Release 3.0.0

.clang-format

@@ -0,0 +1,103 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+# Reiher Group, SCINE subgroup
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+FixNamespaceComments: true
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeBlocks: Merge
+IncludeCategories: 
+  - Regex:           '^".*\.h"'
+    Priority:        1
+  - Regex:           '^".*'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        3
+  - Regex:           '^<.*'
+    Priority:        4
+  - Regex:           '.*'
+    Priority:        5
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+PenaltyBreakBeforeFirstCallParameter: 20
+PenaltyBreakComment: 5
+PenaltyBreakFirstLessLess: 3
+PenaltyBreakString: 100
+PenaltyExcessCharacter: 2
+PenaltyReturnTypeOnItsOwnLine: 40
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...
+

.clang-format-excludes

@@ -0,0 +1 @@
+Dftd3ReferencePairs.h

.clang-tidy

@@ -0,0 +1,63 @@
+---
+# Remarks about the checks:
+# * modernize-use-equals-delete: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-cplusplus.NewDelete: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-cplusplus.NewDeleteLeaks: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-optin.cplusplus.VirtualCall: removed to avoid warnings generated in google-test
+# * cppcoreguidelines-slicing: removed because of PropertyData in Delib
+# * clang-analyzer-core.NullDereference: removed because of warning in clang's headers
+Checks:          '-*,
+                  bugprone-*,
+                  clang-analyzer-*,
+                  -clang-analyzer-cplusplus.NewDelete,
+                  -clang-analyzer-cplusplus.NewDeleteLeaks,
+                  -clang-analyzer-optin.cplusplus.VirtualCall,
+                  -clang-analyzer-core.NullDereference,
+                  cppcoreguidelines-*,
+                  -cppcoreguidelines-owning-memory,
+                  -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+                  -cppcoreguidelines-pro-bounds-constant-array-index,
+                  -cppcoreguidelines-pro-bounds-pointer-arithmetic,
+                  -cppcoreguidelines-pro-type-const-cast,
+                  -cppcoreguidelines-pro-type-member-init,
+                  -cppcoreguidelines-pro-type-vararg,
+                  -cppcoreguidelines-special-member-functions,
+                  -cppcoreguidelines-slicing,
+                  misc-*,
+                  modernize-*,
+                  -modernize-use-equals-delete,
+                  performance-*,
+                  portability-*,
+                  readability-*,
+                  -readability-braces-around-statements,
+                  -readability-else-after-return'
+#HeaderFilterRegex: './src/*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+CheckOptions:
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'
+  - key:             readability-implicit-bool-conversion.AllowPointerConditions # Do not complain for "if (x)" when x is a pointer
+    value:           1
+  - key:             performance-move-const-arg.CheckTriviallyCopyableMove # Do not complain on "std::move(x)" if x is trivially copyable
+    value:           0
+...
+

.conan_test_package/CMakeLists.txt

@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.9)
+
+project(UtilsTestPackage)
+
+find_package(ScineUtilsOS REQUIRED)
+
+add_executable(TestPackageTest ${CMAKE_CURRENT_SOURCE_DIR}/test.cpp)
+target_link_libraries(TestPackageTest PRIVATE Scine::UtilsOS)
+enable_testing()
+add_test(NAME LinkingTest COMMAND TestPackageTest)

.conan_test_package/conanfile.py

@@ -0,0 +1,34 @@
+__copyright__ = """This file is part of SCINE Utilities.
+This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+See LICENSE.txt for details.
+"""
+
+import os
+from conans import ConanFile, CMake
+
+
+def conan_paths_str(build_folder):
+    return os.path.join(build_folder, "conan_paths.cmake")
+
+
+class TestPackageConan(ConanFile):
+    settings = "os", "compiler", "build_type", "arch"
+    generators = "cmake_paths"
+    build_requires = [("cmake/[>3.13.4]@scine/stable")]
+    exports_sources = "CMakeLists.txt", "test.cpp"
+
+    def _configure(self):
+        cmake = CMake(self)
+        cmake.definitions["CMAKE_PROJECT_UtilsTestPackage_INCLUDE"] = conan_paths_str(
+            self.build_folder)
+        cmake.configure()
+        return cmake
+
+    def build(self):
+        cmake = self._configure()
+        cmake.build()
+
+    def test(self):
+        cmake = self._configure()
+        cmake.test()

.conan_test_package/test.cpp

@@ -0,0 +1,11 @@
+#include "Utils/Geometry/ElementInfo.h"
+
+using namespace Scine::Utils;
+
+int main() {
+  if(ElementInfo::element(1) == ElementType::H) {
+    return 0;
+  }
+
+  return 1;
+}

.gitignore

@@ -2,12 +2,14 @@
 build/*
 cmake-build-*
 compile_commands.json
+install/*
 
 # hidden files
 *.swp
 .idea/*
 .lvimrc
 .vscode
+.conan_test_package/build
 
 # python files
 *__pycache__*
@@ -16,4 +18,8 @@ compile_commands.json
 resource/Documentation/*
 
 # generated source files
+externalQC_output_location.h
 orca_output_location.h
+
+# conan ci files
+conan/*

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "cmake"]
-	path = cmake
-	url = https://github.com/qcscine/cmake.git
+[submodule "dev"]
+	path = dev
+	url = https://github.com/qcscine/development-utils.git

CHANGELOG.rst

@@ -0,0 +1,47 @@
+=========
+Changelog
+=========
+
+Release 3.0.0
+=============
+
+- Enable ``conan`` builds and PyPI releases
+- Add Newton-Trajectory type optimizer
+- Add statistics and machine learning tools (PCA, k-fold cross-validation, kernel ridge regression)
+- Add chemical representations for machine-learned force fields
+- Charge Model 5 corrections for Hirshfeld atomic partial charges
+- Add various conceptual DFT quantities
+- Enable access to the density matrix and GTOs in Python
+- Improve Dimer transition state search algorithm
+- Add implicit solvation option to ORCA and Gaussian interfaces
+- Add python bindings sphinx documentation
+- Separate ``Settings`` from its base ``ValueCollection`` in python bindings
+
+Release 2.0.0
+=============
+
+- Add support for internal coordinates
+- Add interface to Gaussian
+- Improve ORCA interface (and make compatible with ORCA 4.2.0)
+- Add BFGS optimizer and G-DIIS convergence accelerator
+- Improve Bofill transition state search algorithm
+- Various bugfixes and improvements
+
+Release 1.0.1
+=============
+
+Hotfix to allow compilation on OSX using Clang.
+
+Release 1.0.0
+=============
+
+Initial release with all necessary functionality to support Sparrow and ReaDuct.
+Among other things, this includes:
+
+- Analytic evaluation of gradients
+- Calculation of bond orders
+- Interface to the ORCA quantum chemistry program
+- Numerical Hessian calculator
+- Optimizers to find minima and transition states on the PES
+- Python bindings
+- SCF algorithm (including convergence accelerators such as DIIS)

CMakeLists.txt

@@ -4,12 +4,12 @@ cmake_minimum_required(VERSION 3.9)
 # tree must then provide a properly namespaced target with the same name as
 # your project.
 project(UtilsOS
-  VERSION 2.0.0
+  VERSION 3.0.0
   DESCRIPTION "Utilities to be used (statically linked) in all other SCINE modules."
 )
 
 # Set the module path for universal cmake files inclusion
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/dev/cmake)
 
 # Component setup
 include(ComponentSetup)
@@ -20,5 +20,17 @@ if(SCINE_BUILD_TESTS)
   enable_testing()
 endif()
 
+# Set rpaths of shared libraries if generated
+if(APPLE)
+  set(CMAKE_BUILD_RPATH "@loader_path")
+  set(CMAKE_INSTALL_RPATH "@loader_path/../lib;@loader_path")
+elseif(UNIX)
+  set(CMAKE_BUILD_RPATH "\$ORIGIN")
+  set(CMAKE_INSTALL_RPATH "\$ORIGIN/../lib;\$ORIGIN")
+endif()
+
 # Subdirectories
 add_subdirectory(src)
+
+# Documentation
+scine_component_documentation(CoreDocumentation)