PR fixes:

- ruff fixes

- docstrings: added description for fixture filled arguments

test/quick_test/common.py

@@ -1,10 +1,12 @@
 import os
-
 from logging import getLogger
 
 logger = getLogger(__name__)
 
 
+__all__ = ["load_test_subjects"]
+
+
 def load_test_subjects():
     """
     Load the test files from the given file path.
@@ -19,7 +21,7 @@ def load_test_subjects():
     test_subjects = []
 
     # Load the reference and test files
-    with open(os.path.join(subjects_dir, subjects_list), "r") as file:
+    with open(os.path.join(subjects_dir, subjects_list)) as file:
         for line in file:
             filename = line.strip()
             logger.debug(filename)

test/quick_test/conftest.py

@@ -3,6 +3,8 @@
 
 import pytest
 
+__all__ = ["subjects_dir", "test_dir", "reference_dir", "subjects_list"]
+
 
 @pytest.fixture
 def subjects_dir():

test/quick_test/test_errors_in_logfiles.py

@@ -1,10 +1,10 @@
-import pytest
-import yaml
+from logging import getLogger
 from pathlib import Path
 
-from .common import *
+import pytest
+import yaml
 
-from logging import getLogger
+from .common import load_test_subjects
 
 logger = getLogger(__name__)
 
@@ -25,7 +25,7 @@ def load_errors():
 
     error_file_path = Path(__file__).parent / "data" / "logfile.errors.yaml"
 
-    with open(error_file_path, "r") as file:
+    with open(error_file_path) as file:
         data = yaml.safe_load(file)
         errors = data.get("errors", [])
         whitelist = data.get("whitelist", [])
@@ -65,8 +65,10 @@ def test_errors(subjects_dir: Path, test_dir: Path, test_subject: Path):
     ----------
     subjects_dir : Path
         Subjects directory.
+        Filled by pytest fixture from conftest.py.
     test_dir : Path
         Tests directory.
+        Filled by pytest fixture from conftest.py.
     test_subject : Path
         Subject to test.
 
@@ -93,22 +95,22 @@ def test_errors(subjects_dir: Path, test_dir: Path, test_subject: Path):
             with log_file.open("r") as file:
                 lines = file.readlines()
                 lines_with_errors = []
-                for line_number, line in enumerate(lines, start=1):
+                for _line_number, line in enumerate(lines, start=1):
                     if any(error in line.lower() for error in errors):
                         if not any(white in line.lower() for white in whitelist):
                             # Get two lines before and after the current line
-                            context = lines[max(0, line_number - 2) : min(len(lines), line_number + 3)]
-                            lines_with_errors.append((line_number, context))
+                            context = lines[max(0, _line_number - 2) : min(len(lines), _line_number + 3)]
+                            lines_with_errors.append((_line_number, context))
                             # print(lines_with_errors)
                             files_with_errors[rel_path] = lines_with_errors
                             error_flag = True
         except FileNotFoundError:
-            raise FileNotFoundError(f"Log file not found at path: {log_file}")
+            raise FileNotFoundError(f"Log file not found at path: {log_file}") from None
 
     # Print the lines and context with errors for each file
     for file, lines in files_with_errors.items():
         logger.debug(f"\nFile {file}, in line {files_with_errors[file][0][0]}:")
-        for line_number, line in lines:
+        for _line_number, line in lines:
             logger.debug(*line, sep="")
 
     # Assert that there are no lines with any of the keywords

test/quick_test/test_file_existence.py

@@ -1,11 +1,10 @@
-import pytest
-
-from .common import *
-
 from logging import getLogger
-
 from pathlib import Path
 
+import pytest
+
+from .common import load_test_subjects
+
 logger = getLogger(__name__)
 
 
@@ -41,10 +40,13 @@ def test_file_existence(subjects_dir: Path, test_dir: Path, reference_dir: Path,
     ----------
     subjects_dir : Path
         Path to the subjects directory.
+        Filled by pytest fixture from conftest.py.
     test_dir : Path
         Name of the test directory.
+        Filled by pytest fixture from conftest.py.
     reference_dir : Path
         Name of the reference directory.
+        Filled by pytest fixture from conftest.py.
     test_subject : Path
         Name of the test subject.
 
@@ -54,8 +56,6 @@ def test_file_existence(subjects_dir: Path, test_dir: Path, reference_dir: Path,
         If a file in the reference list does not exist in the test list.
     """
 
-    print(test_subject)
-
     # Get reference files from the reference subject directory
     reference_subject = subjects_dir / reference_dir / test_subject
     reference_files = get_files_from_folder(reference_subject)

test/quick_test/test_images.py

@@ -1,16 +1,15 @@
-import pytest
+from collections import OrderedDict
+from logging import getLogger
+from pathlib import Path
+
 import nibabel as nib
 import nibabel.cmdline.diff
 import numpy as np
-from pathlib import Path
-
-from collections import OrderedDict
-
-from .common import *
+import pytest
 
 from CerebNet.utils.metrics import dice_score
 
-from logging import getLogger
+from .common import load_test_subjects
 
 logger = getLogger(__name__)
 
@@ -106,10 +105,13 @@ def test_image_headers(subjects_dir: Path, test_dir: Path, reference_dir: Path,
     ----------
     subjects_dir : Path
         Path to the subjects directory.
+        Filled by pytest fixture from conftest.py.
     test_dir : Path
         Name of test directory.
+        Filled by pytest fixture from conftest.py.
     reference_dir: Path
         Name of reference directory.
+        Filled by pytest fixture from conftest.py.
     test_subject : Path
         Name of the test subject.
 
@@ -144,10 +146,13 @@ def test_seg_data(subjects_dir: Path, test_dir: Path, reference_dir: Path, test_
     ----------
     subjects_dir : Path
         Path to the subjects directory.
+        Filled by pytest fixture from conftest.py.
     test_dir : Path
         Name of test directory.
+        Filled by pytest fixture from conftest.py.
     reference_dir : Path
         Name of reference directory.
+        Filled by pytest fixture from conftest.py.
     test_subject : Path
         Name of the test subject.
 
@@ -174,7 +179,7 @@ def test_seg_data(subjects_dir: Path, test_dir: Path, reference_dir: Path, test_
 
     # Check the dice score
     np.testing.assert_allclose(
-        dscore, 0, atol=1e-6, rtol=1e-6, err_msg=f"Dice scores are not within range for all classes"
+        dscore, 0, atol=1e-6, rtol=1e-6, err_msg="Dice scores are not within range for all classes"
     )
 
     # assert dscore == 1, "Dice scores are not 1 for all classes"
@@ -191,10 +196,13 @@ def test_int_data(subjects_dir: Path, test_dir: Path, reference_dir: Path, test_
     ----------
     subjects_dir : Path
         Path to the subjects directory.
+        Filled by pytest fixture from conftest.py.
     test_dir : Path
         Name of test directory.
+        Filled by pytest fixture from conftest.py.
     reference_dir : Path
         Name of reference directory.
+        Filled by pytest fixture from conftest.py.
     test_subject : Path
         Name of the test subject.
 

test/quick_test/test_stats.py

@@ -1,14 +1,12 @@
-from .conftest import *
-
+import os
+from logging import getLogger
 from pathlib import Path
 
 import pandas as pd
 import pytest
 import yaml
 
-from .common import *
-
-from logging import getLogger
+from .common import load_test_subjects
 
 logger = getLogger(__name__)
 
@@ -29,7 +27,7 @@ def thresholds():
     thresholds_file = Path(__file__).parent / "data/thresholds/aseg.stats.yaml"
 
     # Open the file_path and read the thresholds into a dictionary
-    with open(thresholds_file, "r") as file:
+    with open(thresholds_file) as file:
         data = yaml.safe_load(file)
         default_threshold = data.get("default_threshold")
         thresholds = data.get("thresholds", {})
@@ -76,15 +74,15 @@ def load_structs(test_file: Path):
         List of structs.
     """
 
-    if "aseg" in str(test_file):
+    if test_file.name == "aseg.stats":
         structs_file = Path(__file__).parent / "data/thresholds/aseg.stats.yaml"
-    elif "aparc+DKT" in str(test_file):
+    elif test_file.name == "aparc+DKT.stats":
         structs_file = Path(__file__).parent / "data/thresholds/aparc+DKT.stats.yaml"
     else:
         raise ValueError("Unknown test file")
 
     # Open the file_path and read the structs: into a list
-    with open(structs_file, "r") as file:
+    with open(structs_file) as file:
         data = yaml.safe_load(file)
         structs = data.get("structs", [])
 
@@ -112,18 +110,17 @@ def read_measure_stats(file_path: Path):
     measurements = {}
 
     # Retrieve lines starting with "# Measure" from the stats file
-    with open(file_path, "r") as file:
+    with open(file_path) as file:
         # Read each line in the file
-        for i, line in enumerate(file, 1):
+        for _i, line in enumerate(file, 1):
             # Check if the line starts with "# ColHeaders"
             if line.startswith("# ColHeaders"):
-                table_start = i
-                columns = line.strip("# ColHeaders").strip().split(" ")
+                line.removeprefix("# ColHeaders").strip().split(" ")
 
             # Check if the line starts with "# Measure"
             if line.startswith("# Measure"):
                 # Strip "# Measure" from the line
-                line = line.strip("# Measure").strip()
+                line = line.removeprefix("# Measure").strip()
                 # Append the measure to the list
                 line = line.split(", ")
                 measure.append(line[1])
@@ -153,17 +150,16 @@ def read_table(file_path: Path):
     file_path = file_path / "stats" / "aseg.stats"
 
     # Retrieve stats table from the stats file
-    with open(file_path, "r") as file:
+    with open(file_path) as file:
         # Read each line in the file
         for i, line in enumerate(file, 1):
             # Check if the line starts with "# ColHeaders"
             if line.startswith("# ColHeaders"):
                 table_start = i
-                columns = line.strip("# ColHeaders").strip().split(" ")
+                columns = line.removeprefix("# ColHeaders").strip().split(" ")
 
     # Read the reference table into a pandas dataframe
     table = pd.read_table(file_path, skiprows=table_start, sep="\s+", header=None)
-    table_numeric = table.apply(pd.to_numeric, errors="coerce")
     table.columns = columns
     table.set_index(columns[0], inplace=True)
 
@@ -202,8 +198,6 @@ def test_measure_exists(subjects_dir: Path, test_dir: Path, test_subject: Path):
                 f"for struct {struct} the value {data[1].get(struct)} is not close to " f"{ref_data[1].get(struct)}"
             )
 
-    stats_data = read_measure_stats(test_file)
-
     # Check if all measures exist in stats file
     assert len(errors) == 0, ", ".join(errors)