docs

docs/src/reference.md

@@ -8,31 +8,27 @@
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/parameter_linearvalue.jl"]
-Private = false
 ```
 
 ### ParameterQuadraticValue
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/parameter_quadraticvalue.jl"]
-Private = false
 ```
 
 ### ParameterBound
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/parameter_bound.jl"]
-Private = false
 ```
 
 ### ParameterIsozyme
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/parameter_isozyme.jl"]
-Private = false
 ```
 ## Parameterized models
 
@@ -41,30 +37,48 @@ Private = false
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/kinetic_model.jl"]
-Private = false
 ```
 
 ### Solving models
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/solver.jl"]
-Private = false
 ```
 
 ### Pruning models
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/prune.jl"]
-Private = false
 ```
 
 ## Differentiation
 
 ```@autodocs
 Modules = [DifferentiableMetabolism]
 Pages = ["src/differentiate.jl"]
-Private = false
 ```
 
+## Internals
+
+### Constraint tree extensions
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/constraint_trees.jl"]
+```
+
+### Optimization problem builders
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/get_constraints.jl"]
+```
+
+### Symbolics extensions
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/symbolics.jl"]
+```

src/differentiate.jl

@@ -16,6 +16,11 @@ See the License for the specific language governing permissions and
 limitations under the License.
 =#
 
+"""
+$(TYPEDSIGNATURES)
+
+TODO
+"""
 function findall_indeps_qr(A)
     #= 
     Filter out linearly dependent constraints using QR decomposition. Since the
@@ -174,6 +179,11 @@ end
 
 export differentiate
 
+"""
+$(TYPEDSIGNATURES)
+
+TODO
+"""
 function variable_order(m)
     c = []
     ff(p, x::ConstraintTrees.ConstraintTree) = nothing

src/parameter_bound.jl

@@ -20,9 +20,9 @@ limitations under the License.
 $(TYPEDEF)
 
 Representation of an "interval" bound where the lower and upper bound values are
-parameters. Since [`Symbolics.Num`](@ref) is a subtype of `Real`, the bounds
-could also be any real number, but they are converted by the constructors to
-[`Symbolics.Num`](@ref)s. 
+parameters. Since `Symbolics.Num` is a subtype of `Real`, the bounds could also
+be any real number, but they are converted by the constructors to
+`Symbolics.Num`s. 
 
 # Fields
 $(TYPEDFIELDS)
@@ -46,9 +46,8 @@ Base.:*(a::Real, b::ParameterBetween) = ParameterBetween(a * b.lower, a * b.uppe
 $(TYPEDEF)
 
 Representation of an "equality" bound, where the bound value is a parameter.
-Since [`Symbolics.Num`](@ref) is a subtype of `Real`, the bound could also be
-any real number, but it is converted by the constructor to a
-[`Symbolics.Num`](@ref).
+Since `Symbolics.Num` is a subtype of `Real`, the bound could also be any real
+number, but it is converted by the constructor to a `Symbolics.Num`.
 
 # Fields
 $(TYPEDFIELDS)

src/parameter_linearvalue.jl

@@ -21,11 +21,13 @@ Changes from copied code are indicated.
 """
 $(TYPEDEF)
 
-An extension of [`ConstraintTrees.LinearValue`](@ref) where the weights are parameters.
+An extension of `ConstraintTrees.LinearValue` where the weights are parameters.
 
-`ParameterLinearValue`s can be combined additively and multiplied by real-number constants.
+`ParameterLinearValue`s can be combined additively and multiplied by real-number
+constants.
 
-Multiplying two `ParameterLinearValue`s yields a quadratic form (in a [`ParameterQuadraticValue`](@ref)).
+Multiplying two `ParameterLinearValue`s yields a quadratic form (in a
+[`ParameterQuadraticValue`](@ref)).
 
 # Fields
 $(TYPEDFIELDS)

src/parameter_quadraticvalue.jl

@@ -21,10 +21,10 @@ Changes from copied code are indicated.
 """
 $(TYPEDEF)
 
-An extension of [`ConstraintTrees.QuadraticValue`](@ref) where the weights are
+An extension of `ConstraintTrees.QuadraticValue` where the weights are
 parameters.
 
-Behaves similarly to [`ConstraintTrees.QuadraticValue`](@ref). Thus, the
+Behaves similarly to `ConstraintTrees.QuadraticValue`. Thus, the
 cleanest way to construct a `ParameterQuadraticValue` is to multiply
 two [`ParameterLinearValue`](@ref)s.
 

src/solver.jl

@@ -51,7 +51,7 @@ $(TYPEDSIGNATURES)
 
 Construct a JuMP model by substituting `parameters` into the model, `m`. Set the
 `objective` and the `optimizer`, as well as the `sense` similar to
-[`COBREXA.optimization_model`](@ref).
+`COBREXA.optimization_model`.
 
 Converts all inequality constraints to the form `A * x ≤ b`.
 """