Release 6.0.0

qcscine · Nov 20, 2023 · de47ed1 · de47ed1
1 parent a1009ec
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,12 @@
 Changelog
 =========
 
+Release 6.0.0
+-------------
+
+- Improve support for compilation on Windows (MSVC)
+- Update address in license
+
 Release 5.0.0
 -------------
 
@@ -9,10 +15,10 @@ Release 5.0.0
 Release 4.1.0
 -------------
 
-- Add new interface ``EmbeddingCalculator``. This class is derived from 
-  the calculator class and allows for embedding calculations with different 
+- Add new interface ``EmbeddingCalculator``. This class is derived from
+  the calculator class and allows for embedding calculations with different
   underlying calculators.
- 
+
 Release 4.0.2
 -------------
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.9)
 # tree must then provide a properly namespaced target with the same name as
 # your project.
 project(Core
-  VERSION 5.0.0
+  VERSION 6.0.0
   DESCRIPTION "Module management and core interface definitions"
 )
 

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -27,4 +27,4 @@ from members of the Reiher research group.
 Further Contributors
 --------------------
 
-So far, no one else has contributed to this repository.
+- Juuso Lehtivarjo, NMR Solutions Ltd.
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/dev b/dev
diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
@@ -25,6 +25,10 @@ target_link_libraries(Core
     ${CMAKE_DL_LIBS}
 )
 
+if(MSVC)
+  target_compile_definitions(Core PUBLIC BOOST_ALL_NO_LIB)
+endif()
+
 macro(determine_lib_type target)
   get_target_property(LIB_TYPE ${target} TYPE)
   if("${LIB_TYPE}" STREQUAL "UNKNOWN_LIBRARY")

diff --git a/src/Core/Core/BaseClasses/ObjectWithLog.h b/src/Core/Core/BaseClasses/ObjectWithLog.h
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

diff --git a/src/Core/Core/BaseClasses/ObjectWithStructure.h b/src/Core/Core/BaseClasses/ObjectWithStructure.h
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_OBJECTWITHSTRUCTURE_H

diff --git a/src/Core/Core/BaseClasses/StateHandableObject.h b/src/Core/Core/BaseClasses/StateHandableObject.h
@@ -1,7 +1,7 @@
 /**
  * @file StateHandableObject.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_STATEHANDABLEOBJECT_H_
@@ -57,7 +57,7 @@ class StateHandableObject {
    * @brief Get the current state of the object.
    *
    * Note that the state is possibly a mutable representation of the current state
-   * of the object.It is not necessarily a deepcopy, eventhough this is likely the
+   * of the object. It is not necessarily a deepcopy, eventhough this is likely the
    * default behaviour. Please read the documentation of the specific
    * implementation for further details.
    *

diff --git a/src/Core/Core/DerivedModule.h b/src/Core/Core/DerivedModule.h
@@ -2,7 +2,7 @@
  * @file
  * @brief Provides helpers for the general implementation of classes deriving from Module
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

diff --git a/src/Core/Core/Exceptions.h b/src/Core/Core/Exceptions.h
@@ -1,7 +1,7 @@
 /**
  * @file Exceptions.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_EXCEPTIONS_H_

diff --git a/src/Core/Core/ExportControl.h b/src/Core/Core/ExportControl.h
@@ -1,7 +1,7 @@
 /**
  * @file ExportControl.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_EXPORTCONTROL_H_

diff --git a/src/Core/Core/Impl/ModuleManager.h b/src/Core/Core/Impl/ModuleManager.h
@@ -1,6 +1,6 @@
 /**
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

diff --git a/src/Core/Core/Interfaces/Calculator.h b/src/Core/Core/Interfaces/Calculator.h
@@ -1,7 +1,7 @@
 /**
  * @file Calculator.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_CALCULATOR_H_
@@ -119,6 +119,11 @@ class Calculator : public StateHandableObject,
       return calculatorPtr->supportsMethodFamily(methodFamily);
     };
   }
+  /**
+   * @brief Whether the calculator has no underlying Python code and can therefore
+   * release the global interpreter lock in Python bindings
+   */
+  virtual bool allowsPythonGILRelease() const = 0;
 
  private:
   /*

diff --git a/src/Core/Core/Interfaces/CalculatorWithReference.h b/src/Core/Core/Interfaces/CalculatorWithReference.h
@@ -1,7 +1,7 @@
 /**
  * @file Calculator.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_CALCULATORWITHREFERENCE_H

diff --git a/src/Core/Core/Interfaces/EmbeddingCalculator.h b/src/Core/Core/Interfaces/EmbeddingCalculator.h
@@ -1,7 +1,7 @@
 /**
  * @file Calculator.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_EMBEDDINGCALCULATOR_H
@@ -40,7 +40,12 @@ class EmbeddingCalculator : public Calculator {
    * @brief Accessor for the underlying calculators.
    * @return std::vector<std::shared_ptr<Calculator>> A vector of underlying calculators.
    */
-  virtual std::vector<std::shared_ptr<Calculator>> getUnderlyingCalculators() = 0;
+  virtual std::vector<std::shared_ptr<Calculator>> getUnderlyingCalculators() const = 0;
+  /**
+   * @brief Passes the settings of the underlying calculators to the settings of the embedding calculator.
+   * @note In the derived class, care must be taken that the underlying calculators have been set before.
+   */
+  virtual void addUnderlyingSettings() = 0;
   /// @brief Default destructor.
   virtual ~EmbeddingCalculator() = default;
 

diff --git a/src/Core/Core/Interfaces/MMParametrizer.h b/src/Core/Core/Interfaces/MMParametrizer.h
@@ -1,7 +1,7 @@
 /**
  * @file MMParametrizer.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

diff --git a/src/Core/Core/Interfaces/ObjectWithOrbitals.h b/src/Core/Core/Interfaces/ObjectWithOrbitals.h
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_OBJECTWITHORBITALS_H

diff --git a/src/Core/Core/Interfaces/WavefunctionOutputGenerator.h b/src/Core/Core/Interfaces/WavefunctionOutputGenerator.h
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_WAVEFUNCTIONOUTPUTGENERATOR_H

diff --git a/src/Core/Core/Log.h b/src/Core/Core/Log.h
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef INCLUDE_SCINE_UTILS_LOG_H

diff --git a/src/Core/Core/Module.h b/src/Core/Core/Module.h
@@ -1,7 +1,7 @@
 /**
  * @file Module.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef CORE_MODULE_H_

diff --git a/src/Core/Core/ModuleManager.cpp b/src/Core/Core/ModuleManager.cpp
@@ -1,7 +1,7 @@
 /**
  * @file ModuleManager.cpp
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 
@@ -12,6 +12,11 @@
 namespace Scine {
 namespace Core {
 
+ModuleManager& ModuleManager::getInstance() {
+  static ModuleManager instance;
+  return instance;
+}
+
 void ModuleManager::load(const boost::filesystem::path& libraryPath) {
   _impl->load(libraryPath);
 }

diff --git a/src/Core/Core/ModuleManager.h b/src/Core/Core/ModuleManager.h
@@ -1,7 +1,7 @@
 /**
  * @file ModuleManager.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 
@@ -52,10 +52,7 @@ class CORE_EXPORT ModuleManager {
    *
    * @return Returns a reference to the ModuleManager instance.
    */
-  static ModuleManager& getInstance() {
-    static ModuleManager instance;
-    return instance;
-  }
+  static ModuleManager& getInstance();
 
   /**
    * @brief Deleted copy constructor, as required by the singleton design pattern.

diff --git a/src/Core/Tests/CoreTests.cpp b/src/Core/Tests/CoreTests.cpp
@@ -1,7 +1,7 @@
 /**
  * @file CoreTests.cpp
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #include "DummyInterface.h"

diff --git a/src/Core/Tests/DummyInterface.h b/src/Core/Tests/DummyInterface.h
@@ -1,7 +1,7 @@
 /**
  * @file DummyInterfaceAndModels.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef DUMMY_INTERFACE_H

diff --git a/src/Core/Tests/DummyModels.cpp b/src/Core/Tests/DummyModels.cpp
@@ -1,7 +1,7 @@
 /**
  * @file DummyModels.cpp
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #include "DummyModels.h"

diff --git a/src/Core/Tests/DummyModels.h b/src/Core/Tests/DummyModels.h
@@ -1,7 +1,7 @@
 /**
  * @file DummyInterfaceAndModels.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef DUMMY_MODELS_H

diff --git a/src/Core/Tests/Log.cpp b/src/Core/Tests/Log.cpp
@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

diff --git a/src/Core/Tests/SampleModule.cpp b/src/Core/Tests/SampleModule.cpp
@@ -1,7 +1,7 @@
 /**
  * @file SampleModule.cpp
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  *
  * Steps to your own module implementation:

diff --git a/src/Core/Tests/SampleModule.h b/src/Core/Tests/SampleModule.h
@@ -1,7 +1,7 @@
 /**
  * @file SampleModule.h
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  *
  *
+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