PyNEST-NG: A new Python interface for NEST directly connecting Python to C++

.github/workflows/nestbuildmatrix.yml

@@ -581,8 +581,6 @@ jobs:
         # available use flags (all default to "OFF"):
         # openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning, userdoc, music, readline
         use:
-          - "optimize, warning"
-          - "boost, optimize, warning"
           - "openmp, python, gsl, ltdl, boost, optimize, warning"
           - "mpi, python, gsl, ltdl, boost, optimize, warning"
           - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, music, detailed-timers, threaded-timers, mpi-sync-timer"
@@ -778,7 +776,6 @@ jobs:
               -Dwith-python=${{ contains(matrix.use, 'python') && 'ON' || 'OFF' }} \
               -Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' || 'OFF' }} \
               -Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' || 'OFF' }} \
-              -Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' || 'OFF' }} \
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
@@ -910,7 +907,6 @@ jobs:
               -Dwith-python=${{ contains(matrix.use, 'python') && 'ON' || 'OFF' }} \
               -Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' || 'OFF' }} \
               -Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' || 'OFF' }} \
-              -Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' || 'OFF' }} \
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \

.pre-commit-config.yaml

@@ -39,8 +39,8 @@ repos:
           "testsuite/run_test.sh",
           "testsuite/do_tests.sh",
           "testsuite/junit_xml.sh",
-          "examples/run_examples.sh",
-          "examples/list_examples.sh",
+          "pynest/examples/run_examples.sh",
+          "pynest/examples/list_examples.sh",
         ]
 
   - repo: https://github.com/pre-commit/mirrors-clang-format

.pylintrc

@@ -6,7 +6,7 @@
 options = unneeded-not, line-too-long, unnecessary-semicolon, trailing-whitespace, missing-final-newline, bad-indentation, multiple-statements, bare-except
 ignore = CVS .git conda env __pycache__ .pytest_cache .mypy_cache
 
-disable = no-member, redefined-outer-name, invalid-name, consider-using-f-string, wrong-import-order, missing-function-docstring, missing-method-docstring, missing-class-docstring, attribute-defined-outside-init, no-else-return, cell-var-from-loop, import-error, pointless-string-statement, unused-import, redefined-builtin, superfluous-parens, unused-variable, too-many-locals, consider-using-from-import, consider-using-enumerate, no-name-in-module, too-many-arguments, too-many-instance-attributes, import-outside-toplevel, too-few-public-methods, cyclic-import, missing-module-docstring, unidiomatic-typecheck, dangerous-default-value, unused-argument, use-dict-literal, exec-used, no-self-use, too-many-statements, ungrouped-imports, consider-using-sys-exit, too-many-statements, redundant-u-string-prefix, protected-access, consider-using-dict-comprehension, no-else-raise, too-many-nested-blocks, use-a-generator, reimported, undefined-variable, too-many-branches, raise-missing-from, trailing-comma-tuple, unspecified-encoding, consider-using-with, f-string-without-interpolation, broad-except, unnecessary-pass, global-statement, too-many-lines, consider-merging-isinstance, redefined-argument-from-local, global-variable-undefined, use-implicit-booleaness-not-len, inconsistent-return-statements, consider-using-in, inconsistent-return-statements, keyword-arg-before-vararg, consider-using-dict-items, import-self, fixme, c-extension-no-member, too-many-public-methods, consider-iterating-dictionary, consider-using-max-builtin, super-with-arguments, expression-not-assigned, unnecessary-comprehension, no-self-argument, chained-comparison, undefined-loop-variable, empty-docstring, use-maxsplit-arg, pointless-statement, wrong-import-position, redundant-unittest-assert, eval-used, not-callable, invalid-unary-operand-type, consider-using-generator, R0801, unnecessary-dunder-call, logging-fstring-interpolation, consider-using-get, useless-object-inheritance, unrecognized-option, unknown-option-value, useless-option-value
+disable = no-member, redefined-outer-name, invalid-name, consider-using-f-string, wrong-import-order, missing-function-docstring, missing-method-docstring, missing-class-docstring, attribute-defined-outside-init, no-else-return, cell-var-from-loop, import-error, pointless-string-statement, unused-import, redefined-builtin, superfluous-parens, unused-variable, too-many-locals, consider-using-from-import, consider-using-enumerate, no-name-in-module, too-many-arguments, too-many-instance-attributes, too-many-return-statements, import-outside-toplevel, too-few-public-methods, cyclic-import, missing-module-docstring, unidiomatic-typecheck, dangerous-default-value, unused-argument, use-dict-literal, exec-used, no-self-use, too-many-statements, ungrouped-imports, consider-using-sys-exit, too-many-statements, redundant-u-string-prefix, protected-access, consider-using-dict-comprehension, no-else-raise, too-many-nested-blocks, use-a-generator, reimported, undefined-variable, too-many-branches, raise-missing-from, trailing-comma-tuple, unspecified-encoding, consider-using-with, f-string-without-interpolation, broad-except, unnecessary-pass, global-statement, too-many-lines, consider-merging-isinstance, redefined-argument-from-local, global-variable-undefined, use-implicit-booleaness-not-len, inconsistent-return-statements, consider-using-in, inconsistent-return-statements, keyword-arg-before-vararg, consider-using-dict-items, import-self, fixme, c-extension-no-member, too-many-public-methods, consider-iterating-dictionary, consider-using-max-builtin, super-with-arguments, expression-not-assigned, unnecessary-comprehension, no-self-argument, chained-comparison, undefined-loop-variable, empty-docstring, use-maxsplit-arg, pointless-statement, wrong-import-position, redundant-unittest-assert, eval-used, not-callable, invalid-unary-operand-type, consider-using-generator, R0801, unnecessary-dunder-call, logging-fstring-interpolation, consider-using-get, useless-object-inheritance, unrecognized-option, unknown-option-value, useless-option-value
 
 const-naming-style = snake_case
 method-naming-style = PascalCase

CMakeLists.txt

@@ -23,6 +23,11 @@ cmake_minimum_required( VERSION 3.19 )
 list( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake )
 
 project( nest CXX C )
+
+set( CMAKE_CXX_STANDARD 17 )
+set( CMAKE_CXX_STANDARD_REQUIRED True )
+set( CMAKE_CXX_EXTENSIONS OFF )          # -std=c++17 instead of gnu++17
+
 set( NEST_USER_EMAIL "users@nest-simulator.org" )
 
 include( ColorMessages )
@@ -50,15 +55,14 @@ option( cythonize-pynest "Use Cython to cythonize pynestkernel.pyx [default=ON].
 
 # select parallelization scheme
 set( with-mpi OFF CACHE STRING "Build with MPI parallelization [default=OFF]." )
-set( with-openmp ON CACHE BOOL "Build with OpenMP multi-threading [default=ON]. Optionally set OMP compiler flags." )
+set( with-openmp ON CACHE BOOL "Build with OpenMP multi-threading [default=ON]." )
 
 # external libraries
 set( with-libneurosim OFF CACHE STRING "Build with libneurosim [default=OFF]. Optionally give the directory where libneurosim is installed." )
 set( with-music OFF CACHE STRING "Build with MUSIC [default=OFF]. Optionally give the directory where MUSIC is installed." )
 set( with-sionlib OFF CACHE STRING "Build with SIONlib [default=OFF]. Optionally give the directory where sionlib is installed." )
 set( with-boost ON CACHE STRING "Build with Boost [default=ON]. To set a specific Boost installation, give the install path." )
 set( with-hdf5 OFF CACHE STRING "Find a HDF5 library. To set a specific HDF5 installation, set install path. [default=ON]" )
-set( with-readline ON CACHE STRING "Build with GNU Readline library [default=ON]. To set a specific library, give the install path." )
 set( with-ltdl ON CACHE STRING "Build with ltdl library [default=ON]. To set a specific ltdl, give the  install path. NEST uses ltdl for dynamic loading of external user modules." )
 set( with-gsl ON CACHE STRING "Build with the GSL library [default=ON]. To set a specific library, give the install path." )
 
@@ -77,7 +81,6 @@ option( static-libraries "Build static executable and libraries [default=OFF]" O
 set( with-optimize ON CACHE STRING "Enable user defined optimizations [default=ON (uses '-O2')]. When OFF, no '-O' flag is passed to the compiler. Explicit compiler flags can be given; separate multiple flags by ';'." )
 set( with-warning ON CACHE STRING "Enable user defined warnings [default=ON (uses '-Wall')]. Separate  multiple flags by ';'." )
 set( with-debug OFF CACHE STRING "Enable user defined debug flags [default=OFF]. When ON, '-g' is used. Separate  multiple flags by ';'." )
-set( with-cpp-std "c++17" CACHE STRING "C++ standard to use for compilation [default='c++17']." )
 set( with-intel-compiler-flags OFF CACHE STRING "User defined flags for the Intel compiler [default='-fp-model strict']. Separate multiple flags by ';'." )
 set( with-libraries OFF CACHE STRING "Link additional libraries [default=OFF]. Give full path. Separate multiple libraries by ';'." )
 set( with-includes OFF CACHE STRING "Add additional include paths [default=OFF]. Give full path without '-I'. Separate multiple include paths by ';'." )
@@ -130,7 +133,6 @@ get_target_triple( NEST_TARGET_TRIPLE NEST_TARGET_ARCH NEST_TARGET_VENDOR NEST_T
 nest_process_with_python()
 include( GNUInstallDirs )
 nest_post_process_with_python()
-nest_process_with_std()
 nest_process_with_intel_compiler_flags()
 nest_process_with_warning()
 nest_process_with_libraries()
@@ -140,7 +142,6 @@ nest_process_static_libraries()
 nest_process_tics_per_ms()
 nest_process_tics_per_step()
 nest_process_with_libltdl()
-nest_process_with_readline()
 nest_process_with_gsl()
 nest_process_with_openmp()
 nest_process_with_mpi()
@@ -222,13 +223,9 @@ add_custom_target( installcheck
 
 add_subdirectory( doc )
 add_subdirectory( bin )
-add_subdirectory( examples )
 add_subdirectory( build_support )
-add_subdirectory( lib )
 add_subdirectory( libnestutil )
 add_subdirectory( models )
-add_subdirectory( sli )
-add_subdirectory( nest )
 add_subdirectory( nestkernel )
 add_subdirectory( thirdparty )
 add_subdirectory( testsuite )
@@ -275,10 +272,7 @@ endforeach ()
 
 # libraries required to link extension modules
 set( MODULE_LINK_LIBS
-  "-lnest"
-  "-lsli"
   "${LTDL_LIBRARIES}"
-  "${READLINE_LIBRARIES}"
   "${GSL_LIBRARIES}"
   "${LIBNEUROSIM_LIBRARIES}"
   "${MUSIC_LIBRARIES}"
@@ -302,10 +296,10 @@ set( ALL_LIBS
 set( ALL_INCLUDES_tmp
   "${CMAKE_INSTALL_FULL_INCLUDEDIR}/nest"
   "${LTDL_INCLUDE_DIRS}"
-  "${READLINE_INCLUDE_DIRS}"
   "${GSL_INCLUDE_DIRS}"
   "${LIBNEUROSIM_INCLUDE_DIRS}"
   "${MUSIC_INCLUDE_DIRS}"
+  "${OpenMP_CXX_INCLUDE_DIRS}"
   "${MPI_CXX_INCLUDE_PATH}"
   "${BOOST_INCLUDE_DIR}" )
 set( ALL_INCLUDES "" )
@@ -357,6 +351,10 @@ configure_file(
 
 install( FILES LICENSE README.md
     DESTINATION ${CMAKE_INSTALL_DOCDIR}
-    )
+)
+
+install( DIRECTORY examples/
+    DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples
+)
 
 nest_print_config_summary()

bin/nest-config.in

@@ -66,7 +66,7 @@ while test $# -gt 0; do
         echo "@ALL_INCLUDES@"
         ;;
     --cflags)
-        echo "@ALL_CXXFLAGS@"
+        echo "@ALL_CXXFLAGS@ -std=c++@CMAKE_CXX_STANDARD@"
         ;;
     --libs)
         echo "-L${prefix}/@CMAKE_INSTALL_LIBDIR@/nest @MODULE_LINK_LIBS@"

bin/nest-server

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 DAEMON="${NEST_SERVER_DAEMON:-0}"
 HOST="${NEST_SERVER_HOST:-127.0.0.1}"

build_support/check_copyright_headers.py

@@ -54,7 +54,7 @@ def eprint(*args, **kwargs):
 EXIT_NO_SOURCE = 126
 
 try:
-    heuristic_folders = "nest nestkernel build_support models .git"
+    heuristic_folders = "pynest nestkernel build_support models .git"
     if "NEST_SOURCE" not in os.environ:
         if all([name in os.listdir() for name in heuristic_folders.split()]):
             os.environ["NEST_SOURCE"] = "."

build_support/check_forbidden_types.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # check_forbidden_types.sh
 #

build_support/check_unused_names.py

@@ -60,7 +60,7 @@ def eprint(*args, **kwargs):
 EXIT_NO_SOURCE = 126
 
 try:
-    heuristic_folders = "nest nestkernel build_support models .git"
+    heuristic_folders = "pynest nestkernel build_support models .git"
     if "NEST_SOURCE" not in os.environ:
         if all([name in os.listdir() for name in heuristic_folders.split()]):
             os.environ["NEST_SOURCE"] = "."
@@ -93,17 +93,9 @@ def get_names(fname, pattern):
 names_defined = set()
 for names_file in names_files:
     fname = os.path.join(source_dir, names_file)
-
-    names_header = get_names(fname + ".h", r"extern\s+const\s+Name\s+(\w+)\s*;")
-    names_source = get_names(fname + ".cpp", r"const\s+Name\s+(\w+)\(.*")
-
-    for h, s in zip(names_header, names_source):
-        if h != s:
-            eprint(f"[NAME] {names_file}: inconsistent declaration: {h} != {s}")
-            print(f"... {names_file}\\n")
-            sys.exit(EXIT_NAME_H_CPP_MISMATCH)
-        else:
-            names_defined.add(h)
+    names_header = get_names(fname + ".h", r"const\s+std::string\s+(\w+)\(.*")
+    for h in names_header:
+        names_defined.add(h)
 
 
 # We call to recursive grep in the shell here, because that's much

build_support/install_csa-libneurosim.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -euo pipefail
 
 NEUROSIM_INSTALL_PATH="${1:-${HOME}/.cache/libneurosim.install}"

build_support/install_music.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -euo pipefail
 
 MUSIC_INSTALL_PATH="${1:-${HOME}/.cache/music.install}"

build_support/install_sionlib.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -euo pipefail
 
 SIONLIBVERSION="1.7.4"

build_support/version_info.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # version_info.sh
 #

cmake/ConfigureSummary.cmake

@@ -91,11 +91,6 @@ function( NEST_PRINT_CONFIG_SUMMARY )
   message( "" )
   if ( BUILD_DOCS )
     message( "Documentation       : Yes" )
-    if ( BUILD_SLI_DOCS)
-      message( "  SLI doc build     : Yes" )
-    else()
-      message( "  SLI doc build     : No" )
-    endif()
     if ( BUILD_SPHINX_DOCS )
       message( "  Sphinx doc build  : Yes (${SPHINX_EXECUTABLE})" )
     else()
@@ -121,15 +116,6 @@ function( NEST_PRINT_CONFIG_SUMMARY )
     message( "Use GSL             : No" )
   endif ()
 
-  message( "" )
-  if ( HAVE_READLINE )
-    message( "Use Readline        : Yes (GNU Readline ${READLINE_VERSION})" )
-    message( "    Includes        : ${READLINE_INCLUDE_DIRS}" )
-    message( "    Libraries       : ${READLINE_LIBRARIES}" )
-  else ()
-    message( "Use Readline        : No" )
-  endif ()
-
   message( "" )
   if ( HAVE_LIBLTDL )
     message( "Use libltdl         : Yes (LTDL ${LTDL_VERSION})" )

cmake/Platform/Fugaku_FCC.cmake

@@ -26,8 +26,6 @@ set( TRIPLET_VENDOR fujitsu )
 # Set Fugaku for main CMakeList.txt
 #
 set( Fugaku ON CACHE BOOL "Enable Fugaku." FORCE )
-# no readline support on Fugaku
-set( with-readline OFF CACHE BOOL "Find a readline library [default=ON]. To set a specific readline, set install path." FORCE )
 set( with-ltdl OFF CACHE BOOL "Find a ltdl library [default=ON]. To set a specific ltdl, set install path." FORCE )
 # we obviously want to do mpi on Fugaku
 set( with-mpi ON CACHE BOOL "Request compilation with MPI; optionally give directory with MPI installation." FORCE )