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Aleš Erjavec committed 858a15d

Fixed uses of the changed namespace.

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Files changed (16)

-recursive-include orangekit/earth *.svg
+recursive-include orangecontrib/earth *.svg
 recursive-include src *.*
 recursive-include docs *.*
 
-orangekit.earth
-===============
+orangecontrib.earth
+===================
 
-`orangekit.earth` provides a an implementation of
+`orangecontrib.earth` provides a an implementation of
 `Multivariate adaptive regression splines (MARS)`_ for the `Orange`_
 machine learning library. This implementation is based on the C code from
 `R package earth`_ by Stephen Milborrow.
 Prerequisites
 -------------
 
-In order to use `orangekit.earth` you need to have already installed
+In order to use `orangecontrib.earth` you need to have already installed
 `Orange` (version 2.7 or latest).
 
 If you are installing from source you will also need the a working
 
 You can install it using pip or easy_install::
 
-   pip install orangekit.earth
+   pip install orangecontrib.earth
 
 or::
 
-   easy_install orangekit.earth
+   easy_install orangecontrib.earth
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/orangekitearth.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/orangecontribearth.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/orangekitearth.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/orangecontribearth.qhc"
 
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/orangekitearth"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/orangekitearth"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/orangecontribearth"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/orangecontribearth"
 	@echo "# devhelp"
 
 epub:
 	echo.
 	echo.Build finished; now you can run "qcollectiongenerator" with the ^
 .qhcp project file in %BUILDDIR%/qthelp, like this:
-	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\orangekitearth.qhcp
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\orangecontribearth.qhcp
 	echo.To view the help file:
-	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\orangekitearth.ghc
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\orangecontribearth.ghc
 	goto end
 )
 

docs/source/conf.py

 # -*- coding: utf-8 -*-
 #
-# orangekit.earth documentation build configuration file, created by
+# orangecontrib.earth documentation build configuration file, created by
 # sphinx-quickstart on Mon Aug 26 11:49:18 2013.
 #
 # This file is execfile()d with the current directory set to its containing dir.
 # General information about the project.
 project = ast_global_string(setup_ast, "NAME")
 
-# project = u'orangekit.earth'
+# project = u'orangecontrib.earth'
 copyright = u'2013, Bioinformatics Laboratory, FRI UL'
 
 # The version info for the project you're documenting, acts as replacement for
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'orangekitearthdoc'
+htmlhelp_basename = 'orangecontribearthdoc'
 
 
 # -- Options for LaTeX output --------------------------------------------------
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'orangekitearth.tex', u'orangekit.earth Documentation',
+  ('index', 'orangecontribearth.tex', u'orangecontrib.earth Documentation',
    u'Bioinformatics Laboratory, FRI UL', 'manual'),
 ]
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'orangekitearth', u'orangekit.earth Documentation',
+    ('index', 'orangecontribearth', u'orangecontrib.earth Documentation',
      [u'Bioinformatics Laboratory, FRI UL'], 1)
 ]
 
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'orangekitearth', u'orangekit.earth Documentation',
-   u'Bioinformatics Laboratory, FRI UL', 'orangekitearth',
+  ('index', 'orangecontribearth', u'orangecontrib.earth Documentation',
+   u'Bioinformatics Laboratory, FRI UL', 'orangecontribearth',
    'A Python interface for the earth package by Stephen Milborrow.',
    'Miscellaneous'),
 ]
 # -- Options for Epub output ---------------------------------------------------
 
 # Bibliographic Dublin Core info.
-epub_title = u'orangekit.earth'
+epub_title = u'orangecontrib.earth'
 epub_author = u'Bioinformatics Laboratory, FRI UL'
 epub_publisher = u'Bioinformatics Laboratory, FRI UL'
 epub_copyright = u'2013, Bioinformatics Laboratory, FRI UL'

docs/source/index.rst

-.. orangekit.earth documentation master file, created by
+.. orangecontrib.earth documentation master file, created by
    sphinx-quickstart on Mon Aug 26 11:49:18 2013.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to orangekit.earth's documentation!
-===========================================
+Welcome to orangecontrib.earth's documentation!
+===============================================
 
 Contents:
 
 
    overview
 
-   orangekit.earth
+   orangecontrib.earth
 
 
 Widgets
 .. toctree::
    :maxdepth: 1
 
-   Earth <orangekit.earth.widgets.earth>
+   Earth <orangecontrib.earth.widgets.earth>
 
 
 Indices and tables

docs/source/orangecontrib.earth.rst

+========================================
+:mod:`orangecontrib.earth` API reference
+========================================
+
+.. module:: orangecontrib.earth
+
+Learner/Classifier
+------------------
+
+The :class:`EarthLearner` and :class:`EarthClassifier` provide the
+standard Orange learner/classifier pair for model induction/prediction.
+
+.. autoclass:: EarthLearner
+   :show-inheritance:
+   :members:
+   :special-members: __call__
+
+
+.. autoclass:: EarthClassifier
+   :show-inheritance:
+   :members:
+   :special-members: __call__
+
+
+.. seealso:: :mod:`Orange.classification`
+
+
+Example::
+
+    >>> import Orange, orangecontrib.earth
+    >>> data = Orange.data.Table("housing")
+    >>> c = orangecontrib.earth.EarthLearner(data, degree=2, terms=10)
+    >>> print c
+    MEDV =
+       23.587
+       +11.896 * max(0, RM - 6.431)
+       +1.142 * max(0, 6.431 - RM)
+       -0.612 * max(0, LSTAT - 6.120)
+       -228.795 * max(0, NOX - 0.647) * max(0, RM - 6.431)
+       +0.023 * max(0, TAX - 307.000) * max(0, 6.120 - LSTAT)
+       +0.029 * max(0, 307.000 - TAX) * max(0, 6.120 - LSTAT)
+
+
+Feature scoring
+---------------
+
+.. autoclass:: ScoreEarthImportance
+   :show-inheritance:
+   :members:
+   :special-members: __call__
+
+
+.. seealso:: :mod:`Orange.feature.scoring`
+
+
+Utility functions
+-----------------
+
+.. autofunction:: gcv
+
+.. autofunction:: plot_evimp
+
+.. autofunction:: bagged_evimp

docs/source/orangecontrib.earth.widgets.earth.rst

+.. _Earth:
+
+Earth Learner
+=============
+
+.. image:: ../../orangecontrib/earth/widgets/icons/EarthMars.svg
+   :alt: Earth Learner
+
+
+Channels
+--------
+
+Inputs:
+   - Data (Table)
+
+Outputs:
+   - Learner
+         The Earth learning algorithm with parameters as specified in the
+         dialog.
+
+   - Predictor
+        Trained regressor
+
+   - Basis Matrix (Table)
+        A data table of induced basis terms.
+
+Signal ``Predictor`` sends the regressor only if signal ``Data`` is present.
+
+Description
+-----------
+
+This widget constructs a Earth learning algorithm (an implementation of
+the `MARS - Multivariate Adaptive Regression Splines`_). As all widgets
+for classification and regression, this widget provides a learner and
+classifier/regressor on the output. Learner is a learning algorithm with
+settings as specified by the user. It can be fed into widgets for testing
+learners, for instance Test Learners.
+
+.. _`MARS - Multivariate Adaptive Regression Splines`: http://en.wikipedia.org/wiki/Multivariate_adaptive_regression_splines
+
+.. image:: images/Earth.png
+
+
+.. rst-class:: stamp-list
+
+   1. Learner/Predictor can be given a name under which it will appear
+      in other widgets (say ``Test Learners`` or ``Predictions``).
+
+   2. The ``Max. term degree`` parameter specifies the degree of the
+      terms induced in the forward pass. For instance, if set to ``1``
+      the resulting model will contain only linear terms.
+
+   3. The ``Max. terms`` specifies how many terms can be induces in the
+      forward pass. A special value ``Automatic`` instructs the learner
+      to set the limit automatically based on the dimensionality of the
+      data (``min(200, max(20, 2 * NumberOfAttributes)) + 1``)
+
+   4. The ``Knot penalty`` is used in the pruning pass (hinge function
+      penalty for the GCV calculation)
+
+
+After changing one or more settings, you need to push 5 ``Apply``,
+which will put the new learner on the output and, if the training
+examples are given, construct a new predictor and output it as well.
+
+
+Examples
+--------
+
+Lets use the learner to train a model on a data subset and test it on
+unseen instances.
+
+.. image:: images/Earth-Schema.png

docs/source/orangekit.earth.rst

-====================================
-:mod:`orangekit.earth` API reference
-====================================
-
-.. module:: orangekit.earth
-
-Learner/Classifier
-------------------
-
-The :class:`EarthLearner` and :class:`EarthClassifier` provide the
-standard Orange learner/classifier pair for model induction/prediction.
-
-.. autoclass:: EarthLearner
-   :show-inheritance:
-   :members:
-   :special-members: __call__
-
-
-.. autoclass:: EarthClassifier
-   :show-inheritance:
-   :members:
-   :special-members: __call__
-
-
-.. seealso:: :mod:`Orange.classification`
-
-
-Example::
-
-    >>> import Orange, orangekit.earth
-    >>> data = Orange.data.Table("housing")
-    >>> c = orangekit.earth.EarthLearner(data, degree=2, terms=10)
-    >>> print c
-    MEDV =
-       23.587
-       +11.896 * max(0, RM - 6.431)
-       +1.142 * max(0, 6.431 - RM)
-       -0.612 * max(0, LSTAT - 6.120)
-       -228.795 * max(0, NOX - 0.647) * max(0, RM - 6.431)
-       +0.023 * max(0, TAX - 307.000) * max(0, 6.120 - LSTAT)
-       +0.029 * max(0, 307.000 - TAX) * max(0, 6.120 - LSTAT)
-
-
-Feature scoring
----------------
-
-.. autoclass:: ScoreEarthImportance
-   :show-inheritance:
-   :members:
-   :special-members: __call__
-
-
-.. seealso:: :mod:`Orange.feature.scoring`
-
-
-Utility functions
------------------
-
-.. autofunction:: gcv
-
-.. autofunction:: plot_evimp
-
-.. autofunction:: bagged_evimp

docs/source/orangekit.earth.widgets.earth.rst

-.. _Earth:
-
-Earth Learner
-=============
-
-.. image:: ../../orangekit/earth/widgets/icons/EarthMars.svg
-   :alt: Earth Learner
-
-
-Channels
---------
-
-Inputs:
-   - Data (Table)
-
-Outputs:
-   - Learner
-         The Earth learning algorithm with parameters as specified in the
-         dialog.
-
-   - Predictor
-        Trained regressor
-
-   - Basis Matrix (Table)
-        A data table of induced basis terms.
-
-Signal ``Predictor`` sends the regressor only if signal ``Data`` is present.
-
-Description
------------
-
-This widget constructs a Earth learning algorithm (an implementation of
-the `MARS - Multivariate Adaptive Regression Splines`_). As all widgets
-for classification and regression, this widget provides a learner and
-classifier/regressor on the output. Learner is a learning algorithm with
-settings as specified by the user. It can be fed into widgets for testing
-learners, for instance Test Learners.
-
-.. _`MARS - Multivariate Adaptive Regression Splines`: http://en.wikipedia.org/wiki/Multivariate_adaptive_regression_splines
-
-.. image:: images/Earth.png
-
-
-.. rst-class:: stamp-list
-
-   1. Learner/Predictor can be given a name under which it will appear
-      in other widgets (say ``Test Learners`` or ``Predictions``).
-
-   2. The ``Max. term degree`` parameter specifies the degree of the
-      terms induced in the forward pass. For instance, if set to ``1``
-      the resulting model will contain only linear terms.
-
-   3. The ``Max. terms`` specifies how many terms can be induces in the
-      forward pass. A special value ``Automatic`` instructs the learner
-      to set the limit automatically based on the dimensionality of the
-      data (``min(200, max(20, 2 * NumberOfAttributes)) + 1``)
-
-   4. The ``Knot penalty`` is used in the pruning pass (hinge function
-      penalty for the GCV calculation)
-
-
-After changing one or more settings, you need to push 5 ``Apply``,
-which will put the new learner on the output and, if the training
-examples are given, construct a new predictor and output it as well.
-
-
-Examples
---------
-
-Lets use the learner to train a model on a data subset and test it on
-unseen instances.
-
-.. image:: images/Earth-Schema.png

docs/source/overview.rst

 ========
 
 
-:mod:`orangekit.earth` provides a an implementation of
+:mod:`orangecontrib.earth` provides a an implementation of
 `Multivariate adaptive regression splines (MARS)`_ for the `Orange`_
 machine learning library. This implementation is based on the C code from
 `R package earth`_ by Stephen Milborrow.
 Prerequisites
 -------------
 
-In order to use `orangekit.earth` you need to have already installed
+In order to use `orangecontrib.earth` you need to have already installed
 `Orange` (version 2.7 or latest).
 
 If you are installing from source you will also need the a working
 
 You can install it using pip or easy_install::
 
-   pip install orangekit.earth
+   pip install orangecontrib.earth
 
 or::
 
-   easy_install orangekit.earth
+   easy_install orangecontrib.earth
 

orangecontrib/earth/earth.py

 
 Example::
 
-    >>> import Orange, orangekit.earth
+    >>> import Orange, orangecontrib.earth
     >>> data = Orange.data.Table("housing")
-    >>> c = orangekit.earth.EarthLearner(data, degree=2, terms=10)
+    >>> c = orangecontrib.earth.EarthLearner(data, degree=2, terms=10)
     >>> print c.to_string(precision=2)
     MEDV =
        23.59

orangecontrib/earth/evimp.py

 
     ::
 
-        import Orange, orangekit.earth
+        import Orange, orangecontrib.earth
         data = Orange.data.Table("housing")
-        c = orangekit.earth.EarthLearner(data, degree=3)
-        orangekit.earth.plot_evimp(c.evimp())
+        c = orangecontrib.earth.EarthLearner(data, degree=3)
+        orangecontrib.earth.plot_evimp(c.evimp())
 
     .. image:: images/earth-evimp.png
 

orangecontrib/earth/widgets/OWEarth.py

 
 from orngWrap import PreprocessedLearner
 
-from orangekit import earth
+from orangecontrib import earth
 
 NAME = "Earth"
 DESCRIPTION = "Multivariate Adaptive Regression Splines (MARS)"
 all_files = 1
 
 [test]
-test-suite = orangekit.earth.tests
+test-suite = orangecontrib.earth.tests
 from ConfigParser import SafeConfigParser
 
 
-NAME = "orangekit.earth"
+NAME = "orangecontrib.earth"
 VERSION = "0.0.1"
 DESCRIPTION = "A Python interface for the earth package by Stephen Milborrow"
 LONG_DESCRIPTION = open("README.txt", "rb").read()
 AUTHOR = "Bioinformatics Laboratory, FRI UL"
 AUTHOR_EMAIL = "contact@orange.biolab.si"
-URL = "https://bitbucket.org/biolab/orangekit-earth"
+URL = "https://bitbucket.org/biolab/orangecontrib-earth"
 LICENSE = "GPLv3"
 
 PACKAGES = find_packages()
     blas = R = None
     parser = SafeConfigParser()
     parser.read(["site.cfg",
-                 os.path.expanduser("~/.orangekit-earth-site.cfg")])
+                 os.path.expanduser("~/.orangecontrib-earth-site.cfg")])
 
     if parser.has_section("blas_opt"):
         blas = parse_lib_opt(parser, "blas_opt")
 
 ENTRY_POINTS = {
     "orange.addons": (
-        "regression__earth = orangekit.earth.earth",
+        "regression__earth = orangecontrib.earth.earth",
     ),
     "orange.widgets": (
-        "Earth = orangekit.earth.widgets.OWEarth",
+        "Earth = orangecontrib.earth.widgets.OWEarth",
     ),
     "orange.canvas.help": (
-        "intersphinx = orangekit.earth.widgets:intersphinx",
+        "intersphinx = orangecontrib.earth.widgets:intersphinx",
     )
 }
 
 
 def setup_package():
-    config = configuration("orangekit").todict()
+    config = configuration("orangecontrib").todict()
     del config["name"]
 
     setup(name=NAME,