Merge pull request cclib#323 from langner/release-1.5

More v1.5 updates, new DOI and change of license to BSD

ANNOUNCE

@@ -4,12 +4,10 @@ cclib is an open source library, written in Python, for parsing and interpreting
 
 Among other data, cclib extracts:
 
-    * coordinates and energies
-    * geometry optimization data
-    * atomic orbital information
-    * molecular orbital data
-    * vibrational modes
-    * results of TD-DFT calculations
+    * results of SCF, post-Hartree-Fock, TD-DFT and other calculations
+    * coordinates, energies and geometry optimization data
+    * information about atomic and molecular orbitals
+    * vibrational modes, excited states and transitions
     * charges and electrostatic moments
 
 (For a complete list see http://cclib.github.io/data.html).
@@ -18,7 +16,7 @@ cclib also provides some calculation methods for interpreting the electronic pro
 
     * Mulliken and Lowdin population analyses
     * Overlap population analysis
-    * Calculation of Mayer's bond orders. 
+    * Mayer's bond orders
 
 (For a complete list see http://cclib.github.io/methods.html).
 
@@ -31,7 +29,7 @@ If you need help, find a bug, want new features or have any questions, please se
 If your published work uses cclib, please support its development by citing the following article:
     N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for package-independent computational chemistry algorithms, J. Comp. Chem. 29 (5), 839-845 (2008)
 You can also specifically reference this version of cclib as:
-    Eric Berquist, Karol M. Langner, Noel M. O'Boyle, and Adam L. Tenderholt. Release of cclib version 1.4. 2016. http://dx.doi.org/10.5281/zenodo.50324
+    Eric Berquist, Karol M. Langner, Noel M. O'Boyle, and Adam L. Tenderholt. Release of cclib version 1.5. 2016. http://dx.doi.org/10.5281/zenodo.60670
 
 Regards,
 The cclib development team
@@ -40,6 +38,6 @@ The cclib development team
 
 Summary of changes since last version:
     Support for reading and writing CJSON files
-    New parser: cclib nor parses MOPAC files
+    New parser: cclib now parses MOPAC files
     New attribute time for tracking coordinates in trajectories
     New attribute metadata for miscellaneous data not in other attributes 

CHANGELOG

@@ -4,9 +4,10 @@ Features:
     * Support for both reading and writing CJSON (Sanjeed Schamnad)
     * New parser: cclib can now parse MOPAC files (Geoff Hutchison)
     * New attribute time tracks coordinated for dynamics jobs (Ramon Crehuet)
-    * New attribute metadata holds miscellaneous information not in other attributes
+    * New attribute metadata holds miscellaneous information not in other attributes (bwang2453)
     * Extract moments attribute for Gaussian (Geoff Hutchison)
     * Extract atombasis for ADF in simple cases (Felix Plaser)
+    * License change to BSD 3-Clause License
 
 Bugfixes:
     * Correct parsing of several attributes for ROHF calculations

README.md

@@ -1,10 +1,10 @@
 ### cclib
 
-[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.50324.svg)](http://dx.doi.org/10.5281/zenodo.50324)
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.50324.svg)](http://dx.doi.org/10.5281/zenodo.60670)
 [![PyPI version](http://img.shields.io/pypi/v/cclib.svg?style=flat)](https://pypi.python.org/pypi/cclib)
 [![GitHub release](https://img.shields.io/github/release/cclib/cclib.svg?style=flat)](https://github.com/cclib/cclib/releases)
 [![build status](http://img.shields.io/travis/cclib/cclib/master.svg?style=flat)](https://travis-ci.org/cclib/cclib)
-[![license](http://img.shields.io/badge/license-LGPLv2.1-blue.svg?style=flat)](https://github.com/cclib/cclib/blob/master/LICENSE)
+[![license](http://img.shields.io/badge/license-BSD-blue.svg?style=flat)](https://github.com/cclib/cclib/blob/master/LICENSE)
 
 <img src="./logo.png" alt="cclib logo" width="100" />
 

THANKS

@@ -1,45 +1,55 @@
-The developers of cclib would like the thank the following (in alphabetical order) who have contributed in some way to cclib:
+We would like the thank the following who have contributed in some way to cclib:
 
 Nuno Bandeira -- for bug reporting
 Björn Baumeier -- for bug reporting
 Dermot Brougham -- for bug reporting
+bwang2453 -- for patches and new features
 Avril Coghlan -- for designing the cclib logo
+Ramon Crehuet -- for new features
 Björn Dahlgren -- for bug reporting
 Yafei Dai -- for bug reporting
 Abhishek Dey -- for bug reporting
 Matt Ernst -- for patches
 Clyde Fare -- for bug reporting and patches
 Christos Garoufalis -- for bug reporting
-Sagar Gaur -- for bug fixes
+Sagar Gaur -- for patches
 glideht -- for bug reporting
 Edward Holland -- for patches
 Karen Hemelsoet -- for bug reporting
 Ian Hovell -- for bug reporting
+Geoff Hutchison -- for patches, files and a new parser
 Julien Idé -- for bug reporting
 csjacky -- for bug reporting
 Russell Johnson -- for providing CCCBDB (NIST) logfiles
 Jerome Kieffer -- for bug reporting
 Greg Magoon -- for bug reporting and patches
 Scott McKechnie -- for bug reporting
+mkrompiec -- for contributing test files
 mwykes -- for bug reporting and patches
 Alexis Otero-Calvis -- for bug reporting
 Rob Paton -- for creating and running Jaguar test jobs
 Martin Peeks -- for patches
-Felix Plasser -- for bug reporting and contributing files
+Felix Plasser -- for fixes, patches and contributing files
 Martin Rahm -- for bug reporting
 Marius Retegan -- for bug reporting
 Tamilmani S -- for bug reporting
 Melchor Sanchez -- for bug reporting
 Alex Schild -- for ideas and contributing test files
+Sanjeed Schamnad -- for patches new features
 Jen Schwartz -- for helping create and run Jaguar 6.0 test jobs
 Tiago Silva -- for bug reporting
 Pavel Solntsev -- for bug reporting
 Ben Stein -- for patches
 Adam Swanson -- for bug reporting
-Joe Townsend -- for giving multiple GAMESS files to test on
+Joe Townsend -- for contributing multiple GAMESS files to test on
 Chengju Wang -- for bug reporting
 Andrew Warden -- for bug reporting
 Samuel Wilson -- for bug reporting
 Fedor Zhuravlev -- for patches
 
 Please let us know if we have omitted someone from this list.
+Developers of cclib
+Eric J. Berquist
+Karol M. Langner
+Noel M. O'Boyle
+Adam L. Tenderholt

data/regression_download.sh

@@ -1,4 +1,9 @@
 #!/bin/bash
+#
+# Copyright (c) 2016, the cclib development team
+#
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 if [ -d regression/.git ]; then
     if [ -e regression/README.md ] && [ $(head -1 regression/README.md | cut -d " " -f 2) == "cclib-data" ]; then

manifest.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006-2014, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Create a MANIFEST file for distributing soruces with distutils."""
 
@@ -25,7 +22,7 @@
 files.append(os.path.join("src", "scripts", "ccwrite"))
 files.append(os.path.join("src", "scripts", "cda"))
 
-folders = ['bridge', 'method', 'parser', 'progress', 'writer']
+folders = ['bridge', 'io', 'method', 'parser', 'progress']
 for folder in folders:
     files.extend(glob.glob(os.path.join(source,folder,'*.py')))
 

old/downloadwiki.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.sf.net), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 import urllib
 

setup.py

@@ -1,14 +1,9 @@
-#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 #
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# Copyright (c) 2016, the cclib development team
 #
-# Copyright (C) 2006-2016, the cclib development team
-#
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """cclib: parsers and algorithms for computational chemistry
 
@@ -25,7 +20,7 @@
 Environment :: Console
 Intended Audience :: Science/Research
 Intended Audience :: Developers
-License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
+License :: OSI Approved :: BSD License
 Natural Language :: English
 Operating System :: OS Independent
 Programming Language :: Python
@@ -45,11 +40,11 @@ def setup_cclib():
     # The list of packages to be installed.
     cclib_packages = [
         'cclib',
+        'cclib.bridge',
+        'cclib.io',
+        'cclib.method',
         'cclib.parser',
         'cclib.progress',
-        'cclib.method',
-        'cclib.bridge',
-        'cclib.io'
     ]
 
     doclines = __doc__.split("\n")
@@ -62,7 +57,7 @@ def setup_cclib():
         author_email = "[email protected]",
         maintainer = "cclib development team",
         maintainer_email = "[email protected]",
-        license = "LGPL",
+        license = "BSD 3-Clause License",
         description = doclines[0],
         long_description = "\n".join(doclines[2:]),      
         classifiers = classifiers.split("\n"),

src/cclib/__init__.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006-2016 the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """A library for parsing and interpreting results from computational chemistry packages.
 

src/cclib/bridge/__init__.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006-2014, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Facilities for moving parsed data to other cheminformatic libraries."""
 

src/cclib/bridge/cclib2biopython.py

@@ -1,13 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
-
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 """Bridge for using cclib data in biopython (http://biopython.org)."""
 
 try:

src/cclib/bridge/cclib2openbabel.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2009-2015, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Bridge between cclib data and openbabel (http://openbabel.org)."""
 

src/cclib/bridge/cclib2pyquante.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2006-2013, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Bridge for using cclib data in PyQuante (http://pyquante.sourceforge.net)."""
 

src/cclib/io/__init__.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2014-2016, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Contains all writers for standard chemical representations"""
 

src/cclib/io/ccio.py

@@ -1,14 +1,9 @@
 # -*- coding: utf-8 -*-
 #
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# Copyright (c) 2016, the cclib development team
 #
-# Copyright (C) 2009-2016, the cclib development team
-#
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """Tools for identifying, reading and writing files and streams."""
 

src/cclib/io/cjsonreader.py

@@ -1,14 +1,10 @@
 # -*- coding: utf-8 -*-
 #
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# Copyright (c) 2016, the cclib development team
 #
-# Copyright (C) 2007-2016, the cclib development team
-#
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
+
 import json
 
 from ..parser.data import ccData

src/cclib/io/cjsonwriter.py

@@ -1,12 +1,9 @@
-# This file is part of cclib (http://cclib.github.io), a library for parsing
-# and interpreting the results of computational chemistry packages.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2014-2016, the cclib development team
+# Copyright (c) 2016, the cclib development team
 #
-# The library is free software, distributed under the terms of
-# the GNU Lesser General Public version 2.1 or later. You should have
-# received a copy of the license along with cclib. You can also access
-# the full license online at http://www.gnu.org/copyleft/lgpl.html.
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
 
 """A writer for chemical JSON (CJSON) files."""