fix qa

.pre-commit-config.yaml

@@ -1,6 +1,10 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.1.1
     hooks:
       - id: black
-        language_version: python3
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)

bsb_hdf5/__init__.py

@@ -2,24 +2,22 @@
 HDF5 storage engine for the BSB framework.
 """
 
-from bsb import (
-    config,
-    __version__ as bsb_version,
-    MPILock,
-    Engine,
-    StorageNode as IStorageNode,
-    NoopLock,
-)
-from .placement_set import PlacementSet
-from .connectivity_set import ConnectivitySet
-from .file_store import FileStore
-from .morphology_repository import MorphologyRepository
-from datetime import datetime
 import json
-import h5py
 import os
 import shutil
+from datetime import datetime
+
+import h5py
 import shortuuid
+from bsb import Engine, MPILock, NoopLock
+from bsb import StorageNode as IStorageNode
+from bsb import __version__ as bsb_version
+from bsb import config
+
+from .connectivity_set import ConnectivitySet
+from .file_store import FileStore
+from .morphology_repository import MorphologyRepository
+from .placement_set import PlacementSet
 
 __version__ = "4.0.0-rc2"
 __all__ = [

bsb_hdf5/chunks.py

@@ -9,10 +9,12 @@
 objects within them.
 """
 
-from bsb import Chunk, chunklist
-import numpy as np
 import contextlib
-from .resource import handles_handles, HANDLED
+
+import numpy as np
+from bsb import Chunk, chunklist
+
+from .resource import HANDLED, handles_handles
 
 
 class ChunkLoader:

bsb_hdf5/connectivity_set.py

@@ -1,13 +1,12 @@
+import json
+
 import errr
-from bsb import (
-    DatasetNotFoundError,
-    Chunk,
-    chunklist,
-    ConnectivitySet as IConnectivitySet,
-)
-from .resource import Resource, handles_handles, HANDLED
 import numpy as np
-import json
+from bsb import Chunk
+from bsb import ConnectivitySet as IConnectivitySet
+from bsb import DatasetNotFoundError, chunklist
+
+from .resource import HANDLED, Resource, handles_handles
 
 _root = "/connectivity/"
 

bsb_hdf5/file_store.py

@@ -1,11 +1,12 @@
+import json
 import time
+from uuid import uuid4
 
 import numpy as np
-from bsb.storage.interfaces import FileStore as IFileStore
 from bsb.exceptions import MissingActiveConfigError
+from bsb.storage.interfaces import FileStore as IFileStore
+
 from .resource import Resource
-from uuid import uuid4
-import json
 
 _root = "files"
 

bsb_hdf5/morphology_repository.py

@@ -1,14 +1,14 @@
-from bsb.morphologies import Morphology, Branch
-from bsb._encoding import EncodedLabels
-from bsb.exceptions import MorphologyRepositoryError, MissingMorphologyError
-from bsb.storage.interfaces import (
-    MorphologyRepository as IMorphologyRepository,
-    StoredMorphology,
-)
-from .resource import Resource, handles_handles, HANDLED
-import numpy as np
-import json
 import itertools
+import json
+
+import numpy as np
+from bsb._encoding import EncodedLabels
+from bsb.exceptions import MissingMorphologyError, MorphologyRepositoryError
+from bsb.morphologies import Branch, Morphology
+from bsb.storage.interfaces import MorphologyRepository as IMorphologyRepository
+from bsb.storage.interfaces import StoredMorphology
+
+from .resource import HANDLED, Resource, handles_handles
 
 _root = "/morphologies"
 

bsb_hdf5/placement_set.py

@@ -1,19 +1,21 @@
+import itertools
+import json
+
+import numpy as np
+from bsb import config
+from bsb._encoding import EncodedLabels
 from bsb.exceptions import (
-    MissingMorphologyError,
     DatasetExistsError,
     DatasetNotFoundError,
+    MissingMorphologyError,
 )
-from bsb import config
-from bsb.storage._chunks import Chunk, chunklist
-from bsb._encoding import EncodedLabels
-from bsb.storage.interfaces import PlacementSet as IPlacementSet
 from bsb.morphologies import MorphologySet, RotationSet
 from bsb.morphologies.selector import MorphologySelector
-from .resource import Resource, handles_handles, HANDLED
-from .chunks import ChunkLoader, ChunkedProperty, ChunkedCollection
-import numpy as np
-import itertools
-import json
+from bsb.storage._chunks import Chunk, chunklist
+from bsb.storage.interfaces import PlacementSet as IPlacementSet
+
+from .chunks import ChunkedCollection, ChunkedProperty, ChunkLoader
+from .resource import HANDLED, Resource, handles_handles
 
 _root = "/placement/"
 

bsb_hdf5/resource.py

@@ -1,9 +1,9 @@
+import functools
+import inspect
 import typing
 
-import numpy as np
 import h5py
-import inspect
-import functools
+import numpy as np
 
 if typing.TYPE_CHECKING:
     from . import HDF5Engine
@@ -57,7 +57,8 @@ def __init__(self, engine: "HDF5Engine", path: str):
 
     def __eq__(self, other):
         return (
-            self._engine == getattr(other, "_engine", None) and self._path == other._path
+            self._engine == getattr(other, "_engine", None)
+            and self._path == other._path
         )
 
     def require(self, handle):

pyproject.toml

@@ -27,6 +27,9 @@ docs = [
     "sphinx-copybutton==0.5.0"
 ]
 
+[tool.isort]
+profile = "black"
+
 [tool.flit.module]
 name = "bsb_hdf5"
 

test/test_chunks.py

@@ -3,7 +3,7 @@
 import numpy as np
 from bsb.core import Scaffold
 from bsb.storage import Chunk
-from bsb_test import NumpyTestCase, skip_parallel, timeout, RandomStorageFixture
+from bsb_test import NumpyTestCase, RandomStorageFixture, skip_parallel, timeout
 from bsb_test.configs import get_test_config
 
 

test/test_cs.py

@@ -1,8 +1,10 @@
-from bsb.services.pool import WorkflowError
-from bsb_test import FixedPosConfigFixture, RandomStorageFixture, NumpyTestCase
+import unittest
+
 from bsb.core import Scaffold
+from bsb.services.pool import WorkflowError
+from bsb_test import FixedPosConfigFixture, NumpyTestCase, RandomStorageFixture
+
 from bsb_hdf5.connectivity_set import LocationOutOfBoundsError
-import unittest
 
 
 class TestConnectivitySet(

test/test_interface.py

@@ -1,11 +1,10 @@
-from bsb_test.engines import (
-    TestStorage as _TestStorage,
-    TestPlacementSet as _TestPlacementSet,
-    TestMorphologyRepository as _TestMorphologyRepository,
-    TestConnectivitySet as _TestConnectivitySet,
-)
 import unittest
 
+from bsb_test.engines import TestConnectivitySet as _TestConnectivitySet
+from bsb_test.engines import TestMorphologyRepository as _TestMorphologyRepository
+from bsb_test.engines import TestPlacementSet as _TestPlacementSet
+from bsb_test.engines import TestStorage as _TestStorage
+
 
 class TestStorage(_TestStorage, unittest.TestCase, engine_name="hdf5"):
     pass

test/test_mr.py

@@ -1,10 +1,11 @@
-from bsb.services import MPI
-from bsb.storage import Storage
-import numpy as np
-import unittest
 import json
-import h5py
 import os
+import unittest
+
+import h5py
+import numpy as np
+from bsb.services import MPI
+from bsb.storage import Storage
 
 
 class TestHandcrafted(unittest.TestCase):
@@ -60,7 +61,9 @@ def setUpClass(cls):
                 ds = g.create_dataset("data", data=data)
                 ds.attrs["labels"] = json.dumps({1: []})
                 ds.attrs["properties"] = []
-                g.create_dataset("graph", data=[[i + 1, -1] for i in range(4)] + [[5, 0]])
+                g.create_dataset(
+                    "graph", data=[[i + 1, -1] for i in range(4)] + [[5, 0]]
+                )
                 f.create_dataset("morphology_meta", data=json.dumps({"M": {}}))
         MPI.barrier()
 
@@ -121,9 +124,7 @@ def test_multi_branch_single_element(self):
         msg = "Single point unattached branches should still be root."
         self.assertEqual(5, len(m.roots), msg)
         self.assertEqual(5, len(m.branches), "Missing branch")
-        msg = (
-            "Flatten of single point branches should produce n-branch x n-vectors matrix."
-        )
+        msg = "Flatten of single point branches should produce n-branch x n-vectors matrix."
         matrix = m.flatten()
         self.assertEqual((5, 3), matrix.shape, msg)
         msg = "Flatten produced an incorrect matrix"

test/test_setup/__init__.py

@@ -1,4 +1,8 @@
-import os, sys, unittest, threading
+import os
+import sys
+import threading
+import unittest
+
 import numpy as np
 
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", ".."))