Feature/speed optimizations

.github/workflows/ContinuousIntegration.yml

@@ -2,7 +2,10 @@
 name: Continuous Integration
 
 # This workflow is triggered on pushes and pull requests to the repository.
+# This workflow will also run each Monday on the default branch (i.e. master)
 on:
+  schedule:
+    - cron: '0 0 * * 1'
   push:
     branches: '**'
   pull_request:
@@ -14,10 +17,16 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-18.04, macos-10.15 ]
-        cxx: [ g++-9, clang++ ]
+        cxx: [ clang++, g++-9 ]
         build_type: [ Debug, Release ]
 
     steps:
+    - name: Install hdf5 libraries for Linux
+      if: matrix.os == 'ubuntu-18.04'
+      run: sudo apt-get install libhdf5-dev
+    - name: Install hdf5 libraries for MacOS
+      if: matrix.os == 'macos-10.15'
+      run: brew install hdf5
     - name: which CXX
       run: |
         which ${{matrix.cxx}}

CMakeLists.txt

@@ -42,6 +42,7 @@ target_link_libraries( GNDStk
     INTERFACE catch-adapter
     INTERFACE pugixml-adapter
     INTERFACE nlohmann_json::nlohmann_json
+    INTERFACE HighFive
     )
 
 add_executable( json2class.exe
@@ -57,28 +58,162 @@ target_link_libraries( json2class.exe
 # GNDStk : python bindings
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
-include_directories( python/src/ )
+include_directories( python/src/ autogen/prototype/proto/src/ )
 
 pybind11_add_module( GNDStk.python
     EXCLUDE_FROM_ALL
     python/src/GNDStk.python.cpp
     python/src/core/Node.python.cpp
-    python/src/Interpolation.python.cpp
+    python/src/BoundaryCondition.python.cpp
+    python/src/ContributorType.python.cpp
+    python/src/DateType.python.cpp
+    python/src/DecayType.python.cpp
+    python/src/Frame.python.cpp
     python/src/GridStyle.python.cpp
-    python/src/v1.9/containers.python.cpp
-    python/src/v1.9/containers/Axis.python.cpp
-    python/src/v1.9/containers/Values.python.cpp
-    python/src/v1.9/containers/Link.python.cpp
-    python/src/v1.9/containers/Grid.python.cpp
-    python/src/v1.9/containers/Axes.python.cpp
-    python/src/v1.9/containers/XYs1d.python.cpp
-    python/src/v1.9/containers/Regions1d.python.cpp
-    python/src/v1.9/transport/CrossSection.python.cpp
-    python/src/v1.9/transport/Reaction.python.cpp
-    python/src/v1.9/transport/Reactions.python.cpp
-    python/src/v1.9/transport/ReactionSuite.python.cpp
-    python/src/v1.9/transport.python.cpp
-    python/src/v1.9/GNDS.python.cpp
+    python/src/HashAlgorithm.python.cpp
+    python/src/Interaction.python.cpp
+    python/src/Interpolation.python.cpp
+    python/src/InterpolationQualifier.python.cpp
+    python/src/Parity.python.cpp
+    python/src/RelationType.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Axis.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Values.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Link.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Grid.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Axes.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/XYs1d.python.cpp
+    autogen/prototype/proto/python/src/v1.9/containers/Regions1d.python.cpp
+    autogen/prototype/proto/python/src/v1.9/transport/CrossSection.python.cpp
+    autogen/prototype/proto/python/src/v1.9/transport/Reaction.python.cpp
+    autogen/prototype/proto/python/src/v1.9/transport/Reactions.python.cpp
+    autogen/prototype/proto/python/src/v1.9/transport/ReactionSuite.python.cpp
+    autogen/prototype/proto/python/src/v1.9/transport.python.cpp
+    autogen/prototype/proto/python/src/v1.9/proto.python.cpp
+    python/src/v2.0/GNDS.python.cpp
+    python/src/v2.0/containers.python.cpp
+    python/src/v2.0/containers/Array.python.cpp
+    python/src/v2.0/containers/Axes.python.cpp
+    python/src/v2.0/containers/Axis.python.cpp
+    python/src/v2.0/containers/Column.python.cpp
+    python/src/v2.0/containers/ColumnHeaders.python.cpp
+    python/src/v2.0/containers/Constant1d.python.cpp
+    python/src/v2.0/containers/Data.python.cpp
+    python/src/v2.0/containers/Double.python.cpp
+    python/src/v2.0/containers/Fraction.python.cpp
+    python/src/v2.0/containers/Function1ds.python.cpp
+    python/src/v2.0/containers/Function2ds.python.cpp
+    python/src/v2.0/containers/Function3ds.python.cpp
+    python/src/v2.0/containers/Grid.python.cpp
+    python/src/v2.0/containers/Gridded1d.python.cpp
+    python/src/v2.0/containers/Gridded2d.python.cpp
+    python/src/v2.0/containers/Gridded3d.python.cpp
+    python/src/v2.0/containers/Integer.python.cpp
+    python/src/v2.0/containers/Legendre.python.cpp
+    python/src/v2.0/containers/Link.python.cpp
+    python/src/v2.0/containers/Polynomial1d.python.cpp
+    python/src/v2.0/containers/Regions1d.python.cpp
+    python/src/v2.0/containers/Regions2d.python.cpp
+    python/src/v2.0/containers/Regions3d.python.cpp
+    python/src/v2.0/containers/String.python.cpp
+    python/src/v2.0/containers/Table.python.cpp
+    python/src/v2.0/containers/Values.python.cpp
+    python/src/v2.0/containers/XYs1d.python.cpp
+    python/src/v2.0/containers/XYs2d.python.cpp
+    python/src/v2.0/containers/XYs3d.python.cpp
+    python/src/v2.0/containers/Ys1d.python.cpp
+    python/src/v2.0/fissionFragmentData.python.cpp
+    python/src/v2.0/fissionFragmentData/DelayedNeutron.python.cpp
+    python/src/v2.0/fissionFragmentData/DelayedNeutrons.python.cpp
+    python/src/v2.0/fissionFragmentData/FissionFragmentData.python.cpp
+    python/src/v2.0/fpy.python.cpp
+    python/src/v2.0/fpy/ElapsedTime.python.cpp
+    python/src/v2.0/fpy/ElapsedTimes.python.cpp
+    python/src/v2.0/fpy/Energy.python.cpp
+    python/src/v2.0/fpy/IncidentEnergies.python.cpp
+    python/src/v2.0/fpy/IncidentEnergy.python.cpp
+    python/src/v2.0/fpy/Nuclides.python.cpp
+    python/src/v2.0/fpy/ProductYield.python.cpp
+    python/src/v2.0/fpy/ProductYields.python.cpp
+    python/src/v2.0/fpy/Time.python.cpp
+    python/src/v2.0/fpy/Yields.python.cpp
+    python/src/v2.0/fissionFragmentData/Rate.python.cpp
+    python/src/v2.0/pops.python.cpp
+    python/src/v2.0/pops/Alias.python.cpp
+    python/src/v2.0/pops/Aliases.python.cpp
+    python/src/v2.0/pops/Atomic.python.cpp
+    python/src/v2.0/pops/AverageEnergies.python.cpp
+    python/src/v2.0/pops/AverageEnergy.python.cpp
+    python/src/v2.0/pops/Baryon.python.cpp
+    python/src/v2.0/pops/Baryons.python.cpp
+    python/src/v2.0/pops/BindingEnergy.python.cpp
+    python/src/v2.0/pops/Charge.python.cpp
+    python/src/v2.0/pops/ChemicalElement.python.cpp
+    python/src/v2.0/pops/ChemicalElements.python.cpp
+    python/src/v2.0/pops/Configuration.python.cpp
+    python/src/v2.0/pops/Configurations.python.cpp
+    python/src/v2.0/pops/Continuum.python.cpp
+    python/src/v2.0/pops/Decay.python.cpp
+    python/src/v2.0/pops/DecayData.python.cpp
+    python/src/v2.0/pops/DecayMode.python.cpp
+    python/src/v2.0/pops/DecayModes.python.cpp
+    python/src/v2.0/pops/DecayPath.python.cpp
+    python/src/v2.0/pops/Discrete.python.cpp
+    python/src/v2.0/pops/Energy.python.cpp
+    python/src/v2.0/pops/GaugeBoson.python.cpp
+    python/src/v2.0/pops/GaugeBosons.python.cpp
+    python/src/v2.0/pops/Halflife.python.cpp
+    python/src/v2.0/pops/Intensity.python.cpp
+    python/src/v2.0/pops/InternalConversionCoefficients.python.cpp
+    python/src/v2.0/pops/InternalPairFormationCoefficient.python.cpp
+    python/src/v2.0/pops/Isotope.python.cpp
+    python/src/v2.0/pops/Isotopes.python.cpp
+    python/src/v2.0/pops/Lepton.python.cpp
+    python/src/v2.0/pops/Leptons.python.cpp
+    python/src/v2.0/pops/Mass.python.cpp
+    python/src/v2.0/pops/MetaStable.python.cpp
+    python/src/v2.0/pops/Nucleus.python.cpp
+    python/src/v2.0/pops/Nuclide.python.cpp
+    python/src/v2.0/pops/Nuclides.python.cpp
+    python/src/v2.0/pops/Parity.python.cpp
+    python/src/v2.0/pops/PhotonEmissionProbabilities.python.cpp
+    python/src/v2.0/pops/PoPs.python.cpp
+    python/src/v2.0/pops/Probability.python.cpp
+    python/src/v2.0/pops/Product.python.cpp
+    python/src/v2.0/pops/Products.python.cpp
+    python/src/v2.0/pops/Q.python.cpp
+    python/src/v2.0/pops/Shell.python.cpp
+    python/src/v2.0/pops/Spectra.python.cpp
+    python/src/v2.0/pops/Spectrum.python.cpp
+    python/src/v2.0/pops/Spin.python.cpp
+    python/src/v2.0/pops/Unorthodox.python.cpp
+    python/src/v2.0/pops/Unorthodoxes.python.cpp
+    python/src/v2.0/resonances.python.cpp
+    python/src/v2.0/resonances/BreitWigner.python.cpp
+    python/src/v2.0/resonances/Channel.python.cpp
+    python/src/v2.0/resonances/Channels.python.cpp
+    python/src/v2.0/resonances/EnergyInterval.python.cpp
+    python/src/v2.0/resonances/EnergyIntervals.python.cpp
+    python/src/v2.0/resonances/ExternalRMatrix.python.cpp
+    python/src/v2.0/resonances/HardSphereRadius.python.cpp
+    python/src/v2.0/resonances/J.python.cpp
+    python/src/v2.0/resonances/Js.python.cpp
+    python/src/v2.0/resonances/L.python.cpp
+    python/src/v2.0/resonances/LevelSpacing.python.cpp
+    python/src/v2.0/resonances/Ls.python.cpp
+    python/src/v2.0/resonances/RMatrix.python.cpp
+    python/src/v2.0/resonances/Resolved.python.cpp
+    python/src/v2.0/resonances/ResonanceParameters.python.cpp
+    python/src/v2.0/resonances/ResonanceReaction.python.cpp
+    python/src/v2.0/resonances/ResonanceReactions.python.cpp
+    python/src/v2.0/resonances/Resonances.python.cpp
+    python/src/v2.0/resonances/ScatteringRadius.python.cpp
+    python/src/v2.0/resonances/SpinGroup.python.cpp
+    python/src/v2.0/resonances/SpinGroups.python.cpp
+    python/src/v2.0/resonances/TabulatedWidths.python.cpp
+    python/src/v2.0/resonances/Unresolved.python.cpp
+    python/src/v2.0/resonances/Width.python.cpp
+    python/src/v2.0/resonances/Widths.python.cpp
     )
 target_link_libraries( GNDStk.python PRIVATE GNDStk )
 target_compile_options( GNDStk.python PRIVATE "-fvisibility=hidden" )

README.md

@@ -1,5 +1,7 @@
+![Continuous Integration](https://github.com/njoy/GNDStk/workflows/Continuous%20Integration/badge.svg)
+
 # GNDStk
-Generalized Nuclear Database Structure toolkit
+Toolkit for reading and interacting with GNDS formatted files. This toolkit provides a full C++ library along with python bindings.
 
 ## LICENSE
 This software is copyrighted by Los Alamos National Laboratory and distributed according to the conditions in the accompanying [LICENSE](LICENSE) file.

autogen/changes.json

@@ -11,7 +11,6 @@
     "metadata": {
         "type": {
             "Boolean":       "bool",
-            "string":        "std::string",
             "encoding":      "enums::Encoding",
             "frame":         "enums::Frame",
             "interaction":   "enums::Interaction",
@@ -40,7 +39,7 @@
             "nuclear": "enums::Interaction::nuclear",
             "atomic":  "enums::Interaction::atomic",
             "thermalNeutronScatteringLaw":
-                "enums::Interaction::thermalNeutronScatteringLaw",
+            "enums::Interaction::thermalNeutronScatteringLaw",
 
             "// INTERPOLATION": {},
             "flat":              "enums::Interpolation::flat",