Merge branch 'master' into prototype/connection_semantics

# Conflicts:
#	pynest/examples/aeif_cond_beta_multisynapse.py
#	pynest/nest/__init__.py
#	pynest/nest/lib/hl_api_models.py
#	testsuite/pytests/test_compartmental_model.py
#	testsuite/pytests/test_spatial/test_SynapseCollection_distance.py
#	testsuite/pytests/test_urbanczik_synapse.py

.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 +1,11 @@
 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

VERSION

@@ -1 +1 @@
-3.5.0-post0.dev0
+3.6.0-post0.dev0

bin/nest-server

@@ -56,7 +56,7 @@ start() {
     if [ "${DAEMON}" -eq 0 ]; then
       echo "Use CTRL + C to stop this service."
       if [ "${STDOUT}" -eq 1 ]; then
-        echo "-------------------------------------------------"
+        echo "-----------------------------------------------------"
       fi
     fi
 

bin/nest-server-mpi

@@ -16,17 +16,16 @@ Options:
 from docopt import docopt
 from mpi4py import MPI
 
-if __name__ == '__main__':
+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")
 
@@ -35,34 +34,33 @@ rank = comm.Get_rank()
 
 
 def log(call_name, msg):
-    msg = f'==> WORKER {rank}/{time.time():.7f} ({call_name}): {msg}'
+    msg = f"==> WORKER {rank}/{time.time():.7f} ({call_name}): {msg}"
     print(msg, flush=True)
 
 
 if rank == 0:
     print("==> Starting NEST Server Master on rank 0", flush=True)
     nest.server.set_mpi_comm(comm)
-    nest.server.run_mpi_app(host=opt.get('--host', HOST), port=opt.get('--port', PORT))
+    nest.server.run_mpi_app(host=opt.get("--host", HOST), port=opt.get("--port", PORT))
 
 else:
     print(f"==> Starting NEST Server Worker on rank {rank}", flush=True)
     nest.server.set_mpi_comm(comm)
     while True:
-
-        log('spinwait', 'waiting for call bcast')
+        log("spinwait", "waiting for call bcast")
         call_name = comm.bcast(None, root=0)
 
-        log(call_name, 'received call bcast, waiting for data bcast')
+        log(call_name, "received call bcast, waiting for data bcast")
         data = comm.bcast(None, root=0)
 
-        log(call_name, f'received data bcast, data={data}')
+        log(call_name, f"received data bcast, data={data}")
         args, kwargs = data
 
-        if call_name == 'exec':
+        if call_name == "exec":
             response = nest.server.do_exec(args, kwargs)
         else:
             call, args, kwargs = nest.server.nestify(call_name, args, kwargs)
-            log(call_name, f'local call, args={args}, kwargs={kwargs}')
+            log(call_name, f"local call, args={args}, kwargs={kwargs}")
 
             # The following exception handler is useful if an error
             # occurs simulataneously on all processes. If only a
@@ -74,5 +72,5 @@ else:
             except Exception:
                 continue
 
-        log(call_name, f'sending reponse gather, data={response}')
+        log(call_name, f"sending reponse gather, data={response}")
         comm.gather(nest.serializable(response), root=0)

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 +18,12 @@
 #
 # 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 json
-import re
 import glob
+import os
+import re
 
+from sphinx.application import Sphinx
 
 """
 Generate a JSON dictionary that stores the module name as key and corresponding
@@ -106,13 +106,31 @@ def process_directory(directory):
     return api_dict
 
 
-def ExtractPyNESTAPIS():
+def get_pynest_list(app, env, docname):
     directory = "../../pynest/nest/"
-    all_variables_dict = process_directory(directory)
 
-    with open("api_function_list.json", "w") as outfile:
-        json.dump(all_variables_dict, outfile, indent=4)
+    if not hasattr(env, "pynest_dict"):
+        env.pynest_dict = {}
+
+    env.pynest_dict = process_directory(directory)
+
+
+def api_customizer(app, docname, source):
+    env = app.builder.env
+    if docname == "ref_material/pynest_api/index":
+        get_apis = env.pynest_dict
+        html_context = {"api_dict": get_apis}
+        api_source = source[0]
+        rendered = app.builder.templates.render_string(api_source, html_context)
+        source[0] = rendered
+
 
+def setup(app):
+    app.connect("env-before-read-docs", get_pynest_list)
+    app.connect("source-read", api_customizer)
 
-if __name__ == "__main__":
-    ExtractPyNESTAPIS()
+    return {
+        "version": "0.1",
+        "parallel_read_safe": True,
+        "parallel_write_safe": True,
+    }

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"):