Merge pull request #189 from vgteam/packed-edge-count

Fix PackedGraph edge counting

.github/workflows/testmac.yml

@@ -15,7 +15,7 @@ on:
 jobs:
   testmac:
     name: Test on Mac
-    runs-on: macos-10.15
+    runs-on: macos-latest
 
     steps:
       - name: Checkout code with submodules

CMakeLists.txt

@@ -192,7 +192,7 @@ if (BUILD_PYTHON_BINDINGS)
     # Binder (because some generated bindings depend on headers packaged with Binder)
     ExternalProject_Add(binder
       GIT_REPOSITORY "https://github.com/RosettaCommons/binder.git"
-      GIT_TAG "788ab422f9e919478944d79d5890441a964dd1db"
+      GIT_TAG "ee2ecff151d125c3add072a7765aebad6f42a70d"
       # we don't actually build or install Binder via its CMake because we just need its headers
       #CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR}
       CONFIGURE_COMMAND ""
@@ -209,7 +209,7 @@ if (BUILD_PYTHON_BINDINGS)
         if (NOT EXISTS "${PROJECT_SOURCE_DIR}/pybind11")
             message(WARNING "Running on CMake without FetchContent_Declare; attempting to download pybind11 manually")
             execute_process(COMMAND git clone https://github.com/RosettaCommons/pybind11.git "${PROJECT_SOURCE_DIR}/pybind11")
-            execute_process(COMMAND git checkout 4f72ef846fe8453596230ac285eeaa0ce3278bb4
+            execute_process(COMMAND git checkout 5b0a6fc2017fcc176545afe3e09c9f9885283242
                             WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}/pybind11")
         endif()
 
@@ -225,7 +225,7 @@ if (BUILD_PYTHON_BINDINGS)
         FetchContent_Declare(
             pybind11
             GIT_REPOSITORY https://github.com/RosettaCommons/pybind11.git
-            GIT_TAG 4f72ef846fe8453596230ac285eeaa0ce3278bb4
+            GIT_TAG 5b0a6fc2017fcc176545afe3e09c9f9885283242
         )
         FetchContent_GetProperties(pybind11)
         if (NOT pybind11_POPULATED)

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>
@@ -12,20 +13,20 @@ void bind_handlegraph_types(std::function< pybind11::module &(std::string const
 void bind_handlegraph_handle_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_path_metadata(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_path_handle_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
+void bind_std_bdsg_internal_binder_hook_bind(std::function< pybind11::module &(std::string const &namespace_) > &M);
+void bind_handlegraph_mutable_path_metadata(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_mutable_path_mutable_handle_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_graph_proxy(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_graph_proxy_1(std::function< pybind11::module &(std::string const &namespace_) > &M);
 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_mapped_structs_2(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_handlegraph_snarl_decomposition(std::function< pybind11::module &(std::string const &namespace_) > &M);
-void bind_std_bdsg_internal_binder_hook_bind(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);
@@ -50,35 +51,43 @@ 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"},
-		{"bdsg", "yomo"},
 		{"", "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_");
 
 	bind_handlegraph_types(M);
 	bind_handlegraph_handle_graph(M);
 	bind_handlegraph_path_metadata(M);
 	bind_handlegraph_path_handle_graph(M);
+	bind_std_bdsg_internal_binder_hook_bind(M);
+	bind_handlegraph_mutable_path_metadata(M);
 	bind_handlegraph_mutable_path_mutable_handle_graph(M);
 	bind_bdsg_graph_proxy(M);
 	bind_bdsg_graph_proxy_1(M);
 	bind_bdsg_internal_wang_hash(M);
 	bind_bdsg_internal_mapped_structs(M);
 	bind_bdsg_internal_mapped_structs_1(M);
-	bind_bdsg_internal_mapped_structs_2(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_handlegraph_snarl_decomposition(M);
-	bind_std_bdsg_internal_binder_hook_bind(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);

bdsg/cmake_bindings/bdsg.modules

@@ -1 +1 @@
-bdsg bdsg.algorithms bdsg.yomo handlegraph std 
+bdsg bdsg.algorithms handlegraph std 

bdsg/cmake_bindings/bdsg.sources

@@ -3,20 +3,20 @@ handlegraph/types.cpp
 handlegraph/handle_graph.cpp
 handlegraph/path_metadata.cpp
 handlegraph/path_handle_graph.cpp
+std/bdsg/internal/binder_hook_bind.cpp
+handlegraph/mutable_path_metadata.cpp
 handlegraph/mutable_path_mutable_handle_graph.cpp
 bdsg/graph_proxy.cpp
 bdsg/graph_proxy_1.cpp
 bdsg/internal/wang_hash.cpp
 bdsg/internal/mapped_structs.cpp
 bdsg/internal/mapped_structs_1.cpp
-bdsg/internal/mapped_structs_2.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
-handlegraph/snarl_decomposition.cpp
-std/bdsg/internal/binder_hook_bind.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