Fixed lint

BlueBrain · Oct 29, 2024 · fc26f8a · fc26f8a
1 parent 272cf60
commit fc26f8a
Show file tree

Hide file tree

Showing 11 changed files with 17 additions and 4 deletions.
diff --git a/connectome_manipulator/connectome_manipulation/manipulation/conn_extraction.py b/connectome_manipulator/connectome_manipulation/manipulation/conn_extraction.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Connectome extraction module."""
+
 import os
 
 import json

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/conn_removal.py b/connectome_manipulator/connectome_manipulation/manipulation/conn_removal.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Connection removal module."""
+
 import os
 
 import numpy as np

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/conn_rewiring.py b/connectome_manipulator/connectome_manipulation/manipulation/conn_rewiring.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Connectome (re)wiring module (general-purpose)."""
+
 import libsonata
 import neurom as nm
 import numpy as np

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/conn_wiring.py b/connectome_manipulator/connectome_manipulation/manipulation/conn_wiring.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Connectome wiring module (specialized)."""
+
 from datetime import datetime, timedelta
 
 import libsonata

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/null_manipulation.py b/connectome_manipulator/connectome_manipulation/manipulation/null_manipulation.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Null manipulation module - does not do anything."""
+
 from connectome_manipulator import log
 from connectome_manipulator.connectome_manipulation.manipulation import Manipulation
 

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/syn_prop_alteration.py b/connectome_manipulator/connectome_manipulation/manipulation/syn_prop_alteration.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Module for alteration of synapse property values."""
+
 import numpy as np
 
 from connectome_manipulator import log, profiler

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/syn_removal.py b/connectome_manipulator/connectome_manipulation/manipulation/syn_removal.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Synapse removal module."""
+
 import numpy as np
 
 from scipy.sparse import csc_matrix

diff --git a/connectome_manipulator/connectome_manipulation/manipulation/syn_subsampling.py b/connectome_manipulator/connectome_manipulation/manipulation/syn_subsampling.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024 Blue Brain Project/EPFL
 
+"""Synapse subsampling module."""
+
 import numpy as np
 
 from connectome_manipulator import log, profiler

diff --git a/connectome_manipulator/model_building/conn_prob_adj.py b/connectome_manipulator/model_building/conn_prob_adj.py
@@ -43,8 +43,7 @@ def extract(circuit, sel_src=None, sel_dest=None, edges_popul_name=None, CV_dict
 
 
 def build(adj_mat, src_node_ids, tgt_node_ids, inverted=False, **_):
-    """Builds a (deterministic) connection probability model of type ``ConnProbAdjModel`` from an adjacency matrix
-    (i.e., returning probabilities 0.0 or 1.0 only).
+    """Builds a (deterministic) connection probability model of type ``ConnProbAdjModel`` from an adjacency matrix (i.e., returning probabilities 0.0 or 1.0 only).
 
     Args:
         adj_mat (scipy.sparse.csc_matrix): Sparse adjacency matrix with boolean entries (i.e., True...connection, False...no connection)

diff --git a/connectome_manipulator/model_building/model_types.py b/connectome_manipulator/model_building/model_types.py
@@ -1008,7 +1008,6 @@ def draw_cov(self, src_type, tgt_type, size=1):
         (As in Chindemi et al. (2022) "A calcium-based plasticity model for
         predicting long-term potentiation and depression in the neocortex")
         """
-
         if self.prop_cov_mat is None:
             log.warning("No correlated properties!")
             return np.zeros((size, 0))

diff --git a/connectome_manipulator/model_building/pos_mapping_from_table.py b/connectome_manipulator/model_building/pos_mapping_from_table.py
@@ -147,7 +147,6 @@ def plot(out_dir, nrn_ids, nrn_pos, nrn_lay, model, **_):  # pragma: no cover
     Note:
         Only mappings to 2D or 3D space are supported for visualization.
     """
-
     nrn_pos_model = model.apply(gids=nrn_ids)
 
     # Cell positions in 3D original vs. mapped space