Merge pull request #2899 from RaRe-Technologies/pr2821

[MRG] Fix similarity bug in NMSLIB indexer + documentation fixes

docs/src/_matutils.rst

@@ -1,8 +1,8 @@
-:mod:`_matutils` -- Cython matutils
-===================================
+:mod:`_matutils` -- Compiled extension for math utils
+=====================================================
 
 .. automodule:: gensim._matutils
-    :synopsis: Cython math utils
+    :synopsis: Compiled extension for math utils
     :members:
     :inherited-members:
     :undoc-members:

docs/src/apiref.rst

@@ -50,6 +50,7 @@ Modules:
     models/_fasttext_bin
     models/phrases
     models/poincare
+    viz/poincare
     models/coherencemodel
     models/basemodel
     models/callbacks
@@ -63,7 +64,8 @@ Modules:
     models/wrappers/varembed
     similarities/docsim
     similarities/termsim
-    similarities/index
+    similarities/annoy
+    similarities/nmslib
     sklearn_api/atmodel
     sklearn_api/d2vmodel
     sklearn_api/hdp
@@ -102,4 +104,3 @@ Modules:
     summarization/summariser
     summarization/syntactic_unit
     summarization/textcleaner
-    viz/poincare

docs/src/auto_examples/core/run_similarity_queries.py.md5

@@ -1 +1 @@
-a3eaf7347874a32d1d25a455753206dc
+54804120deb345715247f0eed42b5e0e

docs/src/auto_examples/core/run_similarity_queries.rst

@@ -142,7 +142,7 @@ no random-walk static ranks, just a semantic extension over the boolean keyword
 
  .. code-block:: none
 
-    [(0, 0.4618210045327158), (1, 0.07002766527900064)]
+    [(0, 0.46182100453271613), (1, 0.07002766527900031)]
 
 
 
@@ -254,15 +254,15 @@ order, and obtain the final answer to the query `"Human computer interaction"`:
 
  .. code-block:: none
 
-    (2, 0.9984453) Human machine interface for lab abc computer applications
-    (0, 0.998093) A survey of user opinion of computer system response time
-    (3, 0.9865886) The EPS user interface management system
-    (1, 0.93748635) System and human system engineering testing of EPS
-    (4, 0.90755945) Relation of user perceived response time to error measurement
-    (8, 0.050041765) The generation of random binary unordered trees
-    (7, -0.09879464) The intersection graph of paths in trees
-    (6, -0.10639259) Graph minors IV Widths of trees and well quasi ordering
-    (5, -0.12416792) Graph minors A survey
+    0.9984453 The EPS user interface management system
+    0.998093 Human machine interface for lab abc computer applications
+    0.9865886 System and human system engineering testing of EPS
+    0.93748635 A survey of user opinion of computer system response time
+    0.90755945 Relation of user perceived response time to error measurement
+    0.050041765 Graph minors A survey
+    -0.09879464 Graph minors IV Widths of trees and well quasi ordering
+    -0.10639259 The intersection graph of paths in trees
+    -0.12416792 The generation of random binary unordered trees
 
 
 
@@ -319,17 +319,17 @@ on large datasets easily, and to facilitate prototyping of new algorithms for re
 
  .. code-block:: none
 
-    /Volumes/work/workspace/gensim_misha/docs/src/gallery/core/run_similarity_queries.py:194: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
-      plt.show()
+    /Volumes/work/workspace/vew/gensim3.6/lib/python3.6/site-packages/matplotlib/figure.py:445: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
+      % get_backend())
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.663 seconds)
+   **Total running time of the script:** ( 0 minutes  1.211 seconds)
 
-**Estimated memory usage:**  6 MB
+**Estimated memory usage:**  39 MB
 
 
 .. _sphx_glr_download_auto_examples_core_run_similarity_queries.py:

docs/src/auto_examples/core/sg_execution_times.rst

@@ -5,9 +5,9 @@
 
 Computation times
 =================
-**00:00.844** total execution time for **auto_examples_core** files:
+**00:01.211** total execution time for **auto_examples_core** files:
 
-- **00:00.844**: :ref:`sphx_glr_auto_examples_core_run_topics_and_transformations.py` (``run_topics_and_transformations.py``)
+- **00:01.211**: :ref:`sphx_glr_auto_examples_core_run_similarity_queries.py` (``run_similarity_queries.py``)
 - **00:00.000**: :ref:`sphx_glr_auto_examples_core_run_core_concepts.py` (``run_core_concepts.py``)
 - **00:00.000**: :ref:`sphx_glr_auto_examples_core_run_corpora_and_vector_spaces.py` (``run_corpora_and_vector_spaces.py``)
-- **00:00.000**: :ref:`sphx_glr_auto_examples_core_run_similarity_queries.py` (``run_similarity_queries.py``)
+- **00:00.000**: :ref:`sphx_glr_auto_examples_core_run_topics_and_transformations.py` (``run_topics_and_transformations.py``)

docs/src/auto_examples/index.rst

@@ -13,7 +13,7 @@ If you're thinking about contributing documentation, please see :ref:`sphx_glr_a
 
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
@@ -33,9 +33,10 @@ Understanding this functionality is vital for using gensim effectively.
 
 .. only:: html
 
-    .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_core_concepts_thumb.png
+ .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_core_concepts_thumb.png
+     :alt: Core Concepts
 
-        :ref:`sphx_glr_auto_examples_core_run_core_concepts.py`
+     :ref:`sphx_glr_auto_examples_core_run_core_concepts.py`
 
 .. raw:: html
 
@@ -53,9 +54,10 @@ Understanding this functionality is vital for using gensim effectively.
 
 .. only:: html
 
-    .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_corpora_and_vector_spaces_thumb.png
+ .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_corpora_and_vector_spaces_thumb.png
+     :alt: Corpora and Vector Spaces
 
-        :ref:`sphx_glr_auto_examples_core_run_corpora_and_vector_spaces.py`
+     :ref:`sphx_glr_auto_examples_core_run_corpora_and_vector_spaces.py`
 
 .. raw:: html
 
@@ -73,9 +75,10 @@ Understanding this functionality is vital for using gensim effectively.
 
 .. only:: html
 
-    .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_topics_and_transformations_thumb.png
+ .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_topics_and_transformations_thumb.png
+     :alt: Topics and Transformations
 
-        :ref:`sphx_glr_auto_examples_core_run_topics_and_transformations.py`
+     :ref:`sphx_glr_auto_examples_core_run_topics_and_transformations.py`
 
 .. raw:: html
 
@@ -93,9 +96,10 @@ Understanding this functionality is vital for using gensim effectively.
 
 .. only:: html
 
-    .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_similarity_queries_thumb.png
+ .. figure:: /auto_examples/core/images/thumb/sphx_glr_run_similarity_queries_thumb.png
+     :alt: Similarity Queries
 
-        :ref:`sphx_glr_auto_examples_core_run_similarity_queries.py`
+     :ref:`sphx_glr_auto_examples_core_run_similarity_queries.py`
 
 .. raw:: html
 
@@ -108,7 +112,7 @@ Understanding this functionality is vital for using gensim effectively.
    /auto_examples/core/run_similarity_queries
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
@@ -127,9 +131,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_word2vec_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_word2vec_thumb.png
+     :alt: Word2Vec Model
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_word2vec.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_word2vec.py`
 
 .. raw:: html
 
@@ -147,9 +152,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_doc2vec_lee_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_doc2vec_lee_thumb.png
+     :alt: Doc2Vec Model
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_doc2vec_lee.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_doc2vec_lee.py`
 
 .. raw:: html
 
@@ -167,9 +173,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_fasttext_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_fasttext_thumb.png
+     :alt: FastText Model
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_fasttext.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_fasttext.py`
 
 .. raw:: html
 
@@ -187,9 +194,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_annoy_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_annoy_thumb.png
+     :alt: Fast Similarity Queries with Annoy and Word2Vec
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_annoy.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_annoy.py`
 
 .. raw:: html
 
@@ -207,9 +215,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_lda_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_lda_thumb.png
+     :alt: LDA Model
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_lda.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_lda.py`
 
 .. raw:: html
 
@@ -227,9 +236,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_distance_metrics_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_distance_metrics_thumb.png
+     :alt: Distance Metrics
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_distance_metrics.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_distance_metrics.py`
 
 .. raw:: html
 
@@ -247,9 +257,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_wmd_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_wmd_thumb.png
+     :alt: Word Movers' Distance
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_wmd.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_wmd.py`
 
 .. raw:: html
 
@@ -267,9 +278,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_summarization_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_summarization_thumb.png
+     :alt: Text Summarization
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_summarization.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_summarization.py`
 
 .. raw:: html
 
@@ -287,9 +299,10 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
 
 .. only:: html
 
-    .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_pivoted_doc_norm_thumb.png
+ .. figure:: /auto_examples/tutorials/images/thumb/sphx_glr_run_pivoted_doc_norm_thumb.png
+     :alt: Pivoted Document Length Normalization
 
-        :ref:`sphx_glr_auto_examples_tutorials_run_pivoted_doc_norm.py`
+     :ref:`sphx_glr_auto_examples_tutorials_run_pivoted_doc_norm.py`
 
 .. raw:: html
 
@@ -302,7 +315,7 @@ Learning-oriented lessons that introduce a particular gensim feature, e.g. a mod
    /auto_examples/tutorials/run_pivoted_doc_norm
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
@@ -321,9 +334,10 @@ These **goal-oriented guides** demonstrate how to **solve a specific problem** u
 
 .. only:: html
 
-    .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_downloader_api_thumb.png
+ .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_downloader_api_thumb.png
+     :alt: How to download pre-trained models and corpora
 
-        :ref:`sphx_glr_auto_examples_howtos_run_downloader_api.py`
+     :ref:`sphx_glr_auto_examples_howtos_run_downloader_api.py`
 
 .. raw:: html
 
@@ -341,9 +355,10 @@ These **goal-oriented guides** demonstrate how to **solve a specific problem** u
 
 .. only:: html
 
-    .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc_thumb.png
+ .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc_thumb.png
+     :alt: How to Author Gensim Documentation
 
-        :ref:`sphx_glr_auto_examples_howtos_run_doc.py`
+     :ref:`sphx_glr_auto_examples_howtos_run_doc.py`
 
 .. raw:: html
 
@@ -361,9 +376,10 @@ These **goal-oriented guides** demonstrate how to **solve a specific problem** u
 
 .. only:: html
 
-    .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc2vec_imdb_thumb.png
+ .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_doc2vec_imdb_thumb.png
+     :alt: How to Apply Doc2Vec to Reproduce the 'Paragraph Vector' paper
 
-        :ref:`sphx_glr_auto_examples_howtos_run_doc2vec_imdb.py`
+     :ref:`sphx_glr_auto_examples_howtos_run_doc2vec_imdb.py`
 
 .. raw:: html
 
@@ -381,9 +397,10 @@ These **goal-oriented guides** demonstrate how to **solve a specific problem** u
 
 .. only:: html
 
-    .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_compare_lda_thumb.png
+ .. figure:: /auto_examples/howtos/images/thumb/sphx_glr_run_compare_lda_thumb.png
+     :alt: How to Compare LDA Models
 
-        :ref:`sphx_glr_auto_examples_howtos_run_compare_lda.py`
+     :ref:`sphx_glr_auto_examples_howtos_run_compare_lda.py`
 
 .. raw:: html
 
@@ -396,7 +413,7 @@ These **goal-oriented guides** demonstrate how to **solve a specific problem** u
    /auto_examples/howtos/run_compare_lda
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
@@ -440,7 +457,7 @@ Blog posts, tutorial videos, hackathons and other useful Gensim resources, from
 
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div class="sphx-glr-clear"></div>
 
 
 
@@ -450,15 +467,15 @@ Blog posts, tutorial videos, hackathons and other useful Gensim resources, from
     :class: sphx-glr-footer-gallery
 
 
-  .. container:: sphx-glr-download
+  .. container:: sphx-glr-download sphx-glr-download-python
 
-    :download:`Download all examples in Python source code: auto_examples_python.zip <//home/misha/git/gensim/docs/src/auto_examples/auto_examples_python.zip>`
+    :download:`Download all examples in Python source code: auto_examples_python.zip <//Volumes/work/workspace/gensim/trunk/docs/src/auto_examples/auto_examples_python.zip>`
 
 
 
-  .. container:: sphx-glr-download
+  .. container:: sphx-glr-download sphx-glr-download-jupyter
 
-    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//home/misha/git/gensim/docs/src/auto_examples/auto_examples_jupyter.zip>`
+    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//Volumes/work/workspace/gensim/trunk/docs/src/auto_examples/auto_examples_jupyter.zip>`
 
 
 .. only:: html