remove deep bsb imports

.github/workflows/black.yml

@@ -8,6 +8,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Black Check
-      uses: jpetrucciani/black-check@master
+    - uses: actions/checkout@v4
+    - uses: psf/black@stable
+      with:
+        options: "--check --verbose"
+        version: "24.1.1"

.github/workflows/isort.yml

@@ -0,0 +1,20 @@
+name: Run isort
+on:
+  - push
+
+jobs:
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - name: Install apt dependencies
+        # Install `libopenmpi` for mpi4py
+        run: |
+          sudo apt update
+          sudo apt install openmpi-bin libopenmpi-dev
+      # Install dependencies for proper 1st/2nd/3rd party import sorting
+      - run: pip install -e .[parallel]
+      - uses: isort/isort-action@master

bsb_hdf5/__init__.py

@@ -2,9 +2,14 @@
 HDF5 storage engine for the BSB framework.
 """
 
-from bsb import config, __version__ as bsb_version
-from bsb.services import MPILock
-from bsb.storage.interfaces import Engine, StorageNode as IStorageNode, NoopLock
+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

bsb_hdf5/chunks.py

@@ -9,7 +9,7 @@
 objects within them.
 """
 
-from bsb.storage import Chunk, chunklist
+from bsb import Chunk, chunklist
 import numpy as np
 import contextlib
 from .resource import handles_handles, HANDLED

bsb_hdf5/connectivity_set.py

@@ -1,8 +1,11 @@
 import errr
-from bsb.exceptions import DatasetNotFoundError
+from bsb import (
+    DatasetNotFoundError,
+    Chunk,
+    chunklist,
+    ConnectivitySet as IConnectivitySet,
+)
 from .resource import Resource, handles_handles, HANDLED
-from bsb.storage._chunks import Chunk, chunklist
-from bsb.storage.interfaces import ConnectivitySet as IConnectivitySet
 import numpy as np
 import json
 
@@ -475,7 +478,9 @@ def __iter__(self):
                 )
             )
         else:
-            yield self._cs.load_block_connections(self._dir, self._lchunks, self._gchunks)
+            yield self._cs.load_block_connections(
+                self._dir, self._lchunks, self._gchunks
+            )
 
     def get_local_iter(self, direction, local_):
         if local_ is None:

pyproject.toml

@@ -15,6 +15,7 @@ dependencies = ["bsb-core>=4.0.0b0,<=4.0.0b9999"]
 hdf5 = "bsb_hdf5"
 
 [project.optional-dependencies]
+parallel = ["bsb-core[parallel]"]
 test = ["bsb-test>=0.0.0b15,<=0.0.0b9999", "coverage~=7.0", "bsb-core[parallel]"]
 docs = [
     "sphinx==5.0.2",