fix: Revert out-of-scope changes introduced during rebase

Restore all source, header, test, and config files to match main,
removing duplicated code blocks caused by `git rebase -Xours`. Also
removes .readthedocs.yaml and stale nuchic references. This branch
should only contain documentation changes.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jxi24

.github/workflows/cmake.yml

@@ -48,21 +48,6 @@ jobs:
           ln -fs /usr/local/bin/gfortran-14 /usr/local/bin/gfortran
         fi
 
-    - name: Install dependencies (MacOS)
-      if: ${{ matrix.os == 'macos-13' || matrix.os == 'macos-14' }}
-      run: |
-        export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
-        brew update
-        brew install hdf5
-        brew install --force gcc
-        os_ver=$(sw_vers -productVersion | cut -d'.' -f1)
-        # TODO: remove hardcoded gfortran major version
-        if (( "$os_ver" > 13)); then
-          ln -fs /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran
-        else
-          ln -fs /usr/local/bin/gfortran-14 /usr/local/bin/gfortran
-        fi
-
     - name: Set up cache
       id: cache-cpm
       uses: actions/cache@v4

.readthedocs.yaml

@@ -30,13 +30,13 @@ The Achilles code uses CMake as a means to provide a platform agnositic installa
 
 The default options for the building of Achilles requires HepMC3
 and Sherpa. The HepMC3 code provides a means to output events in the convention dictated by the [NuHepMC](https://github.com/NuHepMC/Spec) standard.
-Details on obtaining
-this code can be found in the next [section](#-optional-dependencies).
+The Sherpa interface allows for the simulation of beyond the Standard Model (BSM) processes. Details on obtaining
+these codes can be found in the next [section](#-optional-dependencies).
 
 To build Achilles with these default options can be done with:
 ```bash
 mkdir build && cd build
-cmake .. 
+cmake .. -DACHILLES_ENABLE_SHERPA=ON -DSHERPA_ROOT_DIR=/path/to/sherpa
 make -jN
 ```
 
@@ -63,7 +63,6 @@ To disable the requirement of HepMC3, add the option `-DENABLE_HEPMC3=OFF` to th
 
 #### Sherpa
 
-The Sherpa interface allows for the simulation of beyond the Standard Model (BSM) processes.
 The leptonic currents are calculated as described in [arxiv:2110.15319](https://arxiv.org/abs/2110.15319). This involves calculating
 temrs using the Berends-Giele recursion relations in arbitrary models. The calculation of these is
 implemented into the Comix matrix element generator within the Sherpa codebase.
@@ -72,7 +71,7 @@ The required version of Sherpa is in the process of being made public, but can b
 Achilles authors.
 Note that to enable UFO support from Sherpa, add the option `--enable-ufo' to the configure command.
 
-To enable building with Sherpa, add the option `-DACHILLES_ENABLE_SHERPA=ON -DSHERPA_ROOT_DIR=/path/to/sherpa` to the cmake command.
+To disable the requirement of Sherpa, add the option `-DENABLE_BSM=OFF` to the cmake command.
 
 ### CMake Options
 
@@ -82,7 +81,7 @@ A non-exhaustive list of useful CMake options includes:
 | ------                  | -------                                                                         |
 | `ACHILLES_ENABLE_TESTING`        | Build the Achilles test suite                                                   |
 | `ACHILLES_ENABLE_GZIP`           | Compile the code with the ability to directly compress event files              |
-| `ACHILLES_ENABLE_CASCADE_TEST`   | Build the executable to only run the cascade (hadron-nucleus cross section or transparency) |
+| `ACHILLES_ENABLE_CASCADE_TEST`   | Build the executable to only run the cascade (pA cross section or transparency) |
 | `ACHILLES_ENABLE_POTENTIAL_TEST` | Build executable to test different potentials                                   |
 | `CMAKE_BUILD_TYPE=Debug`         | Build the executable with debug symbols enabled                                |
 ## Running Achilles
@@ -135,37 +134,39 @@ in more details in the [wiki](https://github.com/AchillesGen/Achilles/wiki) and
 
 #### Run card
 
-The run card consists of eight major sections describing how the generation is to be carried out.
+The run card consists of nine major sections describing how the generation is to be carried out.
 These sections are:
 1. The main event section
 2. The process section
-3. The options section 
-4. The incoming beam
-5. Settings for the cascade
-6. Settings for the nuclear interaction model
-7. Settings for the nucleus
-8. Any cuts to apply during the generation of the events
+3. The initialization of the random number generator and precision of the integrator section
+4. The unweighting method to use
+5. The incoming beam
+6. Settings for the cascade
+7. Settings for the nuclear interaction model
+8. Settings for the nucleus
+9. Any cuts to apply during the generation of the events
 
 Each of these sections are described below and in greater detail in the
 [wiki](https://github.com/AchillesGen/Achilles/wiki).
 
-Achilles also provides the option of loading each of these sections from a separate text file. A set of default options for each section is included in the `data/default` directory
-
 The _Main_ section contains options:
  - The number of events (`NEvents`)
  - If cuts should be applied at the generation level (`HardCuts`)
  - The output (`Output`), which contains sub-options:
-    - The event output format (`Format`, currently options are "HepMC3", "NuHepMC", and "Achilles")
+    - The event output format (`Format`, currently options are "HepMC3" and "Achilles")
     - The name of the output file (`Name`)
     - If the file should be written as a gzip file or not (`Zipped`)
 
-The _Processes_ section contains information needed to generate the leptonic current for a given physics model.
+The _Process_ section contains information needed to generate the leptonic current for a given physics model.
 This contains the options for:
- - The incoming and outgoing leptonic states as a list of particle IDs 
+ - The physics model (`Model`)
+ - The output leptonic states as a list of particle IDs (`Final States`)
+
+The _Initialization_ section describes the initialization of the generator, and contains:
+ - The random seed to use for event generation for reproducibility (`Seed`)
+ - The accuracy for the warm-up run of the integrator to achieve before generating events (`Accuracy`)
 
-The _Options_ section contains information on the random number generator, integrator precission, and unweighting methodt to be used in evnet generation. This contains the option for:
- - Initialize which contains the random seed to use for event generation for reproducibility (`Seed`), and the accuracy for the warm-up run of the integrator to achieve before generating events (`Accuracy`) 
- - Unweighting which sets up the methodology for unweighting the events.This has one required setting
+The _Unweighting_ section sets up the methodology for unweighting the events. This has one required setting
 as the `Name` of the unweighting procedure. Each unweighting procedure has their own set of options
 described in detail in the [wiki](https://github.com/AchillesGen/Achilles/wiki/Unweighting).
 
@@ -193,11 +194,11 @@ primary interaction is defined. The required options are:
  - Additional required options depend on the nuclear model used
    and can be found in the [wiki](https://github.com/AchillesGen/Achilles/wiki/Nuclear-Models).
 
-The _Nucleus_ section defines the nucleus for interactions. The required options are:
+The _Nucleus_ section defines the nucleus for interactions. Currently, only a single isotope and nucleus is
+supported to be run at a time. The required options are:
  - The name of the nucleus given as the number of nucleons followed by the chemical symbol (_i.e._ "12C").
  - The Fermi momentum is needed.
- - The Binding energy is needed.
- - The setup for the densities and configuration.
+ - The setup for the density and configuration.
    Details can be found in the [wiki](https://github.com/AchillesGen/Achilles/wiki/Nucleus).
  - The Fermi gas mode for the cascade. Current options are "Local" and "Global".
  - The nuclear potential to use.
@@ -212,27 +213,19 @@ The details of this section are laid out in the [wiki](https://github.com/Achill
 
 The form factor file contains the list of the form factors to use, and the parameters for the different
 parameterization. Currently, the form factors implemented are:
- - vector:
+ - Vector:
     - Dipole
     - Kelly
     - BBBA
     - ArringtonHill
- - axial:
+ - Axial:
     - Dipole
-    - ZExpansion
- - coherent:
+ - Coherent:
     - Helm
     - Lovato (Carbon only)
- 
-Form factors for each of the above can be chosen by editing the `FormFactors.yml` file.
 
 For additional details on the parameters for each form factor, see the [wiki](https://github.com/AchillesGen/Achilles/wiki/Form-Factors).
 
-#### Achilles Rules
-
-To facilitate the user experience, Achilles implements a set of rules which govern run card options. These can be found in `data/Rules.yml`. These rules cover required options in the run card, which if not found, throw a suggestive error notifying the user of the missing options. In addition, to prevent inconsistent physics models from being used together, certain rules are implemented that will additionally throw an error. An example of inconsistent physics modeling is using a propagating Delta baryon in nucleon-nucleon to nucleon-nucleon-pion interactions while also using the DCC model for pion-nucleon to pion-nucleon interactions. These rules can be changed, but we highly recommend users NOT edit these rules unless they know what they are doing. 
-
-
 ### Adding models to Achilles (via Sherpa)
 
 The Beyond the Standard Model handling within Achilles is handled via an interface to Sherpa and Comix.

README.md

@@ -70,25 +70,6 @@ CPMAddPackage(
         "GIT_FAIL_IF_NONZERO_EXIT OFF"
 )
 
-CPMAddPackage(
-    NAME HighFive
-    VERSION 2.6.2
-    GITHUB_REPOSITORY BlueBrain/HighFive
-    OPTIONS
-        "HIGHFIVE_USE_BOOST OFF"
-        "HIGHFIVE_EXAMPLES OFF"
-        "HIGHFIVE_BUILD_DOCS OFF"
-        "HIGHFIVE_UNIT_TESTS OFF"
-)
-
-CPMAddPackage(
-    Name CmakeGitVersion
-    GITHUB_REPOSITORY andrew-hardin/cmake-git-version-tracking
-    GIT_TAG master
-    OPTIONS
-        "GIT_FAIL_IF_NONZERO_EXIT OFF"
-)
-
 # Install testing framework
 if(ACHILLES_ENABLE_TESTING)
     # Catch2

external/CMakeLists.txt

@@ -10,7 +10,6 @@
 #include "Achilles/FourVector.hh"
 #include "Achilles/PDFBase.hh"
 #include "Achilles/ParticleInfo.hh"
-#include "Achilles/PDFBase.hh"
 
 namespace achilles {
 
@@ -125,20 +124,6 @@ class FlatFlux : public FluxType {
     double m_min_energy, m_max_energy;
 };
 
-class PDFBeam : public FluxType {
-    public:
-        PDFBeam(const YAML::Node&);
-        int NVariables() const override { return 1; }
-        FourVector Flux(const std::vector<double>&, double) const override;
-        double GenerateWeight(const FourVector&, std::vector<double>&, double) const override;
-        std::string Type() const override { return "PDFBeam"; }
-        double MaxEnergy() const override { return 0; }
-        double EvaluateFlux(const FourVector&) const override;
-
-    private:
-        std::unique_ptr<PDFBase> p_pdf;
-};
-
 class Beam {
   public:
     using BeamMap = std::map<achilles::PID, std::shared_ptr<FluxType>>;

include/Achilles/Beams.hh

@@ -16,7 +16,6 @@ struct ConfigurationParticle {
     bool is_proton;
     std::array<double, 3> position;
 };
-#endif
 
 struct Configuration {
     std::vector<ConfigurationParticle> nucleons;

include/Achilles/Configuration.hh

@@ -10,7 +10,6 @@
 #include "Achilles/EventHistory.hh"
 #include "Achilles/NuclearRemnant.hh"
 #include "Achilles/ProcessInfo.hh"
-#include "Achilles/EventHistory.hh"
 
 namespace achilles {
 

include/Achilles/Event.hh

@@ -327,29 +327,6 @@ class AxialZExpansion : public FormFactorImpl, RegistrableFormFactor<AxialZExpan
     }
 };
 
-class AxialZExpansion : public FormFactorImpl, RegistrableFormFactor<AxialZExpansion> {
-    public:
-        AxialZExpansion(const YAML::Node&);
-        void Evaluate(double, FormFactor::Values&) const override;
-
-        // Required factory methods
-        static std::unique_ptr<FormFactorImpl> Construct(FFType, const YAML::Node&);
-        static std::string Name() { return "AxialZExpansion"; }
-        static FFType Type() { return FFType::axial; }
-    private:
-        double tcut, t0;
-        std::vector<double> cc_params{}, strange_params{};
-        double ZExpand(std::vector<double> A, double z) const {
-            // Compute the z-expansion, \sum{i=0}^{i_max} a_i z^i
-            double result = 0;
-            for(size_t i = A.size()-1; i > 0; --i) {
-                result += A[i];
-                result *= z;
-            }
-            return result + A[0];
-        }
-};
-
 class Kelly : public FormFactorImpl, RegistrableFormFactor<Kelly> {
   public:
     Kelly(const YAML::Node &);

include/Achilles/FormFactor.hh

@@ -88,27 +88,6 @@ class IntfSpectralMapper
     // static constexpr double dE = 400;
 };
 
-class IntfSpectralMapper
-    : public HadronicBeamMapper,
-      Registrable<HadronicBeamMapper, IntfSpectralMapper, const ProcessInfo &, size_t> {
-  public:
-    IntfSpectralMapper(const ProcessInfo &info, size_t idx);
-    static std::string Name() { return "IntfSpectral"; }
-    static std::unique_ptr<HadronicBeamMapper> Construct(const ProcessInfo &info, size_t idx) {
-        return std::make_unique<IntfSpectralMapper>(info, idx);
-    }
-
-    void GeneratePoint(std::vector<FourVector> &, const std::vector<double> &) override;
-    double GenerateWeight(const std::vector<FourVector> &, std::vector<double> &) override;
-    size_t NDims() const override { return 7; }
-
-  private:
-    static constexpr double dCos2 = 2;
-    static constexpr double dPhi = 2 * M_PI;
-    static constexpr double dp2 = 400; // reduced b/c MF SF has no strength at high P
-    // static constexpr double dE = 400;
-};
-
 } // namespace achilles
 
 #endif

include/Achilles/HadronicMapper.hh

@@ -120,11 +120,6 @@ class MultiChannel {
     void LoadState(std::istream &);
     bool operator==(const MultiChannel &) const;
 
-    // Cache Results
-    void SaveState(std::ostream &) const;
-    void LoadState(std::istream &);
-    bool operator==(const MultiChannel &) const;
-
     // YAML interface
     friend YAML::convert<achilles::MultiChannel>;
 
@@ -214,28 +209,6 @@ double achilles::MultiChannel::GenerateWeight(Integrand<T> &func, const std::vec
     return func.GenerateWeight(channel_weights, point, densities);
 }
 
-template <typename T> std::vector<T> achilles::MultiChannel::GeneratePoint(Integrand<T> &func) {
-    std::vector<double> rans(ndims);
-    std::vector<T> point(ndims);
-
-    // Generate needed random numbers
-    Random::Instance().Generate(rans);
-
-    // Select a channel
-    size_t ichannel = Random::Instance().SelectIndex(channel_weights);
-
-    // Map the point based on the channel
-    func.GeneratePoint(ichannel, rans, point);
-    return point;
-}
-
-template <typename T>
-double achilles::MultiChannel::GenerateWeight(Integrand<T> &func, const std::vector<T> &point) {
-    size_t nchannels = channel_weights.size();
-    std::vector<double> densities(nchannels);
-    return func.GenerateWeight(channel_weights, point, densities);
-}
-
 template <typename T> void achilles::MultiChannel::Optimize(Integrand<T> &func) {
     double rel_err = lim::max();
     while(NeedsOptimization(rel_err)) {