Merge branch 'develop'

.coveragerc

@@ -1,9 +1,3 @@
+# This file is used by coverage command, called from tox.ini 
 [run]
 source = gazelib
-omit =
-    */python?.?/*
-    */lib-python/?.?/*.py
-    */lib_pypy/_*.py
-    */site-packages/ordereddict.py
-    */site-packages/nose/*
-    */unittest2/*

.python-version

@@ -1,7 +1,4 @@
-2.6.9
 2.7.10
-3.1.5
-3.2.6
 3.3.6
 3.4.3
 3.5.0

.travis.yml

@@ -1,23 +1,18 @@
+sudo: false
 language: python
 python:
   - "2.7"
+  - "3.3"
+  - "3.4"
   - "3.5"
-#- "3.5-dev" # 3.5 development branch
-#sudo: true
-before_install:
-  - wget -O miniconda.sh https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda2/bin:$PATH
-  - conda update --yes conda
+
 # command to install dependencies
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION atlas nose
-  - pip install python-coveralls nose-cov unittest2
-  - "pip install $(python setup.py --require)"
+  - pip install tox-travis python-coveralls
+
 # command to run tests
 script:
-  - nosetests --with-cov --cov gazelib --cov-config .coveragerc --logging-level=INFO
+  - tox
 
 after_success:
-  - coveralls --config_file .coveragerc
+  - coveralls

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2015 Jussi Kaatiala, Akseli Palén
+Copyright 2015 Jussi Kaatiala, Akseli Palen
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

README.rst

@@ -23,15 +23,11 @@ With `pip
     $ pip install gazelib
 
 
-
-Usage
-========
-
-API
+Docs
 ======
 
-API docs are available under `docs/
-<https://rawgit.com/infant-cognition-tampere/gazelib/develop/docs/build/>`_.  
+Examples and API docs are available at `http://gazelib.readthedocs.org/
+<http://gazelib.readthedocs.org/>`_.
 
 For developers
 =================
@@ -87,7 +83,7 @@ Follow `instructions to install pyenv
 
 or run comprehensive tests for multiple Python versions listed in ``tox.ini``::
 
-    $ pyenv local 2.6.9 2.7.10 3.1.5 3.2.6 3.3.6 3.4.3 3.5.0
+    $ pyenv local 2.7.10 3.1.5 3.2.6 3.3.6 3.4.3 3.5.0
     $ eval "$(pyenv init -)"
     $ pyenv rehash
     $ tox
@@ -99,6 +95,18 @@ Install new pyenv environments for example by::
 Validate README.rst at `http://rst.ninjs.org/
 <http://rst.ninjs.org/>`_
 
+Tox + Travis CI + `Coveralls
+<https://coveralls.io/github/infant-cognition-tampere/gazelib>`_:
+
+- https://www.rfk.id.au/blog/entry/testing-better-coverage-tox/
+- http://coverage.readthedocs.org/en/latest/
+- https://github.com/z4r/python-coveralls
+- https://github.com/ryanhiebert/tox-travis
+- http://jsatt.com/blog/using-tox-with-travis-ci-to-test-django-apps/
+- http://agiliq.com/blog/2014/05/continuous-integration-with-travis-and-coverallsio/
+- https://github.com/openwebinars-django/testango
+
+
 
 Publishing to PyPI
 -----------------------
@@ -132,6 +140,9 @@ Version release
 5.  Push commits and tags: ``$ git push && git push --tags``
 6.  Publish to PyPI. See *4.4. Publishing to PyPI*.
 
+See also `a successful Git branching model
+<http://nvie.com/posts/a-successful-git-branching-model/>`_.
+
 
 Compile documentation
 ---------------------

docs/conf.py

@@ -53,8 +53,8 @@
 
 # General information about the project.
 project = 'gazelib'
-copyright = '2016, Akseli Palén'
-author = 'Akseli Palén'
+copyright = '2016, Akseli Palen'
+author = 'Akseli Palen'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -229,7 +229,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'gazelib.tex', 'gazelib Documentation',
-     'Akseli Palén', 'manual'),
+     'Akseli Palen', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

gazelib/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Gazelib, a toolkit for gaze analysis.
 '''

gazelib/containers.py

@@ -1,10 +1,12 @@
+# -*- coding: utf-8 -*-
 '''
 Classes that store the gaze data and can be fed to analysis functions.
 '''
-from .validation import has_keys, is_list_of_strings, is_real, ValidationException
+from .validation import has_keys, is_list_of_strings, is_real
 from .settings import min_event_slice_overlap_seconds as min_overlap
 from deepdiff import DeepDiff
 from bisect import bisect_left  # binary tree search tool
+from jsonschema import validate as validate_jsonschema
 
 
 class CommonV1(object):
@@ -21,21 +23,94 @@ class InvalidStreamException(Exception):
     class InvalidEventException(Exception):
         pass
 
+    # JSON Schema to validate raw input
+    SCHEMA = {
+        '$schema': 'http://json-schema.org/draft-04/schema#',
+        'title': 'gazelib/common/v1',
+        'type': 'object',
+        'properties': {
+            'schema': {
+                'type': 'string',
+                'pattern': 'gazelib/common/v1'
+            },
+            'global_posix_time': {
+                'type': 'number'
+            },
+            'environment': {
+                'type': 'object',
+                'patternProperties': {
+                    '.+': {}
+                }
+            },
+            'timelines': {
+                'type': 'object',
+                'patternProperties': {
+                    '.+': {
+                        'type': 'array',
+                        'items': {
+                            'type': 'number'
+                        }
+                    }
+                }
+            },
+            'streams': {
+                'type': 'object',
+                'patternProperties': {
+                    '.+': {
+                        'type': 'object',
+                        'properties': {
+                            'timeline': {
+                                'type': 'string'
+                            },
+                            'values': {
+                                'type': 'array'
+                            },
+                            'confidence': {
+                                'type': 'array',
+                                'items': {
+                                    'type': 'number',
+                                    'maximum': 1.0,
+                                    'minimum': 0.0
+                                }
+                            }
+                        },
+                        'required': ['timeline', 'values']
+                    }
+                }
+            },
+            'events': {
+                'type': 'array',
+                'items': {
+                    'type': 'object',
+                    'properties': {
+                        'tags': {
+                            'type': 'array',
+                            'items': {
+                                'type': 'string'
+                            }
+                        },
+                        'range': {
+                            'type': 'array',
+                            'items': {
+                                'type': 'number'
+                            }
+                        },
+                        'extra': {}
+                    },
+                    'required': ['tags', 'range']
+                }
+            }
+        },
+        'required': ['schema', 'global_posix_time', 'environment',
+                     'timelines', 'streams', 'events']
+    }
+
+    @staticmethod
     def validate(raw_common):
-        keys = [
-          'schema',
-          'global_posix_time',
-          'environment',
-          'timelines',
-          'streams',
-          'events'
-        ]
-
-        if not has_keys(raw_common, keys):
-            raise CommonV1.ValidationException('Keys missing')
-
-        # TODO validate schema value
-        # TODO validate types
+        '''
+        Raises ValidationError if raw_common is not valid gazelib/common/v1
+        '''
+        validate_jsonschema(raw_common, CommonV1.SCHEMA)
 
 
     def __init__(self, raw_common):
@@ -52,13 +127,13 @@ def __eq__(self, other):
     # Accessors
 
     def convert_to_global_time(self, relative_time_seconds):
-        if relative_time_seconds == None:
+        if relative_time_seconds is None:
             return None
         gt = self.raw['global_posix_time']
         return gt + relative_time_seconds
 
     def convert_to_relative_time(self, global_time_seconds):
-        if global_time_seconds == None:
+        if global_time_seconds is None:
             return None
         gt = self.raw['global_posix_time']
         return global_time_seconds - gt
@@ -86,7 +161,7 @@ def iter_events_by_tag(self, tag):
     def slice_by_relative_time(self, rel_start_time, rel_end_time=None):
         '''
         Return new CommonV1 object with data only in the time range.
-          Does not update global_posix_time because easier implementation
+        Does not update global_posix_time because easier implementation.
         '''
 
         # The new copy
@@ -160,15 +235,14 @@ def slice_by_relative_time(self, rel_start_time, rel_end_time=None):
 
         return CommonV1(slice_raw)
 
-
     def slice_by_global_time(self, start_time, end_time=None):
         '''
         Return new CommonV1 object with data only in the time range.
-          Updates the global_posix_time to start_time
-            to minimize representation size.
+            Updates the global_posix_time to start_time
+                to minimize representation size.
         '''
         r_start = self.convert_to_relative_time(start_time)
-        r_end   = self.convert_to_relative_time(end_time)
+        r_end = self.convert_to_relative_time(end_time)
 
         return self.slice_by_relative_time(r_start, r_end)
 
@@ -178,10 +252,11 @@ def slice_by_timeline(self, timeline_name, start_index, end_index=None):
         by the indices of the timeline.
 
         Parameters
-          timeline_name
-          start_index, inclusive
-          end_index (optional), exclusive, first element to not be included.
-            if None given, slice to the end
+            timeline_name
+            start_index: inclusive
+            end_index: optional, exclusive, first element to not be included.
+                If None given, slice to the end.
+
         '''
         timelines = self.raw['timelines']
 
@@ -228,15 +303,15 @@ def slice_by_tag(self, tag, index=0):
         for event in self.raw['events']:
             if tag in event['tags']:
                 if index == i:
-                     target_event = event
-                     break
+                    target_event = event
+                    break
                 i += 1
 
         if target_event is None:
             return None
 
         range_start = target_event['range'][0]
-        range_end   = target_event['range'][1]
+        range_end = target_event['range'][1]
 
         return self.slice_by_relative_time(range_start, range_end)
 
@@ -257,7 +332,7 @@ def iter_slices_by_tag(self, tag, limit_to=None):
 
         for index, event in enumerate(self.iter_events_by_tag(tag)):
             range_start = event['range'][0]
-            range_end   = event['range'][1]
+            range_end = event['range'][1]
             yield self.slice_by_relative_time(range_start, range_end)
             if limit_to is not None:
                 if index + 2 > limit_to:

gazelib/io.py

@@ -1,10 +1,12 @@
+# -*- coding: utf-8 -*-
 '''
-Input-Output functions that help to read and write gazefiles in various formats.
+Input-Output functions that help to read and write gaze data.
 
 '''
 import json
 import csv
 
+
 def load_json(filename):
     # load json-type file
 
@@ -22,7 +24,8 @@ def write_json(filename, data):
 def write_fancy_json(filename, data):
     # Write json so that it is readable by humans (rowchange, indent..).
     with open(filename, 'w') as outfile:
-        json.dump(data, outfile, sort_keys = True, indent = 4, ensure_ascii=False)
+        json.dump(data, outfile, sort_keys=True,
+                  indent=4, ensure_ascii=False)
 
 
 def load_csv_as_dictlist(filename, delimit='\t'):
@@ -37,7 +40,7 @@ def load_csv_as_dictlist(filename, delimit='\t'):
         print("File loading error: " + str(ex))
         return
 
-    reader = csv.reader(ifile, delimiter = delimit)#"\t")
+    reader = csv.reader(ifile, delimiter=delimit)
 
     rownum = 0
     rows = []

gazelib/settings.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Gazelib settings
 '''