Fixed MorphologySet chunk overlap (#708)

* fixed extra simulations name error

* Fixed immutable mapping types

* bumped bsb-hdf5

* a50 - lint & fixes #701

* bumped bsbhdf5

bsb/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "4.0.0a49"
+__version__ = "4.0.0a50"
 
 import functools
 

bsb/cli/commands/_commands.py

@@ -196,6 +196,7 @@ def handler(self, context):
         network = from_storage(context.arguments.network)
         config_option = context.options["config"]
         sim_name = context.arguments.simulation
+        extra_simulations = {}
         if config_option.is_set("cli"):
             extra_simulations = from_file(context.config).simulations
             for name, sim in extra_simulations.items():
@@ -207,7 +208,8 @@ def handler(self, context):
             append = ", " if len(network.simulations) else ""
             append += ", ".join(f"'{name}'" for name in extra_simulations.keys())
             errr.wrap(type(e), e, append=append)
-        result.write(f"{uuid4()}.nio", "ow")
+        else:
+            result.write(f"{uuid4()}.nio", "ow")
 
     def get_options(self):
         return {

bsb/core.py

@@ -100,14 +100,14 @@ class Scaffold:
     """
 
     network: "Network"
-    regions: typing.Mapping[str, "Region"]
-    partitions: typing.Mapping[str, "Partition"]
-    cell_types: typing.Mapping[str, "CellType"]
-    placement: typing.Mapping[str, "PlacementStrategy"]
-    after_placement: typing.Mapping[str, "PostProcessingHook"]
-    connectivity: typing.Mapping[str, "ConnectionStrategy"]
-    after_connectivity: typing.Mapping[str, "PostProcessingHook"]
-    simulations: typing.Mapping[str, "Simulation"]
+    regions: typing.Dict[str, "Region"]
+    partitions: typing.Dict[str, "Partition"]
+    cell_types: typing.Dict[str, "CellType"]
+    placement: typing.Dict[str, "PlacementStrategy"]
+    after_placement: typing.Dict[str, "PostProcessingHook"]
+    connectivity: typing.Dict[str, "ConnectionStrategy"]
+    after_connectivity: typing.Dict[str, "PostProcessingHook"]
+    simulations: typing.Dict[str, "Simulation"]
 
     def __init__(self, config=None, storage=None, clear=False, comm=None):
         """

requirements.txt

@@ -29,4 +29,4 @@ NEURON==8.2.2
 nrn-subprocess==1.3.4
 
 # Plugins
-bsb-hdf5==0.7.2
+bsb-hdf5==0.7.4

setup.py

@@ -17,7 +17,7 @@
     long_description = fh.read()
 
 requires = [
-    "bsb-hdf5~=0.7.2",
+    "bsb-hdf5~=0.7.4",
     "h5py~=3.0",
     "numpy~=1.19",
     "scipy~=1.5",