7.0.2 (#144)

* use nlohmann string conversion not unsafe cast

* remove non-trivial designated initializers

* add more non-trivial designated initializers.

* now use nlohmann_json as a dependecy. it could be installed via conan by using the option multiple_headers=True

* remove expilicit set fPIC flag

* start to add @SpaceIm [patches](https://github.com/SpaceIm/conan-proposal/tree/daeb91349d83d0b8a53b1292eba28a4af728abd5/patches).

add 0001 expected the patch in methods.cxx. There we have to check if the functions are still used.

0002 already added in [7cd5e10](7cd5e10). There seems to be a problem becaus the json_fwd.hpp is not populated if the requirements is installed via conan.

0003 not yet done.

add 0004

0005 already done in [c5118c7](c5118c7)

add 0006

* Fix pypi deploy (#140)

Adapt CC and CXX flag and python version to meet conditions for pypi deploy

* update setup.py to use nlohman multiple_headers

* Make use of extern template.  Use temporary json.hpp instead of json_fwd.hpp which increase build time signifikant, but is temporary required to make CCI run.

* delete unused functions in methdos.h

* fix: take into account that a string wan't be copied if it passe by value

* Move template specification definition from cxx to header

* Revert "Move template specification definition from cxx to header"

This reverts commit ecb7b1f.

* Try different approach in implementing templates

* Revert "Try different approach in implementing templates"

This reverts commit a11b4bf.

* Use macro version to fix templates on windows

* Correct case-insensitive comparison operator
Add missing quotation mark in setup.py

* remove nlohmann_json:multiple_headers  flag

* Set position independent code cmake variable for pypi

* Set CXX_VISIBILTY_PRESET to hidden, should fix #141

* Change CMAKE_CXX_VISIBILITY_PRESET only for static library, otherwise clang won't compile

* Catch negative values for IonizBetheBlochRossi::InelCorrection to avoid negative integrand values. This should avoid sporadic qags-warnings when creating ionization interpolation tables.

* Revert "Catch negative values for IonizBetheBlochRossi::InelCorrection to avoid negative integrand values. This should avoid sporadic qags-warnings when creating ionization interpolation tables."

This reverts commit 273d1c0.

* Change `build_XXX` conan options to `with_XXX` as recommended by conan developers

Co-authored-by: Maximilian Sackel <[email protected]>

.travis.yml

@@ -35,7 +35,7 @@ jobs:
     - os: linux
       dist: focal
       name: Linux gcc 7
-      python: 3.8
+      python: 3.9
       addons:
         apt:
           sources:
@@ -49,7 +49,7 @@ jobs:
     - os: linux
       dist: focal
       name: Linux gcc 10
-      python: 3.8
+      python: 3.9
       addons:
         apt:
           sources:
@@ -63,7 +63,7 @@ jobs:
     - os: linux
       dist: focal
       name: Linux clang 6.0
-      python: 3.8
+      python: 3.9
       addons:
         apt:
           sources:
@@ -78,7 +78,7 @@ jobs:
     - os: linux
       dist: focal
       name: Linux clang 10
-      python: 3.8
+      python: 3.9
       addons:
         apt:
           sources:
@@ -96,7 +96,7 @@ install:
   - conan profile new default --detect
   - conan profile update settings.compiler.libcxx=libstdc++11 default
   - mkdir build && cd build
-  - conan install .. -o build_testing=True --build=missing
+  - conan install .. -o with_testing=True -o nlohmann_json:multiple_headers=True --build=missing
   - conan build ..
   - echo "Searching for test file path"
   - echo $(pwd)
@@ -122,7 +122,7 @@ deploy:
     on:
       repo: tudo-astroparticlephysics/PROPOSAL
       tags: true
-      condition: $CXX = g++-10
+      condition: $CXX = g++
   - provider: pypi
     username: "__token__"
     skip_existing: true
@@ -134,4 +134,4 @@ deploy:
       repo: tudo-astroparticlephysics/PROPOSAL
       tags: true
       branch: master
-      condition: $TRAVIS_PYTHON_VERSION = "3.8"
+      condition: $TRAVIS_PYTHON_VERSION = "3.9"

CMakeLists.txt

@@ -31,6 +31,11 @@ endif()
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+# removes tons of compiler warnings on clang (issue #141). there is probably a cleaner solution.
+if(NOT BUILD_SHARED_LIBS)
+	set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+endif()
+
 option(BUILD_PYTHON "build python interface" OFF)
 option(BUILD_EXAMPLE "build example" OFF)
 option(BUILD_DOCUMENTATION "build documentation" OFF)

INSTALL.md

@@ -31,16 +31,16 @@ $ cd PROPOSAL && mkdir build && cd build
 Use conan to prepare all dependencies. You can pass additional options to conan.
 
 ```sh             
-$ conan install .. -o build_python=True	# other optional dependencies
+$ conan install .. -o with_python=True	# other optional dependencies
 ```
 
 The following options can be passed to `conan install`:
 
-| Option.               | default | Description                                   |
-| --------------------- | ------- | --------------------------------------------- |
-| `build_python`        | False   | Build and install python interface.           |
-| `build_testing`       | False   | Build TestFiles for Python.                   |
-| `build_documentation` | False   | Build doxygen documentation of C++ code (WIP) |
+| Option.              | default | Description                                   |
+| -------------------- | ------- | --------------------------------------------- |
+| `with_python`        | False   | Build and install python interface.           |
+| `with_testing`       | False   | Build TestFiles for Python.                   |
+| `with_documentation` | False   | Build doxygen documentation of C++ code (WIP) |
 
 Build and install PROPOSAL. You may require root privileges when installing, depending on the installation location:
 

conanfile.py

@@ -13,16 +13,16 @@ class PROPOSALConan(ConanFile):
     options = {
         "shared": [True, False],
         "fPIC": [True, False],
-        "build_testing": [True, False],
-        "build_python": [True, False],
-        "build_documentation": [True, False],
+        "with_testing": [True, False],
+        "with_python": [True, False],
+        "with_documentation": [True, False],
     }
     default_options = {
         "shared": False,
         "fPIC": True,
-        "build_testing": False,
-        "build_python": False,
-        "build_documentation": False,
+        "with_testing": False,
+        "with_python": False,
+        "with_documentation": False,
     }
     generators = "cmake_find_package", "cmake_paths"
     _cmake = None
@@ -34,20 +34,21 @@ def config_options(self):
     def requirements(self):
         self.requires("cubicinterpolation/0.1.4")
         self.requires("spdlog/1.8.2")
-        if self.options.build_python:
+        self.requires("nlohmann_json/3.9.1")
+        if self.options.with_python:
             self.requires("pybind11/2.6.2")
-        if self.options.build_testing:
+        if self.options.with_testing:
             self.requires("gtest/1.10.0")
-        if self.options.build_documentation:
+        if self.options.with_documentation:
             self.requires("doxygen/1.8.20")
 
     def _configure_cmake(self):
         if self._cmake:
             return self._cmake
         self._cmake = CMake(self)
-        self._cmake.definitions["BUILD_TESTING"] = self.options.build_testing
-        self._cmake.definitions["BUILD_PYTHON"] = self.options.build_python
-        self._cmake.definitions["BUILD_DOCUMENTATION"] = self.options.build_documentation
+        self._cmake.definitions["BUILD_TESTING"] = self.options.with_testing
+        self._cmake.definitions["BUILD_PYTHON"] = self.options.with_python
+        self._cmake.definitions["BUILD_DOCUMENTATION"] = self.options.with_documentation
         self._cmake.configure()
         return self._cmake
 

conanfile.txt

@@ -0,0 +1 @@
+

setup.cfg

@@ -10,6 +10,7 @@ classifiers=
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
     Programming Language :: Python :: Implementation :: CPython
     Topic :: Scientific/Engineering :: Physics
     Development Status :: 5 - Production/Stable

setup.py

@@ -73,8 +73,8 @@ def build_cmake(self, ext):
                 'conan',
                 'install',
                 ext.source_dir,
-                '-o build_python=True',
-                '-o build_testing=False',
+                '-o with_python=True',
+                '-o with_testing=False'
             ]
             sp.run(conan_call, cwd=self.build_temp, check=True)
             os.remove(self.build_temp + "/Findpybind11.cmake") # bugfix
@@ -85,6 +85,7 @@ def build_cmake(self, ext):
             '-DCMAKE_BUILD_TYPE=' + cfg,
             '-DBUILD_TESTING=OFF',
             '-DBUILD_PYTHON=ON',
+            '-DCMAKE_POSITION_INDEPENDENT_CODE=TRUE',
             '-DBUILD_EXAMPLE=OFF',
             '-DPYTHON_EXECUTABLE=' + sys.executable,
             '-DPYTHON_LIBRARY=' + str(python_lib),

src/PROPOSAL/CMakeLists.txt

@@ -3,9 +3,11 @@ include(GNUInstallDirs)
 add_library(PROPOSAL)
 add_library(PROPOSAL::PROPOSAL ALIAS PROPOSAL)
 
-set_target_properties(PROPOSAL PROPERTIES
-    POSITION_INDEPENDENT_CODE ON
-    )
+if(MSVC)
+    target_compile_options(PROPOSAL PRIVATE "/bigobj" "/EHsc")
+elseif(MINGW)
+    target_compile_options(PROPOSAL PRIVATE "-Wa,-mbig-obj")
+endif()
 
 target_include_directories(PROPOSAL PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
@@ -15,13 +17,15 @@ target_include_directories(PROPOSAL PUBLIC
 
 find_package(CubicInterpolation REQUIRED)
 find_package(spdlog REQUIRED)
+find_package(nlohmann_json REQUIRED)
 
 add_subdirectory(PROPOSAL)
 add_subdirectory(detail)
 
 target_link_libraries(PROPOSAL
     CubicInterpolation::CubicInterpolation
     spdlog::spdlog
+    nlohmann_json::nlohmann_json
     )
 
 install(TARGETS PROPOSAL EXPORT PROPOSALTargets

src/PROPOSAL/Config.cmake.in

@@ -6,5 +6,6 @@ endif()
 
 find_package(CubicInterpolation REQUIRED)
 find_package(spdlog REQUIRED)
+find_package(nlohmann_json REQUIRED)
 
 include ("${CMAKE_CURRENT_LIST_DIR}/PROPOSALTargets.cmake")

src/PROPOSAL/PROPOSAL/EnergyCutSettings.h

@@ -28,7 +28,7 @@
 
 #pragma once
 
-#include "PROPOSAL/json.hpp"
+#include <nlohmann/json.hpp>
 #include <ostream>
 
 namespace PROPOSAL {

src/PROPOSAL/PROPOSAL/Propagator.h

@@ -1,7 +1,7 @@
 #pragma once
 
 #include "PROPOSAL/Secondaries.h"
-#include "PROPOSAL/json.hpp"
+#include <nlohmann/json.hpp>
 #include <unordered_map>
 
 namespace PROPOSAL {

src/PROPOSAL/PROPOSAL/crosssection/CrossSection.h

@@ -77,7 +77,7 @@ namespace detail {
         using dndx_map_t
             = std::unordered_map<size_t, std::tuple<double, dndx_ptr_t>>;
         if (cut)
-            if (cut->GetEcut() == INF and cut->GetVcut() == 1)
+            if (cut->GetEcut() == INF && cut->GetVcut() == 1)
                 return std::unique_ptr<dndx_map_t>();
         auto calc = make_dndx(interpol, param, p, m, cut, hash);
         auto dndx_map = std::make_unique<dndx_map_t>();
@@ -95,7 +95,7 @@ namespace detail {
             = std::unordered_map<size_t, std::tuple<double, dndx_ptr_t>>;
         if (cut) // TODO: is this branch realy necessary, why is a dndx created
                  // for these settings?
-            if (cut->GetEcut() == INF and cut->GetVcut() == 1)
+            if (cut->GetEcut() == INF && cut->GetVcut() == 1)
                 return std::unique_ptr<dndx_map_t>();
         auto dndx_map = std::make_unique<dndx_map_t>();
         for (auto& c : m.GetComponents()) {
@@ -335,7 +335,7 @@ class CrossSection : public CrossSectionBase {
     inline double CalculatedEdx(double energy) override
     {
         auto loss = 0.;
-        if (not dedx)
+        if (!dedx)
             return loss;
         // will produce no working in cpp17
         // for (auto& [weight, calc] : *dedx)
@@ -349,7 +349,7 @@ class CrossSection : public CrossSectionBase {
     inline double CalculatedE2dx(double energy) override
     {
         auto loss = 0.;
-        if (not de2dx)
+        if (!de2dx)
             return loss;
         // will produce no working in cpp17
         // for (auto& [weight, calc] : *de2dx)

src/PROPOSAL/PROPOSAL/crosssection/CrossSectionDNDX/CrossSectionDNDXInterpolant.h

@@ -39,22 +39,27 @@ std::function<double(double, double, double)> retransform_loss<Param>::func
 namespace crosssection {
     struct ComptonKleinNishina;
 }
-template <>
+
+#ifndef CROSSSECTIONDNDXINTERPOLANT_INSTANTIATION
+extern template
 std::function<double(double, double, double)> transform_loss<crosssection::ComptonKleinNishina>::func;
+#endif
 
-template <>
+#ifndef CROSSSECTIONDNDXINTERPOLANT_INSTANTIATION
+extern template
 std::function<double(double, double, double)> retransform_loss<crosssection::ComptonKleinNishina>::func;
+#endif
 
 template <typename T1, typename... Args>
 auto build_dndx_def(T1 const& param, ParticleDef const& p, Args... args)
 {
     auto dndx = std::make_shared<CrossSectionDNDXIntegral>(param, p, args...);
     auto v_lim = AxisBuilderDNDX::v_limits { 0, 1,
         InterpolationSettings::NODES_DNDX_V };
-    auto energy_lim
-        = AxisBuilderDNDX::energy_limits { param.GetLowerEnergyLim(p),
-              InterpolationSettings::UPPER_ENERGY_LIM,
-              InterpolationSettings::NODES_DNDX_E };
+    auto energy_lim = AxisBuilderDNDX::energy_limits();
+    energy_lim.low = param.GetLowerEnergyLim(p);
+    energy_lim.up = InterpolationSettings::UPPER_ENERGY_LIM;
+    energy_lim.nodes = InterpolationSettings::NODES_DNDX_E ;
     auto axis_builder = AxisBuilderDNDX(v_lim, energy_lim);
     axis_builder.refine_definition_range(
         [dndx](double E) { return dndx->Calculate(E); });

src/PROPOSAL/PROPOSAL/crosssection/Factories/AnnihilationFactory.h

@@ -1,5 +1,5 @@
 #pragma once
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 #include <memory>
 
 namespace PROPOSAL {

src/PROPOSAL/PROPOSAL/crosssection/Factories/BremsstrahlungFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/ComptonFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/EpairProductionFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/IonizationFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/MupairProductionFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/PhotoPairProductionFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/PhotonuclearFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/crosssection/Factories/WeakInteractionFactory.h

@@ -1,6 +1,6 @@
 #pragma once
 #include <memory>
-#include "PROPOSAL/json_fwd.hpp"
+#include <nlohmann/json.hpp> // TODO: Use json_fwd.hpp as soon as https://github.com/conan-io/conan-center-index/pull/5149 is merged
 
 namespace PROPOSAL {
     struct CrossSectionBase;

src/PROPOSAL/PROPOSAL/density_distr/density_distr.h

@@ -30,7 +30,7 @@
 #include <functional>
 #include <string>
 #include "PROPOSAL/math/Cartesian3D.h"
-#include "PROPOSAL/json.hpp"
+#include <nlohmann/json.hpp>
 
 namespace PROPOSAL {
 class Axis {
@@ -147,4 +147,4 @@ class Density_distr {
 
 namespace PROPOSAL {
    std::shared_ptr<Density_distr> CreateDensityDistribution(const nlohmann::json&);
-} // namespace PROPOSAL
+} // namespace PROPOSAL

src/PROPOSAL/PROPOSAL/geometry/Box.h

@@ -30,7 +30,7 @@
 #pragma once
 
 #include "PROPOSAL/geometry/Geometry.h"
-#include "PROPOSAL/json.hpp"
+#include <nlohmann/json.hpp>
 
 
 namespace PROPOSAL {