Release 2.0.1

qcscine · Nov 20, 2023 · 21fceb4 · 21fceb4
1 parent 8042bfb
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diff --git a/.clang-format b/.clang-format
@@ -101,10 +101,9 @@ SpacesBeforeTrailingComments: 1
 SpacesInAngles:  false
 SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
-SpacesInContainerLiterals: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
-Standard:        Cpp11
+Standard:        c++17
 TabWidth:        2
 UseTab:          Never
 ...
diff --git a/.conan_test_package/conanfile.py b/.conan_test_package/conanfile.py
@@ -1,5 +1,5 @@
 __copyright__ = """This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

diff --git a/.conan_test_package/test.cpp b/.conan_test_package/test.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -99,6 +99,20 @@ pypi-cp39:
   variables:
     PYABI: cp39-cp39
 
+pypi-cp310:
+  stage: build
+  extends: .manylinux
+  only: [master]
+  variables:
+    PYABI: cp310-cp310
+
+pypi-cp311:
+  stage: build
+  extends: .manylinux
+  only: [master]
+  variables:
+    PYABI: cp311-cp311
+
 # CMake-only build
 cmake-only:
   stage: build

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,6 +6,14 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/spec/v2.0.0.html>`_.
 
+2.0.1
+-----
+
+Changed
+.......
+
+- Update address in license
+
 2.0.0
 -----
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.9)
 
 project(Molassembler
-  VERSION 2.0.0
+  VERSION 2.0.1
   DESCRIPTION "Graph-based molecular toolkit for possibly inorganic molecules"
   LANGUAGES C CXX
 )

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

diff --git a/README.rst b/README.rst
@@ -110,7 +110,7 @@ No dependencies must be preinstalled, and you do not need to download the
 sources. To install/build with Conan::
 
     conan remote add scine https://scine-artifactory.ethz.ch/artifactory/api/conan/public
-    conan install -r scine --build=missing scine_molassembler/2.0.0@
+    conan install -r scine --build=missing scine_molassembler/2.0.1@
 
 Should you want Python bindings, add ``-o scine_molassembler:python=True`` before
 the last argument.
@@ -132,9 +132,9 @@ If ``doxygen`` is found, the C++ library documentation is built. If the Python
 bindings are built and the ``sphinx`` Python module is available, the Python
 binding documentation is generated too.
 
-.. _C++ library: https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.0/cpp/index.html
+.. _C++ library: https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.1/cpp/index.html
 
-.. _Python bindings: https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.0/py/index.html
+.. _Python bindings: https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.1/py/index.html
 
 References
 ----------

diff --git a/analysis/BenchmarkGraphAlgorithms.cpp b/analysis/BenchmarkGraphAlgorithms.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/BenchmarkRefinement.cpp b/analysis/BenchmarkRefinement.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/BenchmarkRefinementFunctions.cpp b/analysis/BenchmarkRefinementFunctions.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/DirectedConformerGeneration.cpp b/analysis/DirectedConformerGeneration.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Gor1Explainer.cpp b/analysis/Gor1Explainer.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Interpret.cpp b/analysis/Interpret.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/MakeIsomorphism.cpp b/analysis/MakeIsomorphism.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/RankingExplainer.cpp b/analysis/RankingExplainer.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/ShapeRecognition.cpp b/analysis/ShapeRecognition.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Shapes/csm.cpp b/analysis/Shapes/csm.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Shapes/shape.cpp b/analysis/Shapes/shape.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Shapes/thomson.cpp b/analysis/Shapes/thomson.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Shapes/writeMappings.cpp b/analysis/Shapes/writeMappings.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Shapes/writeTransitionDotFiles.cpp b/analysis/Shapes/writeTransitionDotFiles.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/Stereopermutations.cpp b/analysis/Stereopermutations.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/analysis/TraceRefinement.cpp b/analysis/TraceRefinement.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  *
  * This file reimplements Distance Geometry with more invasive debug structures

diff --git a/analysis/plot-recognition-data.py b/analysis/plot-recognition-data.py
@@ -1,5 +1,5 @@
 __copyright__ = """This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

diff --git a/cmake/CompilerSpecificSetup.cmake b/cmake/CompilerSpecificSetup.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/cmake/DoxygenSettings.cmake b/cmake/DoxygenSettings.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/cmake/ImportNauty.cmake b/cmake/ImportNauty.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/cmake/ImportOutcome.cmake b/cmake/ImportOutcome.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/cmake/ImportRingDecomposerLib.cmake b/cmake/ImportRingDecomposerLib.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/cmake/LibType.cmake b/cmake/LibType.cmake
@@ -1,6 +1,6 @@
 #
 # This file is licensed under the 3-clause BSD license.
-# Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+# Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 # See LICENSE.txt for details.
 #
 

diff --git a/conanfile.py b/conanfile.py
@@ -1,5 +1,5 @@
 __copyright__ = """This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
@@ -8,9 +8,9 @@
 
 class MolassemblerConan(ScineConan):
     name = "scine_molassembler"
-    version = "2.0.0"
+    version = "2.0.1"
     license = "BSD-3-Clause"
-    author = "ETH Zurich, Laboratory of Physical Chemistry, Reiher Group"
+    author = "ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group"
     url = "https://scine.ethz.ch/download/molassembler"
     description = "Molecular graph interpretation, modification and conformer generation"
     options = {
@@ -45,7 +45,7 @@ class MolassemblerConan(ScineConan):
         "CMakeLists.txt",
     ]
     requires = [
-        "scine_utilities/8.0.0",
+        "scine_utilities/9.0.0",
         "RingDecomposerLib/1.1.3",
         "nauty/2.7r1"
     ]

diff --git a/dev b/dev
diff --git a/doc/examples/construction.cpp b/doc/examples/construction.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 

diff --git a/manual/manual.tex b/manual/manual.tex
@@ -13,7 +13,7 @@
 %%
 % Book metadata
 \title[SCINE Molassembler manual]{User Manual \vskip 0.5em
-{\setlength{\parindent}{0pt} \Huge SCINE Molassembler 2.0.0}}
+{\setlength{\parindent}{0pt} \Huge SCINE Molassembler 2.0.1}}
 \author[The SCINE Molassembler Developers]{The SCINE Molassembler Developers:
 \newline \noindent Moritz Bensberg, Stephanie A.~Grimmel, Jan-Grimo Sobez, Miguel Steiner, Jan P.~Unsleber, and Markus Reiher}
 \publisher{ETH Z\"urich}
@@ -296,7 +296,7 @@ \section{Conan package}
 The base command to install \textsc{Molassembler} is:
 
 \begin{Verbatim}
-conan install scine_molassembler/2.0.0@
+conan install scine_molassembler/2.0.1@
 \end{Verbatim}
 
 Changes to default options can be supplied right after \texttt{conan install}
@@ -305,7 +305,7 @@ \section{Conan package}
 For instance, if you want Python bindings, your install command will be:
 
 \begin{Verbatim}
-conan install -o scine_molassembler:python=True scine_molassembler/2.0.0@
+conan install -o scine_molassembler:python=True scine_molassembler/2.0.1@
 \end{Verbatim}
 
 Conan will proceed to identify your operating system, architecture and compiler.
@@ -395,7 +395,7 @@ \section{From source code with CMake}
 \chapter{Using the C++ library}
 
 \textsc{Molassembler} provides a
-\href{https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.0/cpp}{\texttt{Doxygen}
+\href{https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.1/cpp}{\texttt{Doxygen}
 technical
 documentation}\footnote{\texttt{scine.ethz.ch/download/molassembler}}
 which documents the available functions in detail and also provides an overview
@@ -444,7 +444,7 @@ \chapter{Using the Python module}
 \textsc{Molassembler}. Now you can simply import the module and use it just
 like any other Python module. All functionality available in the Python module
 is
-\href{https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.0/py}{documented with
+\href{https://scine.ethz.ch/static/download/documentation/molassembler/v2.0.1/py}{documented with
 examples}\footnote{\texttt{scine.ethz.ch/download/molassembler}}. You can
 interactively explore the available functionality in an interactive Python shell
 using the \texttt{help} and \texttt{dir} Python functions:

diff --git a/python/AtomStereopermutatorPython.cpp b/python/AtomStereopermutatorPython.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 #include "Molassembler/Temple/Functional.h"

diff --git a/python/BondStereopermutatorPython.cpp b/python/BondStereopermutatorPython.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 #include "TypeCasters.h"

diff --git a/python/CompositePython.cpp b/python/CompositePython.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 #include "TypeCasters.h"

diff --git a/python/ConformersPython.cpp b/python/ConformersPython.cpp
@@ -1,6 +1,6 @@
 /*!@file
  * @copyright This code is licensed under the 3-clause BSD license.
- *   Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+ *   Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
  *   See LICENSE.txt for details.
  */
 #include "Utils/Pybind.h"
-Original file line number
+Diff line change
@@ Expand Up @@
     The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_
     and this project adheres to `Semantic Versioning <http://semver.org/spec/v2.0.0.html>`_.
+.0.1
+    -----
+    Changed
+    .......
+    - Update address in license
 .0.0
     -----
@@ Expand Down @@
+7 −0		CHANGELOG.rst
+1 −1		CONTRIBUTING.rst
+1 −1		LICENSE.txt
+1 −1		cmake/AddEigen.cmake
+1 −1		cmake/CMakeBackports.cmake
+1 −1		cmake/ColorMessages.cmake
+1 −1		cmake/ComponentSetup.cmake
+1 −1		cmake/DownloadFileHelper.cmake
+1 −1		cmake/DoxygenDocumentation.cmake
+1 −1		cmake/FindGMock.cmake
+1 −1		cmake/FindLAPACKE.cmake
+1 −1		cmake/FindMKL.cmake
+3 −3		cmake/FindPythonInterpreter.cmake
+1 −1		cmake/FindPythonModule.cmake
+1 −1		cmake/ImportCereal.cmake
+2 −2		cmake/ImportCore.cmake
+2 −2		cmake/ImportDatabase.cmake
+1 −1		cmake/ImportGTest.cmake
+1 −1		cmake/ImportIRC.cmake
+1 −1		cmake/ImportIntegralEvaluator.cmake
+1 −1		cmake/ImportJSON.cmake
+1 −1		cmake/ImportLBFGSB.cmake
+1 −1		cmake/ImportLibint.cmake
+2 −2		cmake/ImportMolassembler.cmake
+1 −1		cmake/ImportMongoCxx.cmake
+3 −3		cmake/ImportPybind11.cmake
+2 −2		cmake/ImportSparrow.cmake
+1 −1		cmake/ImportSpgLib.cmake
+2 −2		cmake/ImportUtilsOS.cmake
+2 −2		cmake/ImportXtb.cmake
+1 −1		cmake/ImportYamlCpp.cmake
+1 −1		cmake/Licenses.cmake
+1 −1		cmake/SphinxDocumentation.cmake
+27 −4		cmake/TargetLibName.cmake
+1 −1		cmake/Utils.cmake
+1 −1		cmake/doctest_pybind_module.py
+3 −3		conan/base.py
+1 −1		conan/glue/gtest.cmake
+1 −1		conan/hook.cmake
+2 −2		conan/utils.py