Merge branch 'master' into remove_nest_vars_sh

Author: terhorstd

.clang-format

@@ -110,7 +110,7 @@ SpaceBeforeInheritanceColon: true
 SpaceBeforeParens: ControlStatements
 SpaceBeforeRangeBasedForLoopColon: true
 SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
+SpacesBeforeTrailingComments: 2
 SpacesInAngles:  true
 SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: true

.github/workflows/build_nest_wheel.yml

@@ -1,9 +1,6 @@
 name: Build NEST simulator wheels
 
 on:
-  push:
-    branches: [master, pynest-ng, hep_pynest-ng]
-  pull_request:
   release:
     types: [published]
   workflow_dispatch:

.github/workflows/nestbuildmatrix.yml

@@ -10,7 +10,7 @@ jobs:
   clang-format:
     runs-on: "ubuntu-22.04"
     env:
-      CLANG_REQUIRE_VERSION: 17.0.4
+      CLANG_REQUIRE_VERSION: 22.1.0
       CLANG_FORMAT_FILE: ".clang-format"
     steps:
       - name: Harden Runner
@@ -30,7 +30,7 @@ jobs:
 
       - name: "Run clang-format..."
         run: |
-          files=$(find . \( -iname "*.h" -o -iname "*.c" -o -iname "*.cc" -o -iname "*.cpp" \) -not -path "./thirdparty/*")
+          files=$(find . \( -iname "*.h" -o -iname "*.c" -o -iname "*.cc" -o -iname "*.cpp" \) -not -path "./thirdparty/*" -not -path "./cmake/CheckFiles/*")
           diff -u <(cat ${files}) <(clang-format ${files})
 
   shellcheck:
@@ -62,7 +62,7 @@ jobs:
       - name: "Set up Python 3.x"
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: "Install dependencies"
         run: |
@@ -442,7 +442,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Run black..."
-        uses: psf/black@af0ba72a73598c76189d6dd1b21d8532255d5942  # 25.9.0
+        uses: psf/black@6305bf1ae645ab7541be4f5028a86239316178eb  # 26.1.0
         with:
           jupyter: true
 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -15,19 +15,19 @@ repos:
       - id: gitleaks
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 8.0.1
     hooks:
       - id: isort
         args: ["--profile", "black", "--thirdparty", "nest"]
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 26.1.0
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.10.0.1
+    rev: v0.11.0.1
     hooks:
       - id: shellcheck
         # explicitly add input files that are not "*.sh"
@@ -50,7 +50,7 @@ repos:
         ]
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v17.0.4
+    rev: v22.1.0
     hooks:
       - id: clang-format
         types_or: [c++]

build_support/check_copyright_headers.py

@@ -38,7 +38,6 @@
 
 """
 
-
 import os
 import re
 import sys

build_support/generate_modelsmodule.py

@@ -246,16 +246,12 @@ def generate_modelsmodule():
     modeldir.mkdir(parents=True, exist_ok=True)
     with open(modeldir / fname, "w") as file:
         file.write(copyright_header.replace("{{file_name}}", fname))
-        file.write(
-            dedent(
-                """
+        file.write(dedent("""
             #include "models.h"
 
             // Generated includes
             #include "config.h"
-        """
-            )
-        )
+        """))
 
         for model_type, guards_fnames in includes.items():
             file.write(f"\n// {model_type.capitalize()} models\n")

cmake/ProcessOptions.cmake

@@ -173,9 +173,8 @@ function( NEST_PROCESS_STATIC_LIBRARIES )
 
     # Note: "$ORIGIN" (on Linux) and "@loader_path" (on MacOS) are not CMake variables, but special keywords for the
     # Linux resp. the macOS dynamic loader. They refer to the path in which the object is located, e.g.
-    # ``${CMAKE_INSTALL_PREFIX}/bin`` for the nest and sli executables, ``${CMAKE_INSTALL_PREFIX}/lib/nest`` for all
-    # dynamic libraries except PyNEST (libnestkernel.so, etc.), and  something like
-    # ``${CMAKE_INSTALL_PREFIX}/lib/python3.x/site-packages/nest`` for ``pynestkernel.so``. The RPATH is relative to
+    # ``${CMAKE_INSTALL_PREFIX}/bin`` for helper scripts and  something like
+# ``${CMAKE_INSTALL_PREFIX}/lib/python3.x/site-packages/nest`` for ``nestkernel_api.so``. The RPATH is relative to
     # this origin, so the binary ``bin/nest`` can find the files in the relative location ``../lib/nest``, and
     # similarly for PyNEST and the other libraries. For simplicity, we set all the possibilities on all generated
     # objects.

doc/fulldoc.conf.in

@@ -746,13 +746,11 @@ WARN_LOGFILE           = doxygen.log
 INPUT		=	@PROJECT_SOURCE_DIR@/README.md \
 			@PROJECT_SOURCE_DIR@/doc \
 			@PROJECT_SOURCE_DIR@/examples \
-			@PROJECT_SOURCE_DIR@/lib \
 			@PROJECT_SOURCE_DIR@/libnestutil \
 			@PROJECT_SOURCE_DIR@/models \
 			@PROJECT_SOURCE_DIR@/nest \
 			@PROJECT_SOURCE_DIR@/nestkernel \
 			@PROJECT_SOURCE_DIR@/pynest \
-			@PROJECT_SOURCE_DIR@/sli \
 			@PROJECT_SOURCE_DIR@/testsuite
 
 # This tag can be used to specify the character encoding of the source files

doc/htmldoc/conf.py

@@ -68,7 +68,12 @@
     "notfound.extension",
 ]
 
-autodoc_mock_imports = ["nest.pynestkernel", "nest.ll_api"]
+autodoc_mock_imports = [
+    "nest.nestkernel_api",  # compiled binary
+    "flask",  # optional server dependencies not present during docs build
+    "flask_cors",
+    "RestrictedPython",
+]
 mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["templates"]
@@ -100,6 +105,9 @@
 
 # disable require js - mermaid doesn't work if require.js is loaded before it
 nbsphinx_requirejs_path = ""
+# Never execute notebooks during the build; render stored cell outputs as-is.
+# nest is not importable in the docs environment (compiled kernel not present).
+nbsphinx_execute = "never"
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.

doc/htmldoc/developer_space/templates/pynest_api_template.py

@@ -36,7 +36,6 @@
 ]]
 """
 
-
 from msilib.schema import Error