finished merge

mikeizbicki · Jul 22, 2015 · b32ff13 · b32ff13
2 parents 3c4f5e6 + ef36386
commit b32ff13
Show file tree

Hide file tree

Showing 143 changed files with 66,678 additions and 18,151 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,16 @@
 *.Rout
 *.csv
+*.class
+*.o
+
+results
+cover_tree
 
 hlearn-allknn
 hlearn-linear
 *.swp
 *.swo
 dist/
 gitignore/
-examples/
+examples/old/
 scripts/
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,32 @@
+# NB: don't set `language: haskell` here
+
+# The following enables several GHC versions to be tested; often it's enough to test only against the last release in a major GHC version. Feel free to omit lines listings versions you don't need/want testing for.
+env:
+ - CABALVER=1.22 GHCVER=7.10.1 LLVMVER=3.5
+ - CABALVER=1.22 GHCVER=7.10.2 LLVMVER=3.5
+ # - CABALVER=head GHCVER=head   # see section about GHC HEAD snapshots
+
+before_install:
+ -  export PATH="~/.cabal/bin:/opt/ghc/$GHCVER/bin:/opt/cabal/$CABALVER/bin:/usr/bin:$PATH"
+
+install:
+ - travis_retry sudo curl https://raw.githubusercontent.com/mikeizbicki/HLearn/travis/install/ubuntu-precise.sh | sh
+ #- mkdir  /home/travis/.cabal
+ #- echo 'optimization: False' >> /home/travis/.cabal/config
+ # Sometimes GHC uses too much RAM for the travis server, causing the install script to fail.
+ # In this case, we can fix the problem by reinstalling without optimizations.
+
+# Here starts the actual work to be performed for the package under test; any command which exits with a non-zero exit code causes the build to fail.
+script:
+ - if [ -f configure.ac ]; then autoreconf -i; fi
+ - cabal configure -fO0 --enable-tests --enable-benchmarks -v2  # -v2 provides useful information for debugging
+ - cabal build # this builds all libraries and executables (including tests/benchmarks)
+ - cabal test
+ - cabal check
+ - cabal sdist   # tests that a source-distribution can be generated
+
+# Check that the resulting source distribution can be built & installed.
+# If there are no other `.tar.gz` files in `dist`, this can be even simpler:
+# `cabal install --force-reinstalls dist/*-*.tar.gz`
+ - SRC_TGZ=$(cabal info . | awk '{print $2;exit}').tar.gz &&
+   (cd dist && cabal install --force-reinstalls "$SRC_TGZ")
diff --git a/HLearn.cabal b/HLearn.cabal
@@ -0,0 +1,218 @@
+Name:                HLearn
+Version:             2.0.0.0
+Synopsis:            Homomorphic machine learning
+Category:            Data Mining, Machine Learning, Algorithms, Data structures
+License:             BSD3
+License-file:        LICENSE
+Author:              Mike izbicki
+Maintainer:          mike@izbicki.me
+Build-Type:          Simple
+Cabal-Version:       >=1.8
+homepage:            http://github.com/mikeizbicki/HLearn/
+bug-reports:         http://github.com/mikeizbicki/HLearn/issues
+
+Description:
+    HLearn is an experimental, but high performance machine learning library.
+    For example, it currently has the world's fastest nearest neighbor implementation.
+    It uses <http://github.com/mikeizbicki/subhask subhask> for fast numeric computations.
+    The <http://github.com/mikeizbicki/hlearn/blob/master/README.md README> on github contains much more information.
+
+source-repository head
+    type: git
+    location: http://github.com/mikeizbicki/hlearn
+
+--------------------------------------------------------------------------------
+
+Library
+    Build-Depends:
+        -- common dependencies
+        base                >= 4.8 && <4.9,
+        subhask             >= 0.1,
+
+        -- control
+        mtl                 >= 2.1.2,
+
+        -- i/o
+        ansi-terminal       >= 0.6.1.1,
+        directory           >= 1.2,
+        time                >= 1.4.2
+
+        -- visualization
+--         diagrams-svg        >= 0.6,
+--         diagrams-lib        >= 1.3,
+--         process             >= 1.1
+--         graphviz            >= 2999.16
+
+    hs-source-dirs:
+        src
+
+    Exposed-modules:
+
+        HLearn.History
+        HLearn.History.Timing
+
+--         HLearn.Data.Graph
+--         HLearn.Data.Image
+        HLearn.Data.LoadData
+        HLearn.Data.SpaceTree
+        HLearn.Data.SpaceTree.CoverTree
+        HLearn.Data.SpaceTree.CoverTree_Specialized
+        HLearn.Data.SpaceTree.CoverTree.Unsafe
+        HLearn.Data.SpaceTree.Algorithms
+        HLearn.Data.SpaceTree.Algorithms_Specialized
+
+--         HLearn.Evaluation.CrossValidation
+
+        HLearn.Classifiers.Linear
+        HLearn.Models.Distributions
+
+        HLearn.Optimization.Multivariate
+        HLearn.Optimization.Univariate
+
+--         HLearn.Optimization.Amoeba
+--         HLearn.Optimization.Conic
+--         HLearn.Optimization.StepSize
+--         HLearn.Optimization.StochasticGradientDescent
+--         HLearn.Optimization.StepSize.Linear
+--         HLearn.Optimization.StepSize.Const
+--         HLearn.Optimization.StepSize.AlmeidaLanglois
+
+    Other-modules:
+
+    Extensions:
+        FlexibleInstances
+        FlexibleContexts
+        MultiParamTypeClasses
+        FunctionalDependencies
+        UndecidableInstances
+        ScopedTypeVariables
+        BangPatterns
+        TypeOperators
+        GeneralizedNewtypeDeriving
+        TypeFamilies
+        StandaloneDeriving
+        GADTs
+        KindSignatures
+        ConstraintKinds
+        DeriveDataTypeable
+        RankNTypes
+        ImpredicativeTypes
+
+        DataKinds
+        PolyKinds
+        AutoDeriveTypeable
+        TemplateHaskell
+        QuasiQuotes
+        RebindableSyntax
+        NoImplicitPrelude
+        UnboxedTuples
+        MagicHash
+        PolymorphicComponents
+        ExplicitNamespaces
+        EmptyDataDecls
+
+        PartialTypeSignatures
+        MultiWayIf
+
+--------------------------------------------------------------------------------
+
+Test-Suite BashTests
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     test
+    main-is:            BashTests.hs
+    build-depends:      base, process
+
+---------------------------------------
+
+Test-Suite QuickCheck-Unoptimized
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     test
+    main-is:            QuickCheck.hs
+
+    ghc-options:
+        -O0
+
+    build-depends:
+        subhask,
+        HLearn,
+        test-framework-quickcheck2  >= 0.3.0,
+        test-framework              >= 0.8.0
+
+Test-Suite QuickCheck-Optimized
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     test
+    main-is:            QuickCheck.hs
+
+    ghc-options:
+        -O1
+
+    build-depends:
+        subhask,
+        HLearn,
+        test-framework-quickcheck2  >= 0.3.0,
+        test-framework              >= 0.8.0
+
+---------------------------------------
+
+Test-Suite Example0001
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     examples
+    main-is:            example0001-optimization-univariate.hs
+    build-depends:      HLearn, subhask, base
+
+Test-Suite Example0002
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     examples
+    main-is:            example0002-optimization-multivariate.hs
+    build-depends:      HLearn, subhask, base
+
+Test-Suite Example0003
+    type:               exitcode-stdio-1.0
+    hs-source-dirs:     examples
+    main-is:            example0003-classification.hs
+    build-depends:      HLearn, subhask, base
+
+--------------------------------------------------------------------------------
+
+executable hlearn-allknn
+    main-is:            Main.hs
+    hs-source-dirs:     executables/hlearn-allknn
+
+    ghc-options:
+        -threaded
+        -rtsopts
+
+        -funbox-strict-fields
+        -fexcess-precision
+
+--         -prof -osuf p_o -hisuf p_hi
+
+        -fllvm
+        -optlo-O3
+        -optlo-enable-fp-mad
+        -optlo-enable-no-infs-fp-math
+        -optlo-enable-no-nans-fp-math
+        -optlo-enable-unsafe-fp-math
+
+--         -ddump-to-file
+--         -ddump-rule-firings
+--         -ddump-rule-rewrites
+--         -ddump-rules
+--         -ddump-simpl
+--         -ddump-simpl-stats
+--         -dppr-debug
+--         -dsuppress-module-prefixes
+--         -dsuppress-uniques
+--         -dsuppress-idinfo
+--         -dsuppress-coercions
+--         -dsuppress-type-applications
+
+--         -ddump-cmm
+
+    build-depends:
+        base           ,
+        HLearn         ,
+        subhask         ,
+
+        cmdargs,
+        MonadRandom