Release simuPOP 1.1.14

AUTHORS

@@ -1 +1 @@
-Bo Peng <[email protected]>
+Bo Peng <[email protected]>

INSTALL

@@ -1 +1 @@
-Please refer to http://simupop.sourceforge.net/Main/Download for detailed instructions.
+Please refer to https://github.com/BoPeng/simuPOP/Main/Download for detailed instructions.

README.md

@@ -25,6 +25,9 @@ The user guide and reference manual of simuPOP is available at http://bopeng.git
 
 ## Change Log since 1.1.7
 
+### simuPOP 1.1.14
+* [#114](https://github.com/BoPeng/simuPOP/issues/117) Fix compatibility with Python 3.11.
+
 ### simuPOP 1.1.13
 * [#114](https://github.com/BoPeng/simuPOP/issues/114) Allow negative weight of a heterogeneous mating scheme to generate less individuals than calculated.
 

config.h

@@ -4,10 +4,10 @@
  *  $Rev: 3896 $
  *
  *  This file is part of simuPOP, a forward-time population genetics
- *  simulation environment. Please visit http://simupop.sourceforge.net
+ *  simulation environment. Please visit https://github.com/BoPeng/simuPOP
  *  for details.
  *
- *  Copyright (C) 2004 - 2010 Bo Peng ([email protected])
+ *  Copyright (C) 2004 - 2010 Bo Peng ([email protected])
  *
  *  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

development/code-style.cfg

@@ -3,10 +3,10 @@
 # $Rev: 4077 $
 #
 # This file is part of simuPOP, a forward-time population genetics
-# simulation environment. Please visit http://simupop.sourceforge.net
+# simulation environment. Please visit https://github.com/BoPeng/simuPOP
 # for details.
 #
-# Copyright (C) 2004 - 2010 Bo Peng ([email protected])
+# Copyright (C) 2004 - 2010 Bo Peng ([email protected])
 #
 # 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
@@ -38,7 +38,7 @@
 #
 #
 # Remarks:
-# 
+#
 # The main body of this file can be replaced by
 #
 #     > uncrustify -c /path/to/this/file --update-config-with-doc
@@ -967,7 +967,7 @@ pp_define_at_level                       = false    # false/true
 # Example:
 # type myfoo1 myfoo2
 #
-# You can create custom macro-based indentation using macro-open, 
+# You can create custom macro-based indentation using macro-open,
 # macro-else and macro-close.
 # Example:
 # macro-open  BEGIN_TEMPLATE_MESSAGE_MAP

development/conda/meta.yaml

@@ -5,7 +5,7 @@ package:
 source:
   fn: simuPOP-1.1.7.tar.gz
   url: https://binstar.org/bpeng/simuPOP/1.1.7/download/simuPOP-1.1.7-src.tar.gz
-  md5: 
+  md5:
    #  patches:
    # List any patch files here
    # - fix.patch
@@ -52,7 +52,7 @@ test:
     # - nose
 
 about:
-  home: http://simupop.sourceforge.net
+  home: https://github.com/BoPeng/simuPOP
   license: GNU General Public License (GPL)
   summary: 'Forward-time population genetics simulation environment'
 

development/docker/Dockerfile

@@ -3,7 +3,7 @@
 
 FROM    ubuntu:latest
 
-MAINTAINER Bo Peng <[email protected]>
+MAINTAINER Bo Peng <[email protected]>
 
 RUN     apt-get update
 RUN     apt-get -y install swig gcc g++ build-essential bzip2 libbz2-dev libz-dev curl git

development/release.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 
-# make src and binary distribution on all platforms 
+# make src and binary distribution on all platforms
 # (currently mac, linux and solaris) as daily snapshot
 #
 # This is part of simuPOP
-# 
-# Bo Peng ([email protected])
+#
+# Bo Peng ([email protected])
 #
 
 import os
@@ -47,12 +47,12 @@ def setVersionRevision(release):
     execfile('simuPOP_version.py', globals(), ver)
     if release is None:
         release = ver['SIMUPOP_VER']
-    # 
+    #
     # write release file
     with open('simuPOP_version.py', 'w') as version_file:
         version_file.write('SIMUPOP_VER="{}"\nSIMUPOP_REV="{}"\n'
             .format(release, revision))
-    # 
+    #
     # update documents
     for filename in ['doc/userGuide.lyx', 'doc/refManual.lyx']:
         with open(filename) as manual:
@@ -116,7 +116,7 @@ def generateSWIGWrappers():
         (v1, v2, v3) < (2, 0, 4):
         print('Swig >= 2.0.4 is required for Python 3.2 or higher')
         sys.exit(1)
-    # generate header file 
+    # generate header file
     print("Generating external runtime header file src/swigpyrun.h...")
     run_command('%s %s src/swigpyrun.h' % (SWIG, SWIG_RUNTIME_FLAGS))
     # try the first option set with the first library
@@ -174,7 +174,7 @@ def uploadDocuments(ver, rev):
     run_command('make pdf')
     run_command('make dist_release')
     os.chdir(d)
-    
+
 
 
 def buildSourcePackage(ver):
@@ -193,7 +193,7 @@ def build_x86_64(ver):
     if not os.path.isfile(source):
         print 'Source package %s does not exist. Please run "build.py src" first' % source
         sys.exit(1)
-    # 
+    #
     # build
     d = os.getcwd()
     os.chdir(user_tmp_directory)
@@ -248,7 +248,7 @@ def build_remote(ver, remote_machine):
     if not os.path.isfile(source):
         print 'Source package %s does not exist. Please run "build.py src" first' % source
         sys.exit(1)
-    #   
+    #
     print 'Copying source package to remote machine ...'
     run_command("ssh %s '/bin/rm -rf temp &&  mkdir temp && /bin/rm -rf simuPOP'" % remote_machine)
     run_command('scp %s/simuPOP-%s-src.tar.gz %s:temp' % (download_directory, ver, remote_machine))
@@ -274,7 +274,7 @@ def createMacPackage(ver, pyver):
     temp_dir = os.path.expanduser('~/Temp/mpkg')
     if not os.path.isdir(temp_dir):
         os.makedirs(temp_dir)
-    # 
+    #
     src_dir = os.path.join(temp_dir, 'simuPOP-%s' % ver)
     if os.path.isdir(src_dir):
         shutil.rmtree(src_dir)
@@ -286,11 +286,11 @@ def createMacPackage(ver, pyver):
     os.chdir(temp_dir)
     # decompress
     run_command('tar -zxf simuPOP-%s-src.tar.gz' % ver)
-    # 
+    #
     os.chdir(src_dir)
     run_command('python3 setup.py bdist')
     os.chdir(old_dir)
-    # 
+    #
     # Move results to download directory
     dest_targz = os.path.join(download_directory, 'simuPOP-{}-py{}.tar.gz'.format(ver, pyver))
     if os.path.isdir(dest_targz):
@@ -346,7 +346,7 @@ def tagRelease(release):
         cmd = 'svn ci -m "automatic checkin on %s"' % time.asctime()
         run_command(cmd)
     run_command('svn update')
-    cmd = ('svn copy https://sourceforge.net/p/simupop/code/HEAD/tree/trunk ' + 
+    cmd = ('svn copy https://sourceforge.net/p/simupop/code/HEAD/tree/trunk ' +
          'https://sourceforge.net/p/simupop/code/HEAD/tree/trunk/tag/v%s') % release + \
         ' -m "Version %s released at %s"' % (release, time.asctime())
     print cmd
@@ -355,17 +355,17 @@ def tagRelease(release):
 
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='''Create source distribution 
+    parser = argparse.ArgumentParser(description='''Create source distribution
         and binary installers for a simuPOP release. In addition to optional
-        parameters version and tag, extra parameters would be specified and 
+        parameters version and tag, extra parameters would be specified and
         will be passed directly to the 'python setup.py install' process. ''')
     parser.add_argument('--version',
         help='''Modify simuPOP_version.py to the specified version string and
             make the release.''')
     parser.add_argument('actions', nargs='*', default=[
         'build', 'src', 'doc', 'mac'],
         help='Actions to take to make the release.')
-    # go to the top source directory        
+    # go to the top source directory
     os.chdir('..')
     #
     args, argv = parser.parse_known_args()

doc/refManual.lyx

@@ -9,8 +9,8 @@
 % file revision $Rev: 3372$
 \authoraddress{
 {\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
-{\bf Email: } \textsf{[email protected]}\\
-{\bf URL: } \textsf{http://simupop.sourceforge.net} \\
+{\bf Email: } \textsf{[email protected]}\\
+{\bf URL: } \textsf{https://github.com/BoPeng/simuPOP} \\
 {\bf Mailing List: } \textsf{[email protected]}
 }
 \author{Bo Peng}
@@ -39,7 +39,7 @@ Last modified \\
 \subsectionfont{\color{TitleColor}}
 \subsubsectionfont{\color{TitleColor}}
 
-\newlength{\admonitionwidth} 
+\newlength{\admonitionwidth}
 \setlength{\admonitionwidth}{0.7\textwidth}
 \end_preamble
 \use_default_options false
@@ -149,7 +149,7 @@ status open
 
 
 \backslash
-vspace{7.5in} 
+vspace{7.5in}
 \end_layout
 
 \end_inset
@@ -163,26 +163,26 @@ status open
 
 \begin_layout Plain Layout
 
- 
+
 \backslash
-copyright{} 
+copyright{}
 \end_layout
 
 \end_inset
 
- 2004-2008 Bo Peng 
+ 2004-2008 Bo Peng
 \begin_inset ERT
 status open
 
 \begin_layout Plain Layout
 
 
 \backslash
-vspace{.3cm} 
+vspace{.3cm}
 \backslash
-hrule 
+hrule
 \backslash
-vspace{0.1cm} 
+vspace{0.1cm}
 \end_layout
 
 \end_inset
@@ -221,7 +221,7 @@ simuPOP is a general-purpose individual-based forward-time population genetics
  arbitrary nonrandom mating schemes, virtual subpopulations, information
  fields and Python operators, to construct and study almost arbitrarily
  complex evolutionary scenarios.
- 
+
 \end_layout
 
 \begin_layout Abstract
@@ -243,16 +243,16 @@ simuPOP is provided as a number of Python modules, which consist of a large
 \begin_layout Abstract
 This document provides complete references to all classes and functions
  of simuPOP and its utility modules.
- Please refer to the 
+ Please refer to the
 \emph on
 simuPOP user's guide
 \emph default
  for a detailed introduction to simuPOP concepts, and a number of examples
  on how to use simuPOP to perform various simulations.
  All resources, including a pdf version of this guide and a mailing list
- can be found at the simuPOP homepage 
+ can be found at the simuPOP homepage
 \family typewriter
-http://simupop.sourceforge.net
+https://github.com/BoPeng/simuPOP
 \family default
 .
 \end_layout
@@ -267,11 +267,11 @@ How to cite simuPOP:
 \begin_layout Quote
 Bo Peng and Marek Kimmel (2005) simuPOP: a forward-time population genetics
  simulation environment.
- 
+
 \emph on
 bioinformatics
 \emph default
-, 
+,
 \series bold
 21
 \series default
@@ -281,11 +281,11 @@ bioinformatics
 \begin_layout Quote
 Bo Peng and Christopher Amos (2008) Forward-time simulations of nonrandom
  mating populations using simuPOP.
- 
+
 \emph on
 bioinformatics
 \emph default
-, 
+,
 \series bold
 24
 \series default
@@ -1298,7 +1298,7 @@ selection
 
 \end_inset
 
- 
+
 \end_layout
 
 \begin_layout Standard
@@ -1778,7 +1778,7 @@ Utility Modules
 \end_layout
 
 \begin_layout Section
-Module 
+Module
 \family typewriter
 simuOpt
 \end_layout
@@ -1807,7 +1807,7 @@ simuOptsetOptionsRef
 \end_layout
 
 \begin_layout Section
-Module 
+Module
 \family typewriter
 simuPOP.utils
 \end_layout
@@ -1899,7 +1899,7 @@ simuPOPutilsexportRef
 \end_layout
 
 \begin_layout Section
-Module 
+Module
 \family typewriter
 simuPOP.demography
 \end_layout
@@ -2047,7 +2047,7 @@ simuPOPdemographyCosiModelRef
 \end_layout
 
 \begin_layout Section
-Module 
+Module
 \family typewriter
 simuPOP.sampling
 \end_layout
@@ -2209,7 +2209,7 @@ simuPOPsamplingdrawCombinedSamplesRef
 \end_layout
 
 \begin_layout Section
-Module 
+Module
 \family typewriter
 simuPOP.gsl
 \end_layout