fix various stuff in docs

docs/src/index.md

@@ -3,5 +3,5 @@
 
 ```@autodocs
 Modules = [ConstraintTrees]
-Pages = ["ConstraintTrees.jl"]
+Pages = ["src/ConstraintTrees.jl"]
 ```

docs/src/metabolic-modeling.jl

@@ -115,7 +115,7 @@ sum(C.value.(values(c.fluxes)))
 # To demonstrate, let's make a small system with 2 variables.
 system = C.allocate_variables(keys = [:x, :y])
 
-# To add an affine element to a [`Value`](@ref), simply add it as a `Real`
+# To add an affine element to a `Value`, simply add it as a `Real`
 # number, as in the linear transformations below:
 system =
     :original_coords^system *

docs/src/quadratic-optimization.jl

@@ -3,13 +3,13 @@
 #
 # In this example we demonstrate the use of quadratic constraints and values.
 # We assume that the reader is already familiar with the construction of
-# [`ConstraintTree`](@ref)s; if not, it is advisable to read the previous part
+# `ConstraintTree`s; if not, it is advisable to read the previous part
 # of the documentation first.
 #
 # In short, quadratic values and constraints are expressed similarly as other
-# contents of the constraint trees using types [`QValue`](@ref) and
-# [`QConstraint`](@ref), which are quadratic alikes of the linear
-# [`Value`](@ref) and [`Constraint`](@ref).
+# contents of the constraint trees using types `QValue` and
+# `QConstraint`, which are quadratic alikes of the linear
+# `Value` and `Constraint`.
 #
 # ## Working with quadratic values and constraints
 #
@@ -58,7 +58,7 @@ point = C.allocate_variables(keys = [:x, :y])
 ellipse_system = C.make_constraint_tree(
     :point => point,
     :in_area => C.QConstraint(
-        qvalue = squared(point.x.value / 2) + squared(10.0 - point.y.value),
+        qvalue = squared(point.x.value) / 4 + squared(10.0 - point.y.value),
         bound = (-Inf, 1.0),
     ),
 );
@@ -127,6 +127,7 @@ function optimized_vars(cs::C.ConstraintTree, objective::Union{C.Value,C.QValue}
         add_constraint.(values(c))
     end
     add_constraint(cs)
+    JuMP.set_silent(model)
     JuMP.optimize!(model)
     JuMP.value.(model[:x])
 end

docs/src/reference.md

@@ -1,30 +1,53 @@
 
 # Reference
 
-## Values (linear combinations of variables)
+## Values
+
+### Linear and affine values
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["src/value.jl"]
+```
+
+### Quadratic values
 
 ```@autodocs
 Modules = [ConstraintTrees]
-Pages = ["value.jl"]
+Pages = ["src/qvalue.jl"]
 ```
 
 ## Constraints
 
 ```@autodocs
 Modules = [ConstraintTrees]
-Pages = ["constraint.jl"]
+Pages = ["src/bound.jl"]
+```
+
+### Linear and affine constraints
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["src/constraint.jl"]
+```
+
+### Quadratic constraints
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["src/qconstraint.jl"]
 ```
 
 ## Constraint trees
 
 ```@autodocs
 Modules = [ConstraintTrees]
-Pages = ["constraint_tree.jl"]
+Pages = ["src/constraint_tree.jl"]
 ```
 
 ## Solution trees
 
 ```@autodocs
 Modules = [ConstraintTrees]
-Pages = ["solution.jl"]
+Pages = ["src/solution_tree.jl"]
 ```