Use safe_concat function from brainglobe-utils (#148)

* Use safe_concat function from brainglobe-utils

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: willGraham01 <[email protected]>

.github/workflows/test_and_deploy.yml

@@ -35,8 +35,6 @@ jobs:
           python-version: "3.10"
         - os: windows-latest
           python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.8"
 
     steps:
       - name: Cache atlases

pyproject.toml

@@ -3,7 +3,7 @@ name = "brainreg"
 description = "Automated 3D brain registration"
 readme = "README.md"
 authors = [
-    {name = "Adam Tyson, Charly Rousseau", email = "[email protected]"},
+    { name = "Adam Tyson, Charly Rousseau", email = "[email protected]" },
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -16,13 +16,13 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "bg-atlasapi",
     "bg-space",
     "fancylog",
     "imio",
-    "brainglobe-utils",
+    "brainglobe-utils>=0.2.7",
     "numpy",
     "scikit-image",
 ]
@@ -35,22 +35,13 @@ napari = [
     "brainreg-segment>=0.0.2",
     "napari[pyside2]",
 ]
-dev = [
-    "black",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-]
+dev = ["black", "pre-commit", "pytest", "pytest-cov"]
 
 [project.scripts]
 brainreg = "brainreg.cli:main"
 
 [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]
@@ -72,11 +63,9 @@ filterwarnings = [
     "ignore:`np.uint0` is a deprecated alias for `np.uintp`",
     "ignore:`np.void0` is a deprecated alias for `np.void`",
     "ignore:`np.bytes0` is a deprecated alias for `np.bytes_`",
-    "ignore:`np.str0` is a deprecated alias for `np.str_`"
-]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "ignore:`np.str0` is a deprecated alias for `np.str_`",
 ]
+markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 
 [tool.black]
 target-version = ['py38', 'py39', 'py310', 'py311']
@@ -85,6 +74,6 @@ line-length = 79
 
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs"]
+exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 fix = true

src/brainreg/utils/misc.py

@@ -2,8 +2,6 @@
 from argparse import Namespace
 from pathlib import PurePath
 
-import pandas as pd
-
 
 def get_arg_groups(args, parser):
     arg_groups = {}
@@ -26,28 +24,3 @@ def serialise(obj):
 def log_metadata(file_path, args):
     with open(file_path, "w") as f:
         json.dump(args, f, default=serialise)
-
-
-def safe_pandas_concat(df1: pd.DataFrame, df2: pd.DataFrame) -> pd.DataFrame:
-    """
-    Concatenate two DataFrames without relying on deprecated functionality
-    when one of the DataFrames is empty.
-
-    If df1 and df2 are non-empty, return the concatenation.
-    If df1 is empty and df2 is not, return a copy of df2.
-    If df1 is non-empty and df2 is, return a copy of df1.
-    If df1 and df2 are empty, return an empty DataFrame with the same column
-    names as df1.
-
-    :param df1: DataFrame to concatenate.
-    :param df2: DataFrame to concatenate.
-    :returns: DataFrame formed from concatenation of df1 and df2.
-    """
-    if df1.empty and df2.empty:
-        return pd.DataFrame(columns=df1.columns)
-    elif df1.empty:
-        return df2.copy()
-    elif df2.empty:
-        return df1.copy()
-    else:
-        return pd.concat([df1, df2], ignore_index=True)

src/brainreg/utils/volume.py

@@ -10,9 +10,7 @@
 import imio
 import numpy as np
 import pandas as pd
-from brainglobe_utils.pandas.misc import initialise_df
-
-from .misc import safe_pandas_concat
+from brainglobe_utils.pandas.misc import initialise_df, safe_pandas_concat
 
 
 class UnknownAtlasValue(Exception):