Update to v3.7.7

.clang-format

@@ -4,7 +4,7 @@ BasedOnStyle: LLVM
 # To see all the default values of the base style, run: clang-format --style=LLVM --dump-config
 
 Language: Cpp
-Standard: Cpp11
+Standard: c++14
 ColumnLimit: 120
 IndentWidth: 4
 
@@ -17,6 +17,7 @@ AllowShortBlocksOnASingleLine: true
 AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: Empty
 AllowShortLambdasOnASingleLine: Inline
+AllowShortLoopsOnASingleLine: false
 AlwaysBreakTemplateDeclarations: MultiLine
 BinPackArguments: false
 BraceWrapping:

.clang-tidy

@@ -0,0 +1,6 @@
+---
+Checks: '-*,boost-*,bugprone-argument-comment,bugprone-assert-side-effect,bugprone-bad-signal-to-kill-thread,bugprone-bool-pointer-implicit-conversion,bugprone-dangling-handle,bugprone-dynamic-static-initializers,bugprone-fold-init-type,bugprone-forward-declaration-namespace,bugprone-forwarding-reference-overload,bugprone-inaccurate-erase,bugprone-incorrect-roundings,bugprone-infinite-loop,bugprone-integer-division,bugprone-lambda-function-name,bugprone-macro-repeated-side-effects,bugprone-misplaced-*,bugprone-move-forwarding-reference,bugprone-multiple-statement-macro,bugprone-not-null-terminated-result,bugprone-parent-virtual-call,bugprone-posix-return,bugprone-signed-char-misuse,bugprone-sizeof-*,bugprone-string-*,bugprone-suspicious-*,bugprone-swapped-arguments,bugprone-terminating-continue,bugprone-throw-keyword-missing,bugprone-too-small-loop-variable,bugprone-undefined-memory-manipulation,bugprone-undelegated-constructor,bugprone-unhandled-self-assignment,bugprone-unused-return-value,bugprone-use-after-move,bugprone-virtual-near-miss,misc-definitions-in-headers,misc-misplaced-const,misc-new-delete-overloads,misc-non-copyable-objects,misc-redundant-expression,misc-static-assert,misc-unconventional-assign-operator,misc-uniqueptr-reset-release,misc-unused-alias-decls,misc-unused-using-decls,modernize-avoid-bind,modernize-concat-nested-namespaces,modernize-deprecated-*,modernize-loop-convert,modernize-make-*,modernize-raw-string-literal,modernize-redundant-void-arg,modernize-replace-*,modernize-return-braced-init-list,modernize-shrink-to-fit,modernize-unary-static-assert,modernize-use-auto,modernize-use-bool-literals,modernize-use-emplace,modernize-use-equals-*,modernize-use-nodiscard,modernize-use-noexcept,modernize-use-nullptr,modernize-use-override,modernize-use-uncaught-exceptions,modernize-use-using'
+WarningsAsErrors: 'bugprone-*'
+FormatStyle:     none
+CheckOptions:
+...

.gitignore

@@ -56,3 +56,4 @@ cmake_install.cmake
 /*.py
 /*.sh
 /*.gpl
+/**/*.egg-info

CHANGELOG.md

@@ -0,0 +1,120 @@
+# Kassiopeia Changelog
+
+<!--
+Please update the version info when a new Kasper release is published.
+
+When bumping a module version, also provide a date to indicate the last update.
+-->
+
+## Current version
+
+The current Kassiopeia version is v3.7 released on May 1, 2020.
+The latest update v3.7.7 was released on January 13, 2021.
+
+Module versions:
+* **Kassiopeia**       3.7.5 (Jan 13, 2021)
+* **KEMField**         3.7.5 (Jan 13, 2021)
+* **KGeoBag**          3.7.5 (Jan 13, 2021)
+* **Kommon**           1.4.1 (Jan 13, 2021)
+* **UnitTest**         0.2.5 (Nov 30, 2020)
+
+
+<!--
+The changelog files can be updated by the script `gen-changelog.sh` in the `Scripts` folder.
+Please update the release notes below if a new release is published. Make sure to bump any relevant version numbers.
+-->
+
+## Changes in v3.7.7
+
+Kassiopeia v3.7.7 was released on January 13, 2021.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.7)
+
+[*View Changelog*](Changelog/changes-from-v3.7.6-to-v3.7.7.md)
+
+
+## Changes in v3.7.6
+
+Kassiopeia v3.7.6 was released on August 24, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.6)
+
+[*View Changelog*](Changelog/changes-from-v3.7.5-to-v3.7.6.md)
+
+
+## Changes in v3.7.5
+
+Kassiopeia v3.7.5 was released on July 24, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.5)
+
+[*View Changelog*](Changelog/changes-from-v3.7.4-to-v3.7.5.md)
+
+
+## Changes in v3.7.4
+
+Kassiopeia v3.7.4 was released on June 19, 2020. Happy Juneteenth!
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.4)
+
+[*View Changelog*](Changelog/changes-from-v3.7.3-to-v3.7.4.md)
+
+
+## Changes in v3.7.3
+
+Kassiopeia v3.7.3 was released on June 9, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.3)
+
+[*View Changelog*](Changelog/changes-from-v3.7.2-to-v3.7.3.md)
+
+
+## Changes in v3.7.2
+
+Kassiopeia v3.7.2 was released on May 7, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.2)
+
+[*View Changelog*](Changelog/changes-from-v3.7.1-to-v3.7.2.md)
+
+
+## Changes in v3.7.1
+
+Kassiopeia v3.7.1 was released on May 4, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.1)
+
+[*View Changelog*](Changelog/changes-from-v3.7.0-to-v3.7.1.md)
+
+
+## Changes in v3.7.0
+
+Kassiopeia v3.7.0 was released on May 1, 2020.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.7.0)
+
+[*View Changelog*](Changelog/changes-from-v3.6.1-to-v3.7.0.md)
+
+
+## Changes in v3.6.1
+
+Kassiopeia v3.6.1 was released on January 7, 2019.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.6.1)
+
+[*View Changelog*](Changelog/changes-from-v3.5.0-to-v3.6.1.md)
+
+
+## Changes in v3.5.0
+
+Kassiopeia v3.5.0 was released on February 16, 2018.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.5.0)
+
+[*View Changelog*](Changelog/changes-from-v3.4.0-to-v3.5.0.md)
+
+
+## Changes in v3.4.0
+
+Kassiopeia v3.4.0 was released on October 6, 2017.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.4.0)
+
+[*View Changelog*](Changelog/changes-from-v3.1.0-to-v3.4.0.md)
+
+
+## Changes in v3.1.0
+
+Kasper v3.1.0 was released on Jan 14, 2015.
+[Details](https://github.com/KATRIN-Experiment/Kassiopeia/releases/tag/v3.1.0)
+
+This is the first tagged release of the Kassiopeia software.

CMakeLists.txt

@@ -4,17 +4,26 @@ cmake_minimum_required( VERSION ${CMAKE_MINIMUM_VERSION} )
 # project version
 set(KASPER_VERSION_MAJOR 3)
 set(KASPER_VERSION_MINOR 7)
-set(KASPER_VERSION_PATCH 5)
+set(KASPER_VERSION_PATCH 7)
 set(KASPER_VERSION "${KASPER_VERSION_MAJOR}.${KASPER_VERSION_MINOR}.${KASPER_VERSION_PATCH}")
 
 #project( Kasper VERSION ${KASPER_VERSION} )
 project( Kasper )
 
+# Silently try to find major dependencies. This list is not be complete!
+# (Somehow, CMake behaves better if this is done in the root scope before adding modules...)
+find_package(Boost QUIET)
+find_package(HDF5 COMPONENTS CXX QUIET)
+find_package(MPI QUIET)
+find_package(ROOT QUIET)
+find_package(VTK QUIET)
+
 set( BUILD_SHARED_LIBS ON )
 
-set( CMAKE_CXX_STANDARD 14 )
+set( CMAKE_CXX_STANDARD 14 CACHE STRING "The C++ standard whose features are requested to build this target" )
 set( CMAKE_CXX_STANDARD_REQUIRED ON )
 set( CMAKE_CXX_EXTENSIONS OFF )
+set( CMAKE_EXPORT_COMPILE_COMMANDS ON )
 
 # Additional compiler version checks, see https://en.cppreference.com/w/cpp/compiler_support
 if( CMAKE_SYSTEM_NAME STREQUAL "Linux" )
@@ -205,7 +214,7 @@ if( BUILD_KGEOBAG )
 endif( BUILD_KGEOBAG )
 
 # Build modules
-# The order seems to matter! Please place dependent modules at the end.
+# NOTE: The order matters! Please place dependent modules at the end.
 
 if( BUILD_KOMMON )
     add_subdirectory( Kommon )
@@ -227,10 +236,52 @@ if( BUILD_UNIT_TESTS )
     add_subdirectory( UnitTest )
 endif()
 
-#add_subdirectory( Documentation )
+add_subdirectory( Documentation )
+
+# Print some warnings
+
+if( BUILD_KASSIOPEIA OR BUILD_KEMFIELD OR BUILD_KGEOBAG )
+    if( NOT KASPER_USE_VTK )
+        message(WARNING "*** Building without VTK support ***\n"
+            "You won't be able to use 3D visualization tools. Set KASPER_USE_VTK=ON to change this.")
+    endif( NOT KASPER_USE_VTK )
+endif()
+
+if( BUILD_KASSIOPEIA )
+    if( NOT KASPER_USE_ROOT )
+        message(WARNING "*** Building without ROOT support ***\n"
+            "You won't be able to read/write ROOT files. Set KASPER_USE_ROOT=ON to change this.")
+    endif( NOT KASPER_USE_ROOT )
+endif()
+
+if( KASPER_EXPERIMENTAL )
+    message(WARNING "*** Building with experimental code ***\n"
+    "Experimental code is not fully tested and shouldn't be used unless you know what you're doing. Set KASPER_EXPERIMENTAL=OFF to change this.")
+endif( KASPER_EXPERIMENTAL )
+
+if( KASPER_DEPRECATED )
+    message(WARNING "*** Building with deprecated code ***\n"
+    "Deprecated code is no longer maintained and shouldn't be used. Set KASPER_DEPRECATED=OFF to change this.")
+endif( KASPER_DEPRECATED )
+
+get_filename_component(CMAKE_MAKE_PROGRAM_NAME ${CMAKE_MAKE_PROGRAM} NAME)
+message("\n   Build was configured. Run `${CMAKE_MAKE_PROGRAM_NAME}` to start the build,\n"
+    "   `${CMAKE_MAKE_PROGRAM_NAME} install` to install in ${KASPER_INSTALL_DIR},\n"
+    "   or `${CMAKE_MAKE_PROGRAM_NAME} doc` to generate documentation.\n")
+
+# Install common project files
 
 install( EXPORT KasperTargets DESTINATION ${CMAKE_INSTALL_DIR}/${PROJECT_NAME} )
 
+configure_file( KasperVersion.h.in ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.h @ONLY )
+install( FILES ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.h DESTINATION ${INCLUDE_INSTALL_DIR} )
+
+configure_file( KasperVersion.json.in ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.json @ONLY )
+install( FILES ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.json DESTINATION ${CONFIG_INSTALL_DIR} )
+
+configure_file( KasperVersion.xml.in ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.xml @ONLY )
+install( FILES ${CMAKE_CURRENT_BINARY_DIR}/KasperVersion.xml DESTINATION ${CONFIG_INSTALL_DIR} )
+
 configure_file( kasperenv.sh.in ${CMAKE_CURRENT_BINARY_DIR}/kasperenv.sh @ONLY )
 configure_file( create_kasper_user_directory.sh.in ${CMAKE_CURRENT_BINARY_DIR}/create_kasper_user_directory.sh @ONLY )
 install( PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/kasperenv.sh ${CMAKE_CURRENT_BINARY_DIR}/create_kasper_user_directory.sh DESTINATION ${BIN_INSTALL_DIR} )

CONTRIBUTING.md

@@ -0,0 +1,97 @@
+# Kassiopeia
+
+See the [README](README.md) file for basic instructions about setting up Kasper
+and creating the necessary accounts.
+
+
+ Kassiopeia: Simulation of electric and magnetic fields and particle tracking
+==============================================================================
+
+
+ Joining the developers
+------------------------
+
+1.  The primary platform for development is a private GitLab repository that
+    is used internally by the KATRIN collaboration. The Kassiopeia version
+    on GitHub that is publicly available contains a reduced set of Kasper
+    modules without references to KATRIN-specific elements.
+
+    1.  External users of the software are welcome to contribute to its
+        development. Please use the features available on the GitHub
+        platform to update any part of the code. It is suggested to create
+        a personal fork of the code repository, from which pull requests
+        can be initiated.
+
+    2.  Pull requests on GitHub will be reviewed by the core developers,
+        and changes may be required before the updated code can be merged
+        into the main branch. GitHub will be used for all communication.
+
+    3.  Pull requests that were merged into the main branch will also be
+        propagated upstream into the main repository on the KATRIN GitLab.
+        Any updates to the public Kassiopeia version thus become part
+        of the mainline source code, and will benefit both the KATRIN
+        collaboration as well as external users of the software.
+
+2.  Please note that the software is still "work in progress" and it
+    cannot be guaranteed that there are no bugs or other issues.
+
+    1.  To let the core developers know about any problems when building
+        or running the software, please use the GitHub issue tracking
+        system.
+
+3.  To contact the core developers, it is best to use GitHub's features
+    of communication. Alternatively, the following mailing list can
+    be used: katrin-kasper [at] lists.kit.edu
+
+
+ Kasper code structure
+-----------------------
+
+1.  The Kasper source code consists of several modules that implement
+    specific functionality, such as particle tracking or data analysis.
+    The modules are configured by the CMake build system and can be
+    activated individually. Note that although the modules are located
+    in independent directories, they often depend on other Kasper modules.
+    The CMake configuration will take care of activating any necessary
+    dependencies.
+
+    1.  See the [CHANGELOG](CHANGELOG.md) for a list of Kasper modules,
+        their current software versions and recent changes.
+
+    2.  The graph below outlines the module dependencies. Kasper modules
+        that are referenced by other modules are shown as blue boxes,
+        unreferenced modules as red boxes. Code directories that are part
+        of a Kasper module, but have additional dependencies are shown
+        as black circles.
+
+        ![module-deps-graph](module-deps-graph.png "Kasper module dependencies")
+
+    3.  Each module, and thus the Kasper software as a whole, also has
+        dependencies on external packages, such as the ROOT library.
+        See the [README](README.md) for details and a list of required
+        and optional dependencies.
+
+        The graph below outlines the package dependencies. Kasper modules
+        are shown as blue or red boxes, as above. External packages are
+        shown as blue circles. Required dependencies to a package are
+        indicated by a solid line, and optional dependencies by a dashed
+        line. Kasper code directories with additional dependencies are again
+        shown as black circles.
+
+        ![package-deps-graph](package-deps-graph.png "Kasper package dependencies")
+
+    4.  All code in Kasper should follow a consistent coding style. The
+        style-file [.clang-format](.clang-format) is provided for automated
+        code formatting using the clang-format tool. Developers should make
+        sure that any merged code is formatted correctly.
+
+    5.  Code documentation is still unfinished at this point. We are using
+        Doxygen for automated generation of documentation files, which can
+        be enabled in CMake. See the [Documentation/README](Documentation/README)
+        for details.
+
+    5.  A small set of helper scripts is located in the [Scripts](Scripts/)
+        directory. These are intended to support code formatting and
+        automated cleanup (clang-format and clang-tidy), help with code
+        profiling (gperftools), produce dependency graphs (see above),
+        generate documentation and update the Changelog.

Changelog/changes-from-v3.1.0-to-v3.4.0.md

@@ -0,0 +1,24 @@
+# Kasper Changelog
+
+## Changes from v3.1.0 (2015-01-14) to v3.4.0 (2017-10-06)
+### KEMField
+- **2017-10-06:** Update to Kassiopeia 3.4.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//6db81dbc8c7804b8ea56c90bebcedd9f98acb316)
+- **2016-12-06:** fix linking issues with VTK enabled on OSX [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//614862d1916683e1dbe7f664ebb5b0fd15904f21)
+- **2016-12-01:** Update to Kassiopeia 3.3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//56d388dc8fac3017d55cf59a273a9d71e2f59f45)
+- **2016-12-01:** remove use of _GLIBCXX_USE_NOEXCEPT for osx [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//fe42e171c30d361a442e64423b77d44491aecadb)
+- **2016-12-01:** Fixed underlinked libraries in KEMField [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//5c82a197412a7e148b98239ec7c5fd85dfa90cff)
+- **2016-01-28:** Update to Kassiopeia 3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//b36c1fbfd54ab323f303a92c0f713862a4792462)
+### KGeoBag
+- **2017-10-06:** Update to Kassiopeia 3.4.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//6db81dbc8c7804b8ea56c90bebcedd9f98acb316)
+- **2016-12-01:** Update to Kassiopeia 3.3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//56d388dc8fac3017d55cf59a273a9d71e2f59f45)
+- **2016-01-28:** Update to Kassiopeia 3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//b36c1fbfd54ab323f303a92c0f713862a4792462)
+### Kassiopeia
+- **2017-10-06:** Update to Kassiopeia 3.4.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//6db81dbc8c7804b8ea56c90bebcedd9f98acb316)
+- **2016-12-01:** Update to Kassiopeia 3.3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//56d388dc8fac3017d55cf59a273a9d71e2f59f45)
+- **2016-12-01:** Fixed underlinked library in Kassiopeia [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//57bb06d9d66343e58732131e7ced8dee9d8e59db)
+- **2016-01-28:** Update to Kassiopeia 3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//b36c1fbfd54ab323f303a92c0f713862a4792462)
+### Kommon
+- **2017-10-06:** Update to Kassiopeia 3.4.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//6db81dbc8c7804b8ea56c90bebcedd9f98acb316)
+- **2016-12-06:** fix linking issues with VTK enabled on OSX [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//614862d1916683e1dbe7f664ebb5b0fd15904f21)
+- **2016-12-01:** Update to Kassiopeia 3.3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//56d388dc8fac3017d55cf59a273a9d71e2f59f45)
+- **2016-01-28:** Update to Kassiopeia 3.2 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//b36c1fbfd54ab323f303a92c0f713862a4792462)

Changelog/changes-from-v3.4.0-to-v3.5.0.md

@@ -0,0 +1,11 @@
+# Kasper Changelog
+
+## Changes from v3.4.0 (2017-10-06) to v3.5.0 (2018-02-16)
+### KEMField
+- **2018-02-16:** Update to Kassiopeia 3.5.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//82510642da1c01fc6fd0eafbe8a69be5d734cf8b)
+### KGeoBag
+- **2018-02-16:** Update to Kassiopeia 3.5.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//82510642da1c01fc6fd0eafbe8a69be5d734cf8b)
+### Kassiopeia
+- **2018-02-16:** Update to Kassiopeia 3.5.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//82510642da1c01fc6fd0eafbe8a69be5d734cf8b)
+### Kommon
+- **2018-02-16:** Update to Kassiopeia 3.5.0 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//82510642da1c01fc6fd0eafbe8a69be5d734cf8b)

Changelog/changes-from-v3.5.0-to-v3.6.1.md

@@ -0,0 +1,11 @@
+# Kasper Changelog
+
+## Changes from v3.5.0 (2018-02-16) to v3.6.1 (2019-01-07)
+### KEMField
+- **2019-01-07:** Update to Kassiopeia 3.6.1 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//037d938147d14afdf1e0c2c545862a896397e821)
+### KGeoBag
+- **2019-01-07:** Update to Kassiopeia 3.6.1 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//037d938147d14afdf1e0c2c545862a896397e821)
+### Kassiopeia
+- **2019-01-07:** Update to Kassiopeia 3.6.1 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//037d938147d14afdf1e0c2c545862a896397e821)
+### Kommon
+- **2019-01-07:** Update to Kassiopeia 3.6.1 [*(view commit)*](https://github.com/KATRIN-Experiment/Kassiopeia/commit//037d938147d14afdf1e0c2c545862a896397e821)