Merge branch 'radixio-swig' into 'master'

radixio python bindings

See merge request !113

.gitlab-ci.yml

@@ -8,80 +8,120 @@ stages:
 mac_gcc_testing:
   tags:
     - mac
+  artifacts:
+    reports:
+      junit: build/ctest-results.xml
   script:
     - which git
     - git --version
-    - module load cmake gcc/4.8.5 qt/5.9.1 vtk/8.1.0
+    - module load cmake/3.21.0 gcc/4.8.5 qt/5.9.1 vtk/8.1.0
     - which cmake
     - mkdir build
     - cd build
-    - cmake -DTasmanian_DIR=/opt/tasmanian/6.0 ^
-        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Debug-${CI_BUILD_REF_NAME} ^
-        -DCMAKE_BUILD_TYPE=DEBUG ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -DTPL_ENABLE_VTK=ON ^
-        -Dradix_ENABLE_radixplot=OFF ^
+    - cmake -DTasmanian_DIR=/opt/tasmanian/6.0
+        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Debug-${CI_BUILD_REF_NAME}
+        -DCMAKE_BUILD_TYPE=DEBUG
+        -Dradix_ENABLE_TESTS=ON
+        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON
+        -Dradix_ENABLE_TESTS=ON
+        -DTPL_ENABLE_VTK=ON
+        -Dradix_ENABLE_radixplot=OFF
         -Dradix_ENABLE_radixwidgets=OFF ..
-    - ctest --verbose --output-on-failure ^
-        -D ExperimentalStart ^
-        -D ExperimentalBuild ^
+    - ctest --output-on-failure
+        -D ExperimentalStart
+        -D ExperimentalBuild
         -D ExperimentalTest
+        --output-junit ctest-results.xml
 
 mac_llvm_testing:
   tags:
     - mac
+  artifacts:
+    reports:
+      junit: build/ctest-results.xml
   script:
     - which git
     - git --version
-    - module load cmake qt/5.9.1 vtk/8.1.0
+    - module load cmake/3.21.0 qt/5.9.1 vtk/8.1.0
     - mkdir build
     - cd build
     - which cmake
     - export radix_ENABLE_Fortran=OFF
-    - cmake -DTasmanian_DIR=/opt/tasmanian/6.0 ^
-        -DBUILDNAME=$(uname -s)-LLVM-Debug-${CI_BUILD_REF_NAME} ^
-        -DCMAKE_BUILD_TYPE=DEBUG ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -DTPL_ENABLE_VTK=ON ^
-        -Dradix_ENABLE_radixplot=OFF ^
+    - cmake -DTasmanian_DIR=/opt/tasmanian/6.0
+        -DBUILDNAME=$(uname -s)-LLVM-Debug-${CI_BUILD_REF_NAME}
+        -DCMAKE_BUILD_TYPE=DEBUG
+        -Dradix_ENABLE_TESTS=ON
+        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON
+        -Dradix_ENABLE_TESTS=ON
+        -DTPL_ENABLE_VTK=ON
+        -Dradix_ENABLE_radixplot=OFF
         -Dradix_ENABLE_radixwidgets=OFF ..
-    - ctest --verbose --output-on-failure ^
-        -D ExperimentalStart ^
-        -D ExperimentalBuild ^
+    - ctest --output-on-failure
+        -D ExperimentalStart
+        -D ExperimentalBuild
         -D ExperimentalTest
+        --output-junit ctest-results.xml
+
+linux_python_bindings:
+  tags:
+    - linux
+  artifacts:
+    name: ${CI_JOB_NAME}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_SHA}-python-bindings
+    paths:
+      - lib/
+      - python/
+  script:
+    - which git
+    - git --version
+    - mkdir build
+    - cd build
+    - module load swig/4.0.2 cmake
+    - which cmake
+    - cmake
+        -DCMAKE_INSTALL_PREFIX=${CI_PROJECT_DIR}
+        -DBUILD_SHARED_LIBS=ON
+        -DCMAKE_BUILD_TYPE=Release
+        -Dradix_ENABLE_TESTS=ON
+        -DENABLE_PYTHON_WRAPPERS=ON
+        -Dradix_ENABLE_radixmath=ON
+        -Dradix_ENABLE_radixio=ON
+        -Dradix_ENABLE_TESTS=OFF ..
+    - cmake --build . --target install
 
 linux_gcc_testing:
   tags:
     - linux
+  artifacts:
+    reports:
+      junit: build/ctest-results.xml
   script:
     - which git
     - git --version
     - mkdir build
     - cd build
-    - module load cmake qt/5.9.0 vtk/8.1.0
+    - module load swig/4.0.2 cmake/3.21.0 qt/5.9.0 vtk/8.1.0
     - which cmake
-    - cmake -DTasmanian_DIR=/opt/vendors/tasmanian/6.0 ^
-        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Release-${CI_BUILD_REF_NAME} ^
-        -DCMAKE_BUILD_TYPE=Release ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -DENABLE_PYTHON_WRAPPERS=ON ^
-        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON ^
-        -Dradix_ENABLE_TESTS=ON -DTPL_ENABLE_VTK=ON ^
-        -Dradix_ENABLE_radixplot=OFF ^
+    - cmake -DTasmanian_DIR=/opt/vendors/tasmanian/6.0
+        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Release-${CI_BUILD_REF_NAME}
+        -DBUILD_SHARED_LIBS=ON
+        -DCMAKE_BUILD_TYPE=Release
+        -Dradix_ENABLE_TESTS=ON
+        -DENABLE_PYTHON_WRAPPERS=ON
+        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON
+        -Dradix_ENABLE_TESTS=ON -DTPL_ENABLE_VTK=ON
+        -Dradix_ENABLE_radixplot=OFF
         -Dradix_ENABLE_radixwidgets=OFF ..
-    - ctest --verbose --output-on-failure ^
-        -D ExperimentalStart ^
-        -D ExperimentalBuild ^
-        -D ExperimentalTest
+    - cmake --build .
+    - ctest --output-junit ctest-results.xml
 
 linux_analysis:
   stage: analysis
   tags:
     - linux
+  artifacts:
+    name: ${CI_JOB_NAME}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_SHA}-analysis
+    reports:
+      cobertura: build/coverage.xml
   script:
     - which git
     - git --version
@@ -89,23 +129,28 @@ linux_analysis:
     - cd build
     - module load cmake valgrind
     - which cmake
-    - cmake -DTasmanian_DIR=/opt/vendors/tasmanian/6.0/ ^
-        -DCOVERAGE_EXTRA_FLAGS="-s ${CI_PROJECT_DIR}/googletest -d" ^
-        -DMEMCHECK_COMMAND=$(which valgrind) ^
-        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Debug-${CI_BUILD_REF_NAME} ^
-        -DCMAKE_BUILD_TYPE=DEBUG ^
-        -Dradix_ENABLE_COVERAGE_TESTING=ON ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON ^
-        -Dradix_ENABLE_TESTS=ON ^
-        -Dradix_ENABLE_radixplot=OFF ^
+    - cmake -DTasmanian_DIR=/opt/vendors/tasmanian/6.0/
+        -DCOVERAGE_EXTRA_FLAGS="-s ${CI_PROJECT_DIR}/googletest -d"
+        -DMEMCHECK_COMMAND=$(which valgrind)
+        -DBUILDNAME=$(uname -s)-GCC-4.8.5-Debug-${CI_BUILD_REF_NAME}
+        -DCMAKE_BUILD_TYPE=DEBUG
+        -Dradix_ENABLE_COVERAGE_TESTING=ON
+        -Dradix_ENABLE_TESTS=ON
+        -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON
+        -Dradix_ENABLE_TESTS=ON
+        -Dradix_ENABLE_radixplot=OFF
         -Dradix_ENABLE_radixwidgets=OFF ..
-    - ctest --verbose --output-on-failure^
-        -D ExperimentalStart ^
-        -D ExperimentalBuild ^
-        -D ExperimentalTest ^
-        -D ExperimentalMemCheck ^
-        -D ExperimentalCoverage
+    - ctest --output-on-failure
+        -D ExperimentalStart
+        -D ExperimentalBuild
+        -D ExperimentalTest
+        -D ExperimentalMemCheck
+    - gcovr --filter=".*/radix.*"
+        --xml-pretty
+        --print-summary
+        -o coverage.xml
+        -r $CI_PROJECT_DIR
+  coverage: /^\s*lines:\s*\d+.\d+\%/
   allow_failure: true
 
 linux_openmpi_testing:
@@ -127,7 +172,7 @@ linux_openmpi_testing:
         -Dradix_ENABLE_googletest=ON ^
         -Dradix_ENABLE_radixdl=ON ^
         -Dradix_ENABLE_radixcore=ON ..
-    - ctest --verbose --output-on-failure ^
+    - ctest --output-on-failure ^
         -D ExperimentalStart ^
         -D ExperimentalBuild ^
         -D ExperimentalTest

CMakeLists.txt

@@ -14,6 +14,9 @@ IF (NOT TRIBITS_PROCESSING_PACKAGE)
   SET(radix_ENABLE_CXX11 ON CACHE BOOL "Compile using the C++11 standard" FORCE)
   #SET(USE_QT5 TRUE)
 
+  # Disable SONAME VERSION
+  SET(CMAKE_PLATFORM_NO_VERSIONED_SONAME 1)
+
   # disable generating HTML dependencies webpage and xml files
   SET(${PROJECT_NAME}_DEPS_XML_OUTPUT_FILE OFF CACHE BOOL "")
   # disable TriBITS export system to save time configuring
@@ -32,6 +35,9 @@ IF (NOT TRIBITS_PROCESSING_PACKAGE)
   IF(RADIX_DBC)
      ADD_DEFINITIONS("-DRADIX_DBC=${RADIX_DBC}")
   ENDIF()
+  IF(ENABLE_PYTHON_WRAPPERS AND NOT BUILD_SHARED_LIBS)
+     MESSAGE(FATAL_ERROR "ENABLE_PYTHON_WRAPPERS=ON requires BUILD_SHARED_LIBS=ON")
+  ENDIF()
   #
   # For windows with BUILD_SHARED_LIBS we must use CMAKE_RUNTIME_OUTPUT_DIRECTORY
   # to place all *dll and *exe in the same directory so unit tests will work

README.md

+[![pipeline status](https://code.ornl.gov/jap/radix/badges/master/pipeline.svg)](https://code.ornl.gov/jap/radix/-/commits/master)
+[![coverage report](https://code.ornl.gov/jap/radix/badges/master/coverage.svg)](https://code.ornl.gov/jap/radix/-/commits/master)
+
 # Requirements
 * C compiler. gcc 4.8 tested
 * Git
-* CMake. 2.8.12.2 tested.
+* CMake. 3.8.0 tested.
 
 # Getting Started
 * You will need to save your ssh-key in [code.ornl.gov](https://code.ornl.gov/profile/keys).
@@ -43,3 +46,22 @@ cmake ^
 `../configure.sh or ..\configure.bat`
   * I place the configure script in the build directory as opposed to the build/radix directory because it allows me to delete the build/radix
 directory without removing my script.
+
+# Enable Python Bindings
+Example configuration enabling python bindings
+```
+#!/bin/bash
+# Linux bash file example
+rm -rf CMake*
+cmake \
+ -D CMAKE_INSTALL_PREFIX=`pwd`/install \
+ -D CMAKE_BUILD_TYPE:STRING=RELEASE \
+ -D radix_ENABLE_radixio:BOOL=ON \
+ -D radix_ENABLE_radixmath:BOOL=ON \
+ -D radix_ENABLE_TESTS:BOOL=OFF \
+ -G "Unix Makefiles" \
+ ~/radix
+```
+After configuration, compilation, and installation, you need to add the python directory to PYTHONPATH.
+`export PYTHONPATH=~/build/radix/install/python/`
+

cmake/RadixSWIGPyModules.cmake

@@ -9,6 +9,9 @@ FIND_PACKAGE(PythonLibsFromExe REQUIRED)
 # Find the SWIG package for language bindings
 FIND_PACKAGE(SWIG REQUIRED)
 
+IF(CMAKE_VERSION VERSION_GREATER "3.8.0")
+  include(UseSWIG)
+ENDIF()
 #
 # Ensure that PYTHON wrappers are enabled
 IF (ENABLE_PYTHON_WRAPPERS)
@@ -45,8 +48,10 @@ IF (ENABLE_PYTHON_WRAPPERS)
     SET(SWIG_CXX_FLAGS "${SWIG_CXX_FLAGS} -diag-disable 955")
   ENDIF()
 
-  # Tell SWIG to use modern Python code
-  LIST(APPEND CMAKE_SWIG_FLAGS "-modern" "-noproxydel")
+  IF(CMAKE_VERSION VERSION_LESS "3.8.0")
+    # Tell SWIG to use modern Python code
+    LIST(APPEND CMAKE_SWIG_FLAGS "-modern" "-noproxydel")
+  ENDIF()
 
   # If python version is high enough, add -py3 flag
   IF(PYTHON_VERSION_STRING VERSION_GREATER 3.0)
@@ -122,9 +127,7 @@ IF(ENABLE_PYTHON_WRAPPERS)
 
   # Bug fix: version of CMake older than 2.8.8 don't support the
   # INCLUDE_DIRECTORIES property
-  IF(CMAKE_MAJOR_VERSION      LESS 3
-      AND CMAKE_MINOR_VERSION LESS 9
-      AND CMAKE_PATCH_VERSION LESS 9)
+  IF(CMAKE_VERSION VERSION_LESS "2.8.8")
     INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR})
   ENDIF()
 ELSE()
@@ -173,10 +176,11 @@ FUNCTION(_RADIX_ADD_SWIG)
   SET(SWIG_MODULE_${MODULE_NAME}_EXTRA_DEPS ${DEPENDENCIES} )
 
   # Add the new python target
-  IF("${CMAKE_VERSION}" VERSION_LESS "3.8.0")
+  IF(CMAKE_VERSION VERSION_LESS "3.8.0")
     SWIG_ADD_MODULE(${MODULE_NAME} python
       ${SRC_FILE} ${MKSWIG_EXTRASRC})
   ELSE()
+    SET_PROPERTY(SOURCE ${SRC_FILE} PROPERTY CPLUSPLUS ON)
     SWIG_ADD_LIBRARY(${MODULE_NAME}
       LANGUAGE python
       TYPE MODULE

radixio/CMakeLists.txt

@@ -49,5 +49,10 @@ TRIBITS_ADD_TEST_DIRECTORIES(tests)
 # Add example directory
 TRIBITS_ADD_EXAMPLE_DIRECTORIES(examples)
 
+
+IF(ENABLE_PYTHON_WRAPPERS)
+  ADD_SUBDIRECTORY(python)
+ENDIF()
+
 INSTALL(FILES ${HEADERS} DESTINATION "include/radixio/")
 TRIBITS_SUBPACKAGE_POSTPROCESS()

radixio/decaydb.cc

@@ -13517,7 +13517,7 @@ const std::unordered_map<int, DecayDBEntry>& DecayDb::activations() const
 {
   return mActivation;
 }
-const DecayDBEntry& DecayDb::light_element(const int zaid) const
+const DecayDBEntry& DecayDb::light_element(int zaid) const
 {
   const auto& it = mActivation.find(zaid);
   return it->second;
@@ -13530,7 +13530,7 @@ const std::unordered_map<int, DecayDBEntry>& DecayDb::actinides() const
 {
   return mActinide;
 }
-const DecayDBEntry& DecayDb::actinide(const int zaid) const
+const DecayDBEntry& DecayDb::actinide(int zaid) const
 {
   const auto& it = mActinide.find(zaid);
   return it->second;
@@ -13543,14 +13543,14 @@ const std::unordered_map<int, DecayDBEntry>& DecayDb::fission_products() const
 {
   return mFissionProduct;
 }
-const DecayDBEntry& DecayDb::fission_product(const int zaid) const
+const DecayDBEntry& DecayDb::fission_product(int zaid) const
 {
   const auto& it = mFissionProduct.find(zaid);
   return it->second;
 }
 
-const std::unordered_map<int, DecayDBEntry>::iterator DecayDb::find_decayer(
-    const int zaid)
+std::unordered_map<int, DecayDBEntry>::const_iterator DecayDb::find_decayer(
+    int zaid)
 {
   std::unordered_map<int, DecayDBEntry>::iterator decayer;
   const auto& fpI = mFissionProduct.find(zaid);
@@ -13575,7 +13575,7 @@ const std::unordered_map<int, DecayDBEntry>::iterator DecayDb::find_decayer(
   return decayer;
 }
 
-const DecayDBEntry& DecayDb::find_entry(const int zaid) const
+const DecayDBEntry& DecayDb::find_entry(int zaid) const
 {
   if (mFissionProduct.find(zaid) != mFissionProduct.end())
   {

radixio/decaydb.hh

@@ -10,7 +10,7 @@
 
 namespace radix
 {
-struct DecayDBEntry
+struct RADIX_PUBLIC DecayDBEntry
 {
   /**
    * symbol
@@ -140,16 +140,15 @@ class RADIX_PUBLIC DecayDb
   void set_fission_product_title(const std::string& title);
   std::unordered_map<int, DecayDBEntry>& activations();
   const std::unordered_map<int, DecayDBEntry>& activations() const;
-  const DecayDBEntry& light_element(const int zaid) const;
+  const DecayDBEntry& light_element(int zaid) const;
   std::unordered_map<int, DecayDBEntry>& actinides();
   const std::unordered_map<int, DecayDBEntry>& actinides() const;
-  const DecayDBEntry& actinide(const int zaid) const;
+  const DecayDBEntry& actinide(int zaid) const;
   std::unordered_map<int, DecayDBEntry>& fission_products();
   const std::unordered_map<int, DecayDBEntry>& fission_products() const;
-  const DecayDBEntry& fission_product(const int zaid) const;
-  const std::unordered_map<int, DecayDBEntry>::iterator find_decayer(
-      const int zaid);
-  const DecayDBEntry& find_entry(const int zaid) const;
+  const DecayDBEntry& fission_product(int zaid) const;
+  std::unordered_map<int, DecayDBEntry>::const_iterator find_decayer(int zaid);
+  const DecayDBEntry& find_entry(int zaid) const;
 
 };  // class
 }  // namespace radix

radixio/endian.cc

@@ -139,7 +139,8 @@ bool system_is_big_endian()
 #ifdef _WIN32
   typedef unsigned __int32 uint32_t;
 #endif
-  union {
+  union
+  {
     uint32_t i;
     char c[4];
   } bint = {0x01020304};

radixio/hysplitcdump.cc

@@ -9,25 +9,28 @@ void HysplitCDump::setId(const std::string &id) { mId = id; }
 
 void HysplitCDump::dateTime(int &year, int &month, int &day, int &hour) const
 {
-  year  = mYear;
-  month = mMonth;
-  day   = mDay;
-  hour  = mHour;
+  year  = mTime.year;
+  month = mTime.month;
+  day   = mTime.day;
+  hour  = mTime.hour;
 }
 
+const HysplitTime &HysplitCDump::dateTime() const { return mTime; }
+
 void HysplitCDump::setDateTime(int year, int month, int day, int hour)
 {
-  mYear  = year;
-  mMonth = month;
-  mDay   = day;
-  mHour  = hour;
+  mTime.year     = year;
+  mTime.month    = month;
+  mTime.day      = day;
+  mTime.hour     = hour;
+  mTime.forecast = 0;
 }
 
-int HysplitCDump::forecastHour() const { return mForecastHour; }
+int HysplitCDump::forecastHour() const { return mTime.forecast; }
 
 void HysplitCDump::setForecastHour(int forecastHour)
 {
-  mForecastHour = forecastHour;
+  mTime.forecast = forecastHour;
 }
 
 int HysplitCDump::numLocations() const { return int(mStartLocations.size()); }
@@ -38,22 +41,30 @@ void HysplitCDump::location(int i, int &year, int &month, int &day, int &hour,
 {
   radix_check(i < mStartLocations.size());
   radix_check(i >= 0);
-  size_t i_    = size_t(i);
-  Location loc = mStartLocations[i_];
-  year         = loc.year;
-  month        = loc.month;
-  day          = loc.day;
-  hour         = loc.hour;
-  minutes      = loc.minutes;
-  lat          = loc.lat;
-  lon          = loc.lon;
-  z            = loc.z;
+  size_t i_                  = size_t(i);
+  const HysplitLocation &loc = mStartLocations[i_];
+  year                       = loc.year;
+  month                      = loc.month;
+  day                        = loc.day;
+  hour                       = loc.hour;
+  minutes                    = loc.minutes;
+  lat                        = loc.lat;
+  lon                        = loc.lon;
+  z                          = loc.z;
+}
+
+const HysplitLocation &HysplitCDump::location(int i) const
+{
+  radix_check(i < mStartLocations.size());
+  radix_check(i >= 0);
+  size_t i_ = size_t(i);
+  return mStartLocations[i_];
 }
 
 void HysplitCDump::addLocation(int year, int month, int day, int hour,
                                float lat, float lon, float z, int minutes)
 {
-  Location loc;
+  HysplitLocation loc;
   loc.year    = year;
   loc.month   = month;
   loc.day     = day;
@@ -119,7 +130,7 @@ int HysplitCDump::numStartTimes() const { return int(mStartTimes.size()); }
 void HysplitCDump::addStartTime(int year, int month, int day, int hour,
                                 int minute, int forecast)
 {
-  Time t;
+  HysplitTime t;