Include pyAMReX.H & ODR Fix

We provide a single helper include now for all pyAMReX compilation
units (TUs) / cpp files.

This ensures that optional pybind11 includes, e.g., for stl, numpy,
functions and operators, are consistently present in all TUs. This is
required to avoid C++ one-definition-rule (ODR) violations, which are
undefined behavior and thus could cause instabilities down the road.

src/AmrCore/AmrMesh.cpp

@@ -3,19 +3,17 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Config.H>
-#include <AMReX_AmrMesh.H>
+#include "pyAMReX.H"
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include <AMReX_AmrMesh.H>
 
 #include <sstream>
 
-namespace py = pybind11;
-using namespace amrex;
 
+void init_AmrMesh(py::module &m)
+{
+ using namespace amrex;
 
-void init_AmrMesh(py::module &m) {
  py::class_< AmrInfo >(m, "AmrInfo")
  .def("__repr__",
  [](AmrInfo const & amr_info) {
@@ -75,6 +73,5 @@ void init_AmrMesh(py::module &m) {
  .def("finest_level", &AmrMesh::finestLevel)
  .def("ref_ratio", py::overload_cast< >(&AmrMesh::refRatio, py::const_))
  .def("ref_ratio", py::overload_cast< int >(&AmrMesh::refRatio, py::const_))
-
  ;
 }

src/Base/AMReX.cpp

@@ -1,29 +1,27 @@
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX.H>
 #include <AMReX_Vector.H>
 #include <AMReX_ParmParse.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
-
 #include <string>
 
-namespace py = pybind11;
-using namespace amrex;
 
 namespace amrex {
  struct Config {};
 }
 
 void init_AMReX(py::module& m)
 {
+ using namespace amrex;
+
  py::class_<AMReX>(m, "AMReX")
  .def_static("empty", &AMReX::empty)
  .def_static("size", &AMReX::size)
  .def_static("erase", &AMReX::erase)
  .def_static("top", &AMReX::top,
  py::return_value_policy::reference)
-  ;
+ ;
 
  py::class_<Config>(m, "Config")
  .def_property_readonly_static(

src/Base/Arena.cpp

@@ -3,17 +3,14 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Arena.H>
-
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-#include <pybind11/stl.h>
+#include "pyAMReX.H"
 
-namespace py = pybind11;
-using namespace amrex;
+#include <AMReX_Arena.H>
 
 
 void init_Arena(py::module &m) {
+ using namespace amrex;
+
  py::class_< Arena >(m, "Arena");
 
  m.def("The_Arena", &The_Arena, py::return_value_policy::reference)

src/Base/Array4.cpp

@@ -3,24 +3,21 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
+#include "pyAMReX.H"
+
 #include <AMReX_Array4.H>
 #include <AMReX_BLassert.H>
 #include <AMReX_IntVect.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-#include <pybind11/stl.h>
-
 #include <cstdint>
 #include <sstream>
 #include <type_traits>
 
-namespace py = pybind11;
-using namespace amrex;
-
 
 namespace
 {
+ using namespace amrex;
+
  /** CPU: __array_interface__ v3
  *
  * https://numpy.org/doc/stable/reference/arrays.interface.html
@@ -77,6 +74,8 @@ namespace
 template< typename T >
 void make_Array4(py::module &m, std::string typestr)
 {
+ using namespace amrex;
+
  // dispatch simpler via: py::format_descriptor<T>::format() naming
  auto const array_name = std::string("Array4_").append(typestr);
  py::class_< Array4<T> >(m, array_name.c_str())

src/Base/BaseFab.cpp

@@ -3,18 +3,17 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_FArrayBox.H>
+#include "pyAMReX.H"
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include <AMReX_FArrayBox.H>
 
 #include <istream>
 
-namespace py = pybind11;
-using namespace amrex;
 
 namespace
 {
+ using namespace amrex;
+
  template< typename T >
  void init_bf(py::module &m, std::string typestr) {
  auto const bf_name = std::string("BaseFab_").append(typestr);
@@ -122,5 +121,7 @@ namespace
 }
 
 void init_BaseFab(py::module &m) {
+ using namespace amrex;
+
  init_bf<Real>(m, "Real");
 }

src/Base/Box.cpp

@@ -3,22 +3,19 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX_Box.H>
 #include <AMReX_IntVect.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/operators.h>
-#include <pybind11/stl.h>
-
 #include <sstream>
 #include <optional>
 
-namespace py = pybind11;
-using namespace amrex;
 
 namespace
 {
+ using namespace amrex;
+
  /** A little Wrapper class to iterate an amrex::Box via
  * amrex::Box::next().
  */
@@ -66,8 +63,9 @@ namespace
 }
 
 void init_Box(py::module &m) {
- py::class_< Direction >(m, "Direction");
+ using namespace amrex;
 
+ py::class_< Direction >(m, "Direction");
 
 
  py::class_< Box >(m, "Box")

src/Base/BoxArray.cpp

@@ -3,20 +3,17 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX_BoxArray.H>
 #include <AMReX_IntVect.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
-
 #include <sstream>
 
-namespace py = pybind11;
-using namespace amrex;
-
 
 void init_BoxArray(py::module &m) {
+ using namespace amrex;
+
  /* A collection of Boxes stored in an Array. It is a
  * reference-counted concrete class, not a polymorphic one; i.e. you
  * cannot use any of the List member functions with a BoxList

src/Base/CoordSys.cpp

@@ -1,16 +1,12 @@
-#include <AMReX_Config.H>
-#include <AMReX_CoordSys.H>
-
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include "pyAMReX.H"
 
-#include <sstream>
+#include <AMReX_CoordSys.H>
 
-namespace py = pybind11;
-using namespace amrex;
 
 void init_CoordSys(py::module& m)
 {
+ using namespace amrex;
+
  py::class_<CoordSys> coord_sys(m, "CoordSys");
  coord_sys.def("__repr__",
  [](const CoordSys&) {

src/Base/Dim3.cpp

@@ -1,16 +1,14 @@
-#include <AMReX_Config.H>
-#include <AMReX_Dim3.H>
+#include "pyAMReX.H"
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include <AMReX_Dim3.H>
 
 #include <sstream>
 
-namespace py = pybind11;
-using namespace amrex;
 
 void init_Dim3(py::module& m)
 {
+ using namespace amrex;
+
  py::class_<Dim3>(m, "Dim3")
  .def("__repr__",
  [](const Dim3& d) {

src/Base/DistributionMapping.cpp

@@ -3,21 +3,18 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX_BoxArray.H>
 #include <AMReX_DistributionMapping.H>
 #include <AMReX_Vector.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
-
 #include <sstream>
 
-namespace py = pybind11;
-using namespace amrex;
-
 
 void init_DistributionMapping(py::module &m) {
+ using namespace amrex;
+
  py::class_< DistributionMapping >(m, "DistributionMapping")
  .def("__repr__",
  [](DistributionMapping const & dm) {

src/Base/FArrayBox.cpp

@@ -3,20 +3,18 @@
  * Authors: Axel Huebl
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_FArrayBox.H>
+#include "pyAMReX.H"
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
+#include <AMReX_FArrayBox.H>
 
 #include <istream>
 #include <ostream>
 #include <string>
 
-namespace py = pybind11;
-using namespace amrex;
-
 
 void init_FArrayBox(py::module &m) {
+ using namespace amrex;
+
  py::class_< FArrayBox, BaseFab<Real> >(m, "FArrayBox")
  .def("__repr__",
  [](FArrayBox const & /* fab */) {

src/Base/Geometry.cpp

@@ -1,22 +1,19 @@
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX_Geometry.H>
 #include <AMReX_CoordSys.H>
 #include <AMReX_MultiFab.H>
 #include <AMReX_Periodicity.H>
 
-#include <pybind11/pybind11.h>
-// #include <pybind11/operators.h>
-#include <pybind11/stl.h>
-
 #include <sstream>
 #include <string>
 #include <stdexcept>
 
-namespace py = pybind11;
-using namespace amrex;
 
 void init_Geometry(py::module& m)
 {
+ using namespace amrex;
+
  py::class_<GeometryData>(m, "GeometryData")
  .def("__repr__",
  [](const GeometryData&) {

src/Base/IndexType.cpp

@@ -3,21 +3,16 @@
  * Authors: David Grote
  * License: BSD-3-Clause-LBNL
  */
-#include <AMReX_Config.H>
+#include "pyAMReX.H"
+
 #include <AMReX_Dim3.H>
 #include <AMReX_IntVect.H>
 #include <AMReX_IndexType.H>
 
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
-#include <pybind11/numpy.h>
-
 #include <array>
 #include <sstream>
 #include <string>
 
-namespace py = pybind11;
-using namespace amrex;
 
 namespace {
  int check_index(const int i)
@@ -30,6 +25,8 @@ namespace {
 }
 
 void init_IndexType(py::module &m) {
+ using namespace amrex;
+
  py::class_< IndexType > index_type(m, "IndexType");
  index_type.def("__repr__",
  [](py::object& obj) {