Maybe make the bindings properly this time

vgteam · Dec 4, 2024 · 645f0f2 · 645f0f2
1 parent 0a68c99
commit 645f0f2
Show file tree

Hide file tree

Showing 30 changed files with 3,019 additions and 2,779 deletions.
diff --git a/bdsg/cmake_bindings/bdsg.cpp b/bdsg/cmake_bindings/bdsg.cpp
@@ -1,7 +1,8 @@
 #include <map>
+#include <algorithm>
+#include <functional>
 #include <memory>
 #include <stdexcept>
-#include <functional>
 #include <string>
 
 #include <pybind11/pybind11.h>
@@ -20,11 +21,12 @@ void bind_bdsg_graph_proxy_1(std::function< pybind11::module &(std::string const
 void bind_bdsg_internal_wang_hash(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_internal_mapped_structs(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_internal_mapped_structs_1(std::function< pybind11::module &(std::string const &namespace_) > &M);
-void bind_bdsg_internal_utility(std::function< pybind11::module &(std::string const &namespace_) > &M);
+void bind_bdsg_internal_hash_map(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_expanding_overlay_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_strand_split_overlay(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_internal_is_single_stranded(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_internal_eades_algorithm(std::function< pybind11::module &(std::string const &namespace_) > &M);
+void bind_bdsg_internal_base_packed_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_path_position_handle_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_packed_path_position_overlay(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_packed_path_position_overlay_1(std::function< pybind11::module &(std::string const &namespace_) > &M);
@@ -49,13 +51,22 @@ PYBIND11_MODULE(bdsg, root_module) {
 
 	modules[""] = root_module;
 
+	static std::vector<std::string> const reserved_python_words {"nonlocal", "global", };
+
+	auto mangle_namespace_name(
+		[](std::string const &ns) -> std::string {
+			if ( std::find(reserved_python_words.begin(), reserved_python_words.end(), ns) == reserved_python_words.end() ) return ns;
+			else return ns+'_';
+		}
+	);
+
 	std::vector< std::pair<std::string, std::string> > sub_modules {
 		{"", "bdsg"},
 		{"bdsg", "algorithms"},
 		{"", "handlegraph"},
 		{"", "std"},
 	};
-	for(auto &p : sub_modules ) modules[p.first.size() ? p.first+"::"+p.second : p.second] = modules[p.first].def_submodule(p.second.c_str(), ("Bindings for " + p.first + "::" + p.second + " namespace").c_str() );
+	for(auto &p : sub_modules ) modules[p.first.size() ? p.first+"::"+p.second : p.second] = modules[p.first].def_submodule( mangle_namespace_name(p.second).c_str(), ("Bindings for " + p.first + "::" + p.second + " namespace").c_str() );
 
 	//pybind11::class_<std::shared_ptr<void>>(M(""), "_encapsulated_data_");
 
@@ -71,11 +82,12 @@ PYBIND11_MODULE(bdsg, root_module) {
 	bind_bdsg_internal_wang_hash(M);
 	bind_bdsg_internal_mapped_structs(M);
 	bind_bdsg_internal_mapped_structs_1(M);
-	bind_bdsg_internal_utility(M);
+	bind_bdsg_internal_hash_map(M);
 	bind_handlegraph_expanding_overlay_graph(M);
 	bind_bdsg_overlays_strand_split_overlay(M);
 	bind_bdsg_internal_is_single_stranded(M);
 	bind_bdsg_internal_eades_algorithm(M);
+	bind_bdsg_internal_base_packed_graph(M);
 	bind_handlegraph_path_position_handle_graph(M);
 	bind_bdsg_overlays_packed_path_position_overlay(M);
 	bind_bdsg_overlays_packed_path_position_overlay_1(M);

diff --git a/bdsg/cmake_bindings/bdsg.sources b/bdsg/cmake_bindings/bdsg.sources
@@ -11,11 +11,12 @@ bdsg/graph_proxy_1.cpp
 bdsg/internal/wang_hash.cpp
 bdsg/internal/mapped_structs.cpp
 bdsg/internal/mapped_structs_1.cpp
-bdsg/internal/utility.cpp
+bdsg/internal/hash_map.cpp
 handlegraph/expanding_overlay_graph.cpp
 bdsg/overlays/strand_split_overlay.cpp
 bdsg/internal/is_single_stranded.cpp
 bdsg/internal/eades_algorithm.cpp
+bdsg/internal/base_packed_graph.cpp
 handlegraph/path_position_handle_graph.cpp
 bdsg/overlays/packed_path_position_overlay.cpp
 bdsg/overlays/packed_path_position_overlay_1.cpp

diff --git a/bdsg/cmake_bindings/bdsg/graph_proxy.cpp b/bdsg/cmake_bindings/bdsg/graph_proxy.cpp
@@ -19,8 +19,8 @@
 #include <utility>
 #include <vector>
 
-#include <pybind11/pybind11.h>
 #include <functional>
+#include <pybind11/pybind11.h>
 #include <string>
 #include <bdsg/internal/binder_hook_compile.hpp>
 #include <pybind11/stl.h>
@@ -31,9 +31,9 @@
 
 #ifndef BINDER_PYBIND11_TYPE_CASTER
 	#define BINDER_PYBIND11_TYPE_CASTER
-	PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
-	PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
-	PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
+	PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>)
+	PYBIND11_DECLARE_HOLDER_TYPE(T, T*)
+	PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>)
 #endif
 
 void bind_bdsg_graph_proxy(std::function< pybind11::module &(std::string const &namespace_) > &M)

diff --git a/bdsg/cmake_bindings/bdsg/graph_proxy_1.cpp b/bdsg/cmake_bindings/bdsg/graph_proxy_1.cpp
@@ -18,8 +18,8 @@
 #include <utility>
 #include <vector>
 
-#include <pybind11/pybind11.h>
 #include <functional>
+#include <pybind11/pybind11.h>
 #include <string>
 #include <bdsg/internal/binder_hook_compile.hpp>
 #include <pybind11/stl.h>
@@ -30,9 +30,9 @@
 
 #ifndef BINDER_PYBIND11_TYPE_CASTER
 	#define BINDER_PYBIND11_TYPE_CASTER
-	PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
-	PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
-	PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
+	PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>)
+	PYBIND11_DECLARE_HOLDER_TYPE(T, T*)
+	PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>)
 #endif
 
 void bind_bdsg_graph_proxy_1(std::function< pybind11::module &(std::string const &namespace_) > &M)