Merge branch 'master' into develop

FragIt · Nov 13, 2023 · 4b1baf4 · 4b1baf4
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,4 +1,4 @@
-FragIt v2.X.X Release Notes
+FragIt v1.9.0 Release Notes
 ===========================
 
 This is a much-needed major revision to remove bugs
@@ -27,7 +27,7 @@ Updates since  v1.8.0
 ```
 
   * Includes some changes necessary for openbabel
-    cooperation.
+    cooperation with especially version 3.
 
   * Fixed a few errors in the jmol script and template.
 
@@ -37,9 +37,11 @@ Updates since  v1.8.0
 
 Developer Changes
 
-Made substantial changes to align FragIt with how
+ * Made substantial changes to align FragIt with how
 python packages should be organized
 
+ * code updates and improvements all around
+
 FragIt v1.8.0 Release Notes
 ===========================
 

diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 # FragIt
 
 [![GitHub release](https://img.shields.io/github/release/FragIt/fragit-main.svg?style=flat)](https://github.com/FragIt/fragit-main/releases)
-[![Build Status](https://travis-ci.org/FragIt/fragit-main.svg?branch=master)](https://travis-ci.org/FragIt/fragit-main)
 
 FragIt is a python based tool that allows you to quickly fragment ["any"](http://openbabel.org/docs/2.3.0/FileFormats/Overview.html) molecule and use the produced output file(s) as an a starting point for input files in quantum chemistry programs that supports such fragment based methods.
 
@@ -47,4 +46,4 @@ In order to run FragIt, you *need* the following installed on your system:
 * The FragIt source code, look above for information on how to obtain it
 * [Open Babel](http://www.openbabel.org) 2.3 or newer with [python language bindings](http://openbabel.org/docs/dev/Installation/install.html#compile-language-bindings) enabled. Github user [andersx](https://github.com/andersx) [wrote a guide](http://combichem.blogspot.dk/2013/12/compiling-open-babel-with-python.html) to how that is accomplished.
 * [Numpy](http://numpy.scipy.org) 1.5 or newer.
-* [Python](http://www.python.org) version 2.7 or 3.5 (or later).
+* [Python](http://www.python.org) 3.9 (or later).
diff --git a/fragit/cmdline.py b/fragit/cmdline.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2011-2016 Casper Steinmann
+Copyright (C) 2011-2023 Casper Steinmann
 """
 import sys
 import argparse

diff --git a/fragit/config.py b/fragit/config.py
@@ -1,6 +1,6 @@
 """
 Copyright (C) 2010-2011 Mikael W. Ibsen
-Some portions Copyright (C) 2011-2017 Casper Steinmann
+Some portions Copyright (C) 2011-2023 Casper Steinmann
 """
 from configparser import RawConfigParser
 import sys

diff --git a/fragit/fragit_exceptions.py b/fragit/fragit_exceptions.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2016 Casper Steinmann
+Copyright (C) 2016-2023 Casper Steinmann
 """
 
 class OBNotFoundException(ImportError):

diff --git a/fragit/fragmentation.py b/fragit/fragmentation.py
@@ -1,6 +1,6 @@
 """
 Copyright (C) 2010-2011 Mikael W. Ibsen
-Some portions Copyright (C) 2011-2017 Casper Steinmann
+Some portions Copyright (C) 2011-2023 Casper Steinmann
 """
 import sys
 from typing import List, Tuple

diff --git a/fragit/gamessfmo.py b/fragit/gamessfmo.py
@@ -1,6 +1,6 @@
 """
 Copyright (C) 2010-2011 Mikael W. Ibsen
-Some portions Copyright (C) 2011-2017 Casper Steinmann
+Some portions Copyright (C) 2011-2023 Casper Steinmann
 """
 import os
 from typing import Dict, List, Tuple

diff --git a/fragit/mfcc.py b/fragit/mfcc.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2013-2017 Casper Steinmann
+Copyright (C) 2013-2023 Casper Steinmann
 """
 
 from fragit.fragit_exceptions import OBNotFoundException

diff --git a/fragit/openbabelwrapper.py b/fragit/openbabelwrapper.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2011-2016 Casper Steinmann
+Copyright (C) 2011-2023 Casper Steinmann
 """
 
 from fragit.fragit_exceptions import OBNotFoundException

diff --git a/fragit/outputformats.py b/fragit/outputformats.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2011-2016 Casper Steinmann
+Copyright (C) 2011-2023 Casper Steinmann
 """
 
 from fragit.gamessfmo import GamessFMO

diff --git a/fragit/qmmm.py b/fragit/qmmm.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2013-2017 Casper Steinmann
+Copyright (C) 2013-2023 Casper Steinmann
 """
 from typing import List
 

diff --git a/fragit/strings.py b/fragit/strings.py
@@ -2,7 +2,7 @@
 Copyright (C) 2011-2023 Casper Steinmann
 """
 
-version = ("1", "8", "0")
+version = ("1", "9", "0")
 version_str = ".".join(version)
 
 doc_str = """FragIt is a tool to fragment large molecules for use in fragment based quantum chemistry methods.

diff --git a/fragit/template.py b/fragit/template.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2011-2016 Casper Steinmann
+Copyright (C) 2011-2023 Casper Steinmann
 """
 
 import os

diff --git a/fragit/util.py b/fragit/util.py
@@ -1,6 +1,6 @@
 """
 Copyright (C) 2010-2011 Mikael W. Ibsen
-Some portions Copyright (C) 2011-2016 Casper Steinmann
+Some portions Copyright (C) 2011-2023 Casper Steinmann
 """
 import os
 import string

diff --git a/fragit/writer.py b/fragit/writer.py
@@ -1,6 +1,6 @@
 """
 Copyright (C) 2010-2011 Mikael W. Ibsen
-Some portions Copyright (C) 2011-2017 Casper Steinmann
+Some portions Copyright (C) 2011-2023 Casper Steinmann
 """
 from typing import List
 

diff --git a/fragit/xyz.py b/fragit/xyz.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2013-2017 Casper Steinmann
+Copyright (C) 2013-2023 Casper Steinmann
 """
 from typing import List
 

diff --git a/fragit/xyzmfcc.py b/fragit/xyzmfcc.py
@@ -1,5 +1,5 @@
 """
-Copyright (C) 2013-2017 Casper Steinmann
+Copyright (C) 2013-2023 Casper Steinmann
 """
 import numpy as np
 from typing import List, Optional

diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 from fragit.strings import doc_str
 
 __author__ = "Casper Steinmann"
-__copyright__ = "Copyright 2017"
+__copyright__ = "Copyright 2023"
 __license__ = 'GPL2 or later'
 __version__ = version_str
 __email__ = "[email protected]"