Merge remote-tracking branch 'origin/main' into collapsible-widget-pa…

…rent-bug
brainglobe · Jan 8, 2024 · 2a03009 · 2a03009
2 parents 4a24d55 + cb48329
commit 2a03009
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,10 @@
+# Configuring https://pre-commit.ci/ bot
+ci:
+  autoupdate_schedule: monthly
+
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -11,16 +15,16 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.272
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.9
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.12.1
       hooks:
           - id: black
     -   repo: https://github.com/pre-commit/mirrors-mypy
-        rev: v1.4.0
+        rev: v1.8.0
         hooks:
         -   id: mypy
             args: [--config-file, pyproject.toml]

diff --git a/brainglobe_utils/IO/cells.py b/brainglobe_utils/IO/cells.py
@@ -29,11 +29,9 @@ def get_cells(
     cells_only: bool = False,
     cell_type: Optional[int] = None,
 ):
-    # TODO: implement csv read
     if cells_file_path.endswith(".xml"):
         return get_cells_xml(cells_file_path, cells_only=cells_only)
     elif cells_file_path.endswith(".yml"):
-        # Not general
         return get_cells_yml(cells_file_path, ignore_type=True)
     elif os.path.isdir(cells_file_path):
         try:
@@ -211,14 +209,6 @@ def pretty_xml(elem, indentation_str="  "):
     return md_parsed.toprettyxml(indent=indentation_str, encoding="UTF-8")
 
 
-# TRANSCODE
-def transform_xml_file(xml_file_path, output_file_path, transform_params):
-    cells = get_cells(xml_file_path)  # TODO: check if cells_only
-    for cell in cells:
-        cell.transform(*transform_params)
-    cells_to_xml(cells, output_file_path)
-
-
 def find_relevant_tiffs(tiffs, cell_def):
     cells = [UntypedCell(tiff) for tiff in tiffs]
     if os.path.isdir(cell_def):

diff --git a/brainglobe_utils/array/filter.py b/brainglobe_utils/array/filter.py
diff --git a/brainglobe_utils/array/fit.py b/brainglobe_utils/array/fit.py
diff --git a/brainglobe_utils/array/locate.py b/brainglobe_utils/array/locate.py
diff --git a/brainglobe_utils/array/math.py b/brainglobe_utils/array/math.py
diff --git a/brainglobe_utils/array/misc.py b/brainglobe_utils/array/misc.py
diff --git a/brainglobe_utils/array/size.py b/brainglobe_utils/array/size.py