Merge pull request #41 from COBREXA/mk-accessors

add support for Accessors, patch a weird type issue

Project.toml

@@ -1,15 +1,18 @@
 name = "ConstraintTrees"
 uuid = "5515826b-29c3-47a5-8849-8513ac836620"
 authors = ["The developers of ConstraintTrees.jl"]
-version = "1.1.0"
+version = "1.2.0"
 
 [deps]
+ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
+Accessors = "0.1"
 Clarabel = "0.6"
+ConstructionBase = "1.5"
 DataStructures = "0.18"
 DocStringExtensions = "0.8, 0.9"
 GLPK = "1"
@@ -19,6 +22,7 @@ SCIP = "0.11"
 julia = "1"
 
 [extras]
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 Clarabel = "61c947e1-3e6d-4ee4-985a-eec8c727bd6e"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
@@ -28,4 +32,4 @@ SCIP = "82193955-e24f-5292-bf16-6f2c5261a85f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Clarabel", "Downloads", "GLPK", "JuMP", "SBML", "SCIP", "Test"]
+test = ["Accessors", "Clarabel", "Downloads", "GLPK", "JuMP", "SBML", "SCIP", "Test"]

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 Clarabel = "61c947e1-3e6d-4ee4-985a-eec8c727bd6e"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/src/1-metabolic-modeling.jl

@@ -357,14 +357,15 @@ Dict(k => v.fluxes.R_BIOMASS_Ecoli_core_w_GAM for (k, v) in result.community)
 #   change at a single place of the tree may easily change values also in other
 #   parts of any trees, including completely different trees
 # - the "convenient way" of making sure that the above problem never happens is
-#   to deep-copy the whole tree structure, which is typically quite detrimental
-#   to memory use and program efficiency
+#   to copy-on-write the whole tree structure, which is typically quite
+#   detrimental to memory use and program efficiency
 #
 #md # !!! danger "Rules of thumb for safe use of in-place modification"
 #md #     Only use the in-place modifications if:
 #md #     - there is code that explicitly makes sure there is no false sharing via references, e.g. using a deep copy
 #md #     - the in-place modifications are the last thing happening to the constraint tree before it is used by the solver
 #md #     - the in-place modification code is not a part of a re-usable library
+#md #     - you are using a suitable wrapper interface such as [Accessors.jl](https://github.com/JuliaObjects/Accessors.jl)
 #
 # Now, if you are completely sure that ignoring the robustness guidelines will
 # help your code, you can do the in-place tree modifications quite easily using
@@ -391,6 +392,39 @@ result.exchanges
 
 @test result_with_more_oxygen.exchanges.oxygen < -19.0 #src
 
+# ### Alternative: Using Accessors.jl
+#
+# Accessors.jl implement a "lensy" way to update immutable data structures.
+# That comes with a nice outcome of doing the right amount of shallow copyies
+# for you automatically, thus avoiding much of the technical danger of in-place
+# modifications. (You still lose the equational reasoning on your code, but that
+# may not be an issue at all in usual codebases.)
+#
+# Accessors interface is used simply through macros `@set` (which sets a deeply
+# nested field in a structure, returning a modified copy), or with `@reset`
+# which automatically "assigns" the result back to the original variable:
+
+using Accessors
+
+c = @set c.exchanges.biomass.bound = C.Between(-50, 50)
+
+# The above code is equivalent to:
+
+@reset c.exchanges.biomass.bound = C.Between(-50, 50)
+
+# ...and it is also possible to use string and symbol indexes to pick the
+# individual tree items:
+
+@reset c[:exchanges]["biomass"].bound = C.Between(-50, 50)
+
+# All of these operations give us:
+
+c.exchanges.biomass
+
+@test typeof(c.exchanges.biomass.bound) == C.Between #src
+@test c.exchanges.biomass.bound.lower == -50 #src
+@test c.exchanges.biomass.bound.upper == 50 #src
+
 # ## Seeing the differences between the results
 #
 # ConstraintTrees.jl defines its own version of `zip` function that can apply a

src/tree.jl

@@ -13,6 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import ConstructionBase
 import DataStructures: SortedDict, SortedSet
 
 """
@@ -75,10 +76,15 @@ Base.values(x::Tree) = values(elems(x))
 Base.getindex(x::Tree, sym::Symbol) = getindex(elems(x), sym)
 Base.getindex(x::Tree, str::String) = getindex(x, Symbol(str))
 
-Base.setindex!(x::Tree{X}, val::E, sym::Symbol) where {X,E<:X} =
+Base.setindex!(x::Tree{X}, val::E, sym::Symbol) where {X,E<:Union{X,Tree{X}}} =
     setindex!(elems(x), val, sym)
 Base.setindex!(x::Tree, val, str::String) = setindex!(x, val, Symbol(str))
 
+Base.setindex(x::Tree{X}, val::E, sym::Symbol) where {X,E<:Union{X,Tree{X}}} =
+    Tree{X}(elems(x)..., sym => val)
+Base.setindex(x::Tree{X}, val::E, str::String) where {X,E<:Union{X,Tree{X}}} =
+    Base.setindex(x, val, Symbol(str))
+
 Base.delete!(x::Tree, sym::Symbol) = delete!(elems(x), sym)
 Base.delete!(x::Tree, str::String) = delete!(x, Symbol(str))
 
@@ -88,9 +94,12 @@ Base.hasproperty(x::Tree, sym::Symbol) = haskey(x, sym)
 
 Base.getproperty(x::Tree, sym::Symbol) = elems(x)[sym]
 
-Base.setproperty!(x::Tree{X}, sym::Symbol, val::E) where {X,E<:X} =
+Base.setproperty!(x::Tree{X}, sym::Symbol, val::E) where {X,E<:Union{X,Tree{X}}} =
     setindex!(elems(x), val, sym)
 
+ConstructionBase.setproperties(x::Tree{T}, props::NamedTuple) where {T} =
+    Tree{T}(elems(x)..., pairs(props)...)
+
 #
 # Algebraic construction
 #