Merge pull request #47 from yuehhua/develop

Support linear algebra for FeaturedGraph and some refactoring

Author: yuehhua

Manifest.toml

@@ -8,30 +8,36 @@ version = "0.5.0"
 
 [[AbstractTrees]]
 deps = ["Markdown"]
-git-tree-sha1 = "86d092c2599f1f7bb01668bf8eb3412f98d61e47"
+git-tree-sha1 = "33e450545eaf7699da1a6e755f9ea65f14077a45"
 uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.3.2"
+version = "0.3.3"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "c88cfc7f9c1f9f8633cddf0b56e86302b70f64c5"
+git-tree-sha1 = "fd04049c7dd78cfef0b06cdc1f0f181467655712"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "1.0.1"
+version = "1.1.0"
+
+[[ArnoldiMethod]]
+deps = ["DelimitedFiles", "LinearAlgebra", "Random", "SparseArrays", "StaticArrays", "Test"]
+git-tree-sha1 = "2b6845cea546604fb4dca4e31414a6a59d39ddcd"
+uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
+version = "0.0.4"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra"]
-git-tree-sha1 = "bc779df8d73be70e4e05a63727d3a4dfb4c52b1f"
+git-tree-sha1 = "a504dca2ac7eda8761c8f7c1ed52427a1be75a3c"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "0.1.5"
+version = "0.2.6"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[BinaryProvider]]
-deps = ["Libdl", "SHA"]
-git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
+deps = ["Libdl", "Logging", "SHA"]
+git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.5.8"
+version = "0.5.10"
 
 [[CEnum]]
 git-tree-sha1 = "62847acab40e6855a9b5905ccb99c2b5cf6b3ebb"
@@ -82,9 +88,9 @@ version = "0.2.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "067567a322fe466c5ec8d01413eee7127bd11699"
+git-tree-sha1 = "7c4f882c41faa72118841185afc58a2eb00ef612"
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "0.3.1+0"
+version = "0.3.3+0"
 
 [[CuArrays]]
 deps = ["AbstractFFTs", "Adapt", "CEnum", "CUDAapi", "CUDAdrv", "CUDAnative", "DataStructures", "GPUArrays", "Libdl", "LinearAlgebra", "MacroTools", "NNlib", "Printf", "Random", "Requires", "SparseArrays", "TimerOutputs"]
@@ -93,15 +99,15 @@ uuid = "3a865a2d-5b23-5a0f-bc46-62713ec82fae"
 version = "1.7.3"
 
 [[DataAPI]]
-git-tree-sha1 = "674b67f344687a88310213ddfa8a2b3c76cc4252"
+git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.1.0"
+version = "1.3.0"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "5a431d46abf2ef2a4d5d00bd0ae61f651cf854c8"
+git-tree-sha1 = "be680f1ad03c0a03796aa3fda5a2180df7f83b46"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.10"
+version = "0.17.18"
 
 [[Dates]]
 deps = ["Printf"]
@@ -127,23 +133,11 @@ version = "1.0.1"
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
-[[FFTW]]
-deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"]
-git-tree-sha1 = "109d82fa4b00429f9afcce873e9f746f11f018d3"
-uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.2.0"
-
-[[FFTW_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "ddb57f4cf125243b4aa4908c94d73a805f3cbf2c"
-uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a"
-version = "3.3.9+4"
-
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "85c6b57e2680fa28d5c8adc798967377646fbf66"
+git-tree-sha1 = "44f561e293987ffc84272cd3d2b14b0b93123d63"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.8.5"
+version = "0.8.10"
 
 [[FixedPointNumbers]]
 git-tree-sha1 = "4aaea64dd0c30ad79037084f8ca2b94348e65eaa"
@@ -158,9 +152,13 @@ version = "0.10.3"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "88b082d492be6b63f967b6c96b352e25ced1a34c"
+git-tree-sha1 = "869540e4367122fbffaace383a5bdc34d6e5e5ac"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.9"
+version = "0.10.10"
+
+[[Future]]
+deps = ["Random"]
+uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[GPUArrays]]
 deps = ["AbstractFFTs", "Adapt", "LinearAlgebra", "Printf", "Random", "Serialization"]
@@ -170,31 +168,30 @@ version = "2.0.1"
 
 [[IRTools]]
 deps = ["InteractiveUtils", "MacroTools", "Test"]
-git-tree-sha1 = "1a4355e4b5b50be2311ebb644f34f3306dbd0410"
+git-tree-sha1 = "90ee39f9beaaa186e4968417ea2b8ed5673c91c0"
 uuid = "7869d1d1-7146-5819-86e3-90919afe41df"
-version = "0.3.1"
+version = "0.3.3"
 
-[[IntelOpenMP_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "fb8e1c7a5594ba56f9011310790e03b5384998d6"
-uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
-version = "2018.0.3+0"
+[[Inflate]]
+git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c"
+uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9"
+version = "0.1.2"
 
 [[InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Juno]]
 deps = ["Base64", "Logging", "Media", "Profile"]
-git-tree-sha1 = "e1ba2a612645b3e07c773c3a208f215745081fe6"
+git-tree-sha1 = "a686b0cf235fa3e491b79b4783c2d2382292b436"
 uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
-version = "0.8.1"
+version = "0.8.2"
 
 [[LLVM]]
 deps = ["CEnum", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "b6b86801ae2f2682e0a4889315dc76b68db2de71"
+git-tree-sha1 = "72fc0a39d5899091ff2d4cdaa64cb5e4862cf813"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "1.3.4"
+version = "1.5.2"
 
 [[LibGit2]]
 deps = ["Printf"]
@@ -203,19 +200,19 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
+[[LightGraphs]]
+deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
+git-tree-sha1 = "6f85a35d2377cb2db1bc448ed0d6340d2bb1ea64"
+uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
+version = "1.3.3"
+
 [[LinearAlgebra]]
 deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[MKL_jll]]
-deps = ["IntelOpenMP_jll", "Libdl", "Pkg"]
-git-tree-sha1 = "720629cc8cbd12c146ca01b661fd1a6cf66e2ff4"
-uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2019.0.117+2"
-
 [[MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "f7d2e3f654af75f01ec49be82c231c382214223a"
@@ -259,10 +256,9 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.3+3"
 
 [[OrderedCollections]]
-deps = ["Random", "Serialization", "Test"]
-git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
+git-tree-sha1 = "12ce190210d278e12644bcadf5b21cbdcf225cd3"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.1.0"
+version = "1.2.0"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -302,6 +298,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[SimpleTraits]]
+deps = ["InteractiveUtils", "MacroTools"]
+git-tree-sha1 = "2ee666b24ab8be6a922f9d6c11a86e1a703a7dda"
+uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+version = "0.9.2"
+
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
@@ -317,15 +323,15 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["OpenSpecFun_jll"]
-git-tree-sha1 = "e19b98acb182567bcb7b75bb5d9eedf3a3b5ec6c"
+git-tree-sha1 = "d8d8b8a9f4119829410ecd706da4cc8594a1e020"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "0.10.0"
+version = "0.10.3"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
+git-tree-sha1 = "5c06c0aeb81bef54aed4b3f446847905eb6cbda0"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.12.1"
+version = "0.12.3"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -343,9 +349,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TimerOutputs]]
 deps = ["Printf"]
-git-tree-sha1 = "311765af81bbb48d7bad01fb016d9c328c6ede03"
+git-tree-sha1 = "f458ca23ff80e46a630922c555d838303e4b9603"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.3"
+version = "0.5.6"
 
 [[TranscodingStreams]]
 deps = ["Random", "Test"]
@@ -362,21 +368,21 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[ZipFile]]
 deps = ["Libdl", "Printf", "Zlib_jll"]
-git-tree-sha1 = "8748302cfdec02c4ae9c97b112cf10003f7f767f"
+git-tree-sha1 = "254975fef2fc526583bb9b7c9420fe66ffe09f2f"
 uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
-version = "0.9.1"
+version = "0.9.2"
 
 [[Zlib_jll]]
 deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "fd36a6739e256527287c5444960d0266712cd49e"
+git-tree-sha1 = "64b39656c75e67f85b4ac2b336c54674a39f599d"
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+8"
+version = "1.2.11+11"
 
 [[Zygote]]
-deps = ["ArrayLayouts", "DiffRules", "FFTW", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "9688fce24bd8a9468fed12f3d5206099a39054dc"
+deps = ["AbstractFFTs", "ArrayLayouts", "DiffRules", "FillArrays", "ForwardDiff", "Future", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
+git-tree-sha1 = "707ceea58e2bd0ff3077ab13a92f8355181d3ee4"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.4.12"
+version = "0.4.20"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]

Project.toml

@@ -11,6 +11,7 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 IRTools = "7869d1d1-7146-5819-86e3-90919afe41df"
+LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
@@ -28,17 +29,17 @@ DataStructures = "~0.17"
 FillArrays = "^0.8.5"
 Flux = "~0.10"
 IRTools = "~0.3"
+LightGraphs = "1.3"
 Requires = "^1.0.0"
 StaticArrays = "^0.12.1"
 Zygote = "~0.4"
 ZygoteRules = "~0.2"
 julia = "1.4"
 
 [extras]
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "LightGraphs", "SimpleWeightedGraphs", "MetaGraphs"]
+test = ["Test", "SimpleWeightedGraphs", "MetaGraphs"]