Changes after linting with "ruff"

src/sensospot_parser/__init__.py

@@ -21,7 +21,7 @@ DEFAULT_OUTPUT_FILENAME = "collected_data.csv"
 PathLike = Union[str, pathlib.Path]
 
 
-def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
+def parse_folder(source: PathLike, *, quiet: bool = False) -> pandas.DataFrame:
     """parses an assay result folder
 
     The function will first try to use an assay results xml file, and will
@@ -38,7 +38,7 @@ def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
         return parse_xml_folder(source)
     except ValueError:
         pass
-    return parse_csv_folder(source, quiet)
+    return parse_csv_folder(source, quiet=quiet)
 
 
 @click.command()
@@ -68,7 +68,7 @@ def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
     default=False,
     help="Ignore sanity check for csv file parsing",
 )
-def main(sources, output, quiet=False):
+def main(sources, output, quiet=False):  # noqa: FBT002
     """Parses the measurement results of the Sensospot reader
 
     The resulting output is either echoed to stdout or saved to a file.
@@ -77,7 +77,7 @@ def main(sources, output, quiet=False):
     I this doesn't work, the fallback is to parse the csv files.
     """
     paths = (pathlib.Path(source) for source in sources)
-    collection = (parse_folder(source, quiet) for source in paths)
+    collection = (parse_folder(source, quiet=quiet) for source in paths)
     result = (
         pandas.concat(collection, ignore_index=True)
         .reset_index()

src/sensospot_parser/csv_parser.py

@@ -3,10 +3,10 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
-import re
 import pathlib
-from typing import Union, TextIO, Optional, Sequence
+import re
 from collections import namedtuple
+from typing import Optional, Sequence, TextIO, Union
 
 import pandas
 
@@ -74,10 +74,11 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo:
         named tuple FileInfo with parsed metadata
     """
     data_path = pathlib.Path(data_file)
-    *rest, well, exposure = data_path.stem.rsplit("_", 2)  # noqa: F841
+    *rest, well, exposure = data_path.stem.rsplit("_", 2)
     matched = REGEX_WELL.match(well)
     if matched is None:
-        raise ValueError(f"not a valid well: '{well}'")
+        msg = f"not a valid well: '{well}'"
+        raise ValueError(msg)
     row = matched["row"].upper()
     column = int(matched["column"])
     exposure = int(exposure)
@@ -143,7 +144,8 @@ def parse_multiple_csv_files(
         pandas data frame with all parsed data combined
     """
     if not file_list:
-        raise ValueError("Empty file list provided")
+        msg = "Empty file list provided"
+        raise ValueError(msg)
     collection = (_parse_csv_file_silenced(path) for path in file_list)
     filtered = (frame for frame in collection if frame is not None)
     data_frame = pandas.concat(filtered, ignore_index=True).reset_index()
@@ -186,9 +188,8 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
     spot_positions = len(data_frame[columns.POS_ID].unique())
     expected_rows = field_rows * field_cols * exposures * spot_positions
     if expected_rows != len(data_frame):
-        raise ValueError(
-            f"Measurements are missing: {expected_rows} != {len(data_frame)}"
-        )
+        msg = f"Measurements are missing: {expected_rows} != {len(data_frame)}"
+        raise ValueError(msg)
     # set the right data type for measurement columns
     for raw_column in columns.NUMERIC_COLUMNS:
         data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column])
@@ -196,7 +197,7 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
 
 
 def parse_csv_folder(
-    folder: PathLike, quiet: bool = False
+    folder: PathLike, *, quiet: bool = False
 ) -> pandas.DataFrame:
     """parses all csv files in a folder to one large dataframe
 
@@ -214,8 +215,9 @@ def parse_csv_folder(
     file_list = find_csv_files(folder_path)
     try:
         data_frame = parse_multiple_csv_files(file_list)
-    except ValueError:
-        raise ValueError(f"No sensospot data found in folder '{folder}'")
+    except ValueError as e:
+        msg = f"No sensospot data found in folder '{folder}'"
+        raise ValueError(msg) from e
 
     data_frame = add_measurement_parameters(data_frame, folder_path)
 

src/sensospot_parser/parameters.py

@@ -4,8 +4,8 @@ Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
 import pathlib
-from typing import Any, Dict, Union, Optional
-from xml.etree.ElementTree import Element as ElementType  # noqa: S405
+from typing import Any, Dict, Optional, Union
+from xml.etree.ElementTree import Element as ElementType
 
 import numpy
 import pandas
@@ -30,10 +30,7 @@ def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
     if not params_folder.is_dir():
         return None
     param_files = list(params_folder.glob("**/*.svexp"))
-    if len(param_files) == 1:
-        return param_files[0]
-    else:
-        return None
+    return param_files[0] if len(param_files) == 1 else None
 
 
 def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
@@ -45,9 +42,9 @@ def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
     Returns:
         dict with the information
     """
-    # child.tag == "ChannelConfig1"
+    # Example "ChannelConfig1"
     exposure_id = int(channel_node.tag[-1])
-    # channel_description == "[Cy3|Cy5] Green"
+    # Example "Cy3 Green"
     description = channel_node.attrib["Description"]
     exposure_channel = description.rsplit(" ", 1)[-1]
     # floats can be used for exposure times, not only ints

src/sensospot_parser/xml_parser.py

@@ -4,8 +4,8 @@ Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
 import pathlib
-from typing import Union, Optional
 from datetime import datetime
+from typing import Optional, Union
 
 import pandas
 from defusedxml import ElementTree
@@ -76,7 +76,9 @@ class ParserTarget:
 
     def _data_timestamp_parser(self, data: str) -> None:
         """parses the data section of a "Timestamp" tag"""
-        timestamp = datetime.strptime(data.strip(), DATETIME_XML_FORMAT)
+        timestamp = datetime.strptime(  # noqa: DTZ007
+            data.strip(), DATETIME_XML_FORMAT
+        )
         self._current[columns.ANALYSIS_DATETIME] = timestamp
 
     def _data_image_name_parser(self, data: str) -> None:
@@ -108,7 +110,6 @@ class ParserTarget:
 
     def closed(self) -> None:
         """the end of the xml file is reached"""
-        pass
 
 
 def _find_result_xml_file(folder: PathLike) -> Optional[pathlib.Path]:
@@ -154,7 +155,8 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
     """
     xml_file = pathlib.Path(xml_file)
     if not xml_file.is_file():
-        raise ValueError("Xml file does not exist")
+        msg = "Xml file does not exist"
+        raise ValueError(msg)
 
     target = ParserTarget()
     parser = ElementTree.DefusedXMLParser(target=target)
@@ -162,11 +164,13 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
     try:
         parser.feed(xml_file.read_text())
     except (IndexError, KeyError, ValueError, TypeError) as e:
-        raise ValueError("Malformed data in xml file") from e
+        msg = "Malformed data in xml file"
+        raise ValueError(msg) from e
 
     data_frame = pandas.DataFrame(data=target.collected).reset_index()
     if data_frame.empty:
-        raise ValueError("Could not parse assay results xml file")
+        msg = "Could not parse assay results xml file"
+        raise ValueError(msg)
 
     return columns._cleanup_data_columns(data_frame)
 
@@ -186,7 +190,8 @@ def parse_xml_folder(folder: PathLike) -> pandas.DataFrame:
     folder = pathlib.Path(folder)
     xml_file = _find_result_xml_file(folder)
     if xml_file is None:
-        raise ValueError("Could not find assay results xml file")
+        msg = "Could not find assay results xml file"
+        raise ValueError(msg)
     data_frame = parse_xml_file(xml_file)
     data_frame = parameters.add_measurement_parameters(data_frame, folder)
     return columns._cleanup_data_columns(data_frame)

tests/conftest.py

@@ -14,23 +14,23 @@ EXAMPLE_DIR_XML_WITH_PARAMS = "xml_with_parameters"
 @pytest.fixture(scope="session")
 def example_dir(request):
     root_dir = Path(request.config.rootdir)
-    yield root_dir / "example_data"
+    return root_dir / "example_data"
 
 
-@pytest.fixture
+@pytest.fixture()
 def example_file(example_dir):
     data_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS
-    yield data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"
+    return data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"
 
 
-@pytest.fixture
+@pytest.fixture()
 def exposure_df():
     from pandas import DataFrame
 
-    yield DataFrame(data={"Exposure.Id": [1, 2, 3]})
+    return DataFrame(data={"Exposure.Id": [1, 2, 3]})
 
 
-@pytest.fixture
+@pytest.fixture()
 def normalization_data_frame():
     from sensospot_parser.columns import RAW_DATA_NORMALIZATION_MAP
 
@@ -86,10 +86,10 @@ def normalization_data_frame():
     data_frame = pandas.DataFrame(overflow_test_data)
     data_frame["Exposure.Channel"] = "Cy5"
 
-    for value_column in RAW_DATA_NORMALIZATION_MAP.keys():
+    for value_column in RAW_DATA_NORMALIZATION_MAP:
         data_frame[value_column] = data_frame["Value"]
 
-    yield data_frame
+    return data_frame
 
 
 @pytest.fixture(scope="session")
@@ -106,11 +106,11 @@ def parsed_data_frame_without_params(example_dir):
     return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS)
 
 
-@pytest.fixture
+@pytest.fixture()
 def data_frame_with_params(parsed_data_frame_with_params):
     return parsed_data_frame_with_params.copy()
 
 
-@pytest.fixture
+@pytest.fixture()
 def data_frame_without_params(parsed_data_frame_without_params):
     return parsed_data_frame_without_params.copy()

tests/test_columns.py

@@ -1,6 +1,5 @@
 def test_cleanup_data_columns():
     from pandas import DataFrame
-
     from sensospot_parser.columns import _cleanup_data_columns
 
     columns = ["Rect.", "Contour", " ID ", "Found", "Dia."]

tests/test_csv_parser.py

@@ -4,11 +4,11 @@
 import numpy
 import pytest
 
-from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS
+from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
 
 
 @pytest.mark.parametrize(
-    "sub_dir, file_name",
+    ("sub_dir", "file_name"),
     [
         (
             EXAMPLE_DIR_CSV_WO_PARAMS,
@@ -65,14 +65,15 @@ def test_parse_csv_no_array(example_dir):
 
 
 @pytest.mark.parametrize(
-    "input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")]
+    ("provided", "expected"),
+    [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")],
 )
-def test_guess_decimal_separator_returns_correct_separator(input, expected):
+def test_guess_decimal_separator_returns_correct_separator(provided, expected):
     from io import StringIO
 
     from sensospot_parser.csv_parser import _guess_decimal_separator
 
-    handle = StringIO(f"header\n{input}\n")
+    handle = StringIO(f"header\n{provided}\n")
     result = _guess_decimal_separator(handle)
 
     assert result == expected
@@ -98,17 +99,17 @@ def test_well_regex_ok():
     assert result["column"] == "123"
 
 
-@pytest.mark.parametrize("input", ["", "A", "1", "1A", "-1", "A-"])
-def test_well_regex_no_match(input):
+@pytest.mark.parametrize("provided", ["", "A", "1", "1A", "-1", "A-"])
+def test_well_regex_no_match(provided):
     from sensospot_parser.csv_parser import REGEX_WELL
 
-    result = REGEX_WELL.match(input)
+    result = REGEX_WELL.match(provided)
 
     assert result is None
 
 
 @pytest.mark.parametrize(
-    "filename, expected",
+    ("filename", "expected"),
     [("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2))],
 )
 def test_extract_measurement_info_ok(filename, expected):
@@ -123,7 +124,7 @@ def test_extract_measurement_info_ok(filename, expected):
 def test_extract_measurement_info_raises_error(filename):
     from sensospot_parser.csv_parser import _extract_measurement_info
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError):  # noqa: PT011
         _extract_measurement_info(filename)
 
 
@@ -178,7 +179,7 @@ def test_parse_file_raises_error(example_dir):
         / "should_raise_value_error.csv"
     )
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError):  # noqa: PT011
         parse_csv_file(csv_file)
 
 
@@ -223,7 +224,6 @@ def testparse_multiple_files_ok(example_dir, file_list):
     files = [sub_dir / file for file in file_list]
 
     data_frame = parse_multiple_csv_files(files)
-    print(data_frame["Exposure.Id"].unique())
 
     assert len(data_frame) == 100 * len(files)
     assert len(data_frame["Exposure.Id"].unique()) == len(files)
@@ -232,7 +232,7 @@ def testparse_multiple_files_ok(example_dir, file_list):
 def testparse_multiple_files_empty_file_list():
     from sensospot_parser.csv_parser import parse_multiple_csv_files
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError):  # noqa: PT011
         parse_multiple_csv_files([])
 
 
@@ -242,7 +242,6 @@ def testparse_multiple_files_empty_array(example_dir):
     files = [example_dir / "no_array_A1_1.csv"]
 
     data_frame = parse_multiple_csv_files(files)
-    print(data_frame["Exposure.Id"].unique())
 
     assert len(data_frame) == 1
 
@@ -306,5 +305,5 @@ def test_sanity_check_raises_value_error(example_dir):
     data_frame = parse_multiple_csv_files(files)
     data_frame = data_frame.drop(data_frame.index[1])
 
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError):  # noqa: PT011
         _sanity_check(data_frame)

tests/test_parameters.py

@@ -1,6 +1,6 @@
 import pandas
 
-from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS
+from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
 
 
 def test_search_params_file_ok(example_dir):
@@ -32,8 +32,8 @@ def test_ssearch_measurement_params_file_parameters_file(tmpdir):
 
 def test_parse_channel_info(example_dir):
     from sensospot_parser.parameters import (
-        _search_params_file,
         _parse_measurement_params,
+        _search_params_file,
     )
 
     params = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)

tests/test_sensospot_data.py

@@ -5,16 +5,17 @@ from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
 
 
 def test_import_api():
-    from sensospot_parser import main  # noqa: F401
-    from sensospot_parser import columns  # noqa: F401
-    from sensospot_parser import parse_folder  # noqa: F401
-    from sensospot_parser import parse_csv_folder  # noqa: F401
-    from sensospot_parser import parse_xml_folder  # noqa: F401
+    from sensospot_parser import (
+        columns,  # noqa: F401
+        main,  # noqa: F401
+        parse_csv_folder,  # noqa: F401
+        parse_folder,  # noqa: F401
+        parse_xml_folder,  # noqa: F401
+    )
 
 
 def test_compare_xml_to_csv(example_dir):
     import pandas
-
     from sensospot_parser import parse_csv_folder, parse_xml_folder
 
     folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@@ -33,7 +34,7 @@ def test_compare_xml_to_csv(example_dir):
 
 
 @pytest.mark.parametrize(
-    "folder, length, hasnans",
+    ("folder", "length", "hasnans"),
     [
         (EXAMPLE_DIR_XML_WO_PARAMS, 6400, False),
         (EXAMPLE_DIR_CSV_WO_PARAMS, 28800, True),
@@ -41,7 +42,6 @@ def test_compare_xml_to_csv(example_dir):
 )
 def test_parse_folder_switches_parser(example_dir, folder, length, hasnans):
     import pandas
-
     from sensospot_parser import parse_folder
 
     result = parse_folder(example_dir / folder)

tests/test_xml_parser.py

@@ -2,7 +2,7 @@ from datetime import datetime
 
 import pytest
 
-from .conftest import EXAMPLE_DIR_XML_WO_PARAMS, EXAMPLE_DIR_XML_WITH_PARAMS
+from .conftest import EXAMPLE_DIR_XML_WITH_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
 
 
 class DummyDataFunc:
@@ -28,7 +28,7 @@ def test_parser_target_init():
 
 
 @pytest.mark.parametrize(
-    "tag, attributes, expected",
+    ("tag", "attributes", "expected"),
     [
         ("UnknownTag", {"ID": "something"}, {}),
         (
@@ -84,7 +84,7 @@ def test_parser_target_start_image_file_name():
 
 
 @pytest.mark.parametrize(
-    "data_type, value, expected",
+    ("data_type", "value", "expected"),
     [
         ("unknown type", 1, "1"),
         ("System.Int32", "12", 12),
@@ -108,16 +108,40 @@ def test_parser_target_result_attributes_parser(data_type, value, expected):
 
 
 @pytest.mark.parametrize(
-    "value, expected",
+    ("value", "expected"),
     [
-        ("3/7/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)),
-        ("03/7/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)),
-        ("3/07/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)),
-        ("03/07/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)),
-        ("3/7/2022 5:3:47 PM", datetime(2022, 3, 7, 17, 3, 47)),
-        ("3/7/2022 5:31:4 PM", datetime(2022, 3, 7, 17, 31, 4)),
-        ("3/7/2022 5:31:47 pm", datetime(2022, 3, 7, 17, 31, 47)),
-        ("3/7/2022 5:31:47 AM", datetime(2022, 3, 7, 5, 31, 47)),
+        (
+            "3/7/2022 5:31:47 PM",
+            datetime(2022, 3, 7, 17, 31, 47),  # noqa: DTZ001
+        ),
+        (
+            "03/7/2022 5:31:47 PM",
+            datetime(2022, 3, 7, 17, 31, 47),  # noqa: DTZ001
+        ),
+        (
+            "3/07/2022 5:31:47 PM",
+            datetime(2022, 3, 7, 17, 31, 47),  # noqa: DTZ001
+        ),
+        (
+            "03/07/2022 5:31:47 PM",
+            datetime(2022, 3, 7, 17, 31, 47),  # noqa: DTZ001
+        ),
+        (
+            "3/7/2022 5:3:47 PM",
+            datetime(2022, 3, 7, 17, 3, 47),  # noqa: DTZ001
+        ),
+        (
+            "3/7/2022 5:31:4 PM",
+            datetime(2022, 3, 7, 17, 31, 4),  # noqa: DTZ001
+        ),
+        (
+            "3/7/2022 5:31:47 pm",
+            datetime(2022, 3, 7, 17, 31, 47),  # noqa: DTZ001
+        ),
+        (
+            "3/7/2022 5:31:47 AM",
+            datetime(2022, 3, 7, 5, 31, 47),  # noqa: DTZ001
+        ),
     ],
 )
 def test_parser_target_data_timestamp_parser(value, expected):
@@ -203,8 +227,6 @@ def test_find_result_xml_file_ok(tmp_path):
     xml_file = tmp_path / "result.xml"
     xml_file.touch()
 
-    print(list(tmp_path.iterdir()))
-
     result = _find_result_xml_file(tmp_path)
 
     assert result == xml_file
@@ -257,8 +279,6 @@ def test_find_result_hidden_xsl_file(tmp_path):
     xml_file = tmp_path / ".result.xml"
     xml_file.touch()
 
-    print(list(tmp_path.iterdir()))
-
     result = _find_result_xml_file(tmp_path)
 
     assert result is None
@@ -266,10 +286,9 @@ def test_find_result_hidden_xsl_file(tmp_path):
 
 def test_parse_xml_file_ok(example_dir):
     import pandas
-
     from sensospot_parser.xml_parser import (
-        parse_xml_file,
         _find_result_xml_file,
+        parse_xml_file,
     )
 
     folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@@ -288,10 +307,10 @@ def test_parse_xml_file_ok(example_dir):
 
 
 @pytest.mark.parametrize(
-    "file_name, message",
+    ("file_name", "message"),
     [
         ("not_existing.xml", "Xml file does not exist"),
-        ("incomplete.xml", "Could not parse assay results xml file"),
+        ("defect.xml", "Could not parse assay results xml file"),
         ("malformed_data.xml", "Malformed data in xml file"),
     ],
 )
@@ -300,14 +319,14 @@ def test_parse_xml_file_raies_error(file_name, message, example_dir):
 
     xml_file = example_dir / file_name
 
-    with pytest.raises(ValueError) as e:
+    with pytest.raises(ValueError) as e:  # noqa: PT011
         parse_xml_file(xml_file)
-        assert message in str(e)
+
+    assert message in str(e)
 
 
 def test_parse_xml_folder_with_params(example_dir):
     import pandas
-
     from sensospot_parser.xml_parser import parse_xml_folder
 
     folder = example_dir / EXAMPLE_DIR_XML_WITH_PARAMS
@@ -321,7 +340,6 @@ def test_parse_xml_folder_with_params(example_dir):
 
 def test_parse_xml_folder_without_params(example_dir):
     import pandas
-
     from sensospot_parser.xml_parser import parse_xml_folder
 
     folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@@ -336,6 +354,7 @@ def test_parse_xml_folder_without_params(example_dir):
 def test_parse_xml_folder_non_existing_xml_file(tmp_path):
     from sensospot_parser.xml_parser import parse_xml_folder
 
-    with pytest.raises(ValueError) as e:
+    with pytest.raises(ValueError) as e:  # noqa: PT011
         parse_xml_folder(tmp_path)
-        assert "Could not find assay results xml file" in str(e)
+
+    assert "Could not find assay results xml file" in str(e)