Fix ambiguities and test quality with Aqua (#1041)

* Fix ambiguities and test quality with Aqua
* cleanup undefined exports

Author: Affie

Project.toml

@@ -60,6 +60,7 @@ TimeZones = "1.3.1"
 julia = "1.9"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -69,4 +70,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "DataStructures", "GraphPlot", "LinearAlgebra", "Manifolds", "Pkg", "Statistics"]
+test = ["Aqua", "Test", "DataStructures", "GraphPlot", "LinearAlgebra", "Manifolds", "Pkg", "Statistics"]

src/DataBlobs/services/BlobStores.jl

@@ -112,7 +112,7 @@ function addBlob!(dfg::AbstractDFG, entry::BlobEntry, data)
     return addBlob!(getBlobStore(dfg, entry.blobstore), entry, data)
 end
 
-function addBlob!(store::AbstractBlobStore, entry::BlobEntry, data)
+function addBlob!(store::AbstractBlobStore{T}, entry::BlobEntry, data::T) where {T}
     blobId = isnothing(entry.blobId) ? entry.originId : entry.blobId
     return addBlob!(store, blobId, data)
 end
@@ -125,7 +125,9 @@ function addBlob!(store::AbstractBlobStore, blobId::UUID, data, ::String)
     return addBlob!(store, blobId, data)
 end
 
-addBlob!(store::AbstractBlobStore, data, ::String) = addBlob!(store, uuid4(), data)
+function addBlob!(store::AbstractBlobStore{T}, data::T, ::String) where {T}
+    return addBlob!(store, uuid4(), data)
+end
 
 #update
 function updateBlob!(dfg::AbstractDFG, entry::BlobEntry, data::T) where {T}
@@ -336,3 +338,6 @@ end
 function deleteBlob!(store::LinkStore, args...)
     return error("deleteDataBlob(::LinkStore) not supported")
 end
+
+deleteBlob!(store::LinkStore, ::BlobEntry) = deleteBlob!(store)
+deleteBlob!(store::LinkStore, ::UUID) = deleteBlob!(store)

src/Deprecated.jl

@@ -94,9 +94,7 @@ abstract type AbstractBlobEntry end
 @deprecate addDataEntry!(w...; kw...) addBlobEntry!(w...; kw...)
 @deprecate updateDataEntry!(w...; kw...) updateBlobEntry!(w...; kw...)
 @deprecate deleteDataEntry!(w...; kw...) deleteBlobEntry!(w...; kw...)
-@deprecate listDataEntry(w...; kw...) listBlobEntry(w...; kw...)
 @deprecate listDataEntrySequence(w...; kw...) listBlobEntrySequence(w...; kw...)
-@deprecate mergeDataEntry!(w...; kw...) mergeBlobEntry!(w...; kw...)
 
 # @deprecate getData(w...;kw...) getBlob(w...;kw...)
 @deprecate getDataBlob(w...; kw...) getBlob(w...; kw...)

src/DistributedFactorGraphs.jl

@@ -152,7 +152,6 @@ export DFGFactor, DFGFactorSummary, SkeletonDFGFactor, PackedFactor
 
 # Common
 export getSolvable, setSolvable!, isSolvable
-export getInternalId
 export getVariableLabelNumber
 
 # accessors
@@ -164,9 +163,6 @@ export isSolveInProgress, getSolveInProgress
 # CRUD & SET
 export listTags, mergeTags!, removeTags!, emptyTags!
 
-#this isn't acttually implemented. TODO remove or implement
-export addTags!
-
 ##------------------------------------------------------------------------------
 # Variable
 ##------------------------------------------------------------------------------
@@ -185,8 +181,6 @@ export getVariableType
 export getDimension, getManifold, getPointType
 export getPointIdentity, getPoint, getCoordinates
 
-export getManifolds # TODO Deprecate?
-
 # Small Data CRUD
 export SmallDataTypes,
     getSmallData,
@@ -242,12 +236,11 @@ export hasBlobEntry,
     addBlobEntry!,
     updateBlobEntry!,
     deleteBlobEntry!,
-    listBlobEntry,
     listBlobEntrySequence,
-    mergeBlobEntry!
+    mergeBlobEntries!
 export incrDataLabelSuffix
 
-export getBlobEntries, listDataEntries, hasDataEntry, hasDataEntry
+export getBlobEntries, hasDataEntry, hasDataEntry
 export getBlobEntriesVariables
 export listDataEntrySequence
 # convenience wrappers
@@ -319,7 +312,6 @@ export compare,
     compareFactor,
     compareAllVariables,
     compareSimilarVariables,
-    compareSubsetFactorGraph,
     compareSimilarFactors,
     compareFactorGraphs
 

test/runtests.jl

@@ -6,6 +6,7 @@ using Dates
 using TimeZones
 using SHA
 using UUIDs
+using Aqua
 
 # If you want to enable debugging logging (very verbose!)
 # using Logging
@@ -142,3 +143,14 @@ struct NotImplementedDFG{T} <: AbstractDFG{T} end
     @test_throws ErrorException isVariable(dfg, :a)
     @test_throws ErrorException isFactor(dfg, :a)
 end
+
+@testset "Testing Code Quality with Aqua" begin
+    Aqua.test_ambiguities([DistributedFactorGraphs])
+    Aqua.test_unbound_args(DistributedFactorGraphs)
+    Aqua.test_undefined_exports(DistributedFactorGraphs)
+    Aqua.test_piracy(DistributedFactorGraphs)
+    Aqua.test_project_extras(DistributedFactorGraphs)
+    Aqua.test_stale_deps(DistributedFactorGraphs; ignore = [:Colors])
+    Aqua.test_deps_compat(DistributedFactorGraphs)
+    Aqua.test_project_toml_formatting(DistributedFactorGraphs)
+end