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GazzolaLab · Mar 21, 2024 · f57fb1c · f57fb1c
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commit f57fb1c
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Showing 9 changed files with 50 additions and 48 deletions.
diff --git a/src/miv_simulator/interface/connections.py b/src/miv_simulator/interface/connections.py
@@ -62,16 +62,16 @@ def __call__(self):
 
     def on_write_meta_data(self):
         return MPI.COMM_WORLD.Get_rank() == 0
-    
+
     def compute_context(self):
         context = super().compute_context()
-        del context['config']['filepath']
-        del context['config']['forest_filepath']
-        del context['config']['io_size']
-        del context['config']['chunk_size']
-        del context['config']['value_chunk_size']
-        del context['config']['cache_size']
-        del context['config']['write_size']
-        del context['config']['ranks']
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
+        del context["config"]["filepath"]
+        del context["config"]["forest_filepath"]
+        del context["config"]["io_size"]
+        del context["config"]["chunk_size"]
+        del context["config"]["value_chunk_size"]
+        del context["config"]["cache_size"]
+        del context["config"]["write_size"]
+        del context["config"]["ranks"]
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
         return context
diff --git a/src/miv_simulator/interface/distances.py b/src/miv_simulator/interface/distances.py
@@ -52,14 +52,14 @@ def __call__(self):
 
     def on_write_meta_data(self):
         return MPI.COMM_WORLD.Get_rank() == 0
-    
+
     def compute_context(self):
         context = super().compute_context()
-        del context['config']['filepath']
-        del context['config']['io_size']
-        del context['config']['chunk_size']
-        del context['config']['value_chunk_size']
-        del context['config']['cache_size']
-        del context['config']['ranks']
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
+        del context["config"]["filepath"]
+        del context["config"]["io_size"]
+        del context["config"]["chunk_size"]
+        del context["config"]["value_chunk_size"]
+        del context["config"]["cache_size"]
+        del context["config"]["ranks"]
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
         return context
diff --git a/src/miv_simulator/interface/network.py b/src/miv_simulator/interface/network.py
@@ -105,5 +105,5 @@ def launch(self):
 
     def compute_context(self):
         context = super().compute_context()
-        del context['config']
-        return context
+        del context["config"]
+        return context
diff --git a/src/miv_simulator/interface/network_architecture.py b/src/miv_simulator/interface/network_architecture.py
@@ -131,10 +131,10 @@ def generate_connections(self, version=None, uses=None):
 
     def compute_context(self):
         context = super().compute_context()
-        del context['config']['filepath']
-        del context['config']['io_size']
-        del context['config']['chunk_size']
-        del context['config']['value_chunk_size']
-        del context['config']['ranks']
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
-        return context
+        del context["config"]["filepath"]
+        del context["config"]["io_size"]
+        del context["config"]["chunk_size"]
+        del context["config"]["value_chunk_size"]
+        del context["config"]["ranks"]
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
+        return context
diff --git a/src/miv_simulator/interface/neuroh5_graph.py b/src/miv_simulator/interface/neuroh5_graph.py
@@ -95,8 +95,8 @@ def files(self) -> Dict[str, str]:
             "cells": self.graph.cells_filepath,
             "connections": self.graph.connections_filepath,
         }
-        
+
     def compute_context(self):
         context = super().compute_context()
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
         return context
diff --git a/src/miv_simulator/interface/synapse_forest.py b/src/miv_simulator/interface/synapse_forest.py
@@ -3,6 +3,7 @@
 from pydantic import BaseModel, Field, ConfigDict
 from machinable.utils import file_hash
 
+
 class GenerateSynapseForest(Component):
     class Config(BaseModel):
         model_config = ConfigDict(extra="forbid")
@@ -32,7 +33,9 @@ def __call__(self) -> None:
     def compute_context(self):
         # remove filepath in favor of uses
         context = super().compute_context()
-        del context['config']['filepath']
-        context['config']['morphology'] = file_hash(context['config']['morphology'])
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
+        del context["config"]["filepath"]
+        context["config"]["morphology"] = file_hash(
+            context["config"]["morphology"]
+        )
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
         return context
diff --git a/src/miv_simulator/interface/synapses.py b/src/miv_simulator/interface/synapses.py
@@ -67,13 +67,13 @@ def on_write_meta_data(self):
 
     def compute_context(self):
         context = super().compute_context()
-        del context['config']['forest_filepath']
-        del context['config']['template_path']
-        del context['config']['mechanisms_path']
-        del context['config']['io_size']
-        del context['config']['write_size']
-        del context['config']['chunk_size']
-        del context['config']['value_chunk_size']
-        del context['config']['ranks']
-        context['predicate']['uses'] = sorted([u.hash for u in self.uses])
+        del context["config"]["forest_filepath"]
+        del context["config"]["template_path"]
+        del context["config"]["mechanisms_path"]
+        del context["config"]["io_size"]
+        del context["config"]["write_size"]
+        del context["config"]["chunk_size"]
+        del context["config"]["value_chunk_size"]
+        del context["config"]["ranks"]
+        context["predicate"]["uses"] = sorted([u.hash for u in self.uses])
         return context
diff --git a/tests/_machinable/project.py b/tests/_machinable/project.py
@@ -1,7 +1,8 @@
 from machinable import Project
 
+
 class TestEnv(Project):
     def on_resolve_remotes(self):
         return {
             "mpi": "url+https://raw.githubusercontent.com/machinable-org/machinable/2670e9626eb548f6ce2301923be1f49642086d8c/docs/examples/mpi-execution/mpi.py",
-        }
+        }
diff --git a/tests/test_interface.py b/tests/test_interface.py
@@ -12,12 +12,12 @@ def test_interface(tmp_path):
 
     source = os.environ["MIV_SIMULATOR_TEST_INTERFACE_SRC"]
     wd = os.path.dirname(__file__)
-    
+
     debug = True
-    storage_directory = str(tmp_path / 'storage')
+    storage_directory = str(tmp_path / "storage")
     if debug:
         storage_directory = f"{wd}/_machinable/storage"
-    
+
     with get("machinable.index", storage_directory), get(
         "machinable.project", wd
     ):
@@ -31,9 +31,7 @@ def test_interface(tmp_path):
                     "morphology_path": f"{source}/morphology",
                 },
             ).launch()
-        
+
         for component in run.executables:
             print(component)
             assert component.cached()
-
-