Changing names

danspielman · Aug 26, 2018 · ad08368 · ad08368
1 parent 91ea21f
commit ad08368
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Showing 37 changed files with 211 additions and 203 deletions.
diff --git a/Manifest.toml b/Manifest.toml
@@ -1,8 +1,8 @@
 [[Arpack]]
 deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "Random", "SparseArrays", "Test"]
-git-tree-sha1 = "ffc099065b47835213386df346e4a8b807c320cd"
+git-tree-sha1 = "5b046410fb617d9cf2f8bc0edd5da05a2e5a2ad4"
 uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
-version = "0.2.2"
+version = "0.2.3"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -15,9 +15,9 @@ version = "0.8.10"
 
 [[BinaryProvider]]
 deps = ["Libdl", "Pkg", "SHA", "Test"]
-git-tree-sha1 = "ffbf89cc49b073cffdb91381b7ee60557a03ec96"
+git-tree-sha1 = "b530fbeb6f41ab5a83fbe3db1fcbe879334bcd2d"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.4.1"
+version = "0.4.2"
 
 [[BufferedStreams]]
 deps = ["Compat", "Pkg", "Test"]
@@ -33,15 +33,15 @@ version = "0.5.4"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random", "Test"]
-git-tree-sha1 = "b45e62af8eabea138c381c04972c4b25d47e6c69"
+git-tree-sha1 = "0e3209ba7418aed732e5c3818076b4400ee36c08"
 uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.7.3"
+version = "0.7.4"
 
 [[Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Pkg", "Printf", "Reexport", "Test"]
-git-tree-sha1 = "22dbaed87c2b5a2df5caeca48c5f25fe7b6b009a"
+git-tree-sha1 = "26f24e97782dd19d52cf97073c316897ac4d0e30"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.9.2"
+version = "0.9.3"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
@@ -177,10 +177,10 @@ uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
 version = "0.3.1"
 
 [[LibExpat]]
-deps = ["Compat"]
-git-tree-sha1 = "8ba2ca1635ec1755bcf1432c9a2aa6c91a3fb4fd"
+deps = ["Compat", "Pkg"]
+git-tree-sha1 = "fde352ec13479e2f90e57939da2440fb78c5e388"
 uuid = "522f3ed2-3f36-55e3-b6df-e94fee9b0c07"
-version = "0.4.2"
+version = "0.5.0"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -256,15 +256,15 @@ version = "0.3.0"
 
 [[PlotUtils]]
 deps = ["Colors", "Dates", "Printf", "Random", "Reexport", "Test"]
-git-tree-sha1 = "6fd6fafca71798236eccdf5fb1f7e997884e1ad2"
+git-tree-sha1 = "78553a920c4869d20742ba66193e3692369086ec"
 uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "0.5.3"
+version = "0.5.4"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "FixedPointNumbers", "GR", "JSON", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "RecipesBase", "Reexport", "Requires", "Showoff", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "Test", "UUIDs"]
-git-tree-sha1 = "11d668ff24983dd998e264488f4a91a06e11760f"
+git-tree-sha1 = "935241178e80158451cc33f4af7c57f671b881b8"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "0.19.2"
+version = "0.19.3"
 
 [[Printf]]
 deps = ["Unicode"]
@@ -277,16 +277,16 @@ uuid = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
 version = "0.3.0"
 
 [[PyCall]]
-deps = ["Compat", "Conda", "MacroTools", "VersionParsing"]
-git-tree-sha1 = "7a09c45434dff15556ed6b4496390d5c5932ac5d"
+deps = ["Compat", "Conda", "MacroTools", "Statistics", "VersionParsing"]
+git-tree-sha1 = "993d80a2cfd0fc4b2acc698370a4f9761b27cd9e"
 uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-version = "1.18.0"
+version = "1.18.2"
 
 [[PyPlot]]
-deps = ["Colors", "Compat", "LaTeXStrings", "PyCall", "Test", "VersionParsing"]
-git-tree-sha1 = "3a0908224526b378cb0eb1b770385e23b70adb5c"
+deps = ["Base64", "Colors", "Compat", "LaTeXStrings", "PyCall", "VersionParsing"]
+git-tree-sha1 = "1cc673ec375f6fa0e3652e23ba435195f8175387"
 uuid = "d330b81b-6aea-500a-939a-2ce795aea3ee"
-version = "2.6.0"
+version = "2.6.1"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets"]
@@ -328,15 +328,15 @@ version = "0.5.2"
 
 [[Revise]]
 deps = ["Distributed", "FileWatching", "InteractiveUtils", "LibGit2", "OrderedCollections", "Pkg", "REPL", "Random", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "0a98de1780c326498d62a635ebf72654de2c4b24"
+git-tree-sha1 = "97ad3c4ad52b692ae1e0f54b17c517e7c20916e0"
 uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
-version = "0.6.9"
+version = "0.7.2"
 
 [[RoundingIntegers]]
-deps = ["Compat"]
-git-tree-sha1 = "b20dfee859219aadb5dc8f25190212a25d36173b"
+deps = ["Pkg", "Test"]
+git-tree-sha1 = "293ba0ab32218b9ffd596040224228def84f8da0"
 uuid = "d5f540fe-1c90-5db3-b776-2e2f362d9394"
-version = "0.0.3"
+version = "0.2.0"
 
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

diff --git a/compare/baseTest.jl b/compare/baseTest.jl
@@ -8,17 +8,17 @@ include("/Users/spielman/Laplacians/compare/matlabSafe.jl")
 include("/Users/spielman/Laplacians/compare/compare_solvers_TL.jl")
 
 ac_deg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
 end
 ac_wdeg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
 end
 
 
 test1 = SolverTest(ac_deg, "ac")
 test2 = SolverTest(ac_wdeg, "ac_w")
 # removed chol because killing it can cause a crash
-#test3 = SolverTest(cholLap, "chol")
+#test3 = SolverTest(chol_lap, "chol")
 #test4 = SolverTest(cgLapSolver, "cg")
 tests = [test1 test2]
 

diff --git a/compare/st_chimera.jl b/compare/st_chimera.jl
@@ -22,10 +22,10 @@ include("$(lapdir)/compare/compare_solvers_TL.jl")
 
 
 ac_deg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
 end
 ac_wdeg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
 end
 
 
@@ -34,7 +34,7 @@ test_acw = SolverTest(ac_wdeg, "ac_fast")
 test_amg = SolverTest(AMGLapSolver, "pyamg")
 
 # removed chol because killing it can cause a crash
-#test3 = SolverTest(cholLap, "chol")
+#test3 = SolverTest(chol_lap, "chol")
 #test4 = SolverTest(cgLapSolver, "cg")
 tests = [test_ac test_acw test_amg]
 

diff --git a/compare/st_grid2.jl b/compare/st_grid2.jl
@@ -21,17 +21,17 @@ include("$(lapdir)/compare/compare_solvers_TL.jl")
 
 
 ac_deg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
 end
 ac_wdeg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
 end
 
 
 test_ac = SolverTest(ac_deg, "ac")
 test_acw = SolverTest(ac_wdeg, "ac_fast")
 test_amg = SolverTest(AMGLapSolver, "pyamg")
-test_chol = SolverTest(cholLap, "chol")
+test_chol = SolverTest(chol_lap, "chol")
 
 tests = [test_ac test_acw test_amg test_chol]
 

diff --git a/compare/st_grid3.jl b/compare/st_grid3.jl
@@ -21,10 +21,10 @@ include("$(lapdir)/compare/compare_solvers_TL.jl")
 
 
 ac_deg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:deg), verbose=verbose, args...)
 end
 ac_wdeg = function(a; verbose=false, args...)
-    approxCholLap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
+    approxchol_lap(a; params=ApproxCholParams(:wdeg), verbose=verbose, args...)
 end
 
 

diff --git a/devel/develAKPW.ipynb b/devel/develAKPW.ipynb
@@ -90,7 +90,7 @@
     "srand(1)\n",
     "a = grid2(1100)\n",
     "t = akpwU(a)\n",
-    "sum(compStretches(t,a))/nnz(a)"
+    "sum(comp_stretches(t,a))/nnz(a)"
    ]
   },
   {
@@ -115,7 +115,7 @@
     "# this should produce 32.47723881214327\n",
     "#a = grid2(1100)\n",
     "t = akpw(a)\n",
-    "sum(compStretches(t,a))/nnz(a)"
+    "sum(comp_stretches(t,a))/nnz(a)"
    ]
   },
   {
@@ -154,7 +154,7 @@
     " 6.76587  6.80419\n",
     "=#\n",
     "a = wtedChimera(60100,22)\n",
-    "f(t) = sum(compStretches(t,a))/nnz(a)\n",
+    "f(t) = sum(comp_stretches(t,a))/nnz(a)\n",
     "@time t5 = akpw(a);\n",
     "@time t2 = akpw(a, ver=2);\n",
     "[f(t5) f(t2)]\n",
@@ -456,7 +456,7 @@
    ],
    "source": [
     "@time a = wtedChimera(601000,20)\n",
-    "f(t) = sum(compStretches(t,a))/nnz(a)\n",
+    "f(t) = sum(comp_stretches(t,a))/nnz(a)\n",
     "@time t6 = akpwish(a,ver=6)\n",
     "@time t5 = akpwish(a,ver=5)\n",
     "@time t2 = akpwish(a,ver=2)\n",
@@ -489,7 +489,7 @@
    ],
    "source": [
     "@time a = wtedChimera(601000,20)\n",
-    "f(t) = sum(compStretches(t,a))/nnz(a)\n",
+    "f(t) = sum(comp_stretches(t,a))/nnz(a)\n",
     "@time t5 = akpwish(a,ver=5)\n",
     "@time t4 = akpwish(a,ver=4)\n",
     "@time t2 = akpwish(a,ver=2)\n",
@@ -547,7 +547,7 @@
     "\n",
     "for i in 1:10\n",
     "    a = wtedChimera(n,i)\n",
-    "    f(t) = sum(compStretches(t,a))/nnz(a)\n",
+    "    f(t) = sum(comp_stretches(t,a))/nnz(a)\n",
     "    \n",
     "    try\n",
     "    \n",
@@ -657,7 +657,7 @@
    ],
    "source": [
     "a = wtedChimera(301,8)\n",
-    "    f(t) = sum(compStretches(t,a))/nnz(a)\n",
+    "    f(t) = sum(comp_stretches(t,a))/nnz(a)\n",
     "\n",
     "    tic()\n",
     "    tr = akpwish(a,ver=0)\n",
@@ -734,17 +734,17 @@
     "    \n",
     "\n",
     "    t1 = akpwU(a)\n",
-    "    push!(st1, sum(compStretches(t1,a)) / nnz(a) )\n",
+    "    push!(st1, sum(comp_stretches(t1,a)) / nnz(a) )\n",
     "\n",
     "    \n",
     "    t2 = akpwU(a,x->(1/(log(x+1))))\n",
-    "    push!(st2, sum(compStretches(t2,a)) / nnz(a) )\n",
+    "    push!(st2, sum(comp_stretches(t2,a)) / nnz(a) )\n",
     "\n",
     "    t3 = akpwU(a,x->(1/(2*exp(sqrt(log(x))))))\n",
-    "    push!(st3, sum(compStretches(t3,a)) / nnz(a) )\n",
+    "    push!(st3, sum(comp_stretches(t3,a)) / nnz(a) )\n",
     "    \n",
     "    told = akpw(a)\n",
-    "    push!(stold, sum(compStretches(told,a)) / nnz(a) )\n",
+    "    push!(stold, sum(comp_stretches(told,a)) / nnz(a) )\n",
     "\n",
     "end\n",
     "\n",
@@ -790,7 +790,7 @@
     "\n",
     "\n",
     "    t5 = akpwU(a,x->(1/(2*log(x))))\n",
-    "    push!(st5, sum(compStretches(t5,a)) / nnz(a) )\n",
+    "    push!(st5, sum(comp_stretches(t5,a)) / nnz(a) )\n",
     "    \n",
     "\n",
     "end\n",
@@ -856,19 +856,19 @@
     "    tic()\n",
     "    tnew = akpwish(a)\n",
     "    timenew += toq()\n",
-    "    push!(stnew, sum(compStretches(tnew,a)) / nnz(a) )\n",
+    "    push!(stnew, sum(comp_stretches(tnew,a)) / nnz(a) )\n",
     "\n",
     "    \n",
     "    tic()\n",
     "    tp = randishPrim(a)\n",
     "    timep += toq()\n",
-    "    push!(stp, sum(compStretches(tp,a)) / nnz(a) )    \n",
+    "    push!(stp, sum(comp_stretches(tp,a)) / nnz(a) )    \n",
     "    \n",
     "    \n",
     "    tic()\n",
     "    told = akpw(a)\n",
     "    timeold += toq()\n",
-    "    push!(stold, sum(compStretches(told,a)) / nnz(a) )\n",
+    "    push!(stold, sum(comp_stretches(told,a)) / nnz(a) )\n",
     "\n",
     "end\n",
     "\n",
@@ -946,19 +946,19 @@
     "    tic()\n",
     "    tnew = akpwish(a)\n",
     "    timenew += toq()\n",
-    "    push!(stnew, sum(compStretches(tnew,a)) / nnz(a) )\n",
+    "    push!(stnew, sum(comp_stretches(tnew,a)) / nnz(a) )\n",
     "\n",
     "    \n",
     "    tic()\n",
     "    tp = randishPrim(a)\n",
     "    timep += toq()\n",
-    "    push!(stp, sum(compStretches(tp,a)) / nnz(a) )    \n",
+    "    push!(stp, sum(comp_stretches(tp,a)) / nnz(a) )    \n",
     "    \n",
     "    \n",
     "    tic()\n",
     "    told = akpw(a)\n",
     "    timeold += toq()\n",
-    "    push!(stold, sum(compStretches(told,a)) / nnz(a) )\n",
+    "    push!(stold, sum(comp_stretches(told,a)) / nnz(a) )\n",
     "\n",
     "end\n",
     "\n",
@@ -1104,7 +1104,7 @@
     "include(\"../src/akpw.jl\")\n",
     "tnew = akpwish(chimera(50,1))\n",
     "@time tnew = akpwish(a)\n",
-    "sum(compStretches(tnew,a)) / nnz(a)"
+    "sum(comp_stretches(tnew,a)) / nnz(a)"
    ]
   },
   {
@@ -1136,7 +1136,7 @@
     "include(\"../src/akpw.jl\")\n",
     "tnew = akpwish(chimera(50,1))\n",
     "@time tnew = akpwish(a)\n",
-    "sum(compStretches(tnew,a)) / nnz(a)"
+    "sum(comp_stretches(tnew,a)) / nnz(a)"
    ]
   },
   {
@@ -1167,7 +1167,7 @@
    "source": [
     "told = akpw(chimera(50,1))\n",
     "@time told = akpw(a)\n",
-    "sum(compStretches(told,a)) / nnz(a)"
+    "sum(comp_stretches(told,a)) / nnz(a)"
    ]
   },
   {
@@ -1198,7 +1198,7 @@
    "source": [
     "tp = akpw(chimera(50,1))\n",
     "@time tp = randishPrim(a)\n",
-    "sum(compStretches(tp,a)) / nnz(a)"
+    "sum(comp_stretches(tp,a)) / nnz(a)"
    ]
   }
  ],