cclib 1.7.2__tar.gz → 1.8.1rc2__tar.gz

cclib-1.8.1rc2/ANNOUNCE

@@ -0,0 +1,35 @@
+On behalf of the cclib development team, we are pleased to announce the release of cclib 1.8, which is now available for download from https://cclib.github.io. This is a major update that includes Julia bindings (https://github.com/cclib/Cclib.jl), two new parsers (NBO and GAMESS dat files), several new attributes and multiple other improvements and fixes.
+
+cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from 16 different programs: ADF, DALTON, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro, MOLCAS, MOPAC, NBO, NWChem, ORCA, Psi4, QChem and Turbomole.
+
+Among other data, cclib extracts:
+
+    * 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, electrostatic moments and polarizabilities
+(For a complete list see https://cclib.github.io/data.html).
+cclib also provides some calculation methods for interpreting the electronic properties of molecules such as:
+    * Mulliken, Lowdin, Stockholder type, Bader and other population analyses
+    * Overlap population analysis
+    * Mayer's bond orders
+(For a complete list see https://cclib.github.io/methods.html).
+For information on how to use cclib, see our documentation at https://cclib.github.io.
+If you need help, find a bug, want new features or have any questions, please send an email to our mailing list:
+    https://groups.google.com/g/cclib
+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, Amanda Dumi, Geoffrey Hutchison, Karol M. Langner, Oliver S. Lee, Noel M. O'Boyle, Felipe S. S. Schneider, Adam L. Tenderholt, Shiv Upadhyay. Release of cclib version 1.8. 2023. https://doi.org/10.5281/zenodo.8280878
+Regards,
+The cclib development team
+———
+
+Summary of changes since last version:
+* Added Julia language bindings
+* Added parsers for NBO and GAMESS *.dat files
+* New attribute: nmrcouplingtensors for NMR spin-spin couplings
+* New attribute: rotconsts for rotational constants
+* New method: CM5 charges
+* Many improvements and fixes - see CHANGELOG for details

{cclib-1.7.2 → cclib-1.8.1rc2}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017, the cclib development team
+Copyright (c) 2024, the cclib development team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

cclib-1.8.1rc2/MANIFEST.in

@@ -0,0 +1,5 @@
+include ANNOUNCE
+include THANKS
+graft tools
+prune test
+global-exclude *.py[cod]

cclib-1.8.1rc2/PKG-INFO

@@ -0,0 +1,89 @@
+Metadata-Version: 2.1
+Name: cclib
+Version: 1.8.1rc2
+Summary: parsers and algorithms for computational chemistry
+Author-email: cclib development team <cclib@googlegroups.com>
+Maintainer-email: cclib development team <cclib@googlegroups.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, the cclib development team
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Bug Tracker, https://github.com/cclib/cclib/issues
+Project-URL: Changelog, https://github.com/cclib/cclib/blob/master/doc/sphinx/changelog.rst
+Project-URL: Documentation, http://cclib.github.io/
+Project-URL: Homepage, https://github.com/cclib/cclib
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: packaging>=19.0
+Requires-Dist: periodictable
+Requires-Dist: scipy>=1.2.0
+Provides-Extra: bridges
+Requires-Dist: ase>=3.21; extra == "bridges"
+Requires-Dist: biopython; extra == "bridges"
+Requires-Dist: openbabel; extra == "bridges"
+Requires-Dist: pandas; extra == "bridges"
+Requires-Dist: pyscf; extra == "bridges"
+Requires-Dist: qc-iodata>=1.0.0a2; extra == "bridges"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: cclib[bridges,docs,test]; extra == "dev"
+Provides-Extra: all
+Requires-Dist: cclib[bridges]; extra == "all"
+
+### cclib
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8280878.svg)](https://doi.org/10.5281/zenodo.8280878)
+[![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](https://github.com/cclib/cclib/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/cclib/cclib/actions/workflows/cclib_pytest.yml)
+[![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" />
+
+cclib is a Python library that provides parsers for output files of computational chemistry packages. It also provides a platform for computational chemists to implement algorithms in a platform-independent way.
+
+For more information, go to [https://cclib.github.io](https://cclib.github.io). There is a mailing list for questions at https://groups.google.com/g/cclib.

{cclib-1.7.2 → cclib-1.8.1rc2}/README.md

@@ -1,9 +1,9 @@
 ### cclib
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4420433.svg)](https://doi.org/10.5281/zenodo.4420433)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8280878.svg)](https://doi.org/10.5281/zenodo.8280878)
 [![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](https://github.com/cclib/cclib/actions/workflows/cclib_pytest.yml/badge.svg?branch=master)](https://github.com/cclib/cclib/actions/workflows/cclib_pytest.yml)
+[![build status](https://github.com/cclib/cclib/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/cclib/cclib/actions/workflows/cclib_pytest.yml)
 [![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" />

cclib-1.8.1rc2/THANKS

@@ -0,0 +1,101 @@
+Core developers:
+Eric J. Berquist
+Minsik Cho
+Amanda Dumi
+Geoff Hutchison
+Karol M. Langner
+Oliver Lee
+Noel M. O'Boyle (retired)
+Felipe S. S. Schneider
+Adam L. Tenderholt (retired)
+Shiv Upadhyay
+
+Developers that have added at least ~1K SLOC:
+Sagar Gaur
+Andrew S. Rosen
+Sanjeed Schamnad
+Kunal Sharma
+Casper Steinmann
+Jonathon Vandezande
+Weronika Zak
+
+We would like the thank all the following who have contributed to cclib:
+Nuno Bandeira -- for bug reporting
+Björn Baumeier -- for bug reporting
+Dermot Brougham -- for bug reporting
+bwang2453 -- for patches and new features
+Javier Cerezo -- for patches
+Avril Coghlan -- for designing the cclib logo
+computerscienceiscool -- for documentation
+Ramon Crehuet -- for new features
+Michael D'Addario -- for fixes
+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
+Elliot Farrar -- for fixes
+froessler -- for cleanups
+Christos Garoufalis -- for bug reporting
+Alessandro Genova -- for patches and fixes
+Victor Hugo Cano Gil -- for the Julia binding
+glideht -- for bug reporting
+Anselm Hahn -- for code cleanup
+Edward Holland -- for patches
+Karen Hemelsoet -- for bug reporting
+Ian Hovell -- for bug reporting
+Julien Idé -- for bug reporting
+csjacky -- for bug reporting
+Peter St. John -- for patches
+Russell Johnson -- for providing CCCBDB (NIST) logfiles
+Jerome Kieffer -- for bug reporting
+kuriba -- for patches
+Cyrille Lavigne -- for documentation
+Greg Magoon -- for bug reporting and patches
+Alex Maldonado -- for fixes
+Scott McKechnie -- for bug reporting
+migatt -- for bug reporting and patches
+mkrompiec -- for contributing test files
+mwykes -- for bug reporting and patches
+NoviciusVulgaris -- for bug reporting
+Alexis Otero-Calvis -- for bug reporting
+Daniele Padula -- for patches
+Drew Parsons -- for bug reporting
+Rob Paton -- for creating and running Jaguar test jobs
+Mark Payne -- for new features
+Martin Peeks -- for patches
+Andrea Pellegrini -- for bug reporting
+Waylon Peng -- for fixes and improvements
+Mark Perri -- for patches
+Felix Plasser -- for fixes, patches and contributing files
+Sai Murali Karthik Putcha -- for new features
+Mariusz Radon -- for bug reporting
+Martin Rahm -- for bug reporting
+Peter Reinholdt - for patches
+Marius Retegan -- for bug reporting
+Jaime Rodríguez-Guerra - for patches
+Tamilmani S -- for bug reporting
+Melchor Sanchez -- for bug reporting
+Alex Schild -- for ideas and contributing test files
+Jen Schwartz -- for helping create and run Jaguar 6.0 test jobs
+shijunang -- for patches
+Chikashi Shinagawa -- for patches
+simonaxelrod -- for fixes
+Tiago Silva -- for bug reporting
+LoraSM -- for bug reporting
+James E T Smith -- for fixes
+Pavel Solntsev -- for bug reporting
+srtlg -- for fixes
+Ben Stein -- for patches
+Maxim Stolyarchuk - for patches
+Adam Swanson -- for bug reporting
+Joe Townsend -- for contributing multiple GAMESS files to test on
+Chengju Wang -- for bug reporting
+Andrew Warden -- for bug reporting
+Hubert Weißmann -- for fixes
+Dustin Wheeler -- for fixes
+Samuel Wilson -- for bug reporting
+Dave Z. -- for patches
+Fedor Zhuravlev -- for patches
+
+Please let us know if we have omitted someone from this list.

{cclib-1.7.2 → cclib-1.8.1rc2}/cclib/__init__.py

@@ -1,6 +1,4 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright (c) 2022, the cclib development team
+# Copyright (c) 2024, 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.
@@ -12,12 +10,6 @@ computational chemistry programs and typically contained in output files. Specif
 cclib extracts (parses) data from the output files generated by multiple programs
 and provides a consistent interface to access them.
 
-Currently supported programs:
-    ADF, Firefly, GAMESS(US), GAMESS-UK, Gaussian,
-    Jaguar, Molpro, MOPAC, NWChem, ORCA, Psi, Q-Chem
-
-And additionally: formatted checkpoints files (fchk)
-
 Another aim is to facilitate the implementation of algorithms that are not specific
 to any particular computational chemistry package and to maximise interoperability
 with other open source computational chemistry and cheminformatic software libraries.
@@ -25,13 +17,11 @@ To this end, cclib provides a number of bridges to help transfer data to other l
 as well as example methods that take parsed data as input.
 """
 
-__version__ = "1.7.2"
+from cclib._version import __version__
 
-from cclib import parser
-from cclib import progress
-from cclib import method
-from cclib import bridge
-from cclib import io
+# isort: off
+from cclib import parser, progress, method, bridge, io
+# isort: on
 
 # The test module can be imported if it was installed with cclib.
 try:

cclib-1.8.1rc2/cclib/_version.py

@@ -0,0 +1 @@
+__version__ = "1.8.1rc2"

{cclib-1.7.2 → cclib-1.8.1rc2}/cclib/bridge/__init__.py

@@ -1,6 +1,4 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright (c) 2020, the cclib development team
+# Copyright (c) 2024, 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.