Ran ruff on all files

Author: pgleeson

.github/workflows/ci.yml

@@ -39,7 +39,7 @@ jobs:
       if: ${{ matrix.runs-on == 'macos-latest' }}
       run: |
         brew install hdf5
-        
+
     - name: Build package
       run: |
         pip install .[full]

doc/conf.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

doc/devdocs/index.rst

@@ -9,4 +9,3 @@ Contributing
    implementation_of_bindings
    meeting_june_2012
    nodes_segments_sections
-

doc/devdocs/meeting_june_2012.rst

@@ -109,7 +109,7 @@ Mike V was asked to add a clone method to a morphology.
 It was decided that fraction_along should be a property of segment.
 
 The syntax for segment groups should be as follows:
-group=morph.segment_groups['axon_group'] 
+group=morph.segment_groups['axon_group']
 (in connect merge groups should be false by default - throw an exception, tell the user setting merge_groups = True or rename group will fix this)
 
 This was a subject of great debate and has not been completely settled.

doc/devdocs/nodes_segments_sections.rst

@@ -58,7 +58,7 @@ unbranched segmentGroups, which can be used as the basis for sections in any par
 in them, or be ignored by any other application.
 
 In libNeuroML, a section-like concept can be added at API level, to facilitate building cells, to facilitate import/export
-to/from simulators supporting this concept, and to serve as a basis for recompartmentalisation of cells. 
+to/from simulators supporting this concept, and to serve as a basis for recompartmentalisation of cells.
 
 
 
@@ -96,7 +96,7 @@ to the **parent** element, i.e.
     <parent segment="2" fractionAlong="0.5"/>
 
 This is not possible in a node based format, but represents a logically consistent description of what the modeller
-wants. 
+wants.
 
 
 What to do?
@@ -108,4 +108,4 @@ enforce "best practice"?
 PG: I'd argue for the first approach, as it retains as much as possible of what the original reconstructor/simulator specified.
 An API which enforces a policy when it encounters a non optimal morphology (e.g. moving all dendrites to connection points,
 inserting new nodes) will alter the original data in perhaps unintended ways, and that information will be lost by subsequent readers.
-It should be up to each parsing application to decide what to do with the extra information when it reads in a file.
+It should be up to each parsing application to decide what to do with the extra information when it reads in a file.

doc/helpers/nml-core-docs.py

@@ -7,7 +7,6 @@
 Copyright 2023 NeuroML authors
 """
 
-
 import textwrap
 
 print("Generating list of nml classes")

doc/refs.bib

@@ -20,4 +20,3 @@ @Article{Vella2014
   timestamp    = {2019-02-20},
   year         = {2014},
 }
-

doc/userdocs/api.rst

@@ -12,5 +12,3 @@ You can find information on these in the pages below.
    writers
    utils
    arraymorph
-
-

doc/userdocs/arraymorph.rst

@@ -6,5 +6,3 @@
     :members:
     :undoc-members:
     :show-inheritance:
-
-

doc/userdocs/coreclasses_list.txt

@@ -2216,5 +2216,3 @@ basePyNNIaFCondCell
    :undoc-members:
    :show-inheritance:
    :inherited-members:
-
-