Merge branch 'master' into doc_animations

# Conflicts:
#	brian2/sphinxext/generate_examples.py

.devcontainer/dev-requirements.txt

@@ -2,4 +2,6 @@
 scipy >= 0.13.3
 matplotlib >= 2.0
 jupyterlab
-ipympl
+ipympl
+pre-commit == 2.20.*
+black == 22.10.0

.devcontainer/devcontainer.json

@@ -20,8 +20,9 @@
 		"python.defaultInterpreterPath": "/usr/local/bin/python",
 		"python.linting.enabled": true,
 		"python.linting.pylintEnabled": true,
+		"python.formatting.provider": "black",
 		"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
-		"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+		"python.formatting.blackPath": "black",
 		"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
 		"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
 		"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
@@ -46,7 +47,7 @@
 
 	// Use 'postCreateCommand' to run commands after the container is created.
 	// "postCreateCommand": "pip3 install --user -r requirements.txt",
-	"postCreateCommand": "pip3 install --user -e '.[test,doc]' && pip3 freeze > .devcontainer/frozen-requirements.txt",
+	"postCreateCommand": "pre-commit install && pip3 install --user -e '.[test,doc]' && pip3 freeze > .devcontainer/frozen-requirements.txt",
 
 	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",

.git-blame-ignore-revs

@@ -6,3 +6,5 @@
 
 # Unify string formatting and single versus double quotes
 d3ae59251c753ae0737d6ae6242b7e85b60908c4
+# Reformatting with black
+1e9ea598491444fe7c4ee9ece2ec94ad7c5020ec

.github/workflows/publish_to_pypi.yml

@@ -20,15 +20,14 @@ jobs:
       - name: Build source tarball (only on Linux)
         run: |
           python -m pip install --upgrade pip
-          python -m pip install "cython>=0.29" oldest-supported-numpy setuptools
+          python -m pip install "cython>=0.29" oldest-supported-numpy setuptools versioneer
           python setup.py sdist --formats=gztar --with-cython --fail-on-error
         if: ${{ startsWith(matrix.os, 'ubuntu-') }}
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.2.2
         with:
           output-dir: dist
         env:
-          CIBW_BEFORE_BUILD: pip install "cython>=0.29" oldest-supported-numpy setuptools
           CIBW_PROJECT_REQUIRES_PYTHON: ">=3.7"
           CIBW_ARCHS: auto64
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014

.github/workflows/testsuite.yml

@@ -15,9 +15,24 @@ jobs:
         uses: mstimberg/github-calc-nep29@v0.5
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-
+
+  pre-commit:
+    name: Run linters with pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+          cache-dependency-path: .devcontainer/dev-requirements.txt
+      - name: Install deps
+        run: pip3 install -r .devcontainer/dev-requirements.txt
+      - name: Run pre-commit hooks
+        run: pre-commit run --all-files --show-diff-on-failure
+
   testing:
-    needs: [get_python_versions]
+    needs: [get_python_versions, pre-commit]
     name: "Python ${{ matrix.python-version }} on ${{ matrix.os }} (standalone: ${{ matrix.standalone }}, 32bit: ${{ matrix.float_dtype_32 }})"
     runs-on: ${{ matrix.os }}
     strategy:

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: meta
+    hooks:
+      - id: check-hooks-apply
+      - id: check-useless-excludes
+  - repo: https://github.com/psf/black
+    rev: '22.10.0'
+    hooks:
+      - id: black
+        exclude: '^brian2/_version.py$'
+        files: '^brian2/.*\.pyi?$'

AUTHORS

@@ -48,3 +48,4 @@ Abolfazl Ziaeemehr (@Ziaeemehr)
 Étienne Mollier (@emollier)
 Sebastian Schmitt (@schmitts)
 Felix C. Stegerman (@obfusk)
+Oleksii Leonov (@aleksejleonov)

README.rst

@@ -60,6 +60,11 @@ Stimberg, M, Brette, R, Goodman, DFM. “Brian 2, an Intuitive and Efficient Neu
    :alt: Join the chat at https://gitter.im/brian-team/brian2
    :target: https://gitter.im/brian-team/brian2?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
 
+
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :alt: code style: black
+   :target: https://github.com/psf/black
+
 Quickstart
 ----------
 Try out Brian on the `mybinder <https://mybinder.org/>`_ service:

brian2/__init__.py

@@ -6,30 +6,34 @@
 def _check_dependencies():
     """Check basic dependencies"""
     import sys
+
     missing = []
     try:
         import numpy
     except ImportError as ex:
         sys.stderr.write(f"Importing numpy failed: '{ex}'\n")
-        missing.append('numpy')
+        missing.append("numpy")
     try:
         import sympy
     except ImportError as ex:
         sys.stderr.write(f"Importing sympy failed: '{ex}'\n")
-        missing.append('sympy')
+        missing.append("sympy")
     try:
         import pyparsing
     except ImportError as ex:
         sys.stderr.write(f"Importing pyparsing failed: '{ex}'\n")
-        missing.append('pyparsing')
+        missing.append("pyparsing")
     try:
         import jinja2
     except ImportError as ex:
         sys.stderr.write(f"Importing Jinja2 failed: '{ex}'\n")
-        missing.append('jinja2')
+        missing.append("jinja2")
 
     if len(missing):
-        raise ImportError(f"Some required dependencies are missing:\n{', '.join(missing)}")
+        raise ImportError(
+            f"Some required dependencies are missing:\n{', '.join(missing)}"
+        )
+
 
 _check_dependencies()
 
@@ -42,28 +46,30 @@ def _check_dependencies():
     from numpy.random import *
     from numpy.linalg import *
     import numpy.ma as ma
+
     # don't let numpy's datetime hide stdlib
     import datetime
 
 from ._version import get_versions as _get_versions
-__version__ = _get_versions()['version']
-__release_date__ = _get_versions()['date']
+
+__version__ = _get_versions()["version"]
+__release_date__ = _get_versions()["date"]
 
 if __release_date__ is not None:
-    __release_date__ = __release_date__[:10]  #only use date part
-__git_revision__ = _get_versions()['full-revisionid']
+    __release_date__ = __release_date__[:10]  # only use date part
+__git_revision__ = _get_versions()["full-revisionid"]
 
 # Make sure that Brian's unit-aware functions are used, even when directly
 # using names prefixed with numpy or np
 import brian2.numpy_ as numpy
 import brian2.numpy_ as np
 
 # delete some annoying names from the namespace
-if 'x' in globals():
+if "x" in globals():
     del x
-if 'f' in globals():
+if "f" in globals():
     del f
-if 'rate' in globals():
+if "rate" in globals():
     del rate
 
 __docformat__ = "restructuredtext en"
@@ -73,30 +79,32 @@ def _check_dependencies():
 
 # Check for outdated dependency versions
 def _check_dependency_version(name, version):
-    from distutils.version import LooseVersion
+    from packaging.version import Version
     from .core.preferences import prefs
     from .utils.logger import get_logger
     import sys
+
     logger = get_logger(__name__)
 
     module = sys.modules[name]
     if not isinstance(module.__version__, str):  # mocked module
         return
-    if not LooseVersion(module.__version__) >= LooseVersion(version):
-        message = f'{name} is outdated (got version {module.__version__}, need version {version})'
+    if not Version(module.__version__) >= Version(version):
+        message = (
+            f"{name} is outdated (got version {module.__version__}, need version"
+            f" {version})"
+        )
         if prefs.core.outdated_dependency_error:
             raise ImportError(message)
         else:
-
-            logger.warn(message, 'outdated_dependency')
+            logger.warn(message, "outdated_dependency")
 
 
 def _check_dependency_versions():
-    for name, version in [('numpy',  '1.10'),
-                          ('sympy',  '1.2'),
-                          ('jinja2', '2.7')]:
+    for name, version in [("numpy", "1.10"), ("sympy", "1.2"), ("jinja2", "2.7")]:
         _check_dependency_version(name, version)
 
+
 _check_dependency_versions()
 
 # Initialize the logging system
@@ -107,6 +115,7 @@ def _check_dependency_versions():
 # Check the caches
 def _get_size_recursively(dirname):
     import os
+
     total_size = 0
     for dirpath, _, filenames in os.walk(dirname):
         for fname in filenames:
@@ -120,20 +129,24 @@ def _get_size_recursively(dirname):
                 pass  # ignore the file
     return total_size
 
+
 #: Stores the cache directory for code generation targets
 _cache_dirs_and_extensions = {}
 
+
 def check_cache(target):
     cache_dir, _ = _cache_dirs_and_extensions.get(target, (None, None))
     if cache_dir is None:
         return
     size = _get_size_recursively(cache_dir)
-    size_in_mb = int(round(size/1024./1024.))
+    size_in_mb = int(round(size / 1024.0 / 1024.0))
     if size_in_mb > prefs.codegen.max_cache_dir_size:
-        logger.info(f"Cache size for target '{target}': {size_in_mb} MB.\n"
-                    f"You can call clear_cache('{target}') to delete all "
-                    f"files from the cache or manually delete files in the "
-                    f"'{cache_dir}' directory.")
+        logger.info(
+            f"Cache size for target '{target}': {size_in_mb} MB.\n"
+            f"You can call clear_cache('{target}') to delete all "
+            "files from the cache or manually delete files in the "
+            f"'{cache_dir}' directory."
+        )
     else:
         logger.debug(f"Cache size for target '{target}': {size_in_mb} MB")
 
@@ -158,6 +171,7 @@ def clear_cache(target):
     """
     import os
     import shutil
+
     cache_dir, extensions = _cache_dirs_and_extensions.get(target, (None, None))
     if cache_dir is None:
         raise ValueError(f'No cache directory registered for target "{target}".')
@@ -168,10 +182,12 @@ def clear_cache(target):
                 if f.endswith(ext):
                     break
             else:
-                raise IOError(f"The cache directory for target '{target}' contains "
-                              f"the file '{os.path.join(folder, f)}' of an unexpected type and "
-                              f"will therefore not be removed. Delete files in "
-                              f"'{cache_dir}' manually")
+                raise IOError(
+                    f"The cache directory for target '{target}' contains "
+                    f"the file '{os.path.join(folder, f)}' of an unexpected type and "
+                    "will therefore not be removed. Delete files in "
+                    f"'{cache_dir}' manually"
+                )
 
     logger.debug(f"Clearing cache for target '{target}' (directory '{cache_dir}').")
     shutil.rmtree(cache_dir)
@@ -181,9 +197,20 @@ def _check_caches():
     from brian2.codegen.runtime.cython_rt.extension_manager import get_cython_cache_dir
     from brian2.codegen.runtime.cython_rt.extension_manager import get_cython_extensions
 
-    for target, (dirname, extensions) in [('cython', (get_cython_cache_dir(), get_cython_extensions()))]:
+    for target, (dirname, extensions) in [
+        ("cython", (get_cython_cache_dir(), get_cython_extensions()))
+    ]:
         _cache_dirs_and_extensions[target] = (dirname, extensions)
         if prefs.codegen.max_cache_dir_size > 0:
             check_cache(target)
 
+
 _check_caches()
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]