add Prostate data loader

mltb2/data.py

@@ -12,6 +12,7 @@
 
 import os
 from hashlib import sha256
+from io import StringIO
 from typing import Tuple
 
 import joblib
@@ -113,3 +114,46 @@ def load_colon() -> Tuple[pd.Series, pd.DataFrame]:
         result = joblib.load(full_path)
 
     return result
+
+
+def load_prostate() -> Tuple[pd.Series, pd.DataFrame]:
+    """Load prostate data.
+
+    The data is loaded and parsed from `prostate data
+    <https://web.stanford.edu/~hastie/CASI_files/DATA/prostate.html>`_.
+
+    Returns:
+        Tuple containing labels and data.
+    """
+    filename = "prostate.pkl.gz"
+    mltb2_data_home = get_and_create_mltb2_data_dir()
+    full_path = os.path.join(mltb2_data_home, filename)
+    if not os.path.exists(full_path):
+        # download data file
+        url = "https://web.stanford.edu/~hastie/CASI_files/DATA/prostmat.csv"
+        page = requests.get(url, timeout=10)
+        page_str = page.text
+
+        # check checksum of data file
+        page_hash = sha256(page_str.encode("utf-8")).hexdigest()
+        assert page_hash == "f1ccfd3c9a837c002ec5d6489ab139c231739c3611189be14d15ca5541b92036", page_hash
+
+        data_df = pd.read_csv(StringIO(page_str))
+        data_df = data_df.T
+
+        labels = []
+        for label in data_df.index:
+            if "control" in label:
+                labels.append(0)
+            elif "cancer" in label:
+                labels.append(1)
+            else:
+                assert False, "This must not happen!"
+
+        data_df = data_df.reset_index(drop=True)  # reset the index to default integer index
+        label_series = pd.Series(labels)
+        result = (label_series, data_df)
+        joblib.dump(result, full_path, compress=("gzip", 3))
+    else:
+        result = joblib.load(full_path)
+    return result

mltb2/fasttext.py

@@ -43,7 +43,7 @@ def get_model_path_and_download() -> str:
                 url=model_url,
                 sha256_checksum=sha256_checksum,
             )
-            assert fetch_remote_file_path == model_full_path  # noqa: S101
+            assert fetch_remote_file_path == model_full_path
 
         return model_full_path
 

pyproject.toml

@@ -136,7 +136,8 @@ ignore = [
   "S106",  # Possible hardcoded password assigned to argument: "{}"
   "COM812",  # Trailing comma missing
   "S101",  # Use of `assert` detected
-  "PLR2004",  # Magic value used in comparison,
+  "PLR2004",  # Magic value used in comparison
+  "B011",  # Do not `assert False`
 ]
 
 [tool.ruff.per-file-ignores]

tests/test_data.py

@@ -4,7 +4,7 @@
 
 import pandas as pd
 
-from mltb2.data import _load_colon_data, _load_colon_label, load_colon
+from mltb2.data import _load_colon_data, _load_colon_label, load_colon, load_prostate
 
 
 def test_load_colon_data():
@@ -30,3 +30,14 @@ def test_load_colon():
     assert isinstance(result[1], pd.DataFrame)
     assert result[0].shape == (62,)
     assert result[1].shape == (62, 2000)
+
+
+def test_load_prostate_data():
+    result = load_prostate()
+    assert result is not None
+    assert isinstance(result, tuple)
+    assert len(result) == 2
+    assert isinstance(result[0], pd.Series)
+    assert isinstance(result[1], pd.DataFrame)
+    assert result[0].shape == (102,)
+    assert result[1].shape == (102, 6033)