From 4a18ffb98fd70dee12a86927bac0a44e978b3592 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Dec 2024 14:53:43 +0100
Subject: [PATCH 1/2] Fix renaming in case a new section is needed

Fixes #120
---
 src/boutdata/data.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/boutdata/data.py b/src/boutdata/data.py
index 20171e7..247dc3d 100644
--- a/src/boutdata/data.py
+++ b/src/boutdata/data.py
@@ -359,7 +359,7 @@ def get_immediate_parent_and_child(path):
 
             # Renaming a child key just within the same parent section, we can preserve
             # the order
-            if new_parent is old_parent:
+            if new_parent is old_parent and ":" not in new_name:
                 new_parent._keys = rename_key(new_parent._keys, new_child, old_child)
                 new_parent.comments = rename_key(
                     new_parent.comments, new_child, old_child

From e64657104e9f558fdc486520d2b8d8c6935058a7 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Mon, 2 Dec 2024 14:02:29 +0000
Subject: [PATCH 2/2] [skip ci] Apply black/isort changes

---
 src/boutupgrader/bout_v5_factory_upgrader.py  | 20 +++++--------------
 .../bout_v6_coordinates_upgrader.py           |  5 -----
 2 files changed, 5 insertions(+), 20 deletions(-)

diff --git a/src/boutupgrader/bout_v5_factory_upgrader.py b/src/boutupgrader/bout_v5_factory_upgrader.py
index 1558fae..ddb7157 100644
--- a/src/boutupgrader/bout_v5_factory_upgrader.py
+++ b/src/boutupgrader/bout_v5_factory_upgrader.py
@@ -59,9 +59,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -72,9 +70,7 @@ def find_type_pointers(factory, source):
         r"""
         \b{type_name}\s*\*\s*   # Type name and pointer
         ([\w_]+)\s*;            # Variable name
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -104,9 +100,7 @@ def fix_declarations(factory, variables, source):
             (.*?)(class\s*)?         # optional "class" keyword
             \b({type_name})\s*\*\s*  # Type-pointer
             ({variable_name})\s*;    # Variable
-            """.format(
-                type_name=factory["type_name"], variable_name=variable
-            ),
+            """.format(type_name=factory["type_name"], variable_name=variable),
             r"\1std::unique_ptr<\3> \4{nullptr};",
             source,
             flags=re.VERBOSE,
@@ -120,9 +114,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment from factory
             ({factory_name}::.*{create_method}.*);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1auto \4 = \5;",
             source,
             flags=re.VERBOSE,
@@ -136,9 +128,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment
             (0|nullptr|NULL);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1std::unique_ptr<\2> \3{nullptr};",
             source,
             flags=re.VERBOSE,
diff --git a/src/boutupgrader/bout_v6_coordinates_upgrader.py b/src/boutupgrader/bout_v6_coordinates_upgrader.py
index 4dda8f5..8c9feff 100644
--- a/src/boutupgrader/bout_v6_coordinates_upgrader.py
+++ b/src/boutupgrader/bout_v6_coordinates_upgrader.py
@@ -27,7 +27,6 @@
 
 
 def add_parser(subcommand, default_args, files_args):
-
     help_text = textwrap.dedent(
         """\
             Upgrade files to use the refactored Coordinates class.
@@ -85,7 +84,6 @@ def indices_of_matching_lines(pattern, lines):
 
 
 def use_metric_accessors(original_string):
-
     lines = original_string.splitlines()
 
     line_matches = SETTING_METRIC_COMPONENT_REGEX.findall(original_string)
@@ -138,7 +136,6 @@ def remove_geometry_calls(lines):
 
 
 def assignment_regex_pairs(var):
-
     arrow_or_dot = r"\b.+\-\>|\."
     not_followed_by_equals = r"(?!\s?=)"
     equals_something = r"\=\s?(.+)(?=;)"
@@ -174,7 +171,6 @@ def replacement_for_division_assignment(match):
 
 
 def mesh_get_pattern_and_replacement():
-
     # Convert `mesh->get(coord->dx(), "dx")` to `coord->setDx(mesh->get("dx"));`, etc
 
     def replacement_for_assignment_with_mesh_get(match):
@@ -196,7 +192,6 @@ def replacement_for_assignment_with_mesh_get(match):
 
 # Deal with the basic find-and-replace cases that do not involve multiple lines
 def replace_one_line_cases(modified):
-
     metric_component = r"g_?\d\d"
     mesh_spacing = r"d[xyz]"