diff --git a/docs/src/3-parameter-estimation.jl b/docs/src/3-parameter-estimation.jl
index 72bf616..7414e26 100644
--- a/docs/src/3-parameter-estimation.jl
+++ b/docs/src/3-parameter-estimation.jl
@@ -156,4 +156,4 @@ true_parameter_values
 @test abs(estimated_parameters[r3] - true_parameter_values[r3]) <= 0.1 #src
 @test abs(estimated_parameters[r4] - true_parameter_values[r4]) <= 0.1 #src
 @test abs(estimated_parameters[r4] - true_parameter_values[r4]) <= 0.1 #src
-@test all(losses[2:end] .<= losses[1:end-1]) #src strictly decreasing
+@test all(losses[2:end] .<= losses[1:end-1]) #src
diff --git a/docs/src/reference.md b/docs/src/reference.md
index 83d62d7..3eb05fe 100644
--- a/docs/src/reference.md
+++ b/docs/src/reference.md
@@ -12,7 +12,51 @@ Pages = ["src/parameter_linearvalue.jl"]
 
 ### ParameterQuadraticValue
 
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/parameter_quadraticvalue.jl"]
+```
+
 ### ParameterBound
 
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/parameter_bound.jl"]
+```
+
 ### ParameterIsozyme
 
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/parameter_isozyme.jl"]
+```
+## Parameterized models
+
+### Kinetic models
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/kinetic_model.jl"]
+```
+
+### Solving models
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/solver.jl"]
+```
+
+### Pruning models
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/prune.jl"]
+```
+
+## Differentiation
+
+```@autodocs
+Modules = [DifferentiableMetabolism]
+Pages = ["src/differentiate.jl"]
+```
+
diff --git a/src/get_constraints.jl b/src/get_constraints.jl
index 9822e5e..e39722e 100644
--- a/src/get_constraints.jl
+++ b/src/get_constraints.jl
@@ -36,8 +36,6 @@ function equality_constraints(m::ConstraintTrees.ConstraintTree)
     sink
 end
 
-export equality_constraints
-
 function get_equality_constraints(m::ConstraintTrees.ConstraintTree, sink)
     get_equality_constraints.(values(m), Ref(sink))
 end
@@ -75,8 +73,6 @@ function inequality_constraints(m::ConstraintTrees.ConstraintTree)
     ]
 end
 
-export inequality_constraints
-
 function get_inequality_constraints(m::ConstraintTrees.ConstraintTree, sink)
     get_inequality_constraints.(values(m), Ref(sink))
 end
diff --git a/src/kinetic_model.jl b/src/kinetic_model.jl
index 68a2cef..32c6032 100644
--- a/src/kinetic_model.jl
+++ b/src/kinetic_model.jl
@@ -1,3 +1,9 @@
+"""
+$(TYPEDSIGNATURES)
+
+Essentially an enzyme constrained metabolic model, but the kcat can be a
+arbitrary symbolic function.
+"""
 function build_kinetic_model(
     model::AbstractFBCModels.AbstractFBCModel;
     reaction_isozymes::Union{
diff --git a/src/prune.jl b/src/prune.jl
index 84223df..4ee2709 100644
--- a/src/prune.jl
+++ b/src/prune.jl
@@ -14,8 +14,6 @@ distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
-
-Changes from copied code are indicated.
 =#
 
 """
@@ -66,6 +64,11 @@ end
 
 export prune_model
 
+"""
+$(TYPEDSIGNATURES)
+
+TODO
+"""
 function prune_reaction_isozymes(reaction_isozymes, ec_solution, gene_zero_tol)
     active_isozymes = [
         rid => iso_id for iso_amounts in
@@ -99,6 +102,11 @@ end
 
 export prune_reaction_isozymes
 
+"""
+$(TYPEDSIGNATURES)
+
+TODO
+"""
 function prune_gene_product_molar_masses(
     gene_product_molar_masses,
     ec_solution,