Update dependencies, versioning, and add tests to include support for Python 3.13

README.md

@@ -18,6 +18,8 @@ reComBat is a PyPI package which can be installed via `pip`:
 pip install reComBat
 ```
 
+The project supports Python 3.10 through Python 3.13.
+
 You can also clone the repository and install it locally via [Poetry](https://python-poetry.org/) by executing
 ```bash
 poetry install

pyproject.toml

@@ -17,14 +17,16 @@ include = ["LICENSE"]
 packages = [{ include="reComBat", from="." }]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.11"
-numpy = "^1.20.0"
-sklearn = "^0.0"
-tqdm = "^4.62.3"
-fire = "^0.4.0"
-pandas = "^1.3.4"
-
-[tool.poetry.dev-dependencies]
+python = ">=3.10,<3.14"
+numpy = ">=2.2.3,<3.0"
+scikit-learn = ">=1.5.2,<2.0"
+joblib = ">=1.4.2,<2.0"
+tqdm = ">=4.62.3,<5.0"
+fire = ">=0.7.1,<1.0"
+pandas = ">=2.2.3,<4.0"
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=8.3.5,<9.0"
 
 [tool.poetry.scripts]
 reComBat = "reComBat.cli:main"

reComBat/__init__.py

@@ -1,4 +1,4 @@
 # from __future__ import absolute_import
 from .reComBat import reComBat
 
-__version__ = '0.1.0'
+__version__ = "0.1.4"

reComBat/cli.py

@@ -49,7 +49,7 @@ def run_recombat(data_file,
 
     # Read in the data and batch files.
     data = pd.read_csv(os.path.join(data_path,data_file),index_col=0)
-    batch = pd.read_csv(os.path.join(data_path,batch_file),index_col=0,squeeze=True)
+    batch = pd.read_csv(os.path.join(data_path,batch_file),index_col=0).squeeze("columns")
 
     # Read in potential design matrices.
     if X_file is not None:

tests/test_python313_compat.py

@@ -0,0 +1,60 @@
+import pandas as pd
+
+from reComBat import reComBat
+from reComBat.cli import run_recombat
+
+
+def test_fit_transform_smoke():
+    data = pd.DataFrame(
+        [
+            [1.0, 2.0, 3.0, 4.0],
+            [1.2, 2.5, 2.8, 4.5],
+            [0.8, 1.7, 3.5, 3.7],
+            [9.5, 10.5, 12.0, 13.5],
+            [10.4, 11.2, 11.4, 12.8],
+            [8.9, 10.9, 12.6, 13.1],
+        ],
+        index=["s1", "s2", "s3", "s4", "s5", "s6"],
+        columns=["g1", "g2", "g3", "g4"],
+    )
+    batches = pd.Series(["a", "a", "a", "b", "b", "b"], index=data.index, name="batch")
+
+    adjusted = reComBat(verbose=False).fit_transform(data, batches)
+
+    assert isinstance(adjusted, pd.DataFrame)
+    assert adjusted.shape == data.shape
+    assert adjusted.index.equals(data.index)
+    assert adjusted.columns.equals(data.columns)
+
+
+def test_cli_reads_batch_series_and_writes_output(tmp_path):
+    data = pd.DataFrame(
+        [
+            [1.0, 2.0, 3.0, 4.0],
+            [1.2, 2.5, 2.8, 4.5],
+            [0.8, 1.7, 3.5, 3.7],
+            [9.5, 10.5, 12.0, 13.5],
+            [10.4, 11.2, 11.4, 12.8],
+            [8.9, 10.9, 12.6, 13.1],
+        ],
+        index=["s1", "s2", "s3", "s4", "s5", "s6"],
+        columns=["g1", "g2", "g3", "g4"],
+    )
+    batches = pd.Series(["a", "a", "a", "b", "b", "b"], index=data.index, name="batch")
+
+    data.to_csv(tmp_path / "data.csv")
+    batches.to_frame().to_csv(tmp_path / "batches.csv")
+
+    run_recombat(
+        data_file="data.csv",
+        batch_file="batches.csv",
+        data_path=tmp_path,
+        out_path=tmp_path,
+        out_file="adjusted.csv",
+        verbose=False,
+    )
+
+    adjusted = pd.read_csv(tmp_path / "adjusted.csv", index_col=0)
+
+    assert adjusted.shape == data.shape
+    assert list(adjusted.columns) == list(data.columns)