fix(Refactoring): file reorganisation

.clang-format

@@ -21,25 +21,25 @@ AlwaysBreakTemplateDeclarations: true
 BinPackArguments: true
 BinPackParameters: false
 BraceWrapping:
-    AfterClass: true
-    AfterControlStatement: true
-    AfterEnum: true
-    AfterFunction: true
-    AfterNamespace: true
-    AfterObjCDeclaration: true
-    AfterStruct: true
-    AfterUnion: true
-    BeforeCatch: true
-    BeforeElse: true
-    IndentBraces: false
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterObjCDeclaration: true
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: true
+  BeforeElse: true
+  IndentBraces: false
 BreakBeforeBinaryOperators: NonAssignment
 BreakBeforeBraces: Custom
 BreakBeforeTernaryOperators: true
 BreakConstructorInitializers: BeforeColon
 BreakInheritanceList: BeforeColon
 #BreakStringLiterals
 ColumnLimit: 80
-CommentPragmas: ''
+CommentPragmas: ""
 CompactNamespaces: false
 ConstructorInitializerAllOnOneLineOrOnePerLine: true
 ConstructorInitializerIndentWidth: 4

.clang-tidy

@@ -5,29 +5,36 @@
 Checks: >
   *,
   -altera*,
+  -boost*,
   -fuchsia*,
   -llvmlibc*,
   -llvm-header-guard,
+  -llvm-prefer-static-over-anonymous-namespace,
+  -google-readability-todo,
   -misc-no-recursion,
+  -misc-include-cleaner,
+  -misc-const-correctness,
   -modernize-use-trailing-return-type,
+  -portability-avoid-pragma-once,
+  -readability-use-anyofallof,
   -readability-redundant-access-specifiers,
   -readability-convert-member-functions-to-static,
   -cppcoreguidelines-avoid-const-or-ref-data-members
 
 CheckOptions:
-  - key:    misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
-    value:  '1'
+  - key: misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
+    value: "1"
   - key: readability-identifier-length.MinimumLoopCounterNameLength
     value: 1
   - key: readability-identifier-length.IgnoredVariableNames
-    value: '^[defijkptuvw]$'
+    value: "^[_defijkptuvwxyz]$"
   # More options here: https://clang.llvm.org/extra/clang-tidy/checks/readability/identifier-naming.html
   - key: readability-identifier-naming.NamespaceCase
     value: lower_case
   - key: readability-identifier-naming.ClassCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.StructCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.FunctionCase
     value: lower_case
   - key: readability-identifier-naming.VariableCase
@@ -51,14 +58,10 @@ CheckOptions:
   - key: readability-identifier-naming.GlobalFunctionCase
     value: lower_case
   - key: readability-identifier-naming.MemberConstantCase
-    value: CamelCase 
+    value: CamelCase
   - key: readability-identifier-naming.StaticConstantCase
-    value: lower_case 
+    value: lower_case
   - key: readability-function-cognitive-complexity.Threshold
     value: 10
   - key: readability-function-size.ParameterThreshold
     value: 4
-  - key: misc-include-cleaner.IgnoreHeaders
-    value:  utility;cstddef;geode/.*_export\.h;geode/.*/common\.h;geode/basic/types\.h;geode/basic/assert\.h;
-
-

bindings/python/src/common.hpp

@@ -0,0 +1,80 @@
+/*
+ * Copyright (c) 2019 - 2026 Geode-solutions
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ *
+ */
+
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include <absl/container/fixed_array.h>
+#include <absl/container/flat_hash_map.h>
+#include <absl/container/inlined_vector.h>
+#include <absl/types/span.h>
+
+namespace pybind11
+{
+    namespace detail
+    {
+        template < typename Type >
+        struct type_caster< absl::FixedArray< Type > >
+            : list_caster< absl::FixedArray< Type >, Type >
+        {
+        };
+
+        template < typename Type, size_t dimension >
+        struct type_caster< absl::InlinedVector< Type, dimension > >
+            : list_caster< absl::InlinedVector< Type, dimension >, Type >
+        {
+        };
+
+        template < typename Type >
+        struct type_caster< absl::Span< Type > >
+            : list_caster< absl::Span< Type >, Type >
+        {
+            using value_conv = make_caster< Type >;
+
+            bool load( handle src, bool convert )
+            {
+                cpp_.clear();
+                auto s = reinterpret_borrow< sequence >( src );
+                cpp_.reserve( s.size() );
+                for( auto it : s )
+                {
+                    value_conv conv;
+                    if( !conv.load( it, convert ) )
+                        return false;
+                    cpp_.push_back( cast_op< Type&& >( std::move( conv ) ) );
+                }
+                this->value = absl::MakeConstSpan( cpp_ );
+                return true;
+            }
+
+            std::vector< typename std::remove_const< Type >::type > cpp_;
+        };
+
+        template < typename Key, typename Value >
+        struct type_caster< absl::flat_hash_map< Key, Value > >
+            : map_caster< absl::flat_hash_map< Key, Value >, Key, Value >
+        {
+        };
+    } // namespace detail
+} // namespace pybind11

bindings/python/src/stochastic/CMakeLists.txt

@@ -24,7 +24,7 @@ add_geode_python_binding(
         "sampling/mcmc/helpers/fracture_simulation_runner.hpp"
         "sampling/mcmc/helpers/simulation_monitor.hpp"
         "sampling/mcmc/helpers/simulation_printer.hpp"
-        "sampling/mcmc/helpers/simulation_runner.hpp"
+        "sampling/mcmc/simulation_runner.hpp"
         "sampling/direct/double_sampler.hpp"
         "sampling/random_engine.hpp"
         "sampling/distributions.hpp"

bindings/python/src/stochastic/sampling/mcmc/helpers/simulation_runner.hpp → bindings/python/src/stochastic/sampling/mcmc/simulation_runner.hpp

@@ -20,9 +20,10 @@
  * SOFTWARE.
  *
  */
+#include "../../../common.hpp"
 
 #include <geode/stochastic/sampling/mcmc/helpers/simulation_printer.hpp>
-#include <geode/stochastic/sampling/mcmc/helpers/simulation_runner.hpp>
+#include <geode/stochastic/sampling/mcmc/simulation_runner.hpp>
 
 namespace geode
 {

bindings/python/src/stochastic/stochastic.cpp

@@ -29,7 +29,7 @@
 #include "sampling/mcmc/helpers/fracture_simulation_runner.hpp"
 #include "sampling/mcmc/helpers/simulation_monitor.hpp"
 #include "sampling/mcmc/helpers/simulation_printer.hpp"
-#include "sampling/mcmc/helpers/simulation_runner.hpp"
+#include "sampling/mcmc/simulation_runner.hpp"
 
 #include "sampling/distributions.hpp"
 #include "sampling/random_engine.hpp"

include/geode/stochastic/common.hpp

@@ -26,6 +26,7 @@
 #include <geode/basic/common.hpp>
 #include <geode/basic/library.hpp>
 #include <geode/basic/logger.hpp>
+
 #include <geode/stochastic/opengeode_stochastic_stochastic_export.hpp>
 
 namespace geode

include/geode/stochastic/inference/abc_shadow.hpp

@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2019 - 2026 Geode-solutions
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ *
+ */

include/geode/stochastic/models/spatial_model.hpp

@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2019 - 2026 Geode-solutions
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ *
+ */

include/geode/stochastic/sampling/direct/bounding_box_sampler.hpp

@@ -37,8 +37,8 @@
 namespace geode
 {
 
-    template < index_t dimension >
+    template < local_index_t dimension >
     class BoundingBoxSampler
     {
     public:
         explicit BoundingBoxSampler( const BoundingBox< dimension >& box );

include/geode/stochastic/sampling/direct/point_uniform_sampler.hpp

@@ -26,6 +26,8 @@
 
 #include <variant>
 
+#include <geode/stochastic/common.hpp>
+
 namespace geode
 {
     FORWARD_DECLARATION_DIMENSION_CLASS( BoundingBox );

include/geode/stochastic/sampling/mcmc/models/components/density_term.hpp → include/geode/stochastic/sampling/mcmc/energy_terms/density_term.hpp

@@ -24,7 +24,7 @@
 
 #include <geode/stochastic/spatial/object_sets.hpp>
 
-#include <geode/stochastic/sampling/mcmc/models/components/single_object_term.hpp>
+#include <geode/stochastic/sampling/mcmc/energy_terms/single_object_term.hpp>
 
 namespace geode
 {
@@ -46,10 +46,9 @@ namespace geode
                   std::move( targeted_set_ids ),
                   1.0, // scale by domain area to get density per unit
                   []( const ObjectType& obj,
-                      const SpatialDomain< ObjectType::dim >& domain ) {
-                      if( SpatialDomainChecker<
-                              ObjectType >::is_anchored_in_domain( domain,
-                              obj ) )
+                      const SpatialDomain< ObjectType::dim >& spatial_domain ) {
+                      if( SpatialDomainChecker< ObjectType >::
+                              is_anchored_in_domain( spatial_domain, obj ) )
                       {
                           return 1.0;
                       }