Merge pull request #787 from jbarnoud/issue-784-dynamic-authors

Issue #784 -- Dynamic author list

.gitignore

@@ -34,3 +34,5 @@ doc/html/
 *.sw[a-z]
 # Ignore MDAnalysis log files
 MDAnalysis.log
+# Ignore the authors.py files as they are generated files
+authors.py

package/AUTHORS

@@ -49,6 +49,7 @@ Chronological list of authors
   - Robert McGibbon
   - Richard J. Gowers
   - Alejandro Bernardin
+  - Lennard van der Feltz
 2014
   - Matthieu Chavent
   - Joe Jordan

package/CHANGELOG

@@ -13,14 +13,16 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jdetle
+??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jdetle, jbarnoud
 
   * 0.15.0
 
 Metadata
 
   * link download_url to GitHub releases so that Depsy recognizes
     contributors (issue #749)
+  * a __version__ variable is now exposed; it is built by setup.py from the
+    AUTHORS file (Issue #784)
 
 API Changes
 

package/MDAnalysis/__init__.py

@@ -139,7 +139,14 @@
 import logging
 import warnings
 
+logger = logging.getLogger("MDAnalysis.__init__")
+
 from .version import __version__
+try:
+    from .authors import __authors__
+except ImportError:
+    logger.info('Could not find authors.py, __authors__ will be empty.')
+    __authors__ = []
 
 # custom exceptions and warnings
 from .exceptions import (

package/doc/sphinx/source/conf.py

@@ -78,17 +78,8 @@ def __getattr__(cls, name):
 # (take the list from AUTHORS)
 # Ordering: (1) Naveen (2) Elizabeth, then all contributors in alphabetical order
 #           (last) Oliver
-authors = u"""Naveen Michaud-Agrawal, Elizabeth J. Denning, Joshua
-    Adelman, Balasubramanian, Jonathan Barnoud, Christian Beckstein (logo), Alejandro
-    Bernardin, Sébastien Buchoux, David Caplan, Matthieu Chavent,
-    Xavier Deupi, Jan Domański, David L. Dotson, Lennard van der
-    Feltz, Philip Fowler, Joseph Goose, Richard J. Gowers, Lukas
-    Grossar, Benjamin Hall, Joe Jordan, Max Linke, Jinju Lu, Robert
-    McGibbon, Alex Nesterenko, Manuel Nuno Melo, Hai Nguyen,
-    Caio S. Souza, Mattia F. Palermo, Danny Parton, Joshua L. Phillips, Tyler Reddy,
-    Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl,
-    Gorman Stock, Isaac Virshup, Zhuyi Xue, Carlos Yáñez S.,
-    and Oliver Beckstein"""
+author_list = __import__('MDAnalysis').__authors__
+authors = u', '.join(author_list[:-1]) + u', and ' + author_list[-1]
 project = u'MDAnalysis'
 copyright = u'2005-2015, ' + authors
 

package/setup.py

@@ -351,7 +351,78 @@ def extensions(config):
                                 "failed/disabled Cython build.".format(source))
     return extensions, cython_generated
 
+
+def dynamic_author_list():
+    """Generate __authors__ from AUTHORS
+
+    This function generates authors.py that contains the list of the
+    authors from the AUTHORS file. This avoids having that list maintained in
+    several places. Note that AUTHORS is sorted chronologically while we want
+    __authors__ in authors.py to be sorted alphabetically.
+
+    The authors are written in AUTHORS as bullet points under the
+    "Chronological list of authors" title.
+    """
+    authors = []
+    with open('AUTHORS') as infile:
+        # An author is a bullet point under the title "Chronological list of
+        # authors". We first want move the cursor down to the title of
+        # interest.
+        for line_no, line in enumerate(infile, start=1):
+            if line[:-1] == "Chronological list of authors":
+                break
+        else:
+            # If we did not break, it means we did not find the authors.
+            raise IOError('EOF before the list of authors')
+        # Skip the next line as it is the title underlining
+        line = next(infile)
+        line_no += 1
+        if line[:4] != '----':
+            raise IOError('Unexpected content on line {0}, '
+                          'should be a string of "-".'.format(line_no))
+        # Add each bullet point as an author until the next title underlining
+        for line in infile:
+            if line[:4] in ('----', '====', '~~~~'):
+                # The previous line was a title, hopefully it did not start as
+                # a bullet point so it got ignored. Since we hit a title, we
+                # are done reading the list of authors.
+                break
+            elif line.strip()[:2] == '- ':
+                # This is a bullet point, so it should be an author name.
+                name = line.strip()[2:].strip().decode('utf-8')
+                authors.append(name)
+
+    # So far, the list of authors is sorted chronologically. We want it
+    # sorted alphabetically of the last name.
+    authors.sort(key=lambda name: name.split()[-1])
+    # Move Naveen and Elizabeth first, and Oliver last.
+    authors.remove('Naveen Michaud-Agrawal')
+    authors.remove('Elizabeth J. Denning')
+    authors.remove('Oliver Beckstein')
+    authors = (['Naveen Michaud-Agrawal', 'Elizabeth J. Denning']
+               + authors + ['Oliver Beckstein'])
+
+    # Write the authors.py file.
+    with open('MDAnalysis/authors.py', 'w') as outfile:
+        # Write the header
+        header = '''\
+#-*- coding:utf-8 -*-
+
+# This file is generated from the AUTHORS file during the installation process.
+# Do not edit it as your changes will be overwritten.
+'''
+        print(header, file=outfile)
+
+        # Write the list of authors as a python list
+        template = u'__authors__ = [\n{}\n]'
+        author_string = u',\n'.join(u'    u"{}"'.format(name)
+                                    for name in authors)
+        print(template.format(author_string).encode('utf-8'), file=outfile)
+
+
 if __name__ == '__main__':
+    dynamic_author_list()
+
     with open("SUMMARY.txt") as summary:
         LONG_DESCRIPTION = summary.read()
     CLASSIFIERS = [

testsuite/CHANGELOG

@@ -13,13 +13,15 @@ Also see https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests
 and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 
 ------------------------------------------------------------------------------
-??/??/16 orbeckst
+??/??/16 orbeckst, jbarnoud
 
   * 0.15.0
 
     - metadata update: link download_url to GitHub releases so that
       Depsy recognizes contributors (issue #749) and added
       @richardjgowers as maintainer
+    - a __version__ variable is now exposed; it is built by setup.py from the
+      AUTHORS file (Issue #784)
 
 02/28/16 manuel.nuno.melo
 

testsuite/MDAnalysisTests/__init__.py

@@ -106,8 +106,16 @@
 .. _Gromacs: http://www.gromacs.org
 
 """
+import logging
+logger = logging.getLogger("MDAnalysisTests.__init__")
 
 __version__ = "0.14.1-dev0"  # keep in sync with RELEASE in setup.py
+try:
+    from .authors import __authors__
+except ImportError:
+    logger.info('Could not find authors.py, __authors__ will be empty.')
+    __authors__ = []
+
 
 # Do NOT import MDAnalysis at this level. Tests should do it themselves.
 # If MDAnalysis is imported here coverage accounting might fail because all the import

testsuite/MDAnalysisTests/test_authors.py

@@ -0,0 +1,28 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDAnalysis --- http://www.MDAnalysis.org
+# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver
+# Beckstein and contributors (see AUTHORS for the full list)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+from numpy.testing import assert_
+
+import MDAnalysis
+
+def test_package_authors():
+    assert_(len(MDAnalysis.__authors__) > 0,
+            'Could not find the list of authors')
+
+
+def test_testsuite_authors():
+    from . import __authors__
+    assert_(len(__authors__) > 0,
+            'Could not find the list of authors')

testsuite/setup.py

@@ -42,6 +42,75 @@
 import os
 import glob
 
+
+def dynamic_author_list():
+    """Generate __authors__ from AUTHORS
+
+    This function generates authors.py that contains the list of the
+    authors from the AUTHORS file. This avoids having that list maintained in
+    several places. Note that AUTHORS is sorted chronologically while we want
+    __authors__ in authors.py to be sorted alphabetically.
+
+    The authors are written in AUTHORS as bullet points under the
+    "Chronological list of authors" title.
+    """
+    authors = []
+    with open('AUTHORS') as infile:
+        # An author is a bullet point under the title "Chronological list of
+        # authors". We first want move the cursor down to the title of
+        # interest.
+        for line_no, line in enumerate(infile, start=1):
+            if line[:-1] == "Chronological list of authors":
+                break
+        else:
+            # If we did not break, it means we did not find the authors.
+            raise IOError('EOF before the list of authors')
+        # Skip the next line as it is the title underlining
+        line = next(infile)
+        line_no += 1
+        if line[:4] != '----':
+            raise IOError('Unexpected content on line {0}, '
+                          'should be a string of "-".'.format(line_no))
+        # Add each bullet point as an author until the next title underlining
+        for line in infile:
+            if line[:4] in ('----', '====', '~~~~'):
+                # The previous line was a title, hopefully it did not start as
+                # a bullet point so it got ignored. Since we hit a title, we
+                # are done reading the list of authors.
+                break
+            elif line.strip()[:2] == '- ':
+                # This is a bullet point, so it should be an author name.
+                name = line.strip()[2:].strip().decode('utf-8')
+                authors.append(name)
+
+    # So far, the list of authors is sorted chronologically. We want it
+    # sorted alphabetically of the last name.
+    authors.sort(key=lambda name: name.split()[-1])
+    # Move Naveen and Elizabeth first, and Oliver last.
+    authors.remove('Naveen Michaud-Agrawal')
+    authors.remove('Elizabeth J. Denning')
+    authors.remove('Oliver Beckstein')
+    authors = (['Naveen Michaud-Agrawal', 'Elizabeth J. Denning']
+               + authors + ['Oliver Beckstein'])
+
+    # Write the authors.py file.
+    with open('MDAnalysisTests/authors.py', 'w') as outfile:
+        # Write the header
+        header = '''\
+#-*- coding:utf-8 -*-
+
+# This file is generated from the AUTHORS file during the installation process.
+# Do not edit it as your changes will be overwritten.
+'''
+        print(header, file=outfile)
+
+        # Write the list of authors as a python list
+        template = u'__authors__ = [\n{}\n]'
+        author_string = u',\n'.join(u'    u"{}"'.format(name)
+                                    for name in authors)
+        print(template.format(author_string).encode('utf-8'), file=outfile)
+
+
 # Make sure I have the right Python version.
 if sys.version_info[:2] < (2, 7):
     print("MDAnalysis requires Python 2.7 or better. Python {0:d}.{1:d} detected".format(*
@@ -51,6 +120,8 @@
 
 
 if __name__ == '__main__':
+    dynamic_author_list()
+
     RELEASE = "0.14.1-dev0"  # this must be in-sync with MDAnalysis
     LONG_DESCRIPTION = \
         """MDAnalysis is a tool for analyzing molecular dynamics trajectories.