 
 # Trigger extensions:
 using LoopVectorization
@@ -13,6 +12,12 @@ else
     @eval using DynamicExpressions: GraphNode
 end
 
+if PACKAGE_VERSION < v"0.17.0"
+    @eval using DynamicExpressions.EquationUtilsModule: is_constant
+else
+    @eval using DynamicExpressions.NodeUtilsModule: is_constant
+end
+
 include("../test/tree_gen_utils.jl")
 
 const SUITE = BenchmarkGroup()
diff --git a/ext/DynamicExpressionsLoopVectorizationExt.jl b/ext/DynamicExpressionsLoopVectorizationExt.jl
@@ -3,8 +3,8 @@ module DynamicExpressionsLoopVectorizationExt
 using LoopVectorization: @turbo
 using DynamicExpressions: AbstractExpressionNode
 using DynamicExpressions.UtilsModule: ResultOk, fill_similar
-using DynamicExpressions.EvaluateEquationModule: @return_on_check
-import DynamicExpressions.EvaluateEquationModule:
+using DynamicExpressions.EvaluateModule: @return_on_check
+import DynamicExpressions.EvaluateModule:
     deg1_eval,
     deg2_eval,
     deg1_l2_ll0_lr0_eval,
diff --git a/ext/DynamicExpressionsSymbolicUtilsExt.jl b/ext/DynamicExpressionsSymbolicUtilsExt.jl
@@ -1,7 +1,7 @@
 module DynamicExpressionsSymbolicUtilsExt
 
 using SymbolicUtils
-import DynamicExpressions.EquationModule:
+import DynamicExpressions.NodeModule:
     AbstractExpressionNode, Node, constructorof, DEFAULT_NODE_TYPE
 import DynamicExpressions.OperatorEnumModule: AbstractOperatorEnum
 import DynamicExpressions.UtilsModule: isgood, isbad, deprecate_varmap
diff --git a/src/DynamicExpressions.jl b/src/DynamicExpressions.jl
@@ -3,19 +3,19 @@ module DynamicExpressions
 include("Utils.jl")
 include("ExtensionInterface.jl")
 include("OperatorEnum.jl")
-include("Equation.jl")
-include("EquationUtils.jl")
+include("Node.jl")
+include("NodeUtils.jl")
 include("Strings.jl")
-include("EvaluateEquation.jl")
-include("EvaluateEquationDerivative.jl")
+include("Evaluate.jl")
+include("EvaluateDerivative.jl")
 include("EvaluationHelpers.jl")
-include("SimplifyEquation.jl")
+include("Simplify.jl")
 include("OperatorEnumConstruction.jl")
 include("Random.jl")
 
 import PackageExtensionCompat: @require_extensions
 import Reexport: @reexport
-@reexport import .EquationModule:
+@reexport import .NodeModule:
     AbstractNode,
     AbstractExpressionNode,
     GraphNode,
@@ -25,8 +25,8 @@ import Reexport: @reexport
     tree_mapreduce,
     filter_map,
     filter_map!
-import .EquationModule: constructorof, preserve_sharing
-@reexport import .EquationUtilsModule:
+import .NodeModule: constructorof, preserve_sharing
+@reexport import .NodeUtilsModule:
     count_nodes,
     count_constants,
     count_depth,
@@ -40,10 +40,9 @@ import .EquationModule: constructorof, preserve_sharing
 @reexport import .OperatorEnumModule: AbstractOperatorEnum
 @reexport import .OperatorEnumConstructionModule:
     OperatorEnum, GenericOperatorEnum, @extend_operators, set_default_variable_names!
-@reexport import .EvaluateEquationModule: eval_tree_array, differentiable_eval_tree_array
-@reexport import .EvaluateEquationDerivativeModule:
-    eval_diff_tree_array, eval_grad_tree_array
-@reexport import .SimplifyEquationModule: combine_operators, simplify_tree!
+@reexport import .EvaluateModule: eval_tree_array, differentiable_eval_tree_array
+@reexport import .EvaluateDerivativeModule: eval_diff_tree_array, eval_grad_tree_array
+@reexport import .SimplifyModule: combine_operators, simplify_tree!
 @reexport import .EvaluationHelpersModule
 @reexport import .ExtensionInterfaceModule: node_to_symbolic, symbolic_to_node
 @reexport import .RandomModule: NodeSampler
diff --git a/src/Evaluate.jl b/src/Evaluate.jl
@@ -1,10 +1,10 @@
-module EvaluateEquationModule
+module EvaluateModule
 
-import ..EquationModule: AbstractExpressionNode, constructorof
+import ..NodeModule: AbstractExpressionNode, constructorof
 import ..StringsModule: string_tree
 import ..OperatorEnumModule: OperatorEnum, GenericOperatorEnum
 import ..UtilsModule: is_bad_array, fill_similar, counttuple, ResultOk
-import ..EquationUtilsModule: is_constant
+import ..NodeUtilsModule: is_constant
 import ..ExtensionInterfaceModule: bumper_eval_tree_array, _is_loopvectorization_loaded
 
 const OPERATOR_LIMIT_BEFORE_SLOWDOWN = 15
diff --git a/src/EvaluateDerivative.jl b/src/EvaluateDerivative.jl
@@ -1,11 +1,10 @@
-module EvaluateEquationDerivativeModule
+module EvaluateDerivativeModule
 
-import ..EquationModule: AbstractExpressionNode, constructorof
+import ..NodeModule: AbstractExpressionNode, constructorof
 import ..OperatorEnumModule: OperatorEnum
 import ..UtilsModule: is_bad_array, fill_similar, ResultOk2
-import ..EquationUtilsModule: count_constants, index_constants, NodeIndex
-import ..EvaluateEquationModule:
-    deg0_eval, get_nuna, get_nbin, OPERATOR_LIMIT_BEFORE_SLOWDOWN
+import ..NodeUtilsModule: count_constants, index_constants, NodeIndex
+import ..EvaluateModule: deg0_eval, get_nuna, get_nbin, OPERATOR_LIMIT_BEFORE_SLOWDOWN
 import ..ExtensionInterfaceModule: _zygote_gradient
 
 """
diff --git a/src/EvaluationHelpers.jl b/src/EvaluationHelpers.jl
@@ -2,9 +2,9 @@ module EvaluationHelpersModule
 
 import Base: adjoint
 import ..OperatorEnumModule: AbstractOperatorEnum, OperatorEnum, GenericOperatorEnum
-import ..EquationModule: AbstractExpressionNode
-import ..EvaluateEquationModule: eval_tree_array
-import ..EvaluateEquationDerivativeModule: eval_grad_tree_array
+import ..NodeModule: AbstractExpressionNode
+import ..EvaluateModule: eval_tree_array
+import ..EvaluateDerivativeModule: eval_grad_tree_array
 
 # Evaluation:
 """
diff --git a/src/Node.jl b/src/Node.jl
@@ -1,4 +1,4 @@
-module EquationModule
+module NodeModule
 
 import ..OperatorEnumModule: AbstractOperatorEnum
 import ..UtilsModule: @memoize_on, @with_memoize, deprecate_varmap, Undefined
diff --git a/src/NodeUtils.jl b/src/NodeUtils.jl
@@ -1,7 +1,7 @@
-module EquationUtilsModule
+module NodeUtilsModule
 
 import Compat: Returns
-import ..EquationModule:
+import ..NodeModule:
     AbstractNode,
     AbstractExpressionNode,
     Node,
diff --git a/src/OperatorEnumConstruction.jl b/src/OperatorEnumConstruction.jl
@@ -1,10 +1,10 @@
 module OperatorEnumConstructionModule
 
 import ..OperatorEnumModule: AbstractOperatorEnum, OperatorEnum, GenericOperatorEnum
-import ..EquationModule: Node, GraphNode, AbstractExpressionNode, constructorof
+import ..NodeModule: Node, GraphNode, AbstractExpressionNode, constructorof
 import ..StringsModule: string_tree
-import ..EvaluateEquationModule: eval_tree_array, OPERATOR_LIMIT_BEFORE_SLOWDOWN
-import ..EvaluateEquationDerivativeModule: eval_grad_tree_array, _zygote_gradient
+import ..EvaluateModule: eval_tree_array, OPERATOR_LIMIT_BEFORE_SLOWDOWN
+import ..EvaluateDerivativeModule: eval_grad_tree_array, _zygote_gradient
 import ..EvaluationHelpersModule: _grad_evaluator
 
 """Used to set a default value for `operators` for ease of use."""
@@ -110,8 +110,8 @@ function _extend_unary_operator(f::Symbol, type_requirements, internal)
         @gensym _constructorof _AbstractExpressionNode
         quote
             if $$internal
-                import ..EquationModule.constructorof as $_constructorof
-                import ..EquationModule.AbstractExpressionNode as $_AbstractExpressionNode
+                import ..NodeModule.constructorof as $_constructorof
+                import ..NodeModule.AbstractExpressionNode as $_AbstractExpressionNode
             else
                 using DynamicExpressions:
                     constructorof as $_constructorof,
@@ -137,8 +137,8 @@ function _extend_binary_operator(f::Symbol, type_requirements, build_converters,
         @gensym _constructorof _AbstractExpressionNode
         quote
             if $$internal
-                import ..EquationModule.constructorof as $_constructorof
-                import ..EquationModule.AbstractExpressionNode as $_AbstractExpressionNode
+                import ..NodeModule.constructorof as $_constructorof
+                import ..NodeModule.AbstractExpressionNode as $_AbstractExpressionNode
             else
                 using DynamicExpressions:
                     constructorof as $_constructorof,
diff --git a/src/Random.jl b/src/Random.jl
@@ -3,7 +3,7 @@ module RandomModule
 import Compat: Returns, @inline
 import Random: AbstractRNG
 import Base: rand
-import ..EquationModule: AbstractNode, tree_mapreduce, filter_map
+import ..NodeModule: AbstractNode, tree_mapreduce, filter_map
 
 """
     NodeSampler(; tree, filter::Function=Returns(true), weighting::Union{Nothing,Function}=nothing, break_sharing::Val=Val(false))
diff --git a/src/Simplify.jl b/src/Simplify.jl
@@ -1,7 +1,7 @@
-module SimplifyEquationModule
+module SimplifyModule
 
-import ..EquationModule: AbstractExpressionNode, constructorof, Node, copy_node, set_node!
-import ..EquationUtilsModule: tree_mapreduce, is_node_constant
+import ..NodeModule: AbstractExpressionNode, constructorof, Node, copy_node, set_node!
+import ..NodeUtilsModule: tree_mapreduce, is_node_constant
 import ..OperatorEnumModule: AbstractOperatorEnum
 import ..UtilsModule: isbad, isgood
 
diff --git a/src/Strings.jl b/src/Strings.jl
@@ -2,7 +2,7 @@ module StringsModule
 
 using ..UtilsModule: deprecate_varmap
 using ..OperatorEnumModule: AbstractOperatorEnum
-using ..EquationModule: AbstractExpressionNode, tree_mapreduce
+using ..NodeModule: AbstractExpressionNode, tree_mapreduce
 
 const OP_NAMES = Base.ImmutableDict(
     "safe_log" => "log",
diff --git a/src/deprecated.jl b/src/deprecated.jl
@@ -1,5 +1,5 @@
 import Base: @deprecate
-import .EquationModule: Node, GraphNode
+import .NodeModule: Node, GraphNode
 
 @deprecate set_constants set_constants!
 @deprecate simplify_tree simplify_tree!
@@ -69,3 +69,9 @@ for N in (:Node, :GraphNode)
         end
     end
 end
+
+Base.@deprecate_binding EquationModule NodeModule
+Base.@deprecate_binding EquationUtilsModule NodeUtilsModule
+Base.@deprecate_binding EvaluateEquationModule EvaluateModule
+Base.@deprecate_binding EvaluateEquationDerivativeModule EvaluateDerivativeModule
+Base.@deprecate_binding SimplifyEquationModule SimplifyModule
diff --git a/test/test_deprecations.jl b/test/test_deprecations.jl
@@ -1,6 +1,7 @@
 using DynamicExpressions
 using Test
 using Zygote
+using Suppressor: @capture_err
 
 operators = OperatorEnum(; binary_operators=[+, -, *, /], unary_operators=[cos, sin])
 x1, x2 = Node{Float64}(; feature=1), Node{Float64}(; feature=2)
@@ -43,3 +44,11 @@ if VERSION >= v"1.9"
         @assert (n.op == 1 && n.l === x1 && n.r === x2)
     )
 end
+
+# Test deprecated modules
+logs = @capture_err begin
+    @eval using DynamicExpressions.EquationModule
+end
+@test contains(logs, "DynamicExpressions.EquationModule is deprecated,")
+
+DynamicExpressions.EquationModule.Node === DynamicExpressions.NodeModule.Node
diff --git a/test/test_evaluation.jl b/test/test_evaluation.jl
@@ -93,23 +93,23 @@ end
         @test repr(tree) == "cos(cos(3.0))"
         tree = convert(Node{T}, tree)
         truth = cos(cos(T(3.0f0)))
-        @test DynamicExpressions.EvaluateEquationModule.deg1_l1_ll0_eval(tree, [zero(T)]', cos, cos, Val(turbo)).x[1] ≈
+        @test DynamicExpressions.EvaluateModule.deg1_l1_ll0_eval(tree, [zero(T)]', cos, cos, Val(turbo)).x[1] ≈
             truth
 
         # op(<constant>, <constant>)
         tree = Node(1, Node(; val=3.0f0), Node(; val=4.0f0))
         @test repr(tree) == "3.0 + 4.0"
         tree = convert(Node{T}, tree)
         truth = T(3.0f0) + T(4.0f0)
-        @test DynamicExpressions.EvaluateEquationModule.deg2_l0_r0_eval(tree, [zero(T)]', (+), Val(turbo)).x[1] ≈
+        @test DynamicExpressions.EvaluateModule.deg2_l0_r0_eval(tree, [zero(T)]', (+), Val(turbo)).x[1] ≈
             truth
 
         # op(op(<constant>, <constant>))
         tree = Node(1, Node(1, Node(; val=3.0f0), Node(; val=4.0f0)))
         @test repr(tree) == "cos(3.0 + 4.0)"
         tree = convert(Node{T}, tree)
         truth = cos(T(3.0f0) + T(4.0f0))
-        @test DynamicExpressions.EvaluateEquationModule.deg1_l2_ll0_lr0_eval(tree, [zero(T)]', cos, (+), Val(turbo)).x[1] ≈
+        @test DynamicExpressions.EvaluateModule.deg1_l2_ll0_lr0_eval(tree, [zero(T)]', cos, (+), Val(turbo)).x[1] ≈
             truth
 
         # Test for presence of NaNs:
diff --git a/test/test_simplification.jl b/test/test_simplification.jl
@@ -15,8 +15,8 @@ function Base.:≈(a::String, b::String)
     return a == b
 end
 
-simplify_tree! = DynamicExpressions.SimplifyEquationModule.simplify_tree!
-combine_operators = DynamicExpressions.SimplifyEquationModule.combine_operators
+simplify_tree! = DynamicExpressions.SimplifyModule.simplify_tree!
+combine_operators = DynamicExpressions.SimplifyModule.combine_operators
 
 binary_operators = (+, -, /, *)
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-module EquationModule`
	`1`	`+module NodeModule`
`2`	`2`
`3`	`3`	`import ..OperatorEnumModule: AbstractOperatorEnum`
`4`	`4`	`import ..UtilsModule: @memoize_on, @with_memoize, deprecate_varmap, Undefined`