update broken and missing docstrings (#303)

* update broken and missing

* update field accessor ref ♥regex

Author: Affie

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 
 [compat]

docs/make.jl

@@ -1,4 +1,5 @@
 using Documenter
+using GraphPlot
 using DistributedFactorGraphs
 
 makedocs(

docs/src/BuildingGraphs.md

@@ -111,16 +111,16 @@ Reading, updating, and deleting all use DFG functions (as opposed to adding,
 where using the IncrementalInference functions are recommended).
 
 Each variable and factor is uniquely identified by its label. The list of
-variable and factor labels can be retrieved with the `ls`/`getVariableIds` and
-`lsf`/`getFactorIds` functions:
+variable and factor labels can be retrieved with the `ls`/`listVariables` and
+`lsf`/`listFactors` functions:
 
 ```@docs
-getVariableIds
+listVariables
 ls
 ```
 
 ```@docs
-getFactorIds
+listFactors
 lsf
 ```
 

docs/src/GraphData.md

@@ -43,27 +43,24 @@ Labels are the principle identifier of a variable or factor.
 getLabel
 ```
 
-```@docs
-getLabel
-```
-
 #### Timestamps
 
 Each variable or factor can have a timestamp associated with it.
 
 ```@docs
 getTimestamp
-setTimestamp!
+setTimestamp
 ```
 
 #### Tags
 
 Tags are a set of symbols that contain identifiers for the variable or factor.
 
 ```@docs
-addTag
+listTags
 mergeTags!
-deleteTags!
+removeTags!
+emptyTags!
 ```
 
 ### Solvable
@@ -95,7 +92,6 @@ For each PPE structure, there are accessors for getting individual values:
 getMaxPPE
 getMeanPPE
 getSuggestedPPE
-getPPE
 ```
 
 Related functions for getting, adding/updating, and deleting PPE structures:
@@ -106,6 +102,7 @@ getPPE
 addPPE!
 updatePPE!
 deletePPE!
+mergePPEs!
 ```
 
 Example of PPE operations:
@@ -139,6 +136,7 @@ getVariableSolverData
 addVariableSolverData!
 updateVariableSolverData!
 deleteVariableSolverData!
+mergeVariableSolverData!
 ```
 
 Example of solver data operations:
@@ -163,7 +161,7 @@ itself, large entries will slow the graph down, so if data should exceed a
 few bytes/kb, it should rather be saved in bigData.
 
 ```@docs
-getSmallData,
+getSmallData
 setSmallData!
 ```
 

docs/src/TraversingAndQuerying.md

@@ -4,6 +4,5 @@
 getNeighbors
 getSubgraphAroundNode
 getSubgraph
-getIncidenceMatrix
-getIncidenceMatrixSparse
+getBiadjacencyMatrix
 ```

docs/src/func_ref.md

@@ -7,67 +7,6 @@ Pages = [
 Depth = 3
 ```
 
-### Graph Types
-```@docs
-GraphsDFG
-```
-
-### Creating DFG Factor Graphs
-```@docs
-addVariable!
-addFactor!
-```
-
-### Getting Factor Graph Nodes
-```@docs
-getVariables
-getFactors
-getVariable
-getFactor
-getNeighbors
-ls
-lsf
-```
-
-### Updating Factor Graph Nodes
-```@docs
-updateVariable!
-updateFactor!
-```
-
-### Deleting Factor Graph Nodes
-```@docs
-deleteVariable!
-deleteFactor!
-```
-
-### Getting Adjacency Matrix
-```@docs
-getIncidenceMatrix
-getIncidenceMatrixSparse
-```
-
-### Validating Factor Graph Connectivity
-```@docs
-isFullyConnected
-hasOrphans
-```
-
-### Copying Subgraphs
-```@docs
-getSubgraphAroundNode
-getSubgraph
-```
-
-### Summaries
-```@docs
-getSummary
-getSummaryGraph
-```
-
-### Visualization and Plotting
-```@docs
-toDot
-toDotFile
-dfgplot
+```@autodocs
+Modules = [DistributedFactorGraphs, LightDFGs, DFGPlots]
 ```

src/LightDFG/FactorGraphs/FactorGraphs.jl

@@ -95,11 +95,6 @@ zero(g::FactorGraph{T,V,F}) where {T,V,F} = FactorGraph{T,V,F}(0,0)
 
 # TODO issubset(g::T, h::T) where T <: FactorGraph = issubset(g.graph, h.graph)
 
-"""
-    add_edge!(g, u, v)
-    Add an edge `(u, v)` to FactorGraph `g`.
-    return true if the edge has been added, false otherwise
-"""
 @inline add_edge!(g::FactorGraph, x...) = add_edge!(g.graph, x...)
 
 @inline rem_edge!(g::FactorGraph, x...) = rem_edge!(g.graph, x...)

src/entities/DFGFactor.jl

@@ -69,38 +69,38 @@ $(TYPEDFIELDS)
 """
 mutable struct DFGFactor{T, S} <: AbstractDFGFactor
     """Factor label, e.g. :x1f1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Variable timestamp.
-    Accessors: `getTimestamp`, `setTimestamp!`"""
+    Accessors: [`getTimestamp`](@ref), [`setTimestamp`](@ref)"""
     timestamp::DateTime
     """Factor tags, e.g [:FACTOR].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
     """Solver data.
-    Accessors: `getSolverData`, `setSolverData!`"""
+    Accessors: [`getSolverData`](@ref), [`setSolverData!`](@ref)"""
     solverData::GenericFunctionNodeData{T, S}
     """Solvable flag for the factor.
-    Accessors: `getSolvable`, `setSolvable!`
+    Accessors: [`getSolvable`](@ref), [`setSolvable!`](@ref)
     TODO: Switch to `DFGNodeParams`"""
     solvable::Int #TODO we can go with DFGNodeParams or Reference the solvable field with getproperty overload
     """Mutable parameters for the variable. We suggest using accessors to get to this data.
-    Accessors: `getSolvable`, `setSolvable!`"""
+    Accessors: [`getSolvable`](@ref), [`setSolvable!`](@ref)"""
     _dfgNodeParams::DFGNodeParams
     """Internal cache of the ordering of the neighbor variables. Rather use getNeighbors to get the list as this is an internal value.
-    Accessors: `getVariableOrder`"""
+    Accessors: [`getVariableOrder`](@ref)"""
     _variableOrderSymbols::Vector{Symbol}
 end
 
 ##------------------------------------------------------------------------------
 ## Constructors
 
+#TODO _internalId?
 """
 $(SIGNATURES)
 
 Construct a DFG factor given a label.
 """
-#TODO _internalId?
 DFGFactor{T, S}(label::Symbol, internalId::Int64=0, timestamp::DateTime=now()) where {T, S} =
                 DFGFactor(label, timestamp, Set{Symbol}(), GenericFunctionNodeData{T, S}(), 1, DFGNodeParams(1, internalId), Symbol[])
 
@@ -130,18 +130,18 @@ $(TYPEDFIELDS)
 """
 struct DFGFactorSummary <: AbstractDFGFactor
     """Factor label, e.g. :x1f1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Variable timestamp.
-    Accessors: `getTimestamp`"""
+    Accessors: [`getTimestamp`](@ref)"""
     timestamp::DateTime
     """Factor tags, e.g [:FACTOR].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
     """Internal ID used by some of the DFG drivers. We don't suggest using this outside of DFG."""
     _internalId::Int64
     """Internal cache of the ordering of the neighbor variables. Rather use getNeighbors to get the list as this is an internal value.
-    Accessors: `getVariableOrder`"""
+    Accessors: [`getVariableOrder`](@ref)"""
     _variableOrderSymbols::Vector{Symbol}
 end
 
@@ -159,13 +159,13 @@ $(TYPEDFIELDS)
 """
 struct SkeletonDFGFactor <: AbstractDFGFactor
     """Factor label, e.g. :x1f1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Factor tags, e.g [:FACTOR].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
     """Internal cache of the ordering of the neighbor variables. Rather use getNeighbors to get the list as this is an internal value.
-    Accessors: `getVariableOrder`"""
+    Accessors: [`getVariableOrder`](@ref)"""
     _variableOrderSymbols::Vector{Symbol}
 end
 

src/entities/DFGVariable.jl

@@ -178,28 +178,28 @@ $(TYPEDFIELDS)
 """
 struct DFGVariable{T<:InferenceVariable} <: AbstractDFGVariable
     """Variable label, e.g. :x1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Variable timestamp.
-    Accessors: `getTimestamp`, `setTimestamp!`"""
+    Accessors: [`getTimestamp`](@ref), [`setTimestamp`](@ref)"""
     timestamp::DateTime
     """Variable tags, e.g [:POSE, :VARIABLE, and :LANDMARK].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
     """Dictionary of parametric point estimates keyed by solverDataDict keys
-    Accessors: `addPPE!`, `updatePPE!`, and `deletePPE!`"""
+    Accessors: [`addPPE!`](@ref), [`updatePPE!`](@ref), and [`deletePPE!`](@ref)"""
     ppeDict::Dict{Symbol, <: AbstractPointParametricEst}
     """Dictionary of solver data. May be a subset of all solutions if a solver key was specified in the get call.
-    Accessors: `addVariableSolverData!`, `updateVariableSolverData!`, and `deleteVariableSolverData!`"""
+    Accessors: [`addVariableSolverData!`](@ref), [`updateVariableSolverData!`](@ref), and [`deleteVariableSolverData!`](@ref)"""
     solverDataDict::Dict{Symbol, VariableNodeData{T}}
     """Dictionary of small data associated with this variable.
-    Accessors: [`getSmallData!`](@ref), [`setSmallData!`](@ref)"""
+    Accessors: [`getSmallData`](@ref), [`setSmallData!`](@ref)"""
     smallData::Dict{String, String}#Ref{Dict{String, String}} #why was Ref here?
     """Dictionary of large data associated with this variable.
-    Accessors: `addBigDataEntry!`, `getBigDataEntry`, `updateBigDataEntry!`, and `deleteBigDataEntry!`"""
+    Accessors: [`addBigDataEntry!`](@ref), [`getBigDataEntry`](@ref), [`updateBigDataEntry!`](@ref), and [`deleteBigDataEntry!`](@ref)"""
     bigData::Dict{Symbol, AbstractBigDataEntry}
     """Mutable parameters for the variable. We suggest using accessors to get to this data.
-    Accessors: `getSolvable`, `setSolvable!`"""
+    Accessors: [`getSolvable`](@ref), [`setSolvable!`](@ref)"""
     _dfgNodeParams::DFGNodeParams
 end
 
@@ -254,22 +254,22 @@ $(TYPEDFIELDS)
 """
 struct DFGVariableSummary <: AbstractDFGVariable
     """Variable label, e.g. :x1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Variable timestamp.
-    Accessors: `getTimestamp`, `setTimestamp!`"""
+    Accessors: [`getTimestamp`](@ref), [`setTimestamp`](@ref)"""
     timestamp::DateTime
     """Variable tags, e.g [:POSE, :VARIABLE, and :LANDMARK].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
     """Dictionary of parametric point estimates keyed by solverDataDict keys
-    Accessors: `addPPE!`, `updatePPE!`, and `deletePPE!`"""
+    Accessors: [`addPPE!`](@ref), [`updatePPE!`](@ref), and [`deletePPE!`](@ref)"""
     ppeDict::Dict{Symbol, <:AbstractPointParametricEst}
     """Symbol for the softtype for the underlying variable.
-    Accessor: `getSofttype`"""
+    Accessor: [`getSofttype`](@ref)"""
     softtypename::Symbol
     """Dictionary of large data associated with this variable.
-    Accessors: `addBigDataEntry!`, `getBigDataEntry`, `updateBigDataEntry!`, and `deleteBigDataEntry!`"""
+    Accessors: [`addBigDataEntry!`](@ref), [`getBigDataEntry`](@ref), [`updateBigDataEntry!`](@ref), and [`deleteBigDataEntry!`](@ref)"""
     bigData::Dict{Symbol, AbstractBigDataEntry}
     """Internal ID used by some of the DFG drivers. We don't suggest using this outside of DFG."""
     _internalId::Int64
@@ -289,10 +289,10 @@ $(TYPEDFIELDS)
 """
 struct SkeletonDFGVariable <: AbstractDFGVariable
     """Variable label, e.g. :x1.
-    Accessor: `getLabel`"""
+    Accessor: [`getLabel`](@ref)"""
     label::Symbol
     """Variable tags, e.g [:POSE, :VARIABLE, and :LANDMARK].
-    Accessors: `getTags`, `addTags!`, and `deleteTags!`"""
+    Accessors: [`getTags`](@ref), [`mergeTags!`](@ref), and [`removeTags!`](@ref)"""
     tags::Set{Symbol}
 end
 

src/services/AbstractDFG.jl

@@ -966,14 +966,14 @@ end
 
 
 
+# TODO API name get seems wrong maybe just biadjacencyMatrix
 """
     $(SIGNATURES)
 Get a matrix indicating adjacency between variables and factors. Returned as
 a named tuple: B::SparseMatrixCSC{Int}, varLabels::Vector{Symbol)
 facLabels::Vector{Symbol). Rows are the factors, columns are the variables,
 with the corresponding labels in varLabels,facLabels.
 """
-# TODO API name get seems wrong maybe just biadjacencyMatrix
 function getBiadjacencyMatrix(dfg::AbstractDFG; solvable::Int=0)::NamedTuple{(:B, :varLabels, :facLabels), Tuple{SparseMatrixCSC, Vector{Symbol}, Vector{Symbol}}}
     varLabels = map(v->v.label, getVariables(dfg, solvable=solvable))
     factLabels = map(f->f.label, getFactors(dfg, solvable=solvable))