Merge branch 'devel' into polinomial

.gitchangelog.rc

@@ -0,0 +1,191 @@
+##
+## Format
+##
+##   ACTION: [AUDIENCE:] COMMIT_MSG [!TAG ...]
+##
+## Description
+##
+##   ACTION is one of 'chg', 'fix', 'new'
+##
+##       Is WHAT the change is about.
+##
+##       'chg' is for refactor, small improvement, cosmetic changes...
+##       'fix' is for bug fixes
+##       'new' is for new features, big improvement
+##
+##   AUDIENCE is optional and one of 'dev', 'usr', 'pkg', 'test', 'doc'
+##
+##       Is WHO is concerned by the change.
+##
+##       'dev'  is for developpers (API changes, refactors...)
+##       'usr'  is for final users (UI changes)
+##       'pkg'  is for packagers   (packaging changes)
+##       'test' is for testers     (test only related changes)
+##       'doc'  is for doc guys    (doc only changes)
+##
+##   COMMIT_MSG is ... well ... the commit message itself.
+##
+##   TAGs are additionnal adjective as 'refactor' 'minor' 'cosmetic'
+##
+##       They are preceded with a '!' or a '@' (prefer the former, as the
+##       latter is wrongly interpreted in github.) Commonly used tags are:
+##
+##       'refactor' is obviously for refactoring code only
+##       'minor' is for a very meaningless change (a typo, adding a comment)
+##       'cosmetic' is for cosmetic driven change (re-indentation, 80-col...)
+##       'wip' is for partial functionality but complete subfunctionality.
+##
+## Example:
+##
+##   new: usr: support of bazaar implemented
+##   chg: re-indentend some lines !cosmetic
+##   new: dev: updated code to be compatible with last version of killer lib.
+##   fix: pkg: updated year of licence coverage.
+##   new: test: added a bunch of test around user usability of feature X.
+##   fix: typo in spelling my name in comment. !minor
+##
+##   Please note that multi-line commit message are supported, and only the
+##   first line will be considered as the "summary" of the commit message. So
+##   tags, and other rules only applies to the summary.  The body of the commit
+##   message will be displayed in the changelog without reformatting.
+
+
+##
+## ``ignore_regexps`` is a line of regexps
+##
+## Any commit having its full commit message matching any regexp listed here
+## will be ignored and won't be reported in the changelog.
+##
+ignore_regexps = [
+        r'@minor', r'!minor',
+        r'@cosmetic', r'!cosmetic',
+        r'@refactor', r'!refactor',
+        r'@wip', r'!wip',
+        r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*[p|P]kg:',
+        r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*[d|D]ev:',
+        r'^(.{3,3}\s*:)?\s*[fF]irst commit.?\s*$',
+  ]
+
+
+## ``section_regexps`` is a list of 2-tuples associating a string label and a
+## list of regexp
+##
+## Commit messages will be classified in sections thanks to this. Section
+## titles are the label, and a commit is classified under this section if any
+## of the regexps associated is matching.
+##
+    ('New', [
+	r'^[nN]ew\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$',
+     ]),
+    ('Changes', [
+        r'^[cC]hg\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$',
+     ]),
+    ('Fix', [
+        r'^[fF]ix\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n]*)$',
+     ]),
+
+    ('Other', None ## Match all lines
+     ),
+
+]
+
+
+## ``body_process`` is a callable
+##
+## This callable will be given the original body and result will
+## be used in the changelog.
+##
+## Available constructs are:
+##
+##   - any python callable that take one txt argument and return txt argument.
+##
+##   - ReSub(pattern, replacement): will apply regexp substitution.
+##
+##   - Indent(chars="  "): will indent the text with the prefix
+##     Please remember that template engines gets also to modify the text and
+##     will usually indent themselves the text if needed.
+##
+##   - Wrap(regexp=r"\n\n"): re-wrap text in separate paragraph to fill 80-Columns
+##
+##   - noop: do nothing
+##
+##   - ucfirst: ensure the first letter is uppercase.
+##     (usually used in the ``subject_process`` pipeline)
+##
+##   - final_dot: ensure text finishes with a dot
+##     (usually used in the ``subject_process`` pipeline)
+##
+##   - strip: remove any spaces before or after the content of the string
+##
+## Additionally, you can `pipe` the provided filters, for instance:
+#body_process = Wrap(regexp=r'\n(?=\w+\s*:)') | Indent(chars="  ")
+#body_process = Wrap(regexp=r'\n(?=\w+\s*:)')
+#body_process = noop
+body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', r'') | strip
+
+
+## ``subject_process`` is a callable
+##
+## This callable will be given the original subject and result will
+## be used in the changelog.
+##
+## Available constructs are those listed in ``body_process`` doc.
+subject_process = (strip |
+    ReSub(r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n@]*)(@[a-z]+\s+)*$', r'\4') |
+    ucfirst | final_dot)
+
+
+## ``tag_filter_regexp`` is a regexp
+##
+## Tags that will be used for the changelog must match this regexp.
+##
+tag_filter_regexp = r'^v[0-9]+\.[0-9]+(\.[0-9]+)?$'
+
+
+## ``unreleased_version_label`` is a string
+##
+## This label will be used as the changelog Title of the last set of changes
+## between last valid tag and HEAD if any.
+unreleased_version_label = "Unreleased"
+
+
+## ``output_engine`` is a callable
+##
+## This will change the output format of the generated changelog file
+##
+## Available choices are:
+##
+##   - rest_py
+##
+##        Legacy pure python engine, outputs ReSTructured text.
+##        This is the default.
+##
+##   - mustache(<template_name>)
+##
+##        Template name could be any of the available templates in
+##        ``templates/mustache/*.tpl``.
+##        Requires python package ``pystache``.
+##        Examples:
+##           - mustache("markdown")
+##           - mustache("restructuredtext")
+##
+##   - makotemplate(<template_name>)
+##
+##        Template name could be any of the available templates in
+##        ``templates/mako/*.tpl``.
+##        Requires python package ``mako``.
+##        Examples:
+##           - makotemplate("restructuredtext")
+##
+>>>>>>> 287584f0cdac51a674996ff6d7092cc876b25ce6
+#output_engine = rest_py
+#output_engine = mustache("restructuredtext")
+output_engine = mustache("markdown")
+#output_engine = makotemplate("restructuredtext")
+
+
+## ``include_merge`` is a boolean
+##
+## This option tells git-log whether to include merge commits in the log.
+## The default is to include them.
+include_merge = True

CHANGELOG.md

@@ -1,13 +1,64 @@
 # Changelog
 
-## v1.5.3 (2016-09-06)
+## v1.5.5 (2016-10-03)
 
 ### Other
 
+* Bump version: 1.5.4 → 1.5.5. [Max Zwiessele]
+
+
+## v1.5.4 (2016-10-03)
+
+### New
+
+* Added deployment pull request instructions for developers. [mzwiessele]
+
+* Using gitchangelog to keep track of changes and log new features. [mzwiessele]
+
+### Changes
+
+* Version update on paramz. [Max Zwiessele]
+
+* Fixed naming in variational priors : [Max Zwiessele]
+
+* Changelog update. [mzwiessele]
+
+### Fix
+
+* Bug in dataset (in fn download_url) which wrongly interprets the Content-Length meta data, and just takes first character. [Michael T Smith]
+
+* What's new update fix #425 in changelog. [mzwiessele]
+
+### Other
+
+* Bump version: 1.5.3 → 1.5.4. [Max Zwiessele]
+
+* Merge pull request #443 from SheffieldML/dataset_download_url_bugfix. [Max Zwiessele]
+
+  fix: Bug in datasets.py
+
+* Merge branch 'kurtCutajar-devel' into devel. [mzwiessele]
+
 * Bump version: 1.5.2 → 1.5.3. [mzwiessele]
 
 * Merge branch 'devel' into kurtCutajar-devel. [mzwiessele]
 
+* Bump version: 1.5.1 → 1.5.2. [mzwiessele]
+
+* Minor readme changes. [mzwiessele]
+
+* Bump version: 1.5.0 → 1.5.1. [mzwiessele]
+
+* Bump version: 1.4.3 → 1.5.0. [mzwiessele]
+
+* Bump version: 1.4.2 → 1.4.3. [mzwiessele]
+
+* Bump version: 1.4.1 → 1.4.2. [mzwiessele]
+
+* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele]
+
+* [kern] fix #440. [mzwiessele]
+
 * [doc] cleanup. [mzwiessele]
 
 * [merge] into new devel. [Max Zwiessele]
@@ -41,63 +92,6 @@
 * Added core code for GpSSM and GpGrid. [kcutajar]
 
 
-## v1.5.2 (2016-09-06)
-
-### New
-
-* Added deployment pull request instructions for developers. [mzwiessele]
-
-### Other
-
-* Bump version: 1.5.1 → 1.5.2. [mzwiessele]
-
-* Minor readme changes. [mzwiessele]
-
-
-## v1.5.1 (2016-09-06)
-
-### Fix
-
-* What's new update fix #425 in changelog. [mzwiessele]
-
-### Other
-
-* Bump version: 1.5.0 → 1.5.1. [mzwiessele]
-
-
-## v1.5.0 (2016-09-06)
-
-### New
-
-* Using gitchangelog to keep track of changes and log new features. [mzwiessele]
-
-### Other
-
-* Bump version: 1.4.3 → 1.5.0. [mzwiessele]
-
-
-## v1.4.3 (2016-09-06)
-
-### Changes
-
-* Changelog update. [mzwiessele]
-
-### Other
-
-* Bump version: 1.4.2 → 1.4.3. [mzwiessele]
-
-
-## v1.4.2 (2016-09-06)
-
-### Other
-
-* Bump version: 1.4.1 → 1.4.2. [mzwiessele]
-
-* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele]
-
-* [kern] fix #440. [mzwiessele]
-
-
 ## v1.4.1 (2016-09-06)
 
 ### Other
@@ -718,6 +712,11 @@
 
 * [coverage] some more restrictions. [Max Zwiessele]
 
+
+## v1.0.5 (2016-04-08)
+
+### Other
+
 * Merge pull request #365 from SheffieldML/devel. [Max Zwiessele]
 
   patch 1.0.5

GPy/__version__.py

@@ -1 +1 @@
-__version__ = "1.5.3"
+__version__ = "1.5.5"

GPy/core/parameterization/variational.py

@@ -10,7 +10,7 @@ from .param import Param
 from paramz.transformations import Logexp, Logistic,__fixed__
 
 class VariationalPrior(Parameterized):
-    def __init__(self, name='latent space', **kw):
+    def __init__(self, name='latent prior', **kw):
         super(VariationalPrior, self).__init__(name=name, **kw)
 
     def KL_divergence(self, variational_posterior):
@@ -23,6 +23,9 @@ class VariationalPrior(Parameterized):
         raise NotImplementedError("override this for variational inference of latent space")
 
 class NormalPrior(VariationalPrior):
+    def __init__(self, name='normal_prior', **kw):
+        super(VariationalPrior, self).__init__(name=name, **kw)
+
     def KL_divergence(self, variational_posterior):
         var_mean = np.square(variational_posterior.mean).sum()
         var_S = (variational_posterior.variance - np.log(variational_posterior.variance)).sum()

GPy/kern/src/kern.py

@@ -3,7 +3,6 @@
 import sys
 import numpy as np
 from ...core.parameterization.parameterized import Parameterized
-from paramz.core.observable_array import ObsAr
 from paramz.caching import Cache_this
 from .kernel_slice_operations import KernCallsViaSlicerMeta
 from functools import reduce

GPy/kern/src/rbf.py

@@ -42,6 +42,7 @@ class RBF(Stationary):
 
     def dK2_drdr_diag(self):
         return -self.variance # as the diagonal of r is always filled with zeros
+    
     def __getstate__(self):
         dc = super(RBF, self).__getstate__()
         if self.useGPU:

README.md

@@ -246,7 +246,7 @@ Then we are ready to make the last changes for the changelog and versioning:
 Now we can merge the pull request into devel:
 
     $ git checkout devel
-    $ git merge --no-ff kurtCutajar-devel
+    $ git merge --no-ff <pull-origin>-devel
     $ git push origin devel
 
 This will update the devel branch of GPy.

appveyor.yml

@@ -3,7 +3,7 @@ environment:
     secure: 8/ZjXFwtd1S7ixd7PJOpptupKKEDhm2da/q3unabJ00=
   COVERALLS_REPO_TOKEN:
     secure: d3Luic/ESkGaWnZrvWZTKrzO+xaVwJWaRCEP0F+K/9DQGPSRZsJ/Du5g3s4XF+tS
-  gpy_version: 1.5.3
+  gpy_version: 1.5.5
   matrix:
     - PYTHON_VERSION: 2.7
       MINICONDA: C:\Miniconda-x64

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.5.3
+current_version = 1.5.5
 tag = True
 commit = True
 

setup.py

@@ -148,7 +148,7 @@ setup(name = 'GPy',
       include_package_data = True,
       py_modules = ['GPy.__init__'],
       test_suite = 'GPy.testing',
-      install_requires = ['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz>=0.6.8'],
+      install_requires = ['numpy>=1.7', 'scipy>=0.16', 'six', 'paramz>=0.6.9'],
       extras_require = {'docs':['sphinx'],
                         'optional':['mpi4py',
                                     'ipython>=4.0.0',