Replace modshogun by shogun everywhere

shogun-toolbox · Jul 5, 2017 · 75657cb · 75657cb
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diff --git a/.gitignore b/.gitignore
@@ -52,53 +52,6 @@ cpplint.py
 /src/configure-*-*.c*
 /src/build-local
 
-# modular interfaces
-/src/interfaces/*_modular/*.doxy
-/src/interfaces/*_modular/Evaluation.i
-/src/interfaces/*_modular/Regression.i
-/src/interfaces/*_modular/Library.i
-/src/interfaces/*_modular/Distribution.i
-/src/interfaces/*_modular/Structure.i
-/src/interfaces/*_modular/Classifier.i
-/src/interfaces/*_modular/Features.i
-/src/interfaces/*_modular/Kernel.i
-/src/interfaces/*_modular/Preprocessor.i
-/src/interfaces/*_modular/Distance.i
-/src/interfaces/*_modular/Clustering.i
-/src/interfaces/*_modular/SGBase.i
-/src/interfaces/*_modular/IO.i
-/src/interfaces/*_modular/Mathematics.i
-/src/interfaces/*_modular/ModelSelection.i
-/src/interfaces/*_modular/modshogun.i
-/src/interfaces/*_modular/modshogun_ignores.i
-/src/interfaces/*_modular/*_includes.i
-/src/interfaces/*_modular/Makefile
-/src/interfaces/*_modular/Converter.i
-/src/interfaces/*_modular/Multiclass.i
-/src/interfaces/*_modular/Machine.i
-/src/interfaces/*_modular/Transfer.i
-/src/interfaces/*_modular/Loss.i
-/src/interfaces/*_modular/Statistics.i
-/src/interfaces/*_modular/Latent.i
-/src/interfaces/*_modular/GaussianProcess.i
-
-# particular modular ones
-/src/interfaces/csharp_modular/*.cs
-/src/interfaces/csharp_modular/abstract_types_extension.i
-/src/interfaces/csharp_modular/modshogun.dll
-/src/interfaces/java_modular/*.java
-/src/interfaces/java_modular/*.jar
-/src/interfaces/java_modular/*.class
-/src/interfaces/java_modular/org/*
-/src/interfaces/java_modular/shogun/*
-/src/interfaces/python_modular/*.py
-/src/interfaces/python_modular/abstract_types_extension.i
-/src/interfaces/r_modular/*.R
-/src/interfaces/r_modular/*.RData
-/src/interfaces/perl_modular/*.pm
-/src/interfaces/octave_modular/abstract_types_extension.i
-/.duped_py_pl.pb
-
 # /examples/
 *.log
 *.exe
@@ -108,9 +61,9 @@ cpplint.py
 !/examples/undocumented/libshogun/*.cpp
 !/examples/undocumented/libshogun/CMakeLists.txt
 !/examples/undocumented/libshogun/tools/
-!examples/undocumented/python_modular/graphical/
-!examples/undocumented/python_modular/*.py
-!examples/undocumented/python_modular/CMakeLists.txt
+!examples/undocumented/python/graphical/
+!examples/undocumented/python/*.py
+!examples/undocumented/python/CMakeLists.txt
 
 # /tests
 /tests/unit/shogun-unit-test
@@ -120,12 +73,8 @@ cpplint.py
 /tests/unit/*.json
 /tests/unit/combined_kernel.weights
 Testing/
-examples/undocumented/python_modular/serialized_svm.bz2
-examples/undocumented/python_modular/tmp/blaah.asc
-examples/undocumented/python_modular/tmp/blaah.h5
-examples/undocumented/python_modular/tmp/blaah.json
-examples/undocumented/python_modular/tmp/blaah.xml
-examples/undocumented/python_modular/vw_cache.dat.cache
+examples/undocumented/python/serialized_svm.bz2
+examples/undocumented/python/vw_cache.dat.cache
 
 # cmake
 /CMakeFiles/

diff --git a/applications/classification/evaluate_multiclass_labels.py b/applications/classification/evaluate_multiclass_labels.py
@@ -32,7 +32,7 @@
 import argparse
 import logging
 import numpy as np
-from modshogun import (LibSVMFile, MulticlassLabels, MulticlassAccuracy)
+from shogun import (LibSVMFile, MulticlassLabels, MulticlassAccuracy)
 from utils import get_features_and_labels
 
 LOGGER = logging.getLogger(__file__)

diff --git a/applications/classification/predict_multiclass_svm.py b/applications/classification/predict_multiclass_svm.py
@@ -32,7 +32,7 @@
 import argparse
 import logging
 from contextlib import closing
-from modshogun import (LibSVMFile, SparseRealFeatures, MulticlassLabels,
+from shogun import (LibSVMFile, SparseRealFeatures, MulticlassLabels,
 											MulticlassLibSVM, SerializableHdf5File,
 											MulticlassAccuracy)
 from utils import get_features_and_labels

diff --git a/applications/classification/random_fourier_classification.py b/applications/classification/random_fourier_classification.py
@@ -32,7 +32,7 @@ def parse_arguments():
 	return parser.parse_args()
 
 def evaluate(predicted_labels, labels, prefix="Results"):
-	from modshogun import PRCEvaluation, ROCEvaluation, AccuracyMeasure
+	from shogun import PRCEvaluation, ROCEvaluation, AccuracyMeasure
 
 	prc_evaluator = PRCEvaluation()
 	roc_evaluator = ROCEvaluation()
@@ -58,9 +58,9 @@ def load_sparse_data(filename, dimension=None):
 	return {'data':sparse_feats, 'labels':labels}
 
 if __name__=='__main__':
-	from modshogun import SparseRealFeatures, RandomFourierDotFeatures, GAUSSIAN
-	from modshogun import LibSVMFile, BinaryLabels, SVMOcas
-	from modshogun import Time
+	from shogun import SparseRealFeatures, RandomFourierDotFeatures, GAUSSIAN
+	from shogun import LibSVMFile, BinaryLabels, SVMOcas
+	from shogun import Time
 	from numpy import array
 
 	args = parse_arguments()

diff --git a/applications/classification/train_multiclass_svm.py b/applications/classification/train_multiclass_svm.py
@@ -32,7 +32,7 @@
 import argparse
 import logging
 from contextlib import contextmanager, closing
-from modshogun import (LibSVMFile, GaussianKernel, MulticlassLibSVM,
+from shogun import (LibSVMFile, GaussianKernel, MulticlassLibSVM,
 																SerializableHdf5File, LinearKernel)
 from utils import get_features_and_labels, track_execution
 

diff --git a/applications/classification/utils.py b/applications/classification/utils.py
@@ -30,7 +30,7 @@
 
 import logging
 from contextlib import contextmanager
-from modshogun import MulticlassLabels, SparseRealFeatures, Time
+from shogun import MulticlassLabels, SparseRealFeatures, Time
 
 
 logging.basicConfig(level=logging.INFO, format='[%(asctime)-15s %(module)s] %(message)s')

diff --git a/applications/easysvm/galaxy/README b/applications/easysvm/galaxy/README
@@ -1,3 +1,3 @@
 The files in this directory are a copy of
 svn/projects/galaxy/tools/agr.  If you edit them, make sure the
-changes are also integrated into the main version.
+changes are also integrated into the main version.
diff --git a/applications/msplicer/signal_detectors.py b/applications/msplicer/signal_detectors.py
@@ -13,7 +13,7 @@
 import numpy
 import seqdict
 
-from modshogun import KernelMachine,StringCharFeatures,DNA,WeightedDegreeStringKernel
+from shogun import KernelMachine,StringCharFeatures,DNA,WeightedDegreeStringKernel
 
 class svm_splice_model(object):
 	def __init__(self, order, traindat, alphas, b, (window_left,offset,window_right), consensus):

diff --git a/applications/ocr/Ai.py b/applications/ocr/Ai.py
@@ -1,9 +1,9 @@
 # File   : $HeadURL$
 # Version: $Id$
 
-from modshogun import RealFeatures, MulticlassLabels
-from modshogun import GaussianKernel
-from modshogun import GMNPSVM
+from shogun import RealFeatures, MulticlassLabels
+from shogun import GaussianKernel
+from shogun import GMNPSVM
 
 import numpy as np
 import gzip as gz

diff --git a/applications/tapkee/faces_embedding.py b/applications/tapkee/faces_embedding.py
@@ -8,7 +8,7 @@
 # Written (W) 2011 Sergey Lisitsyn
 # Copyright (C) 2011 Sergey Lisitsyn
 
-from modshogun import *
+from shogun import *
 from numpy import *
 from matplotlib.offsetbox import TextArea, DrawingArea, OffsetImage, AnnotationBbox
 import re,os,time

diff --git a/applications/tapkee/samples/dm.py b/applications/tapkee/samples/dm.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 import numpy as np
 

diff --git a/applications/tapkee/samples/hlle.py b/applications/tapkee/samples/hlle.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/samples/isomap.py b/applications/tapkee/samples/isomap.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 import numpy as np
 

diff --git a/applications/tapkee/samples/klle.py b/applications/tapkee/samples/klle.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 import numpy as np
 

diff --git a/applications/tapkee/samples/la.py b/applications/tapkee/samples/la.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 import numpy as np
 

diff --git a/applications/tapkee/samples/lle.py b/applications/tapkee/samples/lle.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/samples/lltsa.py b/applications/tapkee/samples/lltsa.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/samples/lpp.py b/applications/tapkee/samples/lpp.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/samples/ltsa.py b/applications/tapkee/samples/ltsa.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/samples/mds.py b/applications/tapkee/samples/mds.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 import numpy as np
 

diff --git a/applications/tapkee/samples/npe.py b/applications/tapkee/samples/npe.py
@@ -1,4 +1,4 @@
-import modshogun as sg
+import shogun as sg
 import data
 
 # load data

diff --git a/applications/tapkee/words_embedding.py b/applications/tapkee/words_embedding.py
@@ -10,7 +10,7 @@
 
 from numpy import *
 from pylab import *
-from modshogun import *
+from shogun import *
 import random
 import difflib
 

diff --git a/cmake/ShogunInterfaces.cmake b/cmake/ShogunInterfaces.cmake
@@ -37,12 +37,12 @@ ADD_CUSTOM_TARGET(${INTERFACE_TARGET_SRC}
 	COMMENT "copying SWIG files")
 
 INCLUDE(${SWIG_USE_FILE})
-SET_SOURCE_FILES_PROPERTIES(modshogun.i PROPERTIES CPLUSPLUS ON)
+SET_SOURCE_FILES_PROPERTIES(shogun.i PROPERTIES CPLUSPLUS ON)
 IF(DEFINED TARGET_SWIGFLAGS)
-	SET_SOURCE_FILES_PROPERTIES(modshogun.i PROPERTIES SWIG_FLAGS ${TARGET_SWIGFLAGS})
+	SET_SOURCE_FILES_PROPERTIES(shogun.i PROPERTIES SWIG_FLAGS ${TARGET_SWIGFLAGS})
 ENDIF()
 SET(SWIG_MODULE_${INTERFACE_NAME}_EXTRA_DEPS ${INTERFACE_FILES})
-SWIG_ADD_MODULE(${INTERFACE_TARGET} ${INTERFACE_NAME} modshogun.i sg_print_functions.cpp)
+SWIG_ADD_MODULE(${INTERFACE_TARGET} ${INTERFACE_NAME} shogun.i sg_print_functions.cpp)
 SWIG_LINK_LIBRARIES(${INTERFACE_TARGET} shogun::shogun ${INTERFACE_LIBRARIES})
 
 
@@ -52,7 +52,7 @@ SWIG_LINK_LIBRARIES(${INTERFACE_TARGET} shogun::shogun ${INTERFACE_LIBRARIES})
 		#	endforeach()
 
 SET(INTERFACE_REAL_NAME ${SWIG_MODULE_interface_${INTERFACE_NAME}_REAL_NAME})
-SET_TARGET_PROPERTIES(${INTERFACE_REAL_NAME} PROPERTIES OUTPUT_NAME ${PREPEND_TARGET}modshogun)
+SET_TARGET_PROPERTIES(${INTERFACE_REAL_NAME} PROPERTIES OUTPUT_NAME ${PREPEND_TARGET}shogun)
 ADD_DEPENDENCIES(${INTERFACE_REAL_NAME} ${INTERFACE_TARGET_SRC})
 
 #ADD_CUSTOM_COMMAND(TARGETS ${PREPEND_TARGET}interface_${INTERFACE_NAME}
@@ -61,23 +61,23 @@ ADD_DEPENDENCIES(${INTERFACE_REAL_NAME} ${INTERFACE_TARGET_SRC})
 #				   ARGS ${CMAKE_SOURCE_DIR}/src/.scrub_docstrings.py )
 
 IF(DOXYGEN_FOUND)
-	configure_file(${COMMON_INTERFACE_SRC_DIR}/modshogun.doxy.in modshogun.doxy)
+	configure_file(${COMMON_INTERFACE_SRC_DIR}/shogun.doxy.in shogun.doxy)
 
 	ADD_CUSTOM_COMMAND(
-	OUTPUT    modshogun
+	OUTPUT    shogun
 	COMMAND   ${DOXYGEN_EXECUTABLE}
-	ARGS	  modshogun.doxy
+	ARGS	  shogun.doxy
 	DEPENDS   shogun::shogun
 	COMMENT   "Generating doxygen doc"
 	)
 
 	ADD_CUSTOM_COMMAND(
-	OUTPUT    modshogun_doxygen.i
+	OUTPUT    shogun_doxygen.i
 	COMMAND   ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/src/.doxy2swig.py
-	ARGS	  --quiet --no-function-definition modshogun/doxygen_xml/index.xml modshogun_doxygen.i
-	DEPENDS   modshogun
+	ARGS	  --quiet --no-function-definition shogun/doxygen_xml/index.xml shogun_doxygen.i
+	DEPENDS   shogun
 	)
-	ADD_CUSTOM_TARGET(${INTERFACE_NAME}_doxy2swig DEPENDS modshogun_doxygen.i)
+	ADD_CUSTOM_TARGET(${INTERFACE_NAME}_doxy2swig DEPENDS shogun_doxygen.i)
     ADD_DEPENDENCIES(${INTERFACE_REAL_NAME} ${INTERFACE_NAME}_doxy2swig)
 ELSE()
 	#TODO add scrubing

diff --git a/doc/ipython-notebooks/classification/Classification.ipynb b/doc/ipython-notebooks/classification/Classification.ipynb
@@ -48,7 +48,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import os\nSHOGUN_DATA_DIR=os.getenv('SHOGUN_DATA_DIR', '../../../data')\n",
-    "from modshogun import *"
+    "from shogun import *"
    ]
   },
   {

diff --git a/doc/ipython-notebooks/classification/HashedDocDotFeatures.ipynb b/doc/ipython-notebooks/classification/HashedDocDotFeatures.ipynb
@@ -77,7 +77,7 @@
     "The response to that is to read our collection as it is and compute the hash of every token only when it's required, on-the-fly.<br>\n",
     "<h3>On-the-fly Hashing with Shogun</h3>\n",
     "We will now have a look at how the above idea is represented in the Shogun Toolbox. That is we will see how we can load our document collection in memory and consider a hashed document-term matrix with the hashing of every document (or token more specifically) happening on-the-fly, only when it's required to be computed. Altough it may sound a bit tricky, it's actually pretty straightforward and here is how.<br><br>\n",
-    "First of all we import the required components from the modshogun library."
+    "First of all we import the required components from the shogun library."
    ]
   },
   {
@@ -90,7 +90,7 @@
    "source": [
     "%matplotlib inline\n",
     "import os\nSHOGUN_DATA_DIR=os.getenv('SHOGUN_DATA_DIR', '../../../data')\n",
-    "from modshogun import StringCharFeatures, RAWBYTE, HashedDocDotFeatures, NGramTokenizer"
+    "from shogun import StringCharFeatures, RAWBYTE, HashedDocDotFeatures, NGramTokenizer"
    ]
   },
   {
@@ -133,7 +133,7 @@
    },
    "outputs": [],
    "source": [
-    "from modshogun import BinaryLabels\n",
+    "from shogun import BinaryLabels\n",
     "from numpy import array\n",
     "\n",
     "labels = BinaryLabels(array([-1, 1, 1]))"
@@ -199,7 +199,7 @@
    },
    "outputs": [],
    "source": [
-    "from modshogun import SVMOcas\n",
+    "from shogun import SVMOcas\n",
     "\n",
     "C = 0.1\n",
     "epsilon = 0.01\n",

diff --git a/doc/ipython-notebooks/classification/MKL.ipynb b/doc/ipython-notebooks/classification/MKL.ipynb
@@ -48,7 +48,7 @@
     "%matplotlib inline\n",
     "import os\nSHOGUN_DATA_DIR=os.getenv('SHOGUN_DATA_DIR', '../../../data')\n",
     "# import all shogun classes\n",
-    "from modshogun import *"
+    "from shogun import *"
    ]
   },
   {

diff --git a/doc/ipython-notebooks/classification/SupportVectorMachines.ipynb b/doc/ipython-notebooks/classification/SupportVectorMachines.ipynb
@@ -119,7 +119,7 @@
     "import os\nSHOGUN_DATA_DIR=os.getenv('SHOGUN_DATA_DIR', '../../../data')\n",
     "import matplotlib.patches as patches\n",
     "#To import all shogun classes\n",
-    "import modshogun as sg\n",
+    "import shogun as sg\n",
     "import numpy as np\n",
     "\n",
     "#Generate some random data\n",

diff --git a/doc/ipython-notebooks/clustering/GMM.ipynb b/doc/ipython-notebooks/clustering/GMM.ipynb
@@ -114,7 +114,7 @@
     "%matplotlib inline\n",
     "import os\nSHOGUN_DATA_DIR=os.getenv('SHOGUN_DATA_DIR', '../../../data')\n",
     "# import all Shogun classes\n",
-    "from modshogun import *"
+    "from shogun import *"
    ]
   },
   {

diff --git a/doc/ipython-notebooks/clustering/KMeans.ipynb b/doc/ipython-notebooks/clustering/KMeans.ipynb
@@ -111,7 +111,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from modshogun import *\n",
+      "from shogun import *\n",
       "\n",
       "train_features = RealFeatures(rectangle)"
      ],

diff --git a/doc/ipython-notebooks/computer_vision/Scene_classification.ipynb b/doc/ipython-notebooks/computer_vision/Scene_classification.ipynb
@@ -107,7 +107,7 @@
       "import numpy as np\n",
       "import matplotlib.pyplot as plt\n",
       "%matplotlib inline\n",
-      "from modshogun import *\n",
+      "from shogun import *\n",
       "\n",
       "# get the list of all jpg images from the path provided\n",
       "import os\n",