Merge pull request #3 from COBREXA/mk-small-updates

improve tests and description a bit

README.md

@@ -5,11 +5,15 @@
 |:---:|:---:|
 | ![CI status](https://github.com/COBREXA/ConstraintTrees.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/COBREXA/ConstraintTrees.jl/branch/master/graph/badge.svg?token=A2ui7exGIH)](https://codecov.io/gh/COBREXA/ConstraintTrees.jl) | [![stable documentation](https://img.shields.io/badge/docs-stable-blue)](https://cobrexa.github.io/ConstraintTrees.jl/stable) [![dev documentation](https://img.shields.io/badge/docs-dev-cyan)](https://cobrexa.github.io/ConstraintTrees.jl/dev) |
 
-ConstraintTree provides a simple data structure `ConstraintTree` for organizing
-the contents of constraint-based linear problems. As a main goal, it abstracts
-over the distinction between constraints and variables, allowing much tidier
-representation for many kinds of complex constraint systems. The primary
-purpose is to support constraint-based metabolic modeling within COBREXA.jl.
+Package `ConstraintTrees.jl` provides a simple data structure `ConstraintTree`
+for organizing the contents of linear constrained optimization problems. As a
+main goal, it abstracts over the distinction between constraints and variables,
+allowing much tidier representation for many kinds of complex constraint
+systems. The primary purpose is to support constraint-based metabolic modeling
+within [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl).
+
+`ConstraintTrees.jl` is new and under active development. Feel free to discuss
+the changes and ideas.
 
 #### Acknowledgements
 

docs/src/metabolic-modeling.jl

@@ -90,12 +90,22 @@ collect(keys(c))
 
 @test 2 == length((keys(c)))#src
 
-# ## Adding combined constraints
+# ## Value and constraint arithmetics
 
 # Values may be combined additively and multiplied by real constants; which
 # allows us to easily create more complex linear combination of any values
 # already occurring in the model:
-c.fluxes.R_PFK.value - 2 * c.fluxes.R_ACALD.value
+3 * c.fluxes.R_PFK.value - c.fluxes.R_ACALD.value / 2
+
+# For simplicity, you can also scale whole constraints, but it is impossible to
+# add them together because the meaning of the bounds would get broken:
+(3 * c.fluxes.R_PFK, -c.fluxes.R_ACALD / 2)
+
+# To process constraints in bulk, you may use `C.value` for easier access to
+# values and making constraints.
+sum(C.value.(values(c.fluxes)))
+
+# ## Adding combined constraints
 
 # Metabolic modeling relies on the fact that the total rates of any metabolite
 # getting created and consumed by the reaction equals to zero (which

src/constraint.jl

@@ -38,6 +38,7 @@ Base.@kwdef struct Constraint
     bound::Bound = nothing
 end
 
+Base.:-(a::Constraint) = -1 * a
 Base.:*(a::Real, b::Constraint) = b * a
 Base.:*(a::Constraint, b::Real) = Constraint(
     value = a.value * b,

test/misc.jl

@@ -0,0 +1,35 @@
+
+import ConstraintTrees as C
+import SparseArrays as SP
+
+@testset "Values" begin
+    x = C.Value(SP.sparse([5.0, 0, 6.0, 0])) + C.Value(idxs = [2, 3], weights = [5.0, 4.0])
+    @test x.idxs == [1, 2, 3]
+    @test x.weights == [5.0, 5.0, 10.0]
+end
+
+@testset "Constraint tree operations" begin
+    ct1 = C.allocate_variables(keys = [:a, :b])
+    ct2 = C.allocate_variables(keys = [:c, :d])
+
+    @test collect(propertynames(ct1)) == [:a, :b]
+    @test [k for (k, _) in ct2] == [:c, :d]
+    @test eltype(ct2) == Pair{Symbol,C.ConstraintTreeElem}
+    @test collect(keys((:x^ct1 * :x^ct2).x)) == [:a, :b, :c, :d]
+    @test_throws ErrorException ct1 * ct1
+    @test_throws ErrorException :a^ct1 * ct1
+    @test_throws ErrorException ct1 * :a^ct1
+end
+
+@testset "Constraint tree operations" begin
+    ct = C.allocate_variables(keys = [:a, :b])
+    @test_throws BoundsError C.solution_tree(ct, [1.0])
+    st = C.solution_tree(ct, [123.0, 321.0])
+    @test st.a == 123.0
+    @test st[:b] == 321.0
+    @test collect(propertynames(st)) == [:a, :b]
+    @test collect(keys(st)) == [:a, :b]
+    @test sum([v for (_, v) in st]) == 444.0
+    @test sum(values(st)) == 444.0
+    @test eltype(st) == Pair{Symbol,C.SolutionTreeElem}
+end

test/runtests.jl

@@ -3,5 +3,11 @@ import ConstraintTrees
 using Test
 
 @testset "ConstraintTrees tests" begin
-    include("../docs/src/metabolic-modeling.jl")
+    @testset "Metabolic modeling" begin
+        include("../docs/src/metabolic-modeling.jl")
+    end
+
+    @testset "Miscellaneous methods" begin
+        include("misc.jl")
+    end
 end