Remove Multiple Inheritance (#32)

Besides being an anitpattern, Multiple Inheritance is interfering with updating python
bindings to pybind11.

* move getKneeReweightingModel() to FluxFunction with a default to throw
  if model is not "none". Reweightable fluxes override this
* move pion and kaon relative contributions are moved to LegacyConventional
  as those are the only models which use them
* add regression test for pion relative contributions
* [pre-commit.ci] auto fixes from pre-commit.com hooks
* require numpy<2 for meson builds
* remove psudo-cobalts from CI because centos7 is EOL
* fix editorconfig issue

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/tests.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Build nuflux with Meson
         if: matrix.build == 'meson'
         run: |
-          python3 -m pip install meson numpy sphinx breathe sphinx_rtd_theme pytest pytest-tap
+          python3 -m pip install meson 'numpy<2' sphinx breathe sphinx_rtd_theme pytest pytest-tap
           meson setup build . -D b_coverage=true --prefix=${HOME}/inst/
           meson test -C build
       - name: Rename TestLog
@@ -92,71 +92,9 @@ jobs:
         run: docs/docs-upload.sh
         env:
           ICECUBE_PASSWORD: ${{ secrets.ICECUBE_PASSWORD }}
-  cvmfs_meson_tests:
-    name: cvmfs meson tests ${{matrix.cvmfs}}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        cvmfs: [py3-v4.1.1, py3-v4.3.0]
-    steps:
-      - uses: cvmfs-contrib/github-action-cvmfs@v3
-      - name: Checkout nuflux
-        uses: actions/checkout@v4
-      - name: Build and Run Tests in Docker
-        uses: addnab/docker-run-action@v3
-        with:
-          options: -v /cvmfs/icecube.opensciencegrid.org/:/cvmfs/icecube.opensciencegrid.org/ -v /home/runner/work/nuflux/nuflux:/nuflux
-          image: centos:centos7.9.2009
-          run: |
-            yum -y install glibc-headers glibc-devel unzip
-            eval $(/cvmfs/icecube.opensciencegrid.org/${{matrix.cvmfs}}/setup.sh)
-            unset PYTHONPATH
-            export PATH=${HOME}/.local/bin:${PATH}
-            pip install --upgrade --user meson ninja pytest pytest-tap
-            CMAKE_PREFIX_PATH=${SROOT} BOOST_ROOT=${SROOT} meson setup /nuflux/build /nuflux
-            meson test -C/nuflux/build
-      - name: Copy TestLog
-        if: always()
-        run: cp -v build/meson-logs/testlog.junit.xml test-results-meson-cvmfs-${{matrix.cvmfs}}.junit.xml
-      - uses: actions/upload-artifact@v4
-        if: always()
-        with:
-          if-no-files-found: error
-          name: test-results-meson-cvmfs-${{matrix.cvmfs}}
-          path: test-results-meson-cvmfs-${{matrix.cvmfs}}.junit.xml
-  cvmfs_pyproject_tests:
-    name: cvmfs pyproject tests ${{matrix.cvmfs}}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        cvmfs: [py3-v4.1.1, py3-v4.3.0]
-    steps:
-      - uses: cvmfs-contrib/github-action-cvmfs@v3
-      - name: Checkout nuflux
-        uses: actions/checkout@v4
-      - name: Build and Run Tests in Docker
-        uses: addnab/docker-run-action@v3
-        with:
-          options: -v /cvmfs/icecube.opensciencegrid.org/:/cvmfs/icecube.opensciencegrid.org/ -v /home/runner/work/nuflux/nuflux:/nf
-          image: centos:centos7.9.2009
-          run: |
-            yum -y install glibc-headers glibc-devel
-            eval $(/cvmfs/icecube.opensciencegrid.org/${{matrix.cvmfs}}/setup.sh)
-            unset PYTHONPATH
-            python3 -m pip install --upgrade --user pip pytest
-            BOOST_ROOT=${SROOT} python3 -m pip install --user --verbose /nf
-            python3 -m pytest /nf --junit-xml=/nf/test-results-pyproject-cvmfs-${{matrix.cvmfs}}.junit.xml
-      - uses: actions/upload-artifact@v4
-        if: always()
-        with:
-          if-no-files-found: error
-          name: test-results-pyproject-cvmfs-${{matrix.cvmfs}}
-          path: test-results-pyproject-cvmfs-${{matrix.cvmfs}}.junit.xml
   publish-test-results:
     name: "Publish Tests Results"
-    needs: [Tests, cvmfs_meson_tests, cvmfs_pyproject_tests]
+    needs: [Tests]
     runs-on: ubuntu-latest
     permissions:
       checks: write

.pre-commit-config.yaml

@@ -8,11 +8,11 @@ repos:
       - id: prettier
         files: \.ya?ml$
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.5.0
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -37,7 +37,7 @@ repos:
       - id: forbid-crlf
       - id: forbid-tabs
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-builtin-literals

pyproject.toml

@@ -8,7 +8,7 @@ dynamic = ["version"]
 description = "A library for calculating atmospheric neutrino fluxes"
 readme = "README.md"
 requires-python = "~=3.7"
-dependencies = ['numpy']
+dependencies = ['numpy<2']
 license = {file = "LICENSE"}
 keywords = ["python", "science", "astronomy", "astrophysics", "IceCube", "atmospheric", "neutrino"]
 classifiers = [

src/include/nuflux/FluxFunction.h

@@ -29,7 +29,10 @@ namespace nuflux{
   ///The interface for all neutrino fluxes
   class FluxFunction{
   public:
-    FluxFunction(std::string name):name(name){}
+    FluxFunction(std::string name):
+      name(name),
+      kneeCorrectionName("none")
+      {}
     virtual ~FluxFunction(){}
 
     std::string getName() const{ return(name); }
@@ -48,8 +51,16 @@ namespace nuflux{
     virtual double getMaxEnergy() const{ return NAN;}
     virtual double readExtents(ParticleType type) const{ return NAN;}
 
+    virtual void setKneeReweightingModel(std::string reweightModel){
+      if (reweightModel != "none"){
+        throw std::runtime_error("This model does not support knee reweighting");
+      }
+    }
+    std::string getKneeReweightingModel() const{ return(kneeCorrectionName); }
+
   protected:
     std::string name;
+    std::string kneeCorrectionName;
   };
 
   ///Things which are useful or necessary internally for the library but which aren't useful for users
@@ -75,6 +86,14 @@ namespace nuflux{
     };
     std::string getDataPath(std::string fname);
 
+    void registerKneeModel(const std::string baseModel, const std::string name);
+
+    struct KneeRegisterererer{
+      KneeRegisterererer(const std::string baseModel, const std::string name){
+        registerKneeModel(baseModel,name);
+      }
+    };
+
   } //namespace detail
 
 } //namespace nuflux
@@ -83,5 +102,7 @@ namespace nuflux{
   namespace{ nuflux::detail::FluxRegisterererer BOOST_PP_CAT( registerererer , __LINE__ ) (name,factory); }
 #define NNF_REGISTER_DEPRECATED_FLUX(name,factory,reason)\
   namespace{ nuflux::detail::FluxRegisterererer BOOST_PP_CAT( registerererer , __LINE__ ) (name,factory,reason); }
+#define NNF_REGISTER_KNEE(baseModel,name)                               \
+  namespace{ nuflux::detail::KneeRegisterererer BOOST_PP_CAT( registerererer , __LINE__ ) (baseModel,name); }
 
 #endif

src/include/nuflux/LegacyConventionalFlux.h

@@ -7,7 +7,7 @@
 
 namespace nuflux{
 
-  class LegacyConventionalFlux : public FluxFunction, public KneeReweightable, public PionKaonAdjustable{
+  class LegacyConventionalFlux : public FluxFunction{
   public:
     class component{
     public:
@@ -84,6 +84,10 @@ namespace nuflux{
     std::map<ParticleType,component> components;
 
     kneeSpline kneeCorrection;
+    ///the factor by which to boost the pion decay contribution
+    double pionAdjust;
+    ///the factor by which to boost the kaon decay contribution
+    double kaonAdjust;
   public:
     LegacyConventionalFlux(const std::string& fluxName);
     static boost::shared_ptr<FluxFunction> makeFlux(const std::string& fluxName);
@@ -93,8 +97,15 @@ namespace nuflux{
     virtual double getMinEnergy() const;
     virtual double getMaxEnergy() const;
 
-    virtual void setRelativePionContribution(double adjust);
-    virtual void setRelativeKaonContribution(double adjust);
+    ///boosts the contribution from pion decays
+    ///\param adjust the factor by which to increase the pion contribution
+    void setRelativePionContribution(double adjust);
+    double getRelativePionContribution() const{ return(pionAdjust); }
+
+    ///boosts the contribution from kaon decays
+    ///\param adjust the factor by which to increase the kaon contribution
+    void setRelativeKaonContribution(double adjust);
+    double getRelativeKaonContribution() const{ return(kaonAdjust); }
 
     virtual void setKneeReweightingModel(std::string reweightModel);
   };

src/include/nuflux/LegacyPromptFlux.h

@@ -7,7 +7,7 @@
 
 namespace nuflux{
 
-  class LegacyPromptFlux : public FluxFunction, public KneeReweightable{
+  class LegacyPromptFlux : public FluxFunction{
   private:
     class component{
     private:

src/include/nuflux/meson.build

@@ -1,6 +1,6 @@
 nuflux_headers = [
   'ANFlux.h', 'Fluxes.h', 'FluxFunction.h',
-  'Interfaces.h', 'IPLEFlux.h', 'LegacyConventionalFlux.h',
+  'IPLEFlux.h', 'LegacyConventionalFlux.h',
   'LegacyPromptFlux.h', 'nuflux.h',
   'SplineFlux2.h', 'SplineFlux.h',
 ]

src/include/nuflux/nuflux.h

@@ -31,7 +31,6 @@ namespace nuflux{
 
 std::string getDataPath(std::string fname);
 
-#include <nuflux/Interfaces.h>
 #include <nuflux/Fluxes.h>
 
 #endif //NEWNUFLUX_H

src/library/LegacyConventionalFlux.cpp

@@ -21,16 +21,15 @@ namespace nuflux{
   }
 
   LegacyConventionalFlux::LegacyConventionalFlux(const std::string& fluxName):
-    FluxFunction(fluxName),
-    KneeReweightable("none"),
-    PionKaonAdjustable(1.0,1.0){
+    FluxFunction(fluxName)
+  {
     components[NuMu]   =readConvComponent(fluxName+"_numu.dat");
     components[NuMuBar]=readConvComponent(fluxName+"_numubar.dat");
     components[NuE]    =readConvComponent(fluxName+"_nue.dat");
     components[NuEBar] =readConvComponent(fluxName+"_nuebar.dat");
     //this looks dumb but is actually necessary to enforce the continuity constraint
-    setRelativePionContribution(getRelativePionContribution());
-    setRelativeKaonContribution(getRelativeKaonContribution());
+    setRelativePionContribution(1.0);
+    setRelativeKaonContribution(1.0);
   }
 
   boost::shared_ptr<FluxFunction> LegacyConventionalFlux::makeFlux(const std::string& fluxName){

src/library/LegacyPromptFlux.cpp

@@ -19,8 +19,8 @@ namespace nuflux{
   }
 
   LegacyPromptFlux::LegacyPromptFlux(const std::string& fluxName):
-    FluxFunction(fluxName),
-    KneeReweightable("none"){
+    FluxFunction(fluxName)
+  {
     components[NuMu]   =readPromptComponent(detail::getDataPath("LegacyPromptFlux/"+fluxName+"_numupro.dat"));
     components[NuMuBar]=readPromptComponent(detail::getDataPath("LegacyPromptFlux/"+fluxName+"_numubarpro.dat"));
     components[NuE]    =readPromptComponent(detail::getDataPath("LegacyPromptFlux/"+fluxName+"_nuepro.dat"));

src/nuflux/__init__.py

@@ -1,6 +1,5 @@
 __all__ = [
     "FluxFunction",
-    "KneeReweightable",
     "LegacyConventionalFlux",
     "LegacyPromptFlux",
     "NuE",
@@ -10,7 +9,6 @@
     "NuTau",
     "NuTauBar",
     "ParticleType",
-    "PionKaonAdjustable",
     "SplineFlux",
     "SplineFlux2",
     "availableFluxes",
@@ -23,7 +21,6 @@
 
 from _nuflux import (
     FluxFunction,
-    KneeReweightable,
     LegacyConventionalFlux,
     LegacyPromptFlux,
     NuE,
@@ -33,7 +30,6 @@
     NuTau,
     NuTauBar,
     ParticleType,
-    PionKaonAdjustable,
     SplineFlux,
     SplineFlux2,
     availableFluxes,

src/pybindings/module.cxx

@@ -122,24 +122,17 @@ register_FluxFunction()
           (bp::args("particle_type"), "energy", "cos_zen"))
     .add_property("name", &FluxFunction::getName)
     .add_property("energy_range",&energy_range)
-
-    ;
-
-  bp::class_<KneeReweightable, boost::shared_ptr<KneeReweightable>, boost::noncopyable>("KneeReweightable", bp::no_init)
-    .add_property("knee_reweighting_model", &KneeReweightable::getKneeReweightingModel, &KneeReweightable::setKneeReweightingModel)
-    ;
-
-  bp::class_<PionKaonAdjustable, boost::shared_ptr<PionKaonAdjustable>, boost::noncopyable>("PionKaonAdjustable", bp::no_init)
-    .add_property("relative_pion_contribution", &PionKaonAdjustable::getRelativePionContribution, &PionKaonAdjustable::setRelativePionContribution)
-    .add_property("relative_kaon_contribution", &PionKaonAdjustable::getRelativeKaonContribution, &PionKaonAdjustable::setRelativeKaonContribution)
+    .add_property("knee_reweighting_model", &FluxFunction::getKneeReweightingModel, &FluxFunction::setKneeReweightingModel)
     ;
 
-  bp::class_< LegacyConventionalFlux, boost::shared_ptr<LegacyConventionalFlux>,
-              bp::bases<FluxFunction, PionKaonAdjustable, KneeReweightable> >("LegacyConventionalFlux", bp::no_init)
+  bp::class_<LegacyConventionalFlux, boost::shared_ptr<LegacyConventionalFlux>,
+            bp::bases<FluxFunction> >("LegacyConventionalFlux", bp::no_init)
+      .add_property("relative_pion_contribution", &LegacyConventionalFlux::getRelativePionContribution, &LegacyConventionalFlux::setRelativePionContribution)
+      .add_property("relative_kaon_contribution", &LegacyConventionalFlux::getRelativeKaonContribution, &LegacyConventionalFlux::setRelativeKaonContribution)
     ;
 
-  bp::class_< LegacyPromptFlux, boost::shared_ptr<LegacyPromptFlux>,
-              bp::bases<FluxFunction, KneeReweightable> >("LegacyPromptFlux", bp::no_init)
+  bp::class_<LegacyPromptFlux, boost::shared_ptr<LegacyPromptFlux>,
+            bp::bases<FluxFunction> >("LegacyPromptFlux", bp::no_init)
     ;
 
   {