Hello community,
here is the log from the commit of package python-fastcluster for
openSUSE:Factory checked in at 2017-11-10 14:56:44
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-fastcluster (Old)
and /work/SRC/openSUSE:Factory/.python-fastcluster.new (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-fastcluster"
Fri Nov 10 14:56:44 2017 rev:3 rq:539581 version:1.1.24
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-fastcluster/python-fastcluster.changes
2017-05-08 19:03:48.089469839 +0200
+++
/work/SRC/openSUSE:Factory/.python-fastcluster.new/python-fastcluster.changes
2017-11-10 14:57:11.788514229 +0100
@@ -1,0 +2,10 @@
+Sat Nov 4 16:00:03 UTC 2017 - [email protected]
+
+- update to version 1.1.24:
+ * R 3.5 corrects the formula for the “Canberra” metric. See
+ https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17285.
+ The formula in the fastcluster package was changed accordingly. This
+ concerns only the R interface. SciPy and fastcluster's Python interface
+ always had the correct formula.
+
+-------------------------------------------------------------------
Old:
----
fastcluster-1.1.23.tar.gz
New:
----
fastcluster-1.1.24.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-fastcluster.spec ++++++
--- /var/tmp/diff_new_pack.NcSVXo/_old 2017-11-10 14:57:13.132465618 +0100
+++ /var/tmp/diff_new_pack.NcSVXo/_new 2017-11-10 14:57:13.132465618 +0100
@@ -1,7 +1,7 @@
#
# spec file for package python-fastcluster
#
-# Copyright (c) 2017 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -20,20 +20,20 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-fastcluster
-Version: 1.1.23
+Version: 1.1.24
Release: 0
Summary: Hierarchical clustering routines for Python
License: BSD-2-Clause
Group: Development/Languages/Python
Url: http://danifold.net
Source:
https://files.pythonhosted.org/packages/source/f/fastcluster/fastcluster-%{version}.tar.gz
-BuildRequires: gcc-c++
-BuildRequires: fdupes
-BuildRequires: python-rpm-macros
BuildRequires: %{python_module devel}
-BuildRequires: %{python_module setuptools}
BuildRequires: %{python_module numpy-devel}
BuildRequires: %{python_module scipy}
+BuildRequires: %{python_module setuptools}
+BuildRequires: fdupes
+BuildRequires: gcc-c++
+BuildRequires: python-rpm-macros
%if %{with tests}
BuildRequires: %{python_module nose}
%endif
++++++ fastcluster-1.1.23.tar.gz -> fastcluster-1.1.24.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/COPYING.txt
new/fastcluster-1.1.24/COPYING.txt
--- old/fastcluster-1.1.23/COPYING.txt 2015-10-15 22:59:51.000000000 +0200
+++ new/fastcluster-1.1.24/COPYING.txt 2017-08-20 22:49:20.000000000 +0200
@@ -1,4 +1,6 @@
-Copyright © 2011, Daniel Müllner
+Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/INSTALL.txt
new/fastcluster-1.1.24/INSTALL.txt
--- old/fastcluster-1.1.23/INSTALL.txt 2015-10-15 22:59:51.000000000 +0200
+++ new/fastcluster-1.1.24/INSTALL.txt 2017-08-20 22:49:06.000000000 +0200
@@ -1,7 +1,8 @@
fastcluster: Fast hierarchical clustering routines for R and Python
-Copyright © 2011 Daniel Müllner
-<http://danifold.net>
+Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
Installation
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/NEWS.txt
new/fastcluster-1.1.24/NEWS.txt
--- old/fastcluster-1.1.23/NEWS.txt 2017-03-24 22:53:59.000000000 +0100
+++ new/fastcluster-1.1.24/NEWS.txt 2017-08-20 22:49:31.000000000 +0200
@@ -1,7 +1,8 @@
fastcluster: Fast hierarchical clustering routines for R and Python
-Copyright © 2011 Daniel Müllner
-<http://danifold.net>
+Copyright:
+ • Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ • All changes from version 1.1.24 on: © Google Inc. <http://google.com>
Version history
@@ -189,3 +190,11 @@
Version 1.1.23, 03/24/2017
• setup.py: Late NumPy import for better dependency management.
+
+Version 1.1.24, 08/04/2017
+
+ • R 3.5 corrects the formula for the “Canberra” metric. See
+ https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17285.
+ The formula in the fastcluster package was changed accordingly. This
+ concerns only the R interface. SciPy and fastcluster's Python interface
+ always had the correct formula.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/PKG-INFO
new/fastcluster-1.1.24/PKG-INFO
--- old/fastcluster-1.1.23/PKG-INFO 2017-03-28 23:14:27.000000000 +0200
+++ new/fastcluster-1.1.24/PKG-INFO 2017-08-20 23:03:08.000000000 +0200
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: fastcluster
-Version: 1.1.23
+Version: 1.1.24
Summary: Fast hierarchical clustering routines for R and Python.
Home-page: http://danifold.net
Author: Daniel Müllner
@@ -33,24 +33,20 @@
from now on. If some years from now there have not been any updates,
this
does not necessarily mean that the package is unmaintained but maybe
it just
was not necessary to correct anything. Of course, please still report
potential
- bugs and incompatibilities to [email protected]. You may also use
`my GitHub
- repository <https://github.com/dmuellner/fastcluster>`_ for bug
reports, pull
- requests etc.**
+ bugs and incompatibilities to [email protected]. You may also use**
+ `my GitHub repository <https://github.com/dmuellner/fastcluster/>`_
+ **for bug reports, pull requests etc.**
Note that PyPI and my GitHub repository host the source code for the
Python
interface only. The archive with both the R and the Python interface is
available on `CRAN
- <https://cran.r-project.org/web/packages/fastcluster/index.html>`_ and
the
+ <https://CRAN.R-project.org/package=fastcluster>`_ and the
GitHub repository `“cran/fastcluster”
<https://github.com/cran/fastcluster>`_. Even though I appear as the
author also
of this second GitHub repository, this is just an automatic, read-only
mirror
of the CRAN archive, so please do not attempt to report bugs or
contact me via
this repository.
- **Version 1.1.23 had only the file ``setup.py`` changed for better
dependency
- resolution. If version 1.1.22 is installed on your system, this is
perfectly
- fine.**
-
Reference: Daniel Müllner, *fastcluster: Fast Hierarchical,
Agglomerative
Clustering Routines for R and Python*, Journal of Statistical
Software, **53**
(2013), no. 9, 1–18, http://www.jstatsoft.org/v53/i09/.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/README.txt
new/fastcluster-1.1.24/README.txt
--- old/fastcluster-1.1.23/README.txt 2015-10-15 22:59:51.000000000 +0200
+++ new/fastcluster-1.1.24/README.txt 2017-08-20 22:52:38.000000000 +0200
@@ -1,7 +1,8 @@
fastcluster: Fast hierarchical clustering routines for R and Python
-Copyright © 2011 Daniel Müllner
-<http://danifold.net>
+Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
The fastcluster package is a C++ library for hierarchical, agglomerative
clustering. It efficiently implements the seven most widely used clustering
@@ -28,7 +29,7 @@
for the Python interface. The full source distribution with both interfaces
is available on CRAN
- http://cran.r-project.org/web/packages/fastcluster/
+ https://CRAN.R-project.org/package=fastcluster
The Python package can be either installed from PyPI (conveniently with
easy_install) or manually from the source package at CRAN. Both distributions
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/docs/fastcluster.Rtex
new/fastcluster-1.1.24/docs/fastcluster.Rtex
--- old/fastcluster-1.1.23/docs/fastcluster.Rtex 2017-03-24
23:07:39.000000000 +0100
+++ new/fastcluster-1.1.24/docs/fastcluster.Rtex 2017-08-20
22:54:01.000000000 +0200
@@ -1,4 +1,4 @@
-\def\fastclusterversion{1.1.23}
+\def\fastclusterversion{1.1.24}
\documentclass[fontsize=10pt,paper=letter,BCOR=-6mm]{scrartcl}
\usepackage[utf8]{inputenc}
\usepackage{lmodern}
@@ -89,7 +89,7 @@
%\VignetteIndexEntry{User's manual}
\title{The \textit{fastcluster} package: User's manual}
\author{\href{http://danifold.net}{Daniel Müllner}}
-\date{March 24, 2017}
+\date{August 14, 2017}
\subtitle{Version \fastclusterversion}
\maketitle
@@ -295,6 +295,18 @@
\end{quote}
but uses less memory and is equally fast. Ties may be resolved differently,
ie.\ if two pairs of nodes have equal, minimal dissimilarity values at some
point, in the specific computer's representation for floating point numbers,
either pair may be chosen for the next merging step in the dendrogram.
+Note that the formula for the \textit{\q canberra\q} metric changed in R
3.5.0: Before R version 3.5.0, the \textit{\q canberra\q} metric was computed as
+\[
+ d(u,v) = \sum_j\frac{|u_j-v_j|}{|u_j+v_j|}.
+\]
+Starting with R version 3.5.0, the formula was corrected to
+\[
+ d(u,v) = \sum_j\frac{|u_j-v_j|}{|u_j|+|v_j|}.
+\]
+Summands with $u_j=v_j=0$ always contribute 0 to the sum. The second, newer
formula equals SciPy's definition.
+
+The fastcluster package detects the R version at runtime and chooses the
formula accordingly, so that fastcluster and the
\href{http://stat.ethz.ch/R-manual/R-patched/library/stats/html/dist.html}{\texttt{dist}}
method always use the same formula for a given R version.
+
If \textit{method} is one of \textit{\q centroid\q}, \textit{\q median\q},
\textit{\q ward\q}, clustering is performed with respect to Euclidean
distances. In this case, the parameter \textit{metric} must be \textit{\q
euclidean\q}. Notice that \texttt{hclust.vector} operates on Euclidean
distances for compatibility reasons with the \dist{} method, while
\hyperref[hclust]{\texttt{hclust}} assumes \textbf{squared} Euclidean distances
for compatibility with the
\href{http://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html}{\texttt{stats::hclust}}
method! Hence, the call
\phantomsection\label{squared}
\begin{quote}
Binary files old/fastcluster-1.1.23/docs/fastcluster.pdf and
new/fastcluster-1.1.24/docs/fastcluster.pdf differ
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/fastcluster.egg-info/PKG-INFO
new/fastcluster-1.1.24/fastcluster.egg-info/PKG-INFO
--- old/fastcluster-1.1.23/fastcluster.egg-info/PKG-INFO 2017-03-28
23:14:27.000000000 +0200
+++ new/fastcluster-1.1.24/fastcluster.egg-info/PKG-INFO 2017-08-20
23:03:08.000000000 +0200
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: fastcluster
-Version: 1.1.23
+Version: 1.1.24
Summary: Fast hierarchical clustering routines for R and Python.
Home-page: http://danifold.net
Author: Daniel Müllner
@@ -33,24 +33,20 @@
from now on. If some years from now there have not been any updates,
this
does not necessarily mean that the package is unmaintained but maybe
it just
was not necessary to correct anything. Of course, please still report
potential
- bugs and incompatibilities to [email protected]. You may also use
`my GitHub
- repository <https://github.com/dmuellner/fastcluster>`_ for bug
reports, pull
- requests etc.**
+ bugs and incompatibilities to [email protected]. You may also use**
+ `my GitHub repository <https://github.com/dmuellner/fastcluster/>`_
+ **for bug reports, pull requests etc.**
Note that PyPI and my GitHub repository host the source code for the
Python
interface only. The archive with both the R and the Python interface is
available on `CRAN
- <https://cran.r-project.org/web/packages/fastcluster/index.html>`_ and
the
+ <https://CRAN.R-project.org/package=fastcluster>`_ and the
GitHub repository `“cran/fastcluster”
<https://github.com/cran/fastcluster>`_. Even though I appear as the
author also
of this second GitHub repository, this is just an automatic, read-only
mirror
of the CRAN archive, so please do not attempt to report bugs or
contact me via
this repository.
- **Version 1.1.23 had only the file ``setup.py`` changed for better
dependency
- resolution. If version 1.1.22 is installed on your system, this is
perfectly
- fine.**
-
Reference: Daniel Müllner, *fastcluster: Fast Hierarchical,
Agglomerative
Clustering Routines for R and Python*, Journal of Statistical
Software, **53**
(2013), no. 9, 1–18, http://www.jstatsoft.org/v53/i09/.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/fastcluster.py
new/fastcluster-1.1.24/fastcluster.py
--- old/fastcluster-1.1.23/fastcluster.py 2017-03-25 00:02:22.000000000
+0100
+++ new/fastcluster-1.1.24/fastcluster.py 2017-08-20 22:50:39.000000000
+0200
@@ -1,8 +1,9 @@
# -*- coding: utf-8 -*-
__doc__ = """Fast hierarchical clustering routines for R and Python
-Copyright © 2011 Daniel Müllner
-<http://danifold.net>
+Copyright:
+Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+All changes from version 1.1.24 on: © Google Inc. <http://google.com>
This module provides fast hierarchical clustering routines. The "linkage"
method is designed to provide a replacement for the “linkage” function and
@@ -19,7 +20,7 @@
"""
__all__ = ['single', 'complete', 'average', 'weighted', 'ward', 'centroid',
'median', 'linkage', 'linkage_vector']
-__version_info__ = ('1', '1', '23')
+__version_info__ = ('1', '1', '24')
__version__ = '.'.join(__version_info__)
from numpy import double, empty, array, ndarray, var, cov, dot, bool, \
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/setup.py
new/fastcluster-1.1.24/setup.py
--- old/fastcluster-1.1.23/setup.py 2017-03-28 21:24:11.000000000 +0200
+++ new/fastcluster-1.1.24/setup.py 2017-08-20 22:59:44.000000000 +0200
@@ -20,8 +20,9 @@
u('''
fastcluster: Fast hierarchical clustering routines for R and Python
- Copyright © 2011 Daniel Müllner
- <http://danifold.net>
+ Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
''')
with textfileopen('fastcluster.py') as f:
@@ -81,24 +82,20 @@
from now on. If some years from now there have not been any updates, this
does not necessarily mean that the package is unmaintained but maybe it just
was not necessary to correct anything. Of course, please still report potential
-bugs and incompatibilities to [email protected]. You may also use `my GitHub
-repository <https://github.com/dmuellner/fastcluster>`_ for bug reports, pull
-requests etc.**
+bugs and incompatibilities to [email protected]. You may also use**
+`my GitHub repository <https://github.com/dmuellner/fastcluster/>`_
+**for bug reports, pull requests etc.**
Note that PyPI and my GitHub repository host the source code for the Python
interface only. The archive with both the R and the Python interface is
available on `CRAN
-<https://cran.r-project.org/web/packages/fastcluster/index.html>`_ and the
+<https://CRAN.R-project.org/package=fastcluster>`_ and the
GitHub repository `“cran/fastcluster”
<https://github.com/cran/fastcluster>`_. Even though I appear as the author
also
of this second GitHub repository, this is just an automatic, read-only mirror
of the CRAN archive, so please do not attempt to report bugs or contact me via
this repository.
-**Version 1.1.23 had only the file ``setup.py`` changed for better dependency
-resolution. If version 1.1.22 is installed on your system, this is perfectly
-fine.**
-
Reference: Daniel Müllner, *fastcluster: Fast Hierarchical, Agglomerative
Clustering Routines for R and Python*, Journal of Statistical Software, **53**
(2013), no. 9, 1–18, http://www.jstatsoft.org/v53/i09/.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/src/fastcluster.cpp
new/fastcluster-1.1.24/src/fastcluster.cpp
--- old/fastcluster-1.1.23/src/fastcluster.cpp 2016-12-08 00:06:58.000000000
+0100
+++ new/fastcluster-1.1.24/src/fastcluster.cpp 2017-08-20 22:51:02.000000000
+0200
@@ -1,8 +1,9 @@
/*
fastcluster: Fast hierarchical clustering routines for R and Python
- Copyright © 2011 Daniel Müllner
- <http://danifold.net>
+ Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
This library implements various fast algorithms for hierarchical,
agglomerative clustering methods:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/src/fastcluster_python.cpp
new/fastcluster-1.1.24/src/fastcluster_python.cpp
--- old/fastcluster-1.1.23/src/fastcluster_python.cpp 2016-09-19
10:33:00.000000000 +0200
+++ new/fastcluster-1.1.24/src/fastcluster_python.cpp 2017-08-20
22:50:49.000000000 +0200
@@ -1,8 +1,9 @@
/*
fastcluster: Fast hierarchical clustering routines for R and Python
- Copyright © 2011 Daniel Müllner
- <http://danifold.net>
+ Copyright:
+ * Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: © Google Inc. <http://google.com>
*/
// for INT32_MAX in fastcluster.cpp
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/tests/nantest.py
new/fastcluster-1.1.24/tests/nantest.py
--- old/fastcluster-1.1.23/tests/nantest.py 2017-03-24 23:08:49.000000000
+0100
+++ new/fastcluster-1.1.24/tests/nantest.py 2017-08-20 22:50:21.000000000
+0200
@@ -4,11 +4,13 @@
and raises a FloatingPointError.'''
print('''
Test program for the 'fastcluster' package.
-Copyright (c) 2011 Daniel Müllner, <http://danifold.net>''')
+Copyright:
+ * Until package version 1.1.23: (c) 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: (c) Google Inc. <http://google.com>''')
import numpy as np
import fastcluster
-version = '1.1.23'
+version = '1.1.24'
if fastcluster.__version__ != version:
raise ValueError('Wrong module version: {} instead of
{}.'.format(fastcluster.__version__, version))
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/tests/test.py
new/fastcluster-1.1.24/tests/test.py
--- old/fastcluster-1.1.23/tests/test.py 2017-03-24 23:08:58.000000000
+0100
+++ new/fastcluster-1.1.24/tests/test.py 2017-08-20 22:50:27.000000000
+0200
@@ -2,14 +2,16 @@
# -*- coding: utf-8 -*-
print('''
Test program for the 'fastcluster' package.
-Copyright (c) 2011 Daniel Müllner, <http://danifold.net>''')
+Copyright:
+ * Until package version 1.1.23: (c) 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: (c) Google Inc. <http://google.com>''')
import sys
import fastcluster as fc
import numpy as np
from scipy.spatial.distance import pdist, squareform
import math
-version = '1.1.23'
+version = '1.1.24'
if fc.__version__ != version:
raise ValueError('Wrong module version: {} instead of
{}.'.format(fc.__version__, version))
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fastcluster-1.1.23/tests/vectortest.py
new/fastcluster-1.1.24/tests/vectortest.py
--- old/fastcluster-1.1.23/tests/vectortest.py 2017-03-24 23:09:08.000000000
+0100
+++ new/fastcluster-1.1.24/tests/vectortest.py 2017-08-20 22:50:32.000000000
+0200
@@ -4,14 +4,16 @@
# TBD test single on integer matrices for hamming/jaccard
print('''
Test program for the 'fastcluster' package.
-Copyright (c) 2011 Daniel Müllner, <http://danifold.net>''')
+Copyright:
+ * Until package version 1.1.23: (c) 2011 Daniel Müllner <http://danifold.net>
+ * All changes from version 1.1.24 on: (c) Google Inc. <http://google.com>''')
import sys
import fastcluster as fc
import numpy as np
from scipy.spatial.distance import pdist, squareform
import math
-version = '1.1.23'
+version = '1.1.24'
if fc.__version__ != version:
raise ValueError('Wrong module version: {} instead of
{}.'.format(fc.__version__, version))
