Pynest ng

.github/workflows/nestbuildmatrix.yml

@@ -524,7 +524,6 @@ jobs:
         # available use flags (all default to "OFF"):
         # openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning, userdoc, music
         use:
-          - "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"
@@ -565,7 +564,7 @@ jobs:
           sudo apt-get update
           # https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
           sudo apt-get install ccache
-          sudo apt-get install libltdl-dev libreadline6-dev libncurses5-dev libgsl0-dev python3-all-dev jq libpcre3 libpcre3-dev
+          sudo apt-get install libltdl-dev libgsl0-dev python3-all-dev jq libpcre3 libpcre3-dev
           sudo apt-get install tcl8.6 tcl8.6-dev tk8.6-dev
           # Install MPI dependencies regardless of whether we compile NEST with or without MPI, so the installation of MPI4Py works
           sudo apt-get install openmpi-bin libopenmpi-dev
@@ -674,7 +673,6 @@ 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') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
@@ -806,7 +804,6 @@ jobs:
               -Dwith-python=${{ 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

@@ -23,11 +23,6 @@ repos:
       - id: black
         language_version: python3
 
-  - repo: https://github.com/koalaman/shellcheck-precommit
-    rev: v0.9.0
-    hooks:
-      - id: shellcheck
-
   - repo: https://github.com/pre-commit/mirrors-clang-format
     rev: v17.0.4
     hooks:

.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." )
 
@@ -130,7 +134,6 @@ 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 +143,6 @@ 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 +224,9 @@ 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 +273,7 @@ endforeach ()
 
 # libraries required to link extension modules
 set( MODULE_LINK_LIBS
-  "-lnest"
-  "-lsli"
   "${LTDL_LIBRARIES}"
-  "${READLINE_LIBRARIES}"
   "${GSL_LIBRARIES}"
   "${LIBNEUROSIM_LIBRARIES}"
   "${MUSIC_LIBRARIES}"
@@ -302,7 +297,6 @@ set( ALL_LIBS
 set( ALL_INCLUDES_tmp
   "${CMAKE_INSTALL_FULL_INCLUDEDIR}/nest"
   "${LTDL_INCLUDE_DIRS}"
-  "${READLINE_INCLUDE_DIRS}"
   "${GSL_INCLUDE_DIRS}"
   "${LIBNEUROSIM_INCLUDE_DIRS}"
   "${MUSIC_INCLUDE_DIRS}"
@@ -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()

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_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

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 )

cmake/ProcessOptions.cmake

@@ -45,10 +45,6 @@ function( NEST_PROCESS_WITH_DEBUG )
   endif ()
 endfunction()
 
-function( NEST_PROCESS_WITH_STD )
-  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=${with-cpp-std}" PARENT_SCOPE )
-endfunction()
-
 function( NEST_PROCESS_WITH_INTEL_COMPILER_FLAGS )
   if ( NOT with-intel-compiler-flags )
     set( with-intel-compiler-flags "-fp-model strict" )
@@ -143,10 +139,6 @@ function( NEST_PROCESS_STATIC_LIBRARIES )
   # build static or shared libraries
   if ( static-libraries )
 
-    if ( with-readline )
-      printError( "-Dstatic-libraries=ON requires -Dwith-readline=OFF" )
-    endif ()
-
     set( BUILD_SHARED_LIBS OFF PARENT_SCOPE )
     # set RPATH stuff
     set( CMAKE_SKIP_RPATH TRUE PARENT_SCOPE )
@@ -261,30 +253,6 @@ function( NEST_PROCESS_WITH_LIBLTDL )
   endif ()
 endfunction()
 
-function( NEST_PROCESS_WITH_READLINE )
-  # Find readline
-  set( HAVE_READLINE OFF PARENT_SCOPE )
-  if ( with-readline )
-    if ( NOT ${with-readline} STREQUAL "ON" )
-      # a path is set
-      set( Readline_ROOT "${with-readline}" )
-    endif ()
-
-    find_package( Readline )
-    if ( READLINE_FOUND )
-      set( HAVE_READLINE ON PARENT_SCOPE )
-      # export found variables to parent scope
-      set( READLINE_FOUND "${READLINE_FOUND}" PARENT_SCOPE )
-      set( READLINE_LIBRARIES "${READLINE_LIBRARIES}" PARENT_SCOPE )
-      set( READLINE_INCLUDE_DIRS "${READLINE_INCLUDE_DIRS}" PARENT_SCOPE )
-      set( READLINE_VERSION "${READLINE_VERSION}" PARENT_SCOPE )
-
-      include_directories( ${READLINE_INCLUDE_DIRS} )
-      # is linked in sli/CMakeLists.txt
-    endif ()
-  endif ()
-endfunction()
-
 function( NEST_PROCESS_WITH_GSL )
   # Find GSL
   set( HAVE_GSL OFF PARENT_SCOPE )
@@ -667,7 +635,6 @@ function( NEST_PROCESS_USERDOC )
     message( STATUS "Configuring user documentation" )
     find_package( Sphinx REQUIRED)
     find_package( Pandoc REQUIRED)
-    set( BUILD_SLI_DOCS ON PARENT_SCOPE )
     set( BUILD_SPHINX_DOCS ON PARENT_SCOPE )
     set( BUILD_DOCS ON PARENT_SCOPE )
   endif ()