Mcmc config by francoisbonneau · Pull Request #39 · Geode-solutions/OpenGeode-Stochastic

francoisbonneau · 2026-05-25T11:40:50Z

No description provided.

feat(Model): create a factory for energy terms.

feat(EnergyTerm): builder for energy terms

github-actions · 2026-05-25T11:49:45Z

Cpp-Linter Report ⚠️

Some files did not pass the configured checks!

clang-tidy (v20.1.8) reports: 561 concern(s)

bindings/python/src/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:30:9: warning: [google-build-using-namespace]

do not use namespace using-directives; use using-declarations instead
```
   30 |         using namespace geode;
      |         ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:28:37: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   28 |     void define_simulation_monitor( pybind11::module &module )
      |                                     ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:30:9: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   30 |         pybind11::class_< geode::StatisticsTracker >(
      |         ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:30:52: error: [clang-diagnostic-error]

expected '(' for function-style cast or type construction
```
   30 |         pybind11::class_< geode::StatisticsTracker >(
      |                           ~~~~~~~~~~~~~~~~~~~~~~~~ ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:32:19: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   32 |             .def( pybind11::init< geode::index_t >(),
      |                   ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:32:50: error: [clang-diagnostic-error]

expected '(' for function-style cast or type construction
```
   32 |             .def( pybind11::init< geode::index_t >(),
      |                                   ~~~~~~~~~~~~~~ ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:32:52: error: [clang-diagnostic-error]

expected expression
```
   32 |             .def( pybind11::init< geode::index_t >(),
      |                                                    ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:33:17: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   33 |                 pybind11::arg( "nb_energy_terms" ),
      |                 ^
```

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:36:46: error: [clang-diagnostic-error]

use of class template 'geode::StatisticsTracker' requires template arguments

   36 |             .def( "add_realization", &geode::StatisticsTracker::add_realization,
      |                                              ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/inference/statistics_tracker.hpp:13:11: note: template is declared here
   12 |     template < typename ObjectType >
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   13 |     class StatisticsTracker
      |           ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:37:17: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   37 |                 pybind11::arg( "values" ),
      |                 ^
```

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:39:46: error: [clang-diagnostic-error]

use of class template 'geode::StatisticsTracker' requires template arguments

   39 |             .def( "statiscal_count", &geode::StatisticsTracker::statiscal_count,
      |                                              ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/inference/statistics_tracker.hpp:13:11: note: template is declared here
   12 |     template < typename ObjectType >
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   13 |     class StatisticsTracker
      |           ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:41:54: error: [clang-diagnostic-error]

use of class template 'geode::StatisticsTracker' requires template arguments

   41 |             .def_property_readonly( "means", &geode::StatisticsTracker::means,
      |                                                      ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/inference/statistics_tracker.hpp:13:11: note: template is declared here
   12 |     template < typename ObjectType >
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   13 |     class StatisticsTracker
      |           ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:44:25: error: [clang-diagnostic-error]

use of class template 'geode::StatisticsTracker' requires template arguments

   44 |                 &geode::StatisticsTracker::variances,
      |                         ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/inference/statistics_tracker.hpp:13:11: note: template is declared here
   12 |     template < typename ObjectType >
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   13 |     class StatisticsTracker
      |           ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_monitor.hpp:46:41: error: [clang-diagnostic-error]

use of class template 'geode::StatisticsTracker' requires template arguments; argument deduction not allowed in lambda parameter

   46 |             .def( "__repr__", []( const geode::StatisticsTracker &self ) {
      |                                         ^~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/inference/statistics_tracker.hpp:13:11: note: template is declared here
   13 |     class StatisticsTracker
      |           ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:28:37: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   28 |     void define_simulation_printer( pybind11::module &module )
      |                                     ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:30:9: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   30 |         pybind11::class_< SimulationPrinterConfigurator >(
      |         ^
```

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:30:27: error: [clang-diagnostic-error]

'SimulationPrinterConfigurator' does not refer to a value

   30 |         pybind11::class_< SimulationPrinterConfigurator >(
      |                           ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:37:12: note: declared here
   37 |     struct SimulationPrinterConfigurator
      |            ^

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:32:19: error: [clang-diagnostic-error]

use of undeclared identifier 'pybind11'
```
   32 |             .def( pybind11::init<>() )
      |                   ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:32:34: error: [clang-diagnostic-error]

expected expression
```
   32 |             .def( pybind11::init<>() )
      |                                  ^
```
bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:32:36: error: [clang-diagnostic-error]

expected expression
```
   32 |             .def( pybind11::init<>() )
      |                                    ^
```

include/geode/stochastic/inference/statistics_tools.hpp:30:1: warning: [modernize-concat-nested-namespaces]

nested namespaces can be concatenated

   30 | namespace geode
      | ^~~~~~~~~~~~~~~
   31 | {
      | ~
   32 |     namespace statistics
      |     ~~~~~~~~~~~~~~~~~~~~
      |     namespace geode::statistics

include/geode/stochastic/inference/statistics_tracker.hpp:16:9: warning: [google-explicit-constructor]

single-argument constructors must be marked explicit to avoid unintentional implicit conversions
```
   16 |         StatisticsTracker( const Model< ObjectType >& model ) : model_{ model }
      |         ^
      |         explicit 
```
include/geode/stochastic/inference/statistics_tracker.hpp:32:17: warning: [readability-qualified-auto]

'auto &value' can be declared as 'const auto &value'
```
   32 |                 auto& value = values[value_id];
      |                 ^
      |                 const 
```

include/geode/stochastic/inference/target_statistics.hpp:39:42: error: [clang-diagnostic-error]

no template named 'Model'

   39 |         explicit TargetStatistics( const Model< ObjectType >& model )
      |                                          ^

include/geode/stochastic/inference/target_statistics.hpp:47:9: warning: [modernize-use-nodiscard]

function 'model' should be marked [[nodiscard]]
```
   47 |         const Model< ObjectType >& model() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/inference/target_statistics.hpp:47:15: error: [clang-diagnostic-error]

no template named 'Model'
```
   47 |         const Model< ObjectType >& model() const
      |               ^
```
include/geode/stochastic/inference/target_statistics.hpp:63:9: warning: [modernize-use-nodiscard]

function 'has_target' should be marked [[nodiscard]]
```
   63 |         bool has_target( const uuid& term_uuid ) const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/inference/target_statistics.hpp:68:9: warning: [modernize-use-nodiscard]

function 'target' should be marked [[nodiscard]]
```
   68 |         double target( const uuid& term_uuid ) const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/inference/target_statistics.hpp:73:9: warning: [modernize-use-nodiscard]

function 'tolerance' should be marked [[nodiscard]]
```
   73 |         double tolerance( const uuid& term_uuid ) const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/inference/target_statistics.hpp:78:9: warning: [modernize-use-nodiscard]

function 'active_terms' should be marked [[nodiscard]]
```
   78 |         std::vector< uuid > active_terms() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/inference/target_statistics.hpp:94:15: error: [clang-diagnostic-error]

no template named 'Model'
```
   94 |         const Model< ObjectType >& model_;
      |               ^
```

include/geode/stochastic/models/energy_terms/energy_term_builder.hpp:111:35: warning: [hicpp-named-parameter]

all parameters should be named in a function

  111 |         const NewEnergyTypeConfig&,
      |                                   ^
      |                                    /*unused*/
  112 |         const ObjectSets< ObjectType >&,
      |                                        
      |                                         /*unused*/
  113 |         const SpatialDomain< ObjectType::dim >& )
      |                                                  /*unused*/

include/geode/stochastic/models/energy_terms/energy_term_builder.hpp:122:30: warning: [hicpp-named-parameter]

all parameters should be named in a function

  122 |         const std::monostate&,
      |                              ^
      |                               /*unused*/
  123 |         const ObjectSets< ObjectType >&,
      |                                        
      |                                         /*unused*/
  124 |         const SpatialDomain< ObjectType::dim >& )
      |                                                  /*unused*/

include/geode/stochastic/models/model.hpp:51:11: warning: [cppcoreguidelines-special-member-functions]

class 'Model' defines a copy constructor and a copy assignment operator but does not define a destructor, a move constructor or a move assignment operator
```
   51 |     class Model
      |           ^
```
include/geode/stochastic/models/model.hpp:57:9: warning: [google-explicit-constructor]

single-argument constructors must be marked explicit to avoid unintentional implicit conversions
```
   57 |         Model( EnergyTermCollection< ObjectType >&& energy_terms )
      |         ^
      |         explicit 
```
include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp:39:9: warning: [google-explicit-constructor]

single-argument constructors must be marked explicit to avoid unintentional implicit conversions
```
   39 |         UniformPointSetSampler( const SpatialDomain< dimension >& domain )
      |         ^
      |         explicit 
```

include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp:48:13: warning: [cppcoreguidelines-prefer-member-initializer]

'step_move_' should be initialized in a member initializer of the constructor

   40 |             : ObjectSetSampler< Point< dimension > >{}, domain_( domain )
      |                                                                          
      |                                                                          , step_move_(define_step_for_move())
   41 |         {
   42 |             auto volume = domain_.extended_n_volume();
   43 |             OpenGeodeStochasticStochasticException::check_exception(
   44 |                 volume != 0., nullptr, OpenGeodeException::TYPE::data,
   45 |                 "[UniformPointSetSampler] Undefined Extended Bounding "
   46 |                 "Box (volume ==0)." );
   47 |             this->log_pdf_ = -std::log( volume );
   48 |             step_move_ = define_step_for_move();
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp:69:31: warning: [readability-identifier-naming]

invalid case style for constexpr variable 'max_try'

   69 |             constexpr index_t max_try{ 100 };
      |                               ^~~~~~~
      |                               MAX_TRY
   70 |             for( const auto try_id : geode::Range{ max_try } )
      |                                                    ~~~~~~~
      |                                                    MAX_TRY

include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp:88:28: warning: [cppcoreguidelines-avoid-magic-numbers]

0.1 is a magic number; consider replacing it with a named constant
```
   88 |             double ratio = 0.1;
      |                            ^
```

include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:40:13: warning: [bugprone-easily-swappable-parameters]

2 adjacent parameters of 'UniformSegmentSetSampler' of similar type ('const DoubleSampler::Distribution &') are easily swapped by mistake

   40 |             const DoubleSampler::Distribution& length,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   41 |             const DoubleSampler::Distribution& azimuth )
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:40:48: note: the first parameter in the range is 'length'
   40 |             const DoubleSampler::Distribution& length,
      |                                                ^~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:41:48: note: the last parameter in the range is 'azimuth'
   41 |             const DoubleSampler::Distribution& azimuth )
      |                                                ^~~~~~~

include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:65:28: warning: [cppcoreguidelines-avoid-magic-numbers]

0.1 is a magic number; consider replacing it with a named constant
```
   65 |             double ratio = 0.1;
      |                            ^
```

include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:75:31: warning: [readability-identifier-naming]

invalid case style for constexpr variable 'max_try'

   75 |             constexpr index_t max_try{ 100 };
      |                               ^~~~~~~
      |                               MAX_TRY
   76 |             for( const auto try_id : geode::Range{ max_try } )
      |                                                    ~~~~~~~
      |                                                    MAX_TRY

include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:76:29: warning: [clang-analyzer-deadcode.DeadStores]

Value stored to 'try_id' during its initialization is never read

   76 |             for( const auto try_id : geode::Range{ max_try } )
      |                             ^~~~~~ ~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:76:29: note: Value stored to 'try_id' during its initialization is never read
   76 |             for( const auto try_id : geode::Range{ max_try } )
      |                             ^~~~~~ ~

include/geode/stochastic/sampling/direct/object_set_sampler/segment_set_sampler.hpp:94:9: warning: [modernize-use-nodiscard]

function 'is_valid_object' should be marked [[nodiscard]]
```
   94 |         bool is_valid_object( const OwnerSegment2D& obj ) const override
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:28:10: error: [clang-diagnostic-error]

'geode/stochastic/models/energy_terms/density_term.hpp' file not found
```
   28 | #include <geode/stochastic/models/energy_terms/density_term.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
include/geode/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:60:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   60 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:87:9: warning: [cppcoreguidelines-pro-type-member-init]

constructor does not initialize these fields: set_descriptors_, set_name_to_uuid_
```
   87 |         FractureSimulationRunner( const SpatialDomain< 2 >& domain )
      |         ^
```
include/geode/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:87:9: warning: [google-explicit-constructor]

single-argument constructors must be marked explicit to avoid unintentional implicit conversions
```
   87 |         FractureSimulationRunner( const SpatialDomain< 2 >& domain )
      |         ^
      |         explicit 
```
include/geode/stochastic/sampling/mcmc/helpers/fracture_simulation_runner.hpp:174:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
  174 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:47:47: warning: [cppcoreguidelines-avoid-magic-numbers]

100 is a magic number; consider replacing it with a named constant
```
   47 |         index_t realisations_print_frequency{ 100 };
      |                                               ^
```
include/geode/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:51:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   51 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```

include/geode/stochastic/sampling/mcmc/helpers/simulation_printer.hpp:83:13: warning: [modernize-pass-by-value]

pass by value and use std::move

   34 |             const SimulationPrinterConfigurator& config )
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |             SimulationPrinterConfigurator 
   35 |             : model_( model ), config_( config )
      |                                        std::move( )

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:32:17: warning: [performance-enum-size]

enum 'MHDecision' uses a larger base type ('int', size: 4 bytes) than necessary for its value set, consider using 'std::uint8_t' (1 byte) as the base type to reduce its size
```
   32 |     enum struct MHDecision
      |                 ^
```

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:32:17: warning: [readability-identifier-naming]

invalid case style for enum 'MHDecision'

   32 |     enum struct MHDecision
      |                 ^~~~~~~~~~
      |                 MH_DECISION
   33 |     {
   34 |         Accepted,
   35 |         Rejected,
   36 |         Undecided
   37 |     };
   38 | 
   39 |     template < typename ObjectType >
   40 |     struct StepResult
   41 |     {
   42 |         MHDecision decision{ MHDecision::Undecided };
      |         ~~~~~~~~~~           ~~~~~~~~~~
      |         MH_DECISION          MH_DECISION

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:34:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Accepted'
```
   34 |         Accepted,
      |         ^~~~~~~~
      |         accepted
```
include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:35:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Rejected'
```
   35 |         Rejected,
      |         ^~~~~~~~
      |         rejected
```

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:36:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Undecided'

   36 |         Undecided
      |         ^~~~~~~~~
      |         undecided
   37 |     };
   38 | 
   39 |     template < typename ObjectType >
   40 |     struct StepResult
   41 |     {
   42 |         MHDecision decision{ MHDecision::Undecided };
      |                                          ~~~~~~~~~
      |                                          undecided

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:102:9: warning: [modernize-use-nodiscard]

function 'beta' should be marked [[nodiscard]]
```
  102 |         double beta() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:107:31: warning: [readability-identifier-length]

parameter name 'b' is too short, expected at least 3 characters
```
  107 |         void set_beta( double b )
      |                               ^
```

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:141:43: warning: [google-readability-braces-around-statements]

statement should be inside braces

  141 |             if( std::isnan( log_accept ) )
      |                                           ^
      |                                            {
  142 |                 return 0.0;
      |

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:143:36: warning: [google-readability-braces-around-statements]

statement should be inside braces

  143 |             if( log_accept >= 0.0 )
      |                                    ^
      |                                     {
  144 |                 return 1.0;
      |

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:147:39: warning: [google-readability-braces-around-statements]

statement should be inside braces

  147 |             if( log_accept < LOG_MIN )
      |                                       ^
      |                                        {
  148 |                 return 0.0;
      |

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:153:9: warning: [modernize-use-nodiscard]

function 'compute_log_accept' should be marked [[nodiscard]]
```
  153 |         const double compute_log_accept( const double deltaU,
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:153:9: warning: [readability-const-return-type]

return type 'const double' is 'const'-qualified at the top level, which may reduce code readability without improving const correctness
```
  153 |         const double compute_log_accept( const double deltaU,
      |         ^~~~~
```
include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:156:20: warning: [readability-math-missing-parentheses]

'*' has higher precedence than '+'; add parentheses to explicitly specify the order of operations
```
  156 |             return -beta_ * deltaU + proposal_probas.transition_probability();
      |                    ^~~~~~~~~~~~~~~
      |                    (              )
```

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:160:34: warning: [readability-function-size]

function 'accept_or_reject' exceeds recommended size/complexity thresholds

  160 |         StepResult< ObjectType > accept_or_reject(
      |                                  ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:160:34: note: 5 parameters (threshold 4)

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:165:25: warning: [cppcoreguidelines-missing-std-forward]

forwarding reference parameter 'apply_move' is never forwarded inside the function body
```
  165 |             ApplyMove&& apply_move ) const
      |                         ^
```

include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:178:63: warning: [google-readability-braces-around-statements]

statement should be inside braces

  178 |             if( step_result.decision == MHDecision::Accepted )
      |                                                               ^
      |                                                                {
  179 |                 apply_move( state, proposal );
      |

include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp:34:10: warning: [readability-function-size]

function 'add_birth_death_change_moves' exceeds recommended size/complexity thresholds

   34 |     void add_birth_death_change_moves(
      |          ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp:34:10: note: 6 parameters (threshold 4)

include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp:39:9: warning: [bugprone-easily-swappable-parameters]

2 adjacent parameters of 'add_birth_death_change_moves' of similar type ('double') are easily swapped by mistake

   39 |         double death_ratio,
      |         ^~~~~~~~~~~~~~~~~~~
   40 |         double change_ratio )
      |         ~~~~~~~~~~~~~~~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp:39:16: note: the first parameter in the range is 'death_ratio'
   39 |         double death_ratio,
      |                ^~~~~~~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp:40:16: note: the last parameter in the range is 'change_ratio'
   40 |         double change_ratio )
      |                ^~~~~~~~~~~~

include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:31:16: warning: [performance-enum-size]

enum 'MoveType' uses a larger base type ('int', size: 4 bytes) than necessary for its value set, consider using 'std::uint8_t' (1 byte) as the base type to reduce its size
```
   31 |     enum class MoveType
      |                ^
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:31:16: warning: [readability-identifier-naming]

invalid case style for enum 'MoveType'
```
   31 |     enum class MoveType
      |                ^~~~~~~~
      |                MOVE_TYPE
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:33:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Invalid'
```
   33 |         Invalid,
      |         ^~~~~~~
      |         invalid
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:34:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Birth'
```
   34 |         Birth,
      |         ^~~~~
      |         birth
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:35:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Death'
```
   35 |         Death,
      |         ^~~~~
      |         death
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:36:9: warning: [readability-identifier-naming]

invalid case style for enum constant 'Change'
```
   36 |         Change
      |         ^~~~~~
      |         change
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:43:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   43 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:51:9: warning: [modernize-use-nodiscard]

function 'transition_probability' should be marked [[nodiscard]]
```
   51 |         double transition_probability() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:72:9: warning: [modernize-use-nodiscard]

function 'type_string' should be marked [[nodiscard]]
```
   72 |         std::string type_string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:92:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   92 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:112:11: warning: [cppcoreguidelines-special-member-functions]

class 'Move' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
  112 |     class Move
      |           ^
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:132:9: warning: [modernize-use-nodiscard]

function 'proportion_weight' should be marked [[nodiscard]]
```
  132 |         double proportion_weight() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:142:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
  142 |         virtual std::string string() const = 0;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:160:47: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'sampler_' has protected visibility
```
  160 |         const ObjectSetSampler< ObjectType >& sampler_;
      |                                               ^
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:161:16: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'proportion_weight_' has protected visibility
```
  161 |         double proportion_weight_{ 1.0 };
      |                ^
```

include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:169:13: warning: [bugprone-easily-swappable-parameters]

2 adjacent parameters of 'BirthDeathMove' of similar type ('double') are easily swapped by mistake

  169 |             double probability,
      |             ^~~~~~~~~~~~~~~~~~~
  170 |             double birth_ratio )
      |             ~~~~~~~~~~~~~~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:169:20: note: the first parameter in the range is 'probability'
  169 |             double probability,
      |                    ^~~~~~~~~~~
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:170:20: note: the last parameter in the range is 'birth_ratio'
  170 |             double birth_ratio )
      |                    ^~~~~~~~~~~

include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:198:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
  198 |         std::string string() const override
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:246:30: warning: [cppcoreguidelines-avoid-magic-numbers]

0.5 is a magic number; consider replacing it with a named constant
```
  246 |         double birth_ratio_{ 0.5 };
      |                              ^
```
include/geode/stochastic/sampling/mcmc/proposal/moves.hpp:282:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
  282 |         std::string string() const override
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:60:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   60 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:68:11: warning: [cppcoreguidelines-special-member-functions]

class 'ProposalKernel' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
   68 |     class ProposalKernel
      |           ^
```
include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:103:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
  103 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:122:9: warning: [modernize-use-nodiscard]

function 'compute_probabilities' should be marked [[nodiscard]]
```
  122 |         std::vector< double > compute_probabilities() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:144:56: warning: [readability-identifier-length]

parameter name 'p' is too short, expected at least 3 characters
```
  144 |                 probabilities.begin(), [total]( double p ) {
      |                                                        ^
```

include/geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp:160:45: warning: [google-readability-braces-around-statements]

statement should be inside braces

  160 |             if( !cumulative_probs_.empty() )
      |                                             ^
      |                                              {
  161 |                 cumulative_probs_.back() = 1.0; // ensure exact 1.0
      |

include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:40:31: warning: [cppcoreguidelines-avoid-magic-numbers]

1000 is a magic number; consider replacing it with a named constant
```
   40 |         index_t realizations{ 1000 };
      |                               ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:41:43: warning: [cppcoreguidelines-avoid-magic-numbers]

1000 is a magic number; consider replacing it with a named constant
```
   41 |         index_t metropolis_hasting_steps{ 1000 };
      |                                           ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:42:32: warning: [cppcoreguidelines-avoid-magic-numbers]

1000 is a magic number; consider replacing it with a named constant
```
   42 |         index_t burn_in_steps{ 1000 };
      |                                ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:46:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   46 |         std::string string() const
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:65:11: warning: [cppcoreguidelines-special-member-functions]

class 'SimulationRunner' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
   65 |     class SimulationRunner
      |           ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:68:9: warning: [google-explicit-constructor]

single-argument constructors must be marked explicit to avoid unintentional implicit conversions
```
   68 |         SimulationRunner( const SpatialDomain< ObjectType::dim >& domain )
      |         ^
      |         explicit 
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:139:42: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'domain_' has protected visibility
```
  139 |         SpatialDomain< ObjectType::dim > domain_;
      |                                          ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:141:34: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'object_sets_' has protected visibility
```
  141 |         ObjectSets< ObjectType > object_sets_;
      |                                  ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:143:13: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'set_samplers_' has protected visibility
```
  143 |             set_samplers_;
      |             ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:144:48: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'model_' has protected visibility
```
  144 |         std::unique_ptr< Model< ObjectType > > model_;
      |                                                ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:145:68: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'mh_sampler_' has protected visibility
```
  145 |         std::unique_ptr< geode::MetropolisHastings< ObjectType > > mh_sampler_;
      |                                                                    ^
```
include/geode/stochastic/sampling/mcmc/simulation_runner.hpp:147:57: warning: [cppcoreguidelines-non-private-member-variables-in-classes]

member variable 'target_statistics_' has protected visibility
```
  147 |         std::optional< TargetStatistics< ObjectType > > target_statistics_;
      |                                                         ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:30:5: error: [clang-diagnostic-error]

unknown type name 'FORWARD_DECLARATION_DIMENSION_CLASS'
```
   30 |     FORWARD_DECLARATION_DIMENSION_CLASS( BoundingBox );
      |     ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:30:42: warning: [cppcoreguidelines-avoid-non-const-global-variables]

variable 'BoundingBox' is non-const and globally accessible, consider making it const
```
   30 |     FORWARD_DECLARATION_DIMENSION_CLASS( BoundingBox );
      |                                          ^
```

include/geode/stochastic/spatial/object_neighborhood.hpp:30:42: warning: [readability-identifier-naming]

invalid case style for variable 'BoundingBox'

   30 |     FORWARD_DECLARATION_DIMENSION_CLASS( BoundingBox );
      |                                          ^~~~~~~~~~~
      |                                          bounding_box

include/geode/stochastic/spatial/object_neighborhood.hpp:31:1: warning: [llvm-namespace-comment]

namespace 'geode' not terminated with a closing comment

   31 | }
      | ^
      |   // namespace geode
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/spatial/object_neighborhood.hpp:28:11: note: namespace 'geode' starts here
   28 | namespace geode
      |           ^

include/geode/stochastic/spatial/object_neighborhood.hpp:35:12: warning: [cppcoreguidelines-pro-type-member-init]

constructor does not initialize these fields: index, fixed, set_id

   35 |     struct ObjectId
      |            ^
   36 |     {
   37 |         index_t index;
      |                      
      |                      {}
   38 |         bool fixed;
      |                   
      |                   {}
   39 |         uuid set_id;
      |                    
      |                    {}

include/geode/stochastic/spatial/object_neighborhood.hpp:37:9: error: [clang-diagnostic-error]

unknown type name 'index_t'
```
   37 |         index_t index;
      |         ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:39:9: error: [clang-diagnostic-error]

unknown type name 'uuid'
```
   39 |         uuid set_id;
      |         ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:57:16: error: [clang-diagnostic-error]

unknown type name 'index_t'
```
   57 |     template < index_t dimension >
      |                ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:58:11: warning: [cppcoreguidelines-special-member-functions]

class 'ObjectNeighborhood' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
   58 |     class ObjectNeighborhood
      |           ^
```

include/geode/stochastic/spatial/object_neighborhood.hpp:64:25: error: [clang-diagnostic-error]

no template named 'BoundingBox'

   64 |         void add( const BoundingBox< dimension >& box, const ObjectId& id );
      |                         ^

include/geode/stochastic/spatial/object_neighborhood.hpp:64:72: warning: [readability-identifier-length]

parameter name 'id' is too short, expected at least 3 characters

   64 |         void add( const BoundingBox< dimension >& box, const ObjectId& id );
      |                                                                        ^

include/geode/stochastic/spatial/object_neighborhood.hpp:65:28: error: [clang-diagnostic-error]

no template named 'BoundingBox'
```
   65 |         void update( const BoundingBox< dimension >& old_box,
      |                            ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:66:19: error: [clang-diagnostic-error]

no template named 'BoundingBox'
```
   66 |             const BoundingBox< dimension >& new_box,
      |                   ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:67:29: warning: [readability-identifier-length]

parameter name 'id' is too short, expected at least 3 characters
```
   67 |             const ObjectId& id );
      |                             ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:68:28: error: [clang-diagnostic-error]

no template named 'BoundingBox'
```
   68 |         void update( const BoundingBox< dimension >& box,
      |                            ^
```

include/geode/stochastic/spatial/object_neighborhood.hpp:71:28: error: [clang-diagnostic-error]

no template named 'BoundingBox'

   71 |         void remove( const BoundingBox< dimension >& box, const ObjectId& id );
      |                            ^

include/geode/stochastic/spatial/object_neighborhood.hpp:71:75: warning: [readability-identifier-length]

parameter name 'id' is too short, expected at least 3 characters

   71 |         void remove( const BoundingBox< dimension >& box, const ObjectId& id );
      |                                                                           ^

include/geode/stochastic/spatial/object_neighborhood.hpp:73:9: warning: [modernize-use-nodiscard]

function 'get_all_neighbor_ids' should be marked [[nodiscard]]
```
   73 |         std::vector< ObjectId > get_all_neighbor_ids(
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_neighborhood.hpp:74:19: error: [clang-diagnostic-error]

no template named 'BoundingBox'
```
   74 |             const BoundingBox< dimension >& box,
      |                   ^
```
include/geode/stochastic/spatial/object_neighborhood.hpp:75:32: error: [clang-diagnostic-error]

use of undeclared identifier 'uuid'
```
   75 |             const std::vector< uuid >& targeted_set_ids,
      |                                ^
```
include/geode/stochastic/spatial/object_sets.hpp:50:11: warning: [cppcoreguidelines-special-member-functions]

class 'ObjectSets' defines a copy constructor, a copy assignment operator, a move constructor and a move assignment operator but does not define a destructor
```
   50 |     class ObjectSets
      |           ^
```
include/geode/stochastic/spatial/object_sets.hpp:61:9: warning: [modernize-use-nodiscard]

function 'get_all_object' should be marked [[nodiscard]]
```
   61 |         std::vector< ObjectId > get_all_object() const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:62:9: warning: [modernize-use-nodiscard]

function 'get_objects_in_set' should be marked [[nodiscard]]
```
   62 |         std::vector< ObjectId > get_objects_in_set( const uuid& set_id ) const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:64:9: warning: [modernize-use-nodiscard]

function 'nb_sets' should be marked [[nodiscard]]
```
   64 |         index_t nb_sets() const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:65:9: warning: [modernize-use-nodiscard]

function 'nb_objects_in_set' should be marked [[nodiscard]]
```
   65 |         index_t nb_objects_in_set( const uuid& set_id ) const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:66:9: warning: [modernize-use-nodiscard]

function 'nb_objects' should be marked [[nodiscard]]
```
   66 |         index_t nb_objects() const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:78:9: warning: [modernize-use-nodiscard]

function 'string' should be marked [[nodiscard]]
```
   78 |         std::string string() const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:80:9: warning: [modernize-use-nodiscard]

function 'get_set_uuid' should be marked [[nodiscard]]
```
   80 |         uuid get_set_uuid( std::string_view set_name ) const;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:81:9: warning: [modernize-use-nodiscard]

function 'get_set_uuids' should be marked [[nodiscard]]
```
   81 |         std::vector< uuid > get_set_uuids(
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/object_sets.hpp:83:9: warning: [modernize-use-nodiscard]

function 'get_set_uuid_pairs' should be marked [[nodiscard]]
```
   83 |         std::vector< std::pair< uuid, uuid > > get_set_uuid_pairs(
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/pairwise_interactions/distance_cutoff.hpp:51:9: warning: [modernize-use-nodiscard]

function 'neighborhood_searching_distance' should be marked [[nodiscard]]
```
   51 |         double neighborhood_searching_distance() const override;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/pairwise_interactions/distance_cutoff.hpp:74:9: warning: [modernize-use-nodiscard]

function 'neighborhood_searching_distance' should be marked [[nodiscard]]
```
   74 |         double neighborhood_searching_distance() const override;
      |         ^
      |         [[nodiscard]] 
```
include/geode/stochastic/spatial/pairwise_interactions/pairwise_interactions.hpp:38:11: warning: [cppcoreguidelines-special-member-functions]

class 'PairwiseInteraction' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
   38 |     class PairwiseInteraction
      |           ^
```
include/geode/stochastic/spatial/pairwise_interactions/pairwise_interactions.hpp:41:21: warning: [performance-enum-size]

enum 'SCOPE' uses a larger base type ('int', size: 4 bytes) than necessary for its value set, consider using 'std::uint8_t' (1 byte) as the base type to reduce its size
```
   41 |         enum struct SCOPE
      |                     ^
```
include/geode/stochastic/spatial/pairwise_interactions/pairwise_interactions.hpp:68:9: warning: [modernize-use-nodiscard]

function 'neighborhood_searching_distance' should be marked [[nodiscard]]
```
   68 |         virtual double neighborhood_searching_distance() const = 0;
      |         ^
      |         [[nodiscard]] 
```

include/geode/stochastic/spatial/pairwise_interactions/pairwise_interactions_builder.hpp:50:70: warning: [hicpp-named-parameter]

all parameters should be named in a function

   50 |         build_pairwise_interaction_impl( const NewInteractionConfig& )
      |                                                                      ^
      |                                                                       /*unused*/

include/geode/stochastic/spatial/pairwise_interactions/pairwise_interactions_builder.hpp:59:64: warning: [hicpp-named-parameter]

all parameters should be named in a function

   59 |         build_pairwise_interaction_impl( const std::monostate& )
      |                                                                ^
      |                                                                 /*unused*/

include/geode/stochastic/spatial/single_object_features/segment_length_feature.hpp:29:47: error: [clang-diagnostic-error]

variable has incomplete type 'class opengeode_stochastic_stochastic_api'

   29 |     class opengeode_stochastic_stochastic_api SegmentLengthInsideBoxFeature
      |                                               ^
/__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/spatial/single_object_features/segment_length_feature.hpp:29:11: note: forward declaration of 'geode::opengeode_stochastic_stochastic_api'
   29 |     class opengeode_stochastic_stochastic_api SegmentLengthInsideBoxFeature
      |           ^

include/geode/stochastic/spatial/single_object_features/segment_length_feature.hpp:29:47: warning: [cppcoreguidelines-avoid-non-const-global-variables]

variable 'SegmentLengthInsideBoxFeature' is non-const and globally accessible, consider making it const
```
   29 |     class opengeode_stochastic_stochastic_api SegmentLengthInsideBoxFeature
      |                                               ^
```
include/geode/stochastic/spatial/single_object_features/segment_length_feature.hpp:30:9: error: [clang-diagnostic-error]

expected ';' after top level declarator
```
   30 |         : public SingleObjectFeature< OwnerSegment2D >
      |         ^
      |         ;
```

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francoisbonneau and others added 13 commits March 27, 2026 09:04

file reoganisation

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feat(EnergyTerm): builder for energy terms

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github-actions Bot commented May 25, 2026 •

edited

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