From 5ac5dc4a714310569ffc3c43ecac0ad4e79dd427 Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Wed, 1 Nov 2023 10:14:26 +0000
Subject: [PATCH] Fix pandas FutureWarning (#138)

* Fix pandas FutureWarning

* Remove py3.8 support since brainglobe-utils is a hard dependency

---------

Co-authored-by: willGraham01 <1willgraham@gmail.com>
---
 .github/workflows/test_and_deploy.yml |  4 ++--
 brainreg_segment/regions/analysis.py  |  4 ++--
 pyproject.toml                        | 20 ++++++++------------
 3 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 972fd84..f29eba1 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -22,12 +22,12 @@ jobs:
       matrix:
         # Run across a mixture of Python versions and operating systems
         include:
+        - os: ubuntu-latest
+          python-version: "3.11"
         - os: macos-latest
           python-version: "3.10"
         - os: windows-latest
           python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.8"
 
     steps:
       - name: Cache atlases
diff --git a/brainreg_segment/regions/analysis.py b/brainreg_segment/regions/analysis.py
index a99ece4..35a098d 100644
--- a/brainreg_segment/regions/analysis.py
+++ b/brainreg_segment/regions/analysis.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pandas as pd
 from brainglobe_utils.general.list import unique_elements_lists
-from brainglobe_utils.pandas.misc import initialise_df
+from brainglobe_utils.pandas.misc import initialise_df, safe_pandas_concat
 from napari.qt.threading import thread_worker
 from skimage.measure import regionprops_table
 
@@ -248,7 +248,7 @@ def add_structure_volume_to_df(
     }
 
     df_to_append = pd.DataFrame(data_to_append)
-    df = pd.concat([df, df_to_append], ignore_index=True)
+    df = safe_pandas_concat(df, df_to_append)
     return df
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 6778525..2198290 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ name = "brainreg-segment"
 description = "Manual segmentation of 3D brain structures in a common anatomical space"
 readme = "README.md"
 authors = [
-    {name = "Adam Tyson, Horst Obenhaus", email = "code@adamltyson.com"},
+    { name = "Adam Tyson, Horst Obenhaus", email = "code@adamltyson.com" },
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -17,12 +17,12 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
 ]
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 dependencies = [
     "brainglobe-napari-io >= 0.3.0",
     "dask >= 2.15.0",
     "imio",
-    "brainglobe-utils",
+    "brainglobe-utils >=  0.2.7",
     "napari-plugin-engine >= 0.1.4",
     "napari>=0.4.5",
     "numpy",
@@ -30,7 +30,7 @@ dependencies = [
     "scikit-image",
     "tables",
 ]
-license = {text = "BSD-3-Clause"}
+license = { text = "BSD-3-Clause" }
 dynamic = ["version"]
 
 [project.urls]
@@ -49,7 +49,7 @@ dev = [
     "coverage",
     "pytest-cov",
     "pytest-qt",
-    "napari-time-slicer" # to test non ndarray-types
+    "napari-time-slicer", # to test non ndarray-types
 ]
 
 [project.entry-points."napari.manifest"]
@@ -62,11 +62,7 @@ brainreg-segment = "brainreg_segment.segment:main"
 brainreg-segment = "brainreg_segment.plugins"
 
 [build-system]
-requires = [
-    "setuptools>=45",
-    "wheel",
-    "setuptools_scm[toml]>=6.2",
-]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -94,7 +90,7 @@ filterwarnings = [
     # Warning comes from vispy - fixed in vispy 0.12.0. napari 0.5.0 will bump
     # vispy to 0.5.0, so this filter should be removed when napari 0.5.0
     # is released
-    "ignore:distutils Version classes are deprecated:DeprecationWarning"
+    "ignore:distutils Version classes are deprecated:DeprecationWarning",
 ]
 
 [tool.black]
@@ -104,6 +100,6 @@ line-length = 79
 
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs"]
+exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 fix = true