Merge branch 'master' into devel_docs

Conflicts:
	VERSION_HISTORY.md
	doc/api/about.rst

.coveragerc

@@ -1,3 +1,3 @@
 [run]
 source = vis
-omit = vis/tests/*,vis/analyzers/*/template*,*/__init__*
+omit = vis/tests/*,vis/analyzers/*/template*,vis/scripts/*,*/__init__*

.travis.yml

@@ -1,13 +1,14 @@
 # Configuration File for Travis-CI
-
+sudo: false
+addons:
+ apt:
+  packages:
+   - liblapack-dev
+   - gfortran
 language: python
 python:
   - "2.7"
-  - "3.3"
   - "3.4"
-
-install: pip install -r vis/requirements.txt
-
+install: travis_wait pip install -r vis/travis_requirements.txt
 script:  coverage run run_tests.py
-
-after_success: coveralls
+after_success: coveralls

README.txt

@@ -3,10 +3,10 @@ The VIS Framework
 
 The VIS Framework for Music Analysis
 
-[![Build Status](https://travis-ci.org/ELVIS-Project/vis.svg?branch=master)](https://travis-ci.org/ELVIS-Project/vis-framework)
-[![Coverage Status](https://img.shields.io/coveralls/ELVIS-Project/vis.svg)](https://coveralls.io/r/ELVIS-Project/vis-framework)
-[![Latest Version](https://pypip.in/version/vis-framework/badge.svg?text=version)](https://pypi.python.org/pypi/vis-framework/)
-[![License](https://pypip.in/license/vis-framework/badge.svg)](https://www.gnu.org/licenses/agpl-3.0.html)
+[![Build Status](https://travis-ci.org/ELVIS-Project/vis-framework.svg?branch=master)](https://travis-ci.org/ELVIS-Project/vis-framework)
+[![Coverage Status](https://coveralls.io/repos/ELVIS-Project/vis-framework/badge.svg?branch=master&service=github)](https://coveralls.io/github/ELVIS-Project/vis-framework?branch=master)
+[![Latest Version](https://img.shields.io/pypi/v/vis-framework.svg)](https://pypi.python.org/pypi/vis-framework/)
+[![License](https://img.shields.io/badge/license-AGPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.html)
 
 The VIS Framework is a Python package that uses the music21 and pandas libraries to build a ridiculously flexible and preposterously easy system for writing computer music analysis programs.
 
@@ -23,16 +23,18 @@ The VIS Framework uses many software libraries to help with analysis. These are
 - Python 2.7
 - music21
 - pandas
-- mock (for testing)
-- coverage (for testing)
-- python-coveralls (to for automated coverage with coveralls.io)
 
 These are recommended dependencies:
 
 - numexpr (improved performance for pandas)
 - Bottleneck (improved performance for pandas)
 - tables (HDF5 output for pandas)
 - openpyxl (Excel output for pandas)
+- mock (for testing)
+- coverage (for testing)
+- python-coveralls (to for automated coverage with coveralls.io)
+- matplotlib (plotting)
+- scipy (plotting)
 
 Citation
 ========

VERSION_HISTORY.md

@@ -3,13 +3,22 @@ VERSION HISTORY
 This file records version-to-version changes in the VIS Framework. The most recent versions are at
 the top of the file.
 
-
-* 2.2.0 (pending release):
-    - Python 3 compatibility.
+* 2.3.0 (pending release):
     - Importing no longer uses/stores cached pickle files.
     - WorkflowManager.output() produces many table-format results if "count frequency" is False.
     - WorkflowManager.output() changes the column name for table-like outputs, according to the experiment.
     - Greatly improved API documentation.
+* 2.2.1:
+    - set music21 version to 2.1.2 exclusively
+* 2.2.0:
+    - Python 3 compatibility.
+    - New: hierarchical clustering and dendrogram graphical output with dendrogram.py
+    - Refactoring/rewrite: update make_return() method in indexer.py to greatly enhance performance when creating dataframes. Uses pandas.concat() instead of pandas.DataFrame()
+    - Refactoring: simplified the way several indexers and experimenters internally set their settings to make their init methods easier to read. Uses .update() instead of making piecemeal changes.
+    - Tests: includes 15 new tests in a test suite for the dendrogram.py file and comments out 2 tests in offset.py because they are incompatible with the new version of make_return() as they pass magic mock objects to a be concatenated by pandas.concat().
+    - Automated test and code coverage fix
+    - cleanup of dependencies/requirements (big thanks to maxalbert, https://github.com/maxalbert)
+    - 'scripts' directory for helpful scripts
 * 2.1.3
     - can turn on/off multiprocessing
     - fixed issue with Pandas converting strings to floats (or, rather, hacked a solution)

run_tests.py

@@ -7,7 +7,7 @@
 # Filename: run_tests.py
 # Purpose: Run automated tests for the VIS Framework.
 #
-# Copyright (C) 2012, 2013, 2014 Jamie Klassen, Christopher Antila, Ryan Bannon
+# Copyright (C) 2012, 2013, 2014 Jamie Klassen, Christopher Antila, Ryan Bannon, Alexander Morgan
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as
@@ -33,13 +33,16 @@
 from vis.tests import test_indexer
 from vis.tests import test_duration_indexer
 from vis.tests import test_note_beat_strength_indexer
+from vis.tests import test_measure_indexer
 from vis.tests import test_note_rest_indexer
 from vis.tests import test_ngram
+from vis.tests import test_dissonance_indexer
 from vis.tests import test_repeat
 from vis.tests import test_interval_indexer
 from vis.tests import test_frequency_experimenter
 from vis.tests import test_aggregator
 from vis.tests import test_barchart
+from vis.tests import test_dendrogram
 from vis.tests import test_offset
 from vis.tests import test_lilypond
 from vis.tests import test_indexed_piece
@@ -61,12 +64,14 @@
              test_note_rest_indexer.NOTE_REST_INDEXER_SUITE,
              test_duration_indexer.DURATION_INDEXER_SUITE,
              test_note_beat_strength_indexer.NOTE_BEAT_STRENGTH_INDEXER_SUITE,
+             test_measure_indexer.MEASURE_INDEXER_SUITE,
              test_interval_indexer.INTERVAL_INDEXER_SHORT_SUITE,
              test_interval_indexer.INTERVAL_INDEXER_LONG_SUITE,
              test_interval_indexer.INT_IND_INDEXER_SUITE,
              test_interval_indexer.HORIZ_INT_IND_LONG_SUITE,
              test_repeat.REPEAT_INDEXER_SUITE,
              test_ngram.NGRAM_INDEXER_SUITE,
+             test_dissonance_indexer.DISSONANCE_INDEXER_SUITE,
              test_offset.OFFSET_INDEXER_SINGLE_SUITE,
              test_offset.OFFSET_INDEXER_MULTI_SUITE,
              test_lilypond.ANNOTATION_SUITE,
@@ -77,6 +82,7 @@
              test_frequency_experimenter.FREQUENCY_SUITE,
              test_aggregator.COLUMN_AGGREGATOR_SUITE,
              test_barchart.R_BAR_CHART_SUITE,
+             test_dendrogram.DENDROGRAM_SUITE,
              # IndexedPiece and AggregatedPieces
              test_indexed_piece.INDEXED_PIECE_SUITE_A,
              test_indexed_piece.INDEXED_PIECE_SUITE_B,

setup.py

@@ -50,20 +50,13 @@
     platforms = 'any',
     keywords = ['music', 'music analysis', 'music theory', 'counterpoint'],
     requires = [
-        # NB: keep this in sync with vis/requirements.txt and vis/optional_requirements.txt
-        # NB2: I left out the optional requirements and mock, since they aren't *required*
-        'music21 (>=2.0.3, <2.1)',
-        'pandas (>=0.14.1, <0.16)',
+        'music21 (== 2.1.2)',
+        'pandas (>= 0.14.1, < 0.17)'
         ],
     install_requires = [
-        'music21 >= 2.0.3, <2.1',
-        'pandas >=0.14.1, <0.16',
+        'music21 == 2.1.2',
+        'pandas >= 0.14.1, < 0.17'
         ],
-    dependency_links = [
-        # music21 2.0.3 has not been released to PyPl yet (2015-05-20).
-        # This particular commit fixes an issue with exporting fermatas on rests.
-        "https://github.com/cuthbertLab/music21/archive/3fb33def708602485eadc1a655ede2fe22acb766.zip#egg=music21-2.0.3"
-    ],
     packages = [
         'vis',
         'vis.models',

vis/__init__.py

@@ -1,4 +1,4 @@
 _MAJOR = 2
-_MINOR = 1
-_PATCH = 3
+_MINOR = 2
+_PATCH = 1
 __version__ = '{}.{}.{}'.format(_MAJOR, _MINOR, _PATCH)

vis/analyzers/experimenters/barchart.py

@@ -110,32 +110,15 @@ def __init__(self, index, settings=None):
         if 'pathname' not in settings:
             raise RuntimeError(RBarChart._MISSING_SETTINGS)
 
-        self._settings = {'pathname': settings['pathname']}
-
-        # set 'type' ensuring it is valid
+        # Make sure 'type' is valid
         if 'type' in settings:
-            if settings['type'] in RBarChart.OUTPUT_TYPES:
-                self._settings['type'] = settings['type']
-            else:
+            if settings['type'] not in RBarChart.OUTPUT_TYPES:
                 raise RuntimeError(RBarChart._INVALID_TYPE.format(settings['type']))
-        else:
-            self._settings['type'] = RBarChart.default_settings['type']
-
-        # set the other settings
-        if 'column' in settings:
-            self._settings['column'] = settings['column']
-        else:
-            self._settings['column'] = RBarChart.default_settings['column']
 
-        if 'token' in settings:
-            self._settings['token'] = settings['token']
-        else:
-            self._settings['token'] = RBarChart.default_settings['token']
-
-        if 'nr_pieces' in settings:
-            self._settings['nr_pieces'] = str(settings['nr_pieces'])
-        else:
-            self._settings['nr_pieces'] = RBarChart.default_settings['nr_pieces']
+        self._settings = RBarChart.default_settings.copy()
+        self._settings.update(settings)
+        if self._settings['nr_pieces'] is not None:
+        	self._settings['nr_pieces'] = str(self._settings['nr_pieces'])
 
         # set the path to the script
         self._r_bar_chart_path = path.join(vis.__path__[0], 'scripts', 'R_bar_chart.r')