Precommit-updates

.devcontainer/dev-requirements.txt

@@ -4,8 +4,8 @@ matplotlib >= 2.0
 jupyterlab
 ipympl
 pre-commit == 3.3.*
-black == 22.10.0
-isort == 5.12.0
-pyupgrade == 3.4.0
-flake8 == 6.0.0
-flake8-bugbear == 23.5.9
+black == 24.2.0
+isort == 5.13.2
+pyupgrade == 3.15.1
+flake8 == 7.0.0
+flake8-bugbear == 24.2.6

.git-blame-ignore-revs

@@ -14,3 +14,5 @@
 28b02c51545298cb9a76d8295e64a5df391b9207
 # Fix a number of issues flagged by flake8
 0344b005e6ffd232f55e69621630ef01876bc0fb
+# Update to black 24.2.0 and isort 5.13.2
+0d015a50d641edc7709bd89e0ed389e54f1dcab0

.pre-commit-config.yaml

@@ -4,26 +4,26 @@ repos:
       - id: check-hooks-apply
       - id: check-useless-excludes
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.15.1
     hooks:
       - id: pyupgrade
         args: [--py39-plus]
         files: '^brian2/.*\.pyi?$'
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         # We exclude all __init__.py files, since we use wildcard imports, etc.
         exclude: '^brian2/tests/.*$|^brian2/.*__init__[.]py$'
         files: '^brian2/.*\.pyi?$'
-        additional_dependencies: ['flake8-bugbear==23.5.9']
+        additional_dependencies: ['flake8-bugbear==24.2.6']
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         files: '^brian2/.*\.pyi?$'
   - repo: https://github.com/psf/black
-    rev: '22.10.0'
+    rev: '24.2.0'
     hooks:
       - id: black
         files: '^brian2/.*\.pyi?$'

brian2/__init__.py

@@ -1,6 +1,7 @@
 """
 Brian 2
 """
+
 import logging
 
 

brian2/codegen/__init__.py

@@ -1,6 +1,7 @@
 """
 Package providing the code generation framework.
 """
+
 # Import the runtime packages so that they can register their preferences
 
 # isort:skip_file

brian2/codegen/_prefs.py

@@ -5,6 +5,7 @@
 -----------
 .. document_brian_prefs:: codegen
 """
+
 from brian2.core.preferences import BrianPreference, prefs
 
 from .codeobject import CodeObject

brian2/codegen/codeobject.py

@@ -1,6 +1,7 @@
 """
 Module providing the base `CodeObject` and related functions.
 """
+
 import collections
 import copy
 import platform

brian2/codegen/cpp_prefs.py

@@ -6,6 +6,7 @@
 .. document_brian_prefs:: codegen.cpp
 
 """
+
 import distutils
 import json
 import os
@@ -266,9 +267,10 @@ def _determine_flag_compatibility(compiler, flagname):
     import tempfile
     from distutils.errors import CompileError
 
-    with tempfile.TemporaryDirectory(
-        prefix="brian_flag_test_"
-    ) as temp_dir, std_silent():
+    with (
+        tempfile.TemporaryDirectory(prefix="brian_flag_test_") as temp_dir,
+        std_silent(),
+    ):
         fname = os.path.join(temp_dir, "flag_test.cpp")
         with open(fname, "w") as f:
             f.write("int main (int argc, char **argv) { return 0; }")

brian2/codegen/generators/GSL_generator.py

@@ -642,9 +642,9 @@ def to_replace_vector_vars(self, variables_in_vector, ignore=frozenset()):
                 continue
             if isinstance(var_obj, ArrayVariable):
                 pointer_name = self.get_array_name(var_obj, access_data=True)
-                to_replace[
-                    pointer_name
-                ] = f"_GSL_dataholder{access_pointer}{pointer_name}"
+                to_replace[pointer_name] = (
+                    f"_GSL_dataholder{access_pointer}{pointer_name}"
+                )
             else:
                 to_replace[var] = f"_GSL_dataholder{access_pointer}{var}"
 
@@ -933,8 +933,7 @@ def translate(
                     "well-defined: the outcome may depend on the "
                     "order of execution. You can ignore this warning if "
                     "you are sure that the order of operations does not "
-                    "matter. "
-                    + error_msg
+                    "matter. " + error_msg
                 )
 
         # save function names because self.generator.translate_statement_sequence
@@ -1019,9 +1018,7 @@ def translate(
         )
         # rewrite scalar code, keep variables that are needed in scalar code normal
         # and add variables to _dataholder for vector_code
-        GSL_main_code += (
-            f"\n{self.translate_scalar_code(scalar_func_code, variables_in_scalar, variables_in_vector)}"
-        )
+        GSL_main_code += f"\n{self.translate_scalar_code(scalar_func_code, variables_in_scalar, variables_in_vector)}"
         if len(self.variables_to_be_processed) > 0:
             raise AssertionError(
                 "Not all variables that will be used in the vector "

brian2/codegen/generators/base.py

@@ -297,8 +297,7 @@ def translate(self, code, dtype):
                     "well-defined: the outcome may depend on the "
                     "order of execution. You can ignore this warning if "
                     "you are sure that the order of operations does not "
-                    "matter. "
-                    + error_msg
+                    "matter. " + error_msg
                 )
 
         translated = self.translate_statement_sequence(

brian2/codegen/get_cpu_flags.py

@@ -7,7 +7,6 @@
 The CPU flags are printed to stdout encoded as JSON.
 """
 
-
 import json
 
 if __name__ == "__main__":

brian2/codegen/runtime/cython_rt/extension_manager.py

@@ -5,7 +5,6 @@
 https://github.com/ipython/ipython/blob/master/IPython/extensions/cythonmagic.py
 """
 
-
 import glob
 import hashlib
 import importlib.util

brian2/codegen/templates.py

@@ -1,6 +1,7 @@
 """
 Handles loading templates from a directory.
 """
+
 import re
 from collections.abc import Mapping
 

brian2/conftest.py

@@ -1,6 +1,7 @@
 """
 Module containing fixtures and hooks used by the pytest test suite.
 """
+
 import re
 
 import numpy as np

brian2/core/base.py

@@ -1,6 +1,7 @@
 """
 All Brian objects should derive from `BrianObject`.
 """
+
 import functools
 import os
 import sys
@@ -81,8 +82,7 @@ def __init__(
         #: A string indicating where this object was created (traceback with any parts of Brian code removed)
         self._creation_stack = (
             "Object was created here (most recent call only, full details in "
-            "debug log):\n"
-            + creation_stack[-1]
+            "debug log):\n" + creation_stack[-1]
         )
         self._full_creation_stack = "Object was created here:\n" + "\n".join(
             creation_stack

brian2/core/clocks.py

@@ -2,7 +2,6 @@
 Clocks for the simulator.
 """
 
-
 __docformat__ = "restructuredtext en"
 
 import numpy as np

brian2/core/network.py

@@ -217,14 +217,18 @@ def __repr__(self):
             [
                 [
                     f"{entry.name} ({entry.type})",
-                    f"{entry.owner_name} ({entry.owner_type})"
-                    if entry.owner_name is not None
-                    else "--",
+                    (
+                        f"{entry.owner_name} ({entry.owner_type})"
+                        if entry.owner_name is not None
+                        else "--"
+                    ),
                     "{} (every {})".format(
                         str(entry.dt),
-                        "step"
-                        if self.steps[float(entry.dt)] == 1
-                        else f"{self.steps[float(entry.dt)]} steps",
+                        (
+                            "step"
+                            if self.steps[float(entry.dt)] == 1
+                            else f"{self.steps[float(entry.dt)]} steps"
+                        ),
                     ),
                     entry.when,
                     entry.order,
@@ -248,14 +252,18 @@ def _repr_html_(self):
         </tr>
         """.format(
                 f"<b>{entry.name}</b> (<em>{entry.type}</em>)",
-                f"{entry.owner_name} (<em>{entry.owner_type}</em>)"
-                if entry.owner_name is not None
-                else "&ndash;",
+                (
+                    f"{entry.owner_name} (<em>{entry.owner_type}</em>)"
+                    if entry.owner_name is not None
+                    else "&ndash;"
+                ),
                 "{} (every {})".format(
                     str(entry.dt),
-                    "step"
-                    if self.steps[float(entry.dt)] == 1
-                    else f"{self.steps[float(entry.dt)]} steps",
+                    (
+                        "step"
+                        if self.steps[float(entry.dt)] == 1
+                        else f"{self.steps[float(entry.dt)]} steps"
+                    ),
                 ),
                 entry.when,
                 entry.order,

brian2/core/operations.py

@@ -170,6 +170,7 @@ def f():
 
     NetworkOperation, Network, BrianObject
     """
+
     # Notes on this decorator:
     # Normally, a decorator comes in two types, with or without arguments. If
     # it has no arguments, e.g.

brian2/core/preferences.py

@@ -611,8 +611,7 @@ def check_all_validated(self):
                 "The following preferences values have been set but "
                 "are not registered preferences:\n%s\nThis is usually "
                 "because of a spelling mistake or missing library "
-                "import."
-                % ", ".join(self.prefs_unvalidated),
+                "import." % ", ".join(self.prefs_unvalidated),
                 once=True,
             )
 

brian2/core/variables.py

@@ -2,6 +2,7 @@
 Classes used to specify the type of a function, variable or common
 sub-expression.
 """
+
 import collections
 import functools
 import numbers

brian2/devices/__init__.py

@@ -1,5 +1,6 @@
 """
 Package providing the "devices" infrastructure.
 """
+
 from . import device as device_module
 from .device import *

brian2/devices/cpp_standalone/device.py

@@ -1,6 +1,7 @@
 """
 Module implementing the C++ "standalone" device.
 """
+
 import inspect
 import itertools
 import numbers
@@ -233,9 +234,7 @@ def __init__(self):
         self.run_environment_variables = {}
         if sys.platform.startswith("darwin"):
             if "DYLD_LIBRARY_PATH" in os.environ:
-                dyld_library_path = (
-                    f"{os.environ['DYLD_LIBRARY_PATH']}:{os.path.join(sys.prefix, 'lib')}"
-                )
+                dyld_library_path = f"{os.environ['DYLD_LIBRARY_PATH']}:{os.path.join(sys.prefix, 'lib')}"
             else:
                 dyld_library_path = os.path.join(sys.prefix, "lib")
             self.run_environment_variables["DYLD_LIBRARY_PATH"] = dyld_library_path
@@ -387,9 +386,9 @@ def add_array(self, var):
             # use the same name in the two dictionaries, not for example
             # ``_dynamic_array_source_name_2`` and ``_array_source_name_1``
             # (this would work fine, but it would make the code harder to read).
-            orig_dynamic_name = (
-                dynamic_name
-            ) = f"_dynamic_array_{var.owner.name}_{var.name}"
+            orig_dynamic_name = dynamic_name = (
+                f"_dynamic_array_{var.owner.name}_{var.name}"
+            )
             orig_array_name = array_name = f"_array_{var.owner.name}_{var.name}"
             suffix = 0
 

brian2/equations/__init__.py

@@ -2,6 +2,7 @@
 Module handling equations and "code strings", expressions or statements, used
 for example for the reset and threshold definition of a neuron.
 """
+
 from .codestrings import Expression, Statements
 from .equations import Equations
 

brian2/equations/equations.py

@@ -1,6 +1,7 @@
 """
 Differential equations for Brian models.
 """
+
 import keyword
 import re
 import string

brian2/equations/refractory.py

@@ -2,7 +2,6 @@
 Module implementing Brian's refractory mechanism.
 """
 
-
 from brian2.units.allunits import second
 from brian2.units.fundamentalunits import DIMENSIONLESS
 

brian2/groups/group.py

@@ -5,6 +5,7 @@
 objects such as `NeuronGroup` or `StateMonitor` but not `Clock`, and finally
 `CodeRunner`, a class to run code in the context of a `Group`.
 """
+
 import inspect
 import numbers
 import weakref

brian2/groups/neurongroup.py

@@ -1,6 +1,7 @@
 """
 This model defines the `NeuronGroup`, the core of most simulations.
 """
+
 import numbers
 import string
 from collections.abc import MutableMapping, Sequence

brian2/hears.py

@@ -16,7 +16,6 @@
 * time_varying_filter1 (care with units)
 """
 
-
 try:
     import brian as b1
     import brian.hears as b1h

brian2/importexport/dictlike.py

@@ -53,8 +53,7 @@ def export_data(group, variables, units=True, level=0):
         except ImportError as ex:
             raise ImportError(
                 "Exporting to pandas needs a working installation"
-                " of pandas. Importing pandas failed: "
-                + str(ex)
+                " of pandas. Importing pandas failed: " + str(ex)
             )
         if units:
             raise NotImplementedError(

brian2/input/poissongroup.py

@@ -1,6 +1,7 @@
 """
 Implementation of `PoissonGroup`.
 """
+
 import numpy as np
 
 from brian2.core.spikesource import SpikeSource

brian2/input/poissoninput.py

@@ -1,6 +1,7 @@
 """
 Implementation of `PoissonInput`.
 """
+
 from brian2.core.variables import Variables
 from brian2.groups.group import CodeRunner
 from brian2.units.fundamentalunits import (