Sort imports

.github/workflows/nestbuildmatrix.yml

@@ -302,7 +302,7 @@ jobs:
       - name: "Run isort..."
         uses: isort/isort-action@f14e57e1d457956c45a19c05a89cccdf087846e5  # 1.1.0
         with:
-          configuration: --profile black --check-only --diff
+          configuration: --profile=black --thirdparty="nest" --check-only --diff
 
   black:
     runs-on: "ubuntu-20.04"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
-        args: ["--profile", "black", "--check-only", "--diff"]
+        args: ["--profile", "black", "--thirdparty", "nest", "--check-only", "--diff"]
   - repo: https://github.com/psf/black
     rev: 23.7.0
     hooks:

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/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/extractor_userdocs.py

@@ -19,17 +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()

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

@@ -20,15 +20,13 @@
 # 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")

doc/htmldoc/networks/scripts/connections.py

@@ -21,8 +21,8 @@
 
 # create connectivity figures for spatial manual
 
-import nest
 import matplotlib.pyplot as plt
+import nest
 import numpy as np
 
 # seed NumPy RNG to ensure identical results for runs with random placement

doc/htmldoc/resolve_includes.py

@@ -32,10 +32,10 @@
 
 """
 
+import glob
 import os
 import re
 import sys
-import glob
 from fileinput import FileInput
 
 pattern = re.compile("^.. include:: (.*)")

doc/slihelp_generator/generate_help.py

@@ -28,17 +28,21 @@
 The helpindex is built during installation in a separate step.
 """
 
-import os
 import html
 import io
+import os
 import re
 import sys
 import textwrap
 
+from helpers_sli import (
+    check_ifdef,
+    create_helpdirs,
+    cut_it,
+    delete_helpdir,
+    help_generation_required,
+)
 from writers import coll_data
-from helpers_sli import check_ifdef, create_helpdirs, cut_it
-from helpers_sli import delete_helpdir
-from helpers_sli import help_generation_required
 
 if len(sys.argv) != 3:
     print("Usage: python3 generate_help.py <source_dir> <build_dir>")

doc/slihelp_generator/generate_helpindex.py

@@ -30,6 +30,7 @@
 
 import os
 import sys
+
 from writers import write_helpindex
 
 if len(sys.argv) != 2:

doc/slihelp_generator/helpers_sli.py

@@ -19,10 +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 errno
 import os
+import re
 import shutil
-import errno
 
 
 def cut_it(separator, text):

doc/slihelp_generator/writers.py

@@ -31,9 +31,10 @@
 import os
 import re
 import textwrap
-from helpers_sli import cut_it
 from string import Template
 
+from helpers_sli import cut_it
+
 
 def write_help_html(doc_dic, helpdir, fname, sli_command_list, keywords):
     """

examples/nest/Potjans_2014/spike_analysis.py

@@ -21,12 +21,13 @@
 
 # Merges spike files, produces raster plots, calculates and plots firing rates
 
-import numpy as np
 import glob
-import matplotlib.pyplot as plt
 import os
 import re
 
+import matplotlib.pyplot as plt
+import numpy as np
+
 datapath = "."
 
 # get simulation time and numbers of neurons recorded from sim_params.sli

pynest/examples/BrodyHopfield.py

@@ -45,9 +45,9 @@
 #################################################################################
 # First, we import all necessary modules for simulation, analysis, and plotting.
 
+import matplotlib.pyplot as plt
 import nest
 import nest.raster_plot
-import matplotlib.pyplot as plt
 
 ###############################################################################
 # Second, the simulation parameters are assigned to variables.

pynest/examples/CampbellSiegert.py

@@ -51,12 +51,10 @@
 # First, we import all necessary modules for simulation and analysis. Scipy
 # should be imported before nest.
 
-from scipy.special import erf
-from scipy.optimize import fmin
-
-import numpy as np
-
 import nest
+import numpy as np
+from scipy.optimize import fmin
+from scipy.special import erf
 
 ###############################################################################
 # We first set the parameters of neurons, noise and the simulation. First

pynest/examples/Potjans_2014/helpers.py

@@ -27,10 +27,11 @@
 
 """
 
-from matplotlib.patches import Polygon
-import matplotlib.pyplot as plt
 import os
+
+import matplotlib.pyplot as plt
 import numpy as np
+from matplotlib.patches import Polygon
 
 if "DISPLAY" not in os.environ:
     import matplotlib

pynest/examples/Potjans_2014/network.py

@@ -28,11 +28,12 @@
 """
 
 import os
-import numpy as np
-import nest
-import helpers
 import warnings
 
+import helpers
+import nest
+import numpy as np
+
 
 class Network:
     """Provides functions to setup NEST, to create and connect all nodes of

pynest/examples/Potjans_2014/run_microcircuit.py

@@ -30,13 +30,14 @@
 ###############################################################################
 # Import the necessary modules and start the time measurements.
 
-from stimulus_params import stim_dict
-from network_params import net_dict
-from sim_params import sim_dict
-import network
+import time
+
 import nest
+import network
 import numpy as np
-import time
+from network_params import net_dict
+from sim_params import sim_dict
+from stimulus_params import stim_dict
 
 time_start = time.time()
 

pynest/examples/aeif_cond_beta_multisynapse.py

@@ -25,9 +25,9 @@
 
 """
 
+import matplotlib.pyplot as plt
 import nest
 import numpy as np
-import matplotlib.pyplot as plt
 
 neuron = nest.Create("aeif_cond_beta_multisynapse")
 nest.SetStatus(neuron, {"V_peak": 0.0, "a": 4.0, "b": 80.5})

pynest/examples/balancedneuron.py

@@ -46,11 +46,10 @@
 # First, we import all necessary modules for simulation, analysis and
 # plotting. Scipy should be imported before nest.
 
-from scipy.optimize import bisect
-
+import matplotlib.pyplot as plt
 import nest
 import nest.voltage_trace
-import matplotlib.pyplot as plt
+from scipy.optimize import bisect
 
 ###############################################################################
 # Additionally, we set the verbosity using ``set_verbosity`` to