Merge branch 'master' into cornu/modlunit_own_cmake

cmake/ExecuteFindPython/CMakeLists.txt

@@ -2,8 +2,7 @@ cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
 # This is called from PythonHelper.cmake in a subprocess, to allow multiple Python versions to be
 # searched for in the project without CACHE variable hackery.
 project(ExecuteFindPython LANGUAGES C)
-find_package(Python3 COMPONENTS ${Python3_COMPONENTS})
-message(STATUS "Python3_INCLUDE_DIRS=${Python3_INCLUDE_DIRS}")
-message(STATUS "Python3_LIBRARIES=${Python3_LIBRARIES}")
-message(STATUS "Python3_VERSION_MAJOR=${Python3_VERSION_MAJOR}")
-message(STATUS "Python3_VERSION_MINOR=${Python3_VERSION_MINOR}")
+find_package(Python COMPONENTS ${Python_COMPONENTS})
+message(STATUS "Python_INCLUDE_DIRS=${Python_INCLUDE_DIRS}")
+message(STATUS "Python_LIBRARIES=${Python_LIBRARIES}")
+message(STATUS "Python_VERSION=${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}")

cmake/NeuronFileLists.cmake

@@ -349,20 +349,6 @@ set(SCOPMATH_FILES_LIST
 
 set(NRNMPI_FILES_LIST nrnmpi.cpp memory_usage.cpp bbsmpipack.cpp mpispike.cpp)
 
-# nrnpython sources (only if ${NRN_ENABLE_PYTHON_DYNAMIC} is OFF}
-set(NRNPYTHON_FILES_LIST
-    nrnpython.cpp
-    nrnpy_hoc.cpp
-    nrnpy_nrn.cpp
-    nrnpy_p2h.cpp
-    grids.cpp
-    rxd.cpp
-    rxd_extracellular.cpp
-    rxd_intracellular.cpp
-    rxd_vol.cpp
-    rxd_marching_cubes.cpp
-    rxd_llgramarea.cpp)
-
 set(IVOS_FILES_LIST observe.cpp resource.cpp)
 
 set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.inc)
@@ -416,8 +402,6 @@ nrn_create_file_list(NRN_SPARSE_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sparse ${SPA
 nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath
                      ${SCOPMATH_FILES_LIST})
 nrn_create_file_list(NRN_NRNMPI_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi ${NRNMPI_FILES_LIST})
-nrn_create_file_list(NRN_NRNPYTHON_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnpython
-                     ${NRNPYTHON_FILES_LIST})
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/ivoc/ nrnmain.cpp)
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/oc/ ockludge.cpp modlreg.cpp)
 nrn_create_file_list(NRNMPI_DYNAMIC_INCLUDE_FILE ${PROJECT_SOURCE_DIR}/src/nrnmpi

cmake/PythonHelper.cmake

@@ -51,8 +51,7 @@ endif()
 # * nrnpy_EXECUTABLE
 # * nrnpy_INCLUDES
 # * nrnpy_LIBRARIES
-# * nrnpy_VERSION_MAJOR
-# * nrnpy_VERSION_MINOR
+# * nrnpy_VERSION
 #
 # If NRN_ENABLE_PYTHON is *not* set then only nrnpy_EXECUTABLE will be set. There is some special
 # handling on macOS when sanitizers are enabled:
@@ -73,7 +72,7 @@ function(nrn_find_python)
     message(FATAL_ERROR "${opt_KEYWORDS_MISSING_VALUES} values are required")
   endif()
   if(NOT IS_ABSOLUTE "${opt_NAME}")
-    # Find the full path to ${opt_NAME} as Python3_EXECUTABLE does not accept relative paths.
+    # Find the full path to ${opt_NAME} as Python_EXECUTABLE does not accept relative paths.
     find_program(
       "${opt_NAME}_full" "${opt_NAME}"
       PATHS ENV PATH
@@ -88,14 +87,14 @@ function(nrn_find_python)
   endif()
   # Only bother finding version/include/library information if NRN_ENABLE_PYTHON is set.
   if(NRN_ENABLE_PYTHON)
-    # Run find_package(Python3 ...) in a subprocess, so there is no pollution of CMakeCache.txt and
+    # Run find_package(Python ...) in a subprocess, so there is no pollution of CMakeCache.txt and
     # so on. Our desire to include multiple Python versions in one build means we have to handle
     # lists of versions/libraries/... manually. Unfortunately one cannot safely use find_package in
     # CMake script mode, so we configure an extra project.
     string(SHA1 pyexe_hash "${opt_NAME}")
     string(SUBSTRING "${pyexe_hash}" 0 6 pyexe_hash)
     # Which attributes we're trying to learn about this Python
-    set(python_vars Python3_INCLUDE_DIRS Python3_VERSION_MAJOR Python3_VERSION_MINOR)
+    set(python_vars Python_INCLUDE_DIRS Python_VERSION)
     if(NRN_ENABLE_PYTHON_DYNAMIC AND NOT NRN_LINK_AGAINST_PYTHON)
       # Do not link against Python, so we don't need the library -- just as well, it's not available
       # in manylinux
@@ -106,15 +105,15 @@ function(nrn_find_python)
         )
       endif()
       set(dev_component "Development.Module")
-      set(Python3_LIBRARIES "do-not-link-against-libpython-in-dynamic-python-builds")
+      set(Python_LIBRARIES "do-not-link-against-libpython-in-dynamic-python-builds")
     else()
       set(dev_component "Development")
-      list(APPEND python_vars Python3_LIBRARIES)
+      list(APPEND python_vars Python_LIBRARIES)
     endif()
     execute_process(
       COMMAND
-        ${CMAKE_COMMAND} "-DPython3_EXECUTABLE:STRING=${opt_NAME}"
-        "-DPython3_COMPONENTS=${dev_component};Interpreter" -S
+        ${CMAKE_COMMAND} "-DPython_EXECUTABLE:STRING=${opt_NAME}"
+        "-DPython_COMPONENTS=${dev_component};Interpreter" -S
         ${CMAKE_SOURCE_DIR}/cmake/ExecuteFindPython -B
         ${CMAKE_BINARY_DIR}/ExecuteFindPython_${pyexe_hash}
       RESULT_VARIABLE result
@@ -133,16 +132,13 @@ function(nrn_find_python)
       set(${var} "${CMAKE_MATCH_1}")
     endforeach()
     set("${opt_PREFIX}_INCLUDES"
-        "${Python3_INCLUDE_DIRS}"
+        "${Python_INCLUDE_DIRS}"
         PARENT_SCOPE)
     set("${opt_PREFIX}_LIBRARIES"
-        "${Python3_LIBRARIES}"
+        "${Python_LIBRARIES}"
         PARENT_SCOPE)
-    set("${opt_PREFIX}_VERSION_MAJOR"
-        "${Python3_VERSION_MAJOR}"
-        PARENT_SCOPE)
-    set("${opt_PREFIX}_VERSION_MINOR"
-        "${Python3_VERSION_MINOR}"
+    set("${opt_PREFIX}_VERSION"
+        "${Python_VERSION}"
         PARENT_SCOPE)
   endif()
   # Finally do our special treatment for macOS + sanitizers
@@ -195,7 +191,6 @@ foreach(pyexe ${python_executables})
   nrn_find_python(NAME "${pyexe}" PREFIX nrnpy)
   if(NRN_ENABLE_PYTHON)
     # If NRN_ENABLE_PYTHON=OFF then we're only using Python to run build scripts etc.
-    set(nrnpy_VERSION "${nrnpy_VERSION_MAJOR}.${nrnpy_VERSION_MINOR}")
     if(${nrnpy_VERSION} VERSION_LESS NRN_MINIMUM_PYTHON_VERSION)
       message(FATAL_ERROR "${pyexe} too old (${nrnpy_VERSION} < ${NRN_MINIMUM_PYTHON_VERSION})")
     endif()
@@ -207,7 +202,7 @@ foreach(pyexe ${python_executables})
       message(FATAL_ERROR "Cannot handle multiple Python include dirs: ${nrnpy_INCLUDES}")
     endif()
     if(NOT num_lib_dirs EQUAL 1)
-      message(FATAL_ERROR "Cannot handle multiple Python libraries: ${Python3_LIBRARIES}")
+      message(FATAL_ERROR "Cannot handle multiple Python libraries: ${Python_LIBRARIES}")
     endif()
     if(nrnpy_VERSION IN_LIST NRN_PYTHON_VERSIONS)
       # We cannot build against multiple copies of the same pythonX.Y version.
@@ -236,7 +231,6 @@ if(NRN_ENABLE_TESTS AND NRN_ENABLE_PYTHON)
   set(NRN_PYTHON_EXTRA_FOR_TESTS_VERSIONS)
   foreach(pyexe ${NRN_PYTHON_EXTRA_FOR_TESTS})
     nrn_find_python(NAME "${pyexe}" PREFIX nrnpy)
-    set(nrnpy_VERSION "${nrnpy_VERSION_MAJOR}.${nrnpy_VERSION_MINOR}")
     if(nrnpy_VERSION IN_LIST NRN_PYTHON_VERSIONS)
       string(JOIN ", " versions ${NRN_PYTHON_VERSIONS})
       message(FATAL_ERROR "NRN_PYTHON_EXTRA_FOR_TESTS=${NRN_PYTHON_EXTRA_FOR_TESTS} cannot contain"

src/nrniv/CMakeLists.txt

@@ -62,12 +62,6 @@ if(MINGW)
   list(APPEND NRN_NRNIV_LIB_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/dlfcn.c)
 endif()
 
-# NRN_ENABLE_MODULE_INSTALL will create a separate nrnpython lib
-if(NRN_ENABLE_PYTHON AND NOT NRN_ENABLE_PYTHON_DYNAMIC)
-  # Include nrnpython in nrniv - useful for single lib neuron and wheels
-  list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_NRNPYTHON_SRC_FILES})
-endif()
-
 if(NOT NRN_ENABLE_INTERVIEWS)
   list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_IVOS_SRC_FILES})
 endif()
@@ -305,7 +299,7 @@ cpp_cc_configure_sanitizers(TARGET nrniv_lib)
 # Source-directory .cpp needs to find generated .hpp.
 target_include_directories(nrniv_lib PUBLIC "${NRN_OC_GEN}")
 if(NRN_ENABLE_PYTHON AND NOT NRN_ENABLE_PYTHON_DYNAMIC)
-  target_include_directories(nrniv_lib PUBLIC "${NRN_DEFAULT_PYTHON_INCLUDES}")
+  target_link_libraries(nrniv_lib nrnpython)
 endif()
 if(NRN_ENABLE_THREADS)
   target_link_libraries(nrniv_lib Threads::Threads)
@@ -346,10 +340,6 @@ endif()
 # =============================================================================
 # Link with all libraries
 # =============================================================================
-if(NRN_ENABLE_PYTHON AND NOT NRN_ENABLE_PYTHON_DYNAMIC)
-  target_link_libraries(nrniv_lib ${NRN_DEFAULT_PYTHON_LIBRARIES})
-endif()
-
 if(NRN_ENABLE_MPI)
   if(NRN_ENABLE_MPI_DYNAMIC)
     list(LENGTH NRN_MPI_LIBNAME_LIST _num_mpi)
@@ -392,7 +382,7 @@ if(NRN_ENABLE_INTERVIEWS)
   include_directories(${IV_INCLUDE_DIR})
   target_link_libraries(nrniv_lib interviews)
 else()
-  target_include_directories(nrniv_lib PUBLIC ${NRN_IVOS_SRC_DIR} ${PROJECT_BINARY_DIR}/src/ivos)
+  target_include_directories(nrniv_lib PUBLIC ${NRN_IVOS_SRC_DIR})
 endif()
 
 if(IV_ENABLE_X11_DYNAMIC)

src/nrnpython/CMakeLists.txt

@@ -15,30 +15,41 @@ install(TARGETS rxdmath DESTINATION ${NRN_INSTALL_SHARE_LIB_DIR})
 # =============================================================================
 set(nrnpython_lib_list)
 
+set(NRNPYTHON_FILES_LIST
+    nrnpython.cpp
+    nrnpy_hoc.cpp
+    nrnpy_nrn.cpp
+    nrnpy_p2h.cpp
+    grids.cpp
+    rxd.cpp
+    rxd_extracellular.cpp
+    rxd_intracellular.cpp
+    rxd_vol.cpp
+    rxd_marching_cubes.cpp
+    rxd_llgramarea.cpp)
+
+set(INCLUDE_DIRS
+    ..
+    ../oc
+    ../nrnoc
+    ../ivoc
+    ../nrniv
+    ../nrnmpi
+    ${CMAKE_CURRENT_BINARY_DIR}
+    ${PROJECT_BINARY_DIR}/src/oc)
+if(NRN_ENABLE_INTERVIEWS)
+  list(APPEND INCLUDE_DIRS ${IV_INCLUDE_DIR})
+else()
+  list(APPEND INCLUDE_DIRS ../ivos)
+endif()
+
 # user has selected dynamic python support (could be multiple versions)
 if(NRN_ENABLE_PYTHON_DYNAMIC)
-  set(INCLUDE_DIRS
-      .
-      ..
-      ../oc
-      ../nrnoc
-      ../ivoc
-      ../nrniv
-      ../gnu
-      ../nrnmpi
-      ${PROJECT_BINARY_DIR}/src/nrnpython
-      ${PROJECT_BINARY_DIR}/src/ivos
-      ${PROJECT_BINARY_DIR}/src/oc)
-  if(NRN_ENABLE_INTERVIEWS)
-    list(APPEND INCLUDE_DIRS ${IV_INCLUDE_DIR})
-  else()
-    list(APPEND INCLUDE_DIRS ../ivos)
-  endif()
   foreach(val RANGE ${NRN_PYTHON_ITERATION_LIMIT})
     list(GET NRN_PYTHON_VERSIONS ${val} pyver)
     list(GET NRN_PYTHON_INCLUDES ${val} pyinc)
     list(GET NRN_PYTHON_LIBRARIES ${val} pylib)
-    add_library(nrnpython${pyver} SHARED ${NRN_NRNPYTHON_SRC_FILES})
+    add_library(nrnpython${pyver} SHARED ${NRNPYTHON_FILES_LIST})
     target_include_directories(nrnpython${pyver} BEFORE PUBLIC ${pyinc} ${INCLUDE_DIRS})
     target_link_libraries(nrnpython${pyver} nrniv_lib ${Readline_LIBRARY})
     if(NRN_LINK_AGAINST_PYTHON)
@@ -48,6 +59,15 @@ if(NRN_ENABLE_PYTHON_DYNAMIC)
     list(APPEND nrnpython_lib_list nrnpython${pyver})
     install(TARGETS nrnpython${pyver} DESTINATION ${NRN_INSTALL_SHARE_LIB_DIR})
   endforeach()
+else()
+  add_library(nrnpython OBJECT ${NRNPYTHON_FILES_LIST})
+  add_dependencies(nrnpython generated_source_files)
+  set_property(TARGET nrnpython PROPERTY POSITION_INDEPENDENT_CODE ON)
+  target_include_directories(nrnpython PUBLIC ${INCLUDE_DIRS})
+  target_include_directories(nrnpython PUBLIC "${NRN_DEFAULT_PYTHON_INCLUDES}")
+  target_link_libraries(nrnpython ${NRN_DEFAULT_PYTHON_LIBRARIES})
+  target_include_directories(nrnpython PUBLIC ${PROJECT_SOURCE_DIR}/${NRN_3RDPARTY_DIR}/eigen)
+  target_include_directories(nrnpython PUBLIC ${PROJECT_BINARY_DIR}/src/nrniv/oc_generated)
 endif()
 
 configure_file(_config_params.py.in "${PROJECT_BINARY_DIR}/lib/python/neuron/_config_params.py"

src/nrnpython/nrnpy_hoc.cpp

@@ -110,7 +110,7 @@ static void add2topdict(PyObject*);
 static const char* hocobj_docstring = "class neuron.hoc.HocObject - Hoc Object wrapper";
 
 #if 1
-#include <hoccontext.h>
+#include "hoccontext.h"
 #else
 extern Object* hoc_thisobject;
 #define HocTopContextSet  \

src/nrnpython/nrnpy_p2h.cpp

@@ -4,8 +4,8 @@
 #include <InterViews/resource.h>
 #include <nrnoc2iv.h>
 #include <classreg.h>
-#include <nrnpython.h>
-#include <hoccontext.h>
+#include "nrnpython.h"
+#include "hoccontext.h"
 #include "nrnpy.h"
 #include "nrnpy_utils.h"
 #include "oc_ansi.h"

src/nrnpython/nrnpy_utils.h

@@ -1,6 +1,6 @@
 #pragma once
 
-#include <nrnwrap_Python.h>
+#include "nrnwrap_Python.h"
 #include <cassert>
 
 inline bool is_python_string(PyObject* python_string) {

src/nrnpython/nrnpython.cpp

@@ -1,13 +1,13 @@
-#include <nrnpython.h>
-#include <nrnpy_utils.h>
+#include "nrnpython.h"
+#include "nrnpy_utils.h"
 #include "oc_ansi.h"
 #include <stdio.h>
 #include <InterViews/resource.h>
 #if HAVE_IV
 #include <InterViews/session.h>
 #endif
 #include <nrnoc2iv.h>
-#include <hoccontext.h>
+#include "hoccontext.h"
 #include <ocfile.h>  // bool isDirExist(const std::string& path);
 
 #include <hocstr.h>

src/nrnpython/nrnpython.h

@@ -12,7 +12,7 @@
 #if defined(USE_PYTHON)
 #undef _POSIX_C_SOURCE
 #undef _XOPEN_SOURCE
-#include <nrnwrap_Python.h>
+#include "nrnwrap_Python.h"
 
 #endif /*USE_PYTHON*/
 

src/nrnpython/rxd.cpp

@@ -8,8 +8,8 @@
 #include <../nrnoc/section.h>
 #include <../nrnoc/nrn_ansi.h>
 #include <../nrnoc/multicore.h>
-#include <nrnwrap_Python.h>
-#include <nrnpython.h>
+#include "nrnwrap_Python.h"
+#include "nrnpython.h"
 
 #include <thread>
 #include <vector>

src/nrnpython/rxd_extracellular.cpp

@@ -4,7 +4,7 @@
 #include <string.h>
 #include "grids.h"
 #include "rxd.h"
-#include <nrnwrap_Python.h>
+#include "nrnwrap_Python.h"
 #include <cmath>
 #include <ocmatrix.h>
 #include <cfloat>

src/nrnpython/rxd_intracellular.cpp

@@ -4,7 +4,7 @@
 #include <string.h>
 #include "grids.h"
 #include "rxd.h"
-#include <nrnwrap_Python.h>
+#include "nrnwrap_Python.h"
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

src/nrnpython/rxd_vol.cpp

@@ -3,7 +3,7 @@
 #include <assert.h>
 #include "grids.h"
 #include "rxd.h"
-#include <nrnwrap_Python.h>
+#include "nrnwrap_Python.h"
 
 /*Tortuous diffusion coefficients*/
 #define DcX(x, y, z) (g->dc_x * PERM(x, y, z))

test/pyinit/CMakeLists.txt

@@ -167,7 +167,6 @@ foreach(val RANGE ${NRN_PYTHON_COUNT})
           # Not an error if a user's system doesn't have all the names in ${search_names}
           continue()
         endif()
-        set(nrnpy_VERSION "${nrnpy_VERSION_MAJOR}.${nrnpy_VERSION_MINOR}")
         if(NOT nrnpy_VERSION IN_LIST NRN_PYTHON_VERSIONS)
           # e.g. python or python3 points to a version we didn't build against
           continue()