fixup docs

stelmo · Aug 11, 2024 · c2d31b8 · c2d31b8
1 parent c1bdcae
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Showing 5 changed files with 61 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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,