Merge branch 'master' into nest-server-cleanup

Author: terhorstd

.github/workflows/nestbuildmatrix.yml

@@ -290,6 +290,19 @@ jobs:
       - name: "Run pylint..."
         run: |
           pylint --jobs=$(nproc) pynest/ testsuite/pytests/*.py testsuite/regressiontests/*.py
+  
+  isort:
+    runs-on: "ubuntu-20.04"
+    steps:
+      - name: "Checkout repository content"
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: "Run isort..."
+        uses: isort/isort-action@f14e57e1d457956c45a19c05a89cccdf087846e5  # 1.1.0
+        with:
+          configuration: --profile=black --thirdparty="nest" --check-only --diff
 
   black:
     runs-on: "ubuntu-20.04"
@@ -298,8 +311,9 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
+
       - name: "Run black..."
-        uses: psf/black@bf7a16254ec96b084a6caf3d435ec18f0f245cc7   # 23.3.0
+        uses: psf/black@193ee766ca496871f93621d6b58d57a6564ff81b  # 23.7.0
         with:
           jupyter: true
 
@@ -405,7 +419,7 @@ jobs:
   build_linux:
     if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
     runs-on: ${{ matrix.os }}
-    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, black, flake8]
+    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
     env:
       CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
       NEST_VPATH: "build"
@@ -607,7 +621,7 @@ jobs:
   build_macos:
     if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
     runs-on: ${{ matrix.os }}
-    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, black, flake8]
+    needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
     env:
       CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
       NEST_VPATH: "build"

.pre-commit-config.yaml

@@ -1,6 +1,22 @@
 repos:
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--thirdparty", "nest", "--diff"]
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v13.0.0
+    hooks:
+      - id: clang-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

bin/nest-server-mpi

@@ -19,14 +19,13 @@ from mpi4py import MPI
 if __name__ == "__main__":
     opt = docopt(__doc__)
 
-import time
+import os
 import sys
+import time
 
 import nest
 import nest.server
 
-import os
-
 HOST = os.getenv("NEST_SERVER_HOST", "127.0.0.1")
 PORT = os.getenv("NEST_SERVER_PORT", "52425")
 

build_support/check_copyright_headers.py

@@ -40,8 +40,8 @@
 
 
 import os
-import sys
 import re
+import sys
 
 
 def eprint(*args, **kwargs):

build_support/check_unused_names.py

@@ -40,8 +40,8 @@
 """
 
 import os
-import sys
 import re
+import sys
 from subprocess import check_output
 
 

build_support/format_all_c_c++_files.sh

@@ -2,10 +2,15 @@
 
 # With this script you can easily format all C/C++ files contained in
 # any (sub)directory of NEST. Internally it uses clang-format to do
-# the actual formatting. You can give a different clang-format command,
-# e.g. by executing `CLANG_FORMAT=clang-format-14 ./format_all_c_c++_files.sh`.
+# the actual formatting. 
+# 
+# NEST C/C++ code should be formatted according to clang-format version 13.0.0.
+# If you would like to see how the code will be formatted with a different
+# clang-format version, execute e.g. `CLANG_FORMAT=clang-format-14 ./format_all_c_c++_files.sh`.
+#
 # By default the script starts at the current working directory ($PWD), but
 # supply a different starting directory as the first argument to the command.
+
 CLANG_FORMAT=${CLANG_FORMAT:-clang-format}
 CLANG_FORMAT_FILE=${CLANG_FORMAT_FILE:-.clang-format}
 

build_support/generate_modelsmodule.py

@@ -26,10 +26,9 @@
 compiled by CMake.
 """
 
+import argparse
 import os
 import sys
-import argparse
-
 from pathlib import Path
 from textwrap import dedent
 

doc/htmldoc/_ext/HoverXTooltip.py

@@ -19,9 +19,10 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
-import re
 import os
+import re
 import sys
+
 from docutils import nodes
 from docutils.parsers.rst import Directive, directives
 

doc/htmldoc/_ext/VersionSyncRole.py

@@ -21,6 +21,7 @@
 
 import json
 from pathlib import Path
+
 from docutils import nodes
 
 

doc/htmldoc/_ext/add_button_notebook.py

@@ -22,9 +22,10 @@
 import glob
 import os
 import sys
-from sphinx.application import Sphinx
 from pathlib import Path
 
+from sphinx.application import Sphinx
+
 
 def add_button_to_examples(app, env, docnames):
     """Find all examples and include a link to launch notebook.

doc/htmldoc/_ext/extract_api_functions.py

@@ -18,12 +18,11 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
-import os
 import ast
+import glob
 import json
+import os
 import re
-import glob
-
 
 """
 Generate a JSON dictionary that stores the module name as key and corresponding

doc/htmldoc/_ext/extractor_userdocs.py

@@ -19,18 +19,17 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
-import re
-from tqdm import tqdm
-from pprint import pformat
-from math import comb
-
-import os
 import glob
 import json
-from itertools import chain, combinations
 import logging
+import os
+import re
 from collections import Counter
+from itertools import chain, combinations
+from math import comb
+from pprint import pformat
 
+from tqdm import tqdm
 
 logging.basicConfig(level=logging.WARNING)
 log = logging.getLogger(__name__)

doc/htmldoc/_ext/list_examples.py

@@ -19,15 +19,14 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
+import glob
+import logging
+import os
+
 from docutils import nodes
 from docutils.parsers.rst import Directive, Parser
-
 from sphinx.application import Sphinx
 from sphinx.util.docutils import SphinxDirective
-import os
-import glob
-
-import logging
 
 logging.basicConfig(level=logging.WARNING)
 log = logging.getLogger(__name__)

doc/htmldoc/clean_source_dirs.py

@@ -19,8 +19,8 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 import os
-import shutil
 import pathlib
+import shutil
 from glob import glob
 
 for dir_ in ("auto_examples", "models"):

doc/htmldoc/conf.py

@@ -20,22 +20,20 @@
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
 
-import sys
-import os
 import json
+import os
 import subprocess
-
-from urllib.request import urlretrieve
-
+import sys
 from pathlib import Path
 from shutil import copyfile
+from urllib.request import urlretrieve
 
 # Add the extension modules to the path
 extension_module_dir = os.path.abspath("./_ext")
 sys.path.append(extension_module_dir)
 
-from extractor_userdocs import ExtractUserDocs, relative_glob  # noqa
 from extract_api_functions import ExtractPyNESTAPIS  # noqa
+from extractor_userdocs import ExtractUserDocs, relative_glob  # noqa
 
 repo_root_dir = os.path.abspath("../..")
 pynest_dir = os.path.join(repo_root_dir, "pynest")
@@ -172,6 +170,7 @@
     "globaltoc_collapse": True,
     # If True, show hidden TOC entries
     "globaltoc_includehidden": True,
+    "version_dropdown": False,
 }
 
 html_static_path = ["static"]