ChangeLog

+2019.08.30
+Fixed the clustercentroids routine in python/clustermodule.c.
+Changed src/cluster.c and python/clustermodule.c to be consistent with PEP7.
+Added tests to the Python unit tests.
+
+2019.04.26
+Moved Windows-specific code from src/cluster.c to windows/library.c.
+Fixed a memory leak in X11/gui.c.
+Expanded doctests in python/__init__.py.
+Fixed a bug in the treecluster routine in python/clustermodule.c that caused
+the weight argument to be checked if the distance matrix was provided.
+Cleaned up formatting in python/test/test_Cluster.py.
+
 2018.11.22
 Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in
 Hierarchical and KMeans in src/command.c; these memory leaks occurred when

INSTALL

@@ -92,7 +92,7 @@ You may need to log in as root the install Pycluster.
 If you do not have root access, do
   python setup.py install --prefix=/some/other/directory
 and set the environment variable
-  PYTHONPATH=/some/other/directory/lib/python2.2/site-packages
+  PYTHONPATH=/some/other/directory/lib/python2.6/site-packages
 The exact command depends on which shell you are using; the exact path will
 depend on the version of Python you are using.
 To use Pycluster, you will also need numpy (Numerical Python). Pycluster was

Makefile.am

@@ -3,7 +3,8 @@
 DOCDIST = doc/cluster.pdf doc/cluster3.pdf doc/cluster.texinfo \
   doc/cluster3.texinfo doc/structure.eps doc/Makefile
 WINDIST = windows/cluster.hhp windows/cluster.ico windows/cluster.iss \
-  windows/main.c windows/gui.c windows/format.bmp windows/Makefile \
+  windows/main.c windows/gui.c windows/library.c \
+  windows/format.bmp windows/Makefile \
   windows/resources.h windows/resources.rc
 MACDIST = mac/main.m mac/Controller.h mac/Controller.m mac/cluster.icns \
   mac/English.lproj/InfoPlist.strings \

Makefile.in

@@ -297,7 +297,8 @@ DOCDIST = doc/cluster.pdf doc/cluster3.pdf doc/cluster.texinfo \
   doc/cluster3.texinfo doc/structure.eps doc/Makefile
 
 WINDIST = windows/cluster.hhp windows/cluster.ico windows/cluster.iss \
-  windows/main.c windows/gui.c windows/format.bmp windows/Makefile \
+  windows/main.c windows/gui.c windows/library.c \
+  windows/format.bmp windows/Makefile \
   windows/resources.h windows/resources.rc
 
 MACDIST = mac/main.m mac/Controller.h mac/Controller.m mac/cluster.icns \

NEWS

-2018.11.22
-Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in
-Hierarchical and KMeans in src/command.c; these memory leaks occurred when
-memory allocation failed.
-Fixed a bug in the distancematrix function Bio/Cluster/__init__.py, where the 
-weight argument was not properly initialized if it had the default value None,
-causing the function to fail.
+2019.08.30
+Fixed the clustercentroids routine in python/clustermodule.c.
+Changed src/cluster.c and python/clustermodule.c to be consistent with PEP7.
+Added tests to the Python unit tests.

X11/gui.c

@@ -1452,10 +1452,12 @@ static void KMeans(Widget w, XtPointer client_data, XtPointer call_data)
                 kGenes = GetWidgetItemInt(page, "KMeansGeneK");
                 if (kGenes==0)
                 {   Statusbar(NULL, "Choose a nonzero number of clusters");
+                    free(path);
                     return;
                 }
                 if (Rows < kGenes)
                 {   Statusbar(NULL, "More clusters than genes available");
+                    free(path);
                     return;
                 }
                 n += strlen("_G");
@@ -1468,10 +1470,12 @@ static void KMeans(Widget w, XtPointer client_data, XtPointer call_data)
                 kArrays = GetWidgetItemInt(page, "KMeansArrayK");
                 if (kArrays==0)
                 {   Statusbar(NULL, "Choose a nonzero number of clusters");
+                    free(path);
                     return;
                 }
                 if (Columns < kArrays)
                 {   Statusbar(NULL, "More clusters than arrays available");
+                    free(path);
                     return;
                 }
                 n += strlen("_A");

compile

 #! /bin/sh
 # Wrapper for compilers which do not understand '-c -o'.
 
-scriptversion=2012-10-14.11; # UTC
+scriptversion=2018-03-07.03; # UTC
 
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2018 Free Software Foundation, Inc.
 # Written by Tom Tromey <tromey@cygnus.com>.
 #
 # This program is free software; you can redistribute it and/or modify
@@ -17,7 +17,7 @@ scriptversion=2012-10-14.11; # UTC
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
@@ -255,7 +255,8 @@ EOF
     echo "compile $scriptversion"
     exit $?
     ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe | \
+  icl | *[/\\]icl | icl.exe | *[/\\]icl.exe )
     func_cl_wrapper "$@"      # Doesn't return...
     ;;
 esac
@@ -339,9 +340,9 @@ exit $ret
 # Local Variables:
 # mode: shell-script
 # sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'before-save-hook 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
+# time-stamp-time-zone: "UTC0"
 # time-stamp-end: "; # UTC"
 # End:

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for cluster 1.57.
+# Generated by GNU Autoconf 2.69 for cluster 1.59.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -577,8 +577,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='cluster'
 PACKAGE_TARNAME='cluster'
-PACKAGE_VERSION='1.57'
-PACKAGE_STRING='cluster 1.57'
+PACKAGE_VERSION='1.59'
+PACKAGE_STRING='cluster 1.59'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1273,7 +1273,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures cluster 1.57 to adapt to many kinds of systems.
+\`configure' configures cluster 1.59 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1343,7 +1343,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of cluster 1.57:";;
+     short | recursive ) echo "Configuration of cluster 1.59:";;
    esac
   cat <<\_ACEOF
 
@@ -1440,7 +1440,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-cluster configure 1.57
+cluster configure 1.59
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1859,7 +1859,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by cluster $as_me 1.57, which was
+It was created by cluster $as_me 1.59, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2723,7 +2723,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='cluster'
- VERSION='1.57'
+ VERSION='1.59'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -6009,7 +6009,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by cluster $as_me 1.57, which was
+This file was extended by cluster $as_me 1.59, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -6075,7 +6075,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-cluster config.status 1.57
+cluster config.status 1.59
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

 # Process this file with autoconf to produce a configure script.
-AC_INIT(cluster, 1.57)
+AC_INIT(cluster, 1.59)
 AC_CONFIG_SRCDIR(src/cluster.c)
 AM_INIT_AUTOMAKE
 AC_CONFIG_HEADERS(config.h)

debian/changelog

+cluster3 (1.59-2) UNRELEASED; urgency=medium
+
+  * Excluding autogenerated files from archive in d/copyright
+  * Instructed d/watch to repack.
+
+ -- Steffen Moeller <moeller@debian.org>  Sun, 19 Jan 2020 01:15:41 +0100
+
+cluster3 (1.59-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12 (routine-update)
+  * Standards-Version: 4.4.1 (routine-update)
+  * Remove trailing whitespace in debian/copyright (routine-update)
+  * Remove trailing whitespace in debian/rules (routine-update)
+  * Trim trailing whitespace.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata
+    (already present in machine-readable debian/copyright).
+  * Rely on pre-initialized dpkg-architecture variables.
+  * Fix day-of-week for changelog entry 1.25-0.2.
+  * python2 -> python3
+
+ -- Steffen Moeller <moeller@debian.org>  Sun, 19 Jan 2020 00:45:36 +0100
+
 cluster3 (1.57-1) unstable; urgency=medium
 
   * New upstream version.
@@ -83,11 +106,10 @@ cluster3 (1.25-0.2) UNRELEASED; urgency=low
 
   * Provides both the motif gui and command line interface.
 
- -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Tue,  7 Apr 2004 18:31:37 +0200
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Wed, 07 Apr 2004 18:31:37 +0200
 
 cluster3 (1.25-0.1) UNRELEASED; urgency=low
 
   * Initial Release.
 
  -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Tue,  6 Apr 2004 18:31:37 +0200
-

debian/compat

-11

debian/control

@@ -7,7 +7,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
 Section: non-free/science
 XS-Autobuild: yes
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libmotif-dev,
                perl,
                libx11-dev,
@@ -15,10 +15,10 @@ Build-Depends: debhelper (>= 11~),
                libxext-dev,
                libsm-dev,
                libxt-dev,
-               python-minimal,
-               python-setuptools,
-               python-numpy
-Standards-Version: 4.3.0
+               python3-all,
+               python3-setuptools,
+               python3-numpy
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/cluster3
 Vcs-Git: https://salsa.debian.org/med-team/cluster3.git
 Homepage: http://bonsai.hgc.jp/~mdehoon/software/cluster/

debian/copyright

@@ -5,6 +5,19 @@ Source: http://bonsai.hgc.jp/~mdehoon/software/cluster/
 Comment: The GUI part of this program is non-free.  This was discussed
  on the Debian Med mailing list with upstream
    https://lists.debian.org/debian-med/2016/02/msg00000.html
+Files-Excluded:
+ X11/.deps/
+ config.cache
+ config.h
+ config.log
+ config.status
+ src/.deps/
+ stamp-h1
+ INSTALL
+ Makefile.in
+ X11/Makefile.in
+ configure
+ src/Makefile.in
 
 Files: *
 Copyright: M. J. L. de Hoon <mdehoon@ims.u-tokyo.ac.jp>, S. Imoto, J. Nolan, and S. Miyano, Michael Eisen

debian/patches/python3.patch

+Index: cluster3/html/Makefile
+===================================================================
+--- cluster3.orig/html/Makefile
++++ cluster3/html/Makefile
+@@ -2,7 +2,7 @@ docdir = ../doc
+ 
+ index.html: $(docdir)/cluster3.texinfo
+ 	makeinfo --html $(docdir)/cluster3.texinfo --output=.
+-	python mac.py
++	python3 mac.py
+ 
+ distdir: .
+ 
+Index: cluster3/setup.py
+===================================================================
+--- cluster3.orig/setup.py
++++ cluster3/setup.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ from distutils.core import setup, Extension, Command
+ import sys

debian/patches/series

 build-on-arm.patch
+python3.patch

debian/rules

@@ -7,14 +7,13 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 # These are used for cross-compiling and for saving the configure script
 # from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE   ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE  ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+include /usr/share/dpkg/architecture.mk
 
 CFLAGS += -flto
 LDFLAGS += -flto
 
 %:
-	dh $@
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_configure:
 	# build nox version first
@@ -27,7 +26,8 @@ override_dh_auto_configure:
 
 override_dh_auto_build-arch:
 	# $(MAKE) CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
-	dh_auto_build
+	$(MAKE) -C X11
+	$(MAKE) -C src
 	cp src/cluster cluster.x
 
 override_dh_auto_build-indep:
@@ -43,8 +43,10 @@ cluster3.1: debian/cluster3.sgml
 xcluster3.1: debian/xcluster3.sgml
 	docbook-to-man $< > $@
 
-override_dh_clean:
-	dh_clean src/*.o X11/*.o src/cluster X11/cluster src/Makefile src/Makefile.old X11/Makefile Makefile MANIFEST
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f cluster.nox cluster.x src/*.o X11/*.o X11/*.a src/cluster X11/cluster src/Makefile src/Makefile.old X11/Makefile Makefile MANIFEST
+	rm -rf X11/.deps/ config.cache config.h config.log config.status src/.deps/ stamp-h1
 
 override_dh_install:
 	dh_install

debian/upstream/metadata

-Contact: M. J. L. de Hoon <mdehoon@ims.u-tokyo.ac.jp>
-Name: cluster3
 Reference:
   Debian-package: cluster3
   Author: M. J. L. de Hoon AND S. Imoto AND J. Nolan AND S. Miyano
@@ -15,8 +13,7 @@ Reference:
   PMID: 14871861
   URL: >
     http://bioinformatics.oxfordjournals.org/content/20/9/1453.long
- ePrint: "https://academic.oup.com/bioinformatics/article-pdf/\
-  20/9/1453/488286/bth078.pdf"
+  ePrint: https://academic.oup.com/bioinformatics/article-pdf/20/9/1453/488286/bth078.pdf
 Registry:
 - Name: OMICtools
   Entry: OMICS_01571

debian/watch

 version=3
+opts= "repack,compression=xz,oversionmangle=s/$/+ds/" \
 http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm cluster-(.*)\.tar\.gz