feat(Sampler): add genericity

[francoisbonneau]

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Cpp-Linter Report ⚠️

Some files did not pass the configured checks!

clang-tidy (v20.1.8) reports: 12 concern(s)

• include/geode/stochastic/inference/statistics_tracker.hpp:38:9: warning: [google-explicit-constructor]

  single-argument constructors must be marked explicit to avoid unintentional implicit conversions

     38 |         StatisticsTracker( const Model< ObjectType >& model ) : model_{ model }
        |         ^
        |         explicit 

• include/geode/stochastic/inference/statistics_tracker.hpp:54:17: warning: [readability-qualified-auto]

  'auto &value' can be declared as 'const auto &value'

     54 |                 auto& value = values[value_id];
        |                 ^
        |                 const 

• include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:168:34: warning: [readability-function-size]

  function 'accept_or_reject' exceeds recommended size/complexity thresholds

    168 |         StepResult< ObjectType > accept_or_reject(
        |                                  ^
  /__w/OpenGeode-Stochastic/OpenGeode-Stochastic/include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp:168:34: note: 5 parameters (threshold 4)

• 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 )
        |                ^~~~~~~~~~~~

• src/geode/stochastic/spatial/object_sets.cpp:36:14: warning: [readability-identifier-length]

  variable name 'it' is too short, expected at least 3 characters

     36 |         auto it = uuid_to_index_.find( set_id );
        |              ^

• src/geode/stochastic/spatial/object_sets.cpp:205:43: warning: [cppcoreguidelines-avoid-magic-numbers]

  2. is a magic number; consider replacing it with a named constant

    205 |         box.extends( searching_distance * 2. );
        |                                           ^

• tests/stochastic/sampling/mcmc/proposal/test-proposal-kernel.cpp:115:25: warning: [bugprone-unchecked-optional-access]

  unchecked access to optional value

    115 |                         proposed_move.old_object_id.value()
        |                         ^

• tests/stochastic/sampling/mcmc/proposal/test-proposal-kernel.cpp:135:25: warning: [bugprone-unchecked-optional-access]

  unchecked access to optional value

    135 |                         proposed_move.old_object_id.value()
        |                         ^

• tests/stochastic/sampling/mcmc/test-metropolis-hasting-sampler.cpp:25:10: error: [clang-diagnostic-error]

  'geode/stochastic/models/energy_terms/density_term.hpp' file not found

     25 | #include <geode/stochastic/models/energy_terms/density_term.hpp>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• tests/stochastic/sampling/test-random-engine.cpp:183:10: warning: [readability-function-size]

  function 'test_truncated_gaussian' exceeds recommended size/complexity thresholds

    183 |     void test_truncated_gaussian( double mean_value,
        |          ^
  /__w/OpenGeode-Stochastic/OpenGeode-Stochastic/tests/stochastic/sampling/test-random-engine.cpp:183:10: note: 5 parameters (threshold 4)

• tests/stochastic/sampling/test-random-engine.cpp:183:35: warning: [bugprone-easily-swappable-parameters]

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

    183 |     void test_truncated_gaussian( double mean_value,
        |                                   ^~~~~~~~~~~~~~~~~~
    184 |         double std_value,
        |         ~~~~~~~~~~~~~~~~
  /__w/OpenGeode-Stochastic/OpenGeode-Stochastic/tests/stochastic/sampling/test-random-engine.cpp:183:42: note: the first parameter in the range is 'mean_value'
    183 |     void test_truncated_gaussian( double mean_value,
        |                                          ^~~~~~~~~~
  /__w/OpenGeode-Stochastic/OpenGeode-Stochastic/tests/stochastic/sampling/test-random-engine.cpp:184:16: note: the last parameter in the range is 'std_value'
    184 |         double std_value,
        |                ^~~~~~~~~

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