updated documentation, updated package with relative paths. running well, but sphinx unsuccessful

Author: stephenhky

docs/Makefile

@@ -19,8 +19,7 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
-
+.PHONY: help
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       to make standalone HTML files"
@@ -48,40 +47,48 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 	@echo "  coverage   to run coverage check of the documentation (if enabled)"
 
+.PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
 
+.PHONY: html
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
+.PHONY: dirhtml
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
+.PHONY: singlehtml
 singlehtml:
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
+.PHONY: pickle
 pickle:
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
+.PHONY: json
 json:
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
+.PHONY: htmlhelp
 htmlhelp:
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 	@echo
 	@echo "Build finished; now you can run HTML Help Workshop with the" \
 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
 
+.PHONY: qthelp
 qthelp:
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 	@echo
@@ -91,6 +98,7 @@ qthelp:
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/shorttext.qhc"
 
+.PHONY: applehelp
 applehelp:
 	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
 	@echo
@@ -99,6 +107,7 @@ applehelp:
 	      "~/Library/Documentation/Help or install it in your application" \
 	      "bundle."
 
+.PHONY: devhelp
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
@@ -108,84 +117,99 @@ devhelp:
 	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/shorttext"
 	@echo "# devhelp"
 
+.PHONY: epub
 epub:
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
+.PHONY: latex
 latex:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
 	@echo "Run \`make' in that directory to run these through (pdf)latex" \
 	      "(use \`make latexpdf' here to do that automatically)."
 
+.PHONY: latexpdf
 latexpdf:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through pdflatex..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
+.PHONY: latexpdfja
 latexpdfja:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through platex and dvipdfmx..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
+.PHONY: text
 text:
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
+.PHONY: man
 man:
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
+.PHONY: texinfo
 texinfo:
 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
 	@echo
 	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
 	@echo "Run \`make' in that directory to run these through makeinfo" \
 	      "(use \`make info' here to do that automatically)."
 
+.PHONY: info
 info:
 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
 	@echo "Running Texinfo files through makeinfo..."
 	make -C $(BUILDDIR)/texinfo info
 	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
 
+.PHONY: gettext
 gettext:
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
+.PHONY: changes
 changes:
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
+.PHONY: linkcheck
 linkcheck:
 	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
 	@echo
 	@echo "Link check complete; look for any errors in the above output " \
 	      "or in $(BUILDDIR)/linkcheck/output.txt."
 
+.PHONY: doctest
 doctest:
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
+.PHONY: coverage
 coverage:
 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
 	@echo "Testing of coverage in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/coverage/python.txt."
 
+.PHONY: xml
 xml:
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
+.PHONY: pseudoxml
 pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo

docs/conf.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # shorttext documentation build configuration file, created by
-# sphinx-quickstart on Fri Nov 11 18:11:01 2016.
+# sphinx-quickstart on Tue Nov 15 15:25:44 2016.
 #
 # This file is execfile()d with the current directory set to its
 # containing dir.
@@ -14,14 +14,17 @@
 
 import sys
 import os
-import shlex
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../shorttext'))
 sys.path.insert(0, os.path.abspath('../shorttext/data'))
 sys.path.insert(0, os.path.abspath('../shorttext/utils'))
+sys.path.insert(0, os.path.abspath('../shorttext/classifiers'))
+sys.path.insert(0, os.path.abspath('../shorttext/classifiers/embed'))
+sys.path.insert(0, os.path.abspath('../shorttext/classifiers/embed/autoencode'))
 sys.path.insert(0, os.path.abspath('../shorttext/classifiers/embed/sumvec'))
 sys.path.insert(0, os.path.abspath('../shorttext/classifiers/embed/nnlib'))
 
@@ -62,9 +65,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.0'
+version = u'0.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.0b5'
+release = u'0.0b5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -229,8 +232,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'shorttext.tex', u'shorttext Documentation',
-   u'Kwan-Yuet Ho', 'manual'),
+    (master_doc, 'shorttext.tex', u'shorttext Documentation',
+     u'Kwan-Yuet Ho', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -273,9 +276,9 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'shorttext', u'shorttext Documentation',
-   author, 'shorttext', 'One line description of project.',
-   'Miscellaneous'),
+    (master_doc, 'shorttext', u'shorttext Documentation',
+     author, 'shorttext', 'One line description of project.',
+     'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.

setup.py

@@ -21,13 +21,15 @@ def readme():
       author_email="stephenhky@yahoo.com.hk",
       license='MIT',
       packages=['shorttext',
+                'shorttext.utils',
                 'shorttext.classifiers',
                 'shorttext.classifiers.embed',
                 'shorttext.classifiers.embed.autoencode',
                 'shorttext.classifiers.embed.nnlib',
                 'shorttext.classifiers.embed.sumvec',
-                'shorttext.data',
-                'shorttext.utils',],
+                'shorttext.data',],
+      package_dir={'shorttext': 'shorttext'},
+      package_data={'shorttext': ['data/*.csv']},
       install_requires=[
           'numpy', 'scipy', 'keras', 'theano', 'nltk', 'gensim', 'pandas',
       ],

shorttext/__init__.py

@@ -1,2 +1,3 @@
-
-
+import data
+import utils
+import classifiers

shorttext/classifiers/__init__.py

@@ -1,6 +1,9 @@
-from classifiers.embed.autoencode import AutoencoderEmbedVecClassification
-from classifiers.embed.nnlib import CNNEmbedVecClassification
-from classifiers.embed.sumvec import SumWord2VecClassification
+from ..utils import classification_exceptions
+from ..utils import kerasmodel_io as kerasmodel_io
+
+from .embed.autoencode import AutoencoderEmbedVecClassification
+from .embed.nnlib import CNNEmbedVecClassification
+from .embed.sumvec import SumWord2VecClassification
 
 # allowed algorithms
-allowed_algos = {'sumword2vec', 'autoencoder', 'cnn', 'vnn'}
+allowed_algos = {'sumword2vec', 'autoencoder', 'cnn', 'vnn'}

shorttext/classifiers/embed/autoencode/AutoencoderEmbedVecClassification.py

@@ -8,8 +8,8 @@
 from nltk import word_tokenize
 from scipy.spatial.distance import cosine
 
-from utils import kerasmodel_io as kerasio
-from utils import ModelNotTrainedException
+from ... import kerasmodel_io as kerasio
+from ... import classification_exceptions as e
 
 
 # Reference: Francois Chollet, "Building Autoencoders in Keras"
@@ -76,7 +76,7 @@ def train(self):
 
     def savemodel(self, nameprefix, save_complete_autoencoder=False):
         if not self.trained:
-            raise ModelNotTrainedException()
+            raise e.ModelNotTrainedException()
         kerasio.save_model(nameprefix+'_encoder', self.encoder)
         if save_complete_autoencoder:
             kerasio.save_model(nameprefix+'_decoder', self.decoder)
@@ -99,7 +99,7 @@ def shorttext_to_embedvec(self, shorttext):
 
     def encode(self, shorttext):
         if not self.trained:
-            raise ModelNotTrainedException()
+            raise e.ModelNotTrainedException()
         embedvec = self.shorttext_to_embedvec(shorttext)
         return self.encoder.predict(np.array([embedvec]))
 

shorttext/classifiers/embed/nnlib/CNNEmbedVecClassification.py

@@ -1,10 +1,13 @@
 import VarNNEmbedVecClassification as vnn
-from classifiers.embed.nnlib import frameworks as fr
+import frameworks as fr
 
 
 # wrapper for VarNNEmbedVecClassification for using CNN only
 # backward compatible with the previous version of this class
 class CNNEmbeddedVecClassifier:
+    """
+    This class is a wrapper that runs {@link vnn}, but carries backward compatibility.
+    """
     def __init__(self,
                  wvmodel,
                  classdict=None,