Update pybind11 version to v2.8.1 release

.gitmodules

@@ -2,7 +2,7 @@
 	path = 3rdparty/HighFive
 	url = https://github.com/BlueBrain/HighFive.git
 [submodule "3rdparty/pybind11"]
-	path = 3rdparty/pybind11
+	path = binds/python/pybind11
 	url = https://github.com/pybind/pybind11.git
 [submodule "3rdparty/GSL_LITE"]
 	path = 3rdparty/GSL_LITE

3rdparty/CMakeLists.txt

@@ -14,9 +14,3 @@ target_include_directories(gsl-lite SYSTEM INTERFACE)
 
 add_library(lexertl INTERFACE)
 target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)
-
-if(BUILD_BINDINGS)
-  add_subdirectory(pybind11)
-  target_include_directories(pybind11 SYSTEM INTERFACE
-    pybind11)
-endif()

CHANGELOG.md

@@ -1,16 +1,36 @@
+v3.3.3
+======
+
+New Features
+    * Vasculature section_offsets & section_connectivity (#352)
+    * n_points method for immutable Morphology and Vasculature (#359)
+
+Fixes:
+    * Fixed documentation links (#350)
+    * Python version check >=3.7 (#356)
+    * Updated pybind11 submodule to v2.8.1 (#362)
+
+v3.3.2
+======
+
+Fixes:
+    * Fixed wheel uploading (#355)
+
 v3.3.1
+======
 
 New Features:
     * Dendritic spine (#321)
 
 Fixes:
-    * updated tests
-    * use std::make_unique (#333)
-    * don't compile c++ tests when creating python package (#332)
-    * remove unused AccessMode enum (#331)
     * Imbue enums with numeric operations (#330)
-    * allow lowercase neurite names
-    * allow whitespace in CellBody neurite
+    * Remove unused AccessMode enum (#331)
+    * Don't compile c++ tests when creating python package (#332)
+    * Use std::make_unique (#333)
+    * Updated tests (#340)
+    * Allow lowercase neurite names
+    * Allow whitespace in CellBody neurite
+    * Excluded musslinux wheels from building (#354)
 
 Previously:
 - The first neurite point is no longer connected to the soma. It was previously

CMakeLists.txt

@@ -27,6 +27,9 @@ set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
 include(CompilerFlags)
 set(CMAKE_CXX_FLAGS "${FLAGS}")
 
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 if (EXTERNAL_HIGHFIVE)
   find_package(HighFive REQUIRED)
 endif()

MANIFEST.in

@@ -1,7 +1,9 @@
-recursive-include src *
-recursive-include binds *
-recursive-include include *
+# MorphIO c++
+graft src
+graft include
+include CMakeLists.txt
 
+# MorphIO submodule dependencies
 include 3rdparty/GSL_LITE/CMakeLists.txt 3rdparty/GSL_LITE/gsl-lite.natvis
 recursive-include 3rdparty/GSL_LITE/cmake/ *
 recursive-include 3rdparty/GSL_LITE/include/ *
@@ -11,11 +13,20 @@ recursive-include 3rdparty/HighFive/include/ *
 recursive-include 3rdparty/HighFive/CMake/ *
 recursive-include 3rdparty/HighFive/doc/ *
 
-recursive-include 3rdparty/pybind11/include/ *
-include 3rdparty/pybind11/CMakeLists.txt
-
 include 3rdparty/lexertl14/CMakeLists.txt
 recursive-include 3rdparty/lexertl14/include/lexertl/ *
 
-recursive-include 3rdparty/pybind11/tools/ *
-include CMakeLists.txt
+# pybind11 for python bindings
+recursive-include binds/python/pybind11/include *
+recursive-include binds/python/pybind11/tools *.cmake
+include binds/python/pybind11/CMakeLists.txt
+include binds/python/pybind11/LICENSE
+
+# setuptools_scm forces all SCM files to be packaged into sdist
+# we need to manually exclude them to prevent their inclusion
+# see https://github.com/pypa/setuptools_scm/issues/190
+prune ci
+prune doc
+prune tests
+prune scripts
+prune examples

binds/python/CMakeLists.txt

@@ -1,18 +1,15 @@
-pybind11_add_module(_morphio
-    SYSTEM
+add_subdirectory(pybind11 EXCLUDE_FROM_ALL)
+
+pybind11_add_module(_morphio SYSTEM
     morphio.cpp
     bind_immutable.cpp
     bindings_utils.cpp
     bind_misc.cpp
     bind_mutable.cpp
     bind_vasculature.cpp
-    )
-
-target_include_directories(_morphio
-  PRIVATE
-  ${CMAKE_CURRENT_SOURCE_DIR}/../../include
-  )
+)
 
 target_link_libraries(_morphio
-    PRIVATE
-    morphio_static)
+    PRIVATE morphio_static
+    PRIVATE pybind11::module
+)