.gitignore

@@ -39,7 +39,6 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache

.pre-commit-config.yaml

@@ -11,18 +11,33 @@ repos:
     -   id: detect-private-key
 -   repo: local
     hooks:
+    -   id: isort-project
+        name: isort project
+        entry: isort -rc src
+        language: system
+        pass_filenames: false
+    -   id: isort-test
+        name: isort test
+        entry: isort -rc tests
+        language: system
+        pass_filenames: false
     -   id: black
-        name: Autoformatting code with "black"
+        name: black
         entry: black src tests
         language: system
         pass_filenames: false
-    -   id: ruff
-        name: Linting code with "ruff"
-        entry: ruff src tests
+    -   id: flake8
+        name: flake8 project
+        entry: flake8 --ignore E231,W503 src
+        language: system
+        pass_filenames: false
+    -   id: flake8
+        name: flake8 test
+        entry: flake8 --ignore S101,W503 tests
         language: system
         pass_filenames: false
     -   id: pytest
-        name: Testing the project with "pytest"
+        name: pytest
         entry: pytest tests
-        language: system
         pass_filenames: false
+        language: system

CHANGES.md

@@ -1,18 +1,3 @@
-2.0.0 - xml parsing
--------------------
-
-- The assay results xml file is now parsed first
-- CSV parsing is still available as fallback if the XML could not be parsed
-
-
-1.0.0 - cli cleanup
--------------------
-
- - the cli interface was cleaned up a lot
- - default output of cli is now stdout
- - multiple sources can be specified instead of the clumsy '-r' option before
-
-
 0.7.0 - simplifications
 -----------------------
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean coverage coverall docs devenv install lint prepareenv repo serve-docs test testall testfunctional nox tox
+.PHONY: clean coverage coverall docs devenv install lint prepareenv repo serve-docs test testall testfunctional tox
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -54,8 +54,11 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 
 lint: ## reformat with black and check style with flake8
+	isort src
+	isort tests
 	black src tests
-	ruff src tests
+	flake8 --ignore E231,W503,E402 src
+	flake8 --ignore S101,W503 tests
 
 test: lint ## run tests quickly, stop on first error
 	pytest tests -x -l --last-failed --disable-warnings -m "not functional"
@@ -76,11 +79,8 @@ coverall: lint ## full test suite, check code coverage and open coverage report
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
-nox:  ## run fully isolated tests with nox
-	nox
-
-tox:  ## old habits die hard: typo-squatting to use nox
-	nox
+tox:  ## run fully isolated tests with tox
+	tox
 
 docs:  ## build the documentation using mkdocs
 	mkdocs build
@@ -88,14 +88,14 @@ docs:  ## build the documentation using mkdocs
 serve-docs: docs  ## build the documentation and serve them in a web server
 	mkdocs serve
 
-install:  ## install updated project.toml
-	.venv/bin/pip3 install -e ".[docs,dev,test]"
+install:  ## install updated project.toml with flint
+	flit install --pth-file
 
 prepareenv: ## setup virtual environment and install packages
-	rm -fr .venv/
 	python3 -m venv --prompt sensospot .venv
-	.venv/bin/pip3 install --upgrade pip wheel
-	.venv/bin/pip3 install -e ".[docs,dev,test]"
+	.venv/bin/pip3 install --upgrade pip
+	.venv/bin/pip3 install "flit>3.2"
+	.venv/bin/flit install --pth-file
 
 devenv: prepareenv ## setup development environment including precommit hooks
 	.venv/bin/pre-commit install --install-hooks
@@ -107,4 +107,5 @@ repo: prepareenv ## complete project setup with development environment and git
 	git branch -m main
 	git remote add origin https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_parser.git
 	git push -u origin main --no-verify
+
 	.venv/bin/pre-commit install --install-hooks

README.md

@@ -43,11 +43,6 @@ There is a `columns` module available, providing constans that define the column
 
 ## Avaliable public functions:
 
-All public functions return a [pandas DataFrame][pandas] object.
-
-Be aware that some columns might contain no values. This is depending on the parsing 
-method (xml or csv) and if a parameters file could be found or not.
-
  - **parse_folder(path_to_folder)**
    Tries the `parse_xml_folder()` function first and if an error occurs, 
    it falls back to the `parse_csv_folder()`
@@ -93,4 +88,3 @@ To generate the documentation pages use `make docs` or `make serve-docs` for
 starting a webserver with the generated documentation
 
 [sensospot]: https://www.miltenyi-imaging.com/products/sensospot
-[pandas]: https://pandas.pydata.org/docs/reference/frame.html

noxfile.py

@@ -1,8 +0,0 @@
-import nox
-
-
-@nox.session(python=["3.9", "3.10", "3.11"])
-def tests(session):
-    session.install(".[test]")
-
-    session.run("pytest", *session.posargs)

pyproject.toml

@@ -27,10 +27,10 @@ classifiers = [
 ]
 
 dependencies = [
-    "click",
-    "defusedxml >=0.6.0",
     "pandas >=1.0.0",
+    "defusedxml >=0.6.0",
     "tables >=3.6.1",
+    "click",
 ]
 [project.urls]
 Source = "https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_parser.git"
@@ -39,34 +39,26 @@ Source = "https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_parser.git"
 sensospot_parse = "sensospot_parser:main"
 
 [project.optional-dependencies]
+test = [
+    "pytest >=4.0.0",
+    "pytest-cov",
+    "pytest-mock",
+    "pytest-randomly >=3.5.0",
+    "tox",
+]
 dev = [
     "black",
-    "flit",
+    "flake8",
+    "flake8-comprehensions",
+    "flake8-bandit",
+    "isort >= 5.0.0",
     "keyring",
     "pre-commit",
-    "ruff",
 ]
 docs = [
     "mkdocs",
     "mkdocstrings[python]",
 ]
-test = [
-    "pytest >=4.0.0",
-    "pytest-cov",
-    "pytest-mock",
-    "pytest-randomly >=3.5.0",
-    "nox",
-]
-
-
-[tool.pytest.ini_options]
-markers = [
-    "functional: marks tests as functional (deselect with '-m \"not functional\"')",
-]
-addopts = [
-    "--strict-markers",
-]
-
 
 [tool.black]
 line-length = 79
@@ -82,39 +74,16 @@ extend-exclude = '''
 ^/.dist
 '''
 
-[tool.ruff]
-# see https://github.com/charliermarsh/ruff
-select = ["ALL"]
-ignore = [
-    # ignored for now, should be activated in the future
-    # docstrings
-    "D",
-    # flake8-annotations
-    "ANN",
-    # flake8-type-checking
-    "TCH",
-
-    # ignored, "black" will handle this
-    # flake8-commas
-    "COM",
+[tool.isort]
+line_length=79
+multi_line_output=3
+length_sort="True"
+include_trailing_comma="True"
 
-    # ignored, due to Windows / WSL2 setup
-    # flake8-executable
-    "EXE",
-
-    # project specific ignores
-    # flake8-import-conventions
-    "ICN",
+[tool.pytest.ini_options]
+markers = [
+    "functional: marks tests as functional (deselect with '-m \"not functional\"')",
+]
+addopts = [
+    "--strict-markers",
 ]
-fixable = ["I"]
-fix = true
-line-length=79
-target-version = "py38"
-
-[tool.ruff.per-file-ignores]
-# see https://github.com/charliermarsh/ruff
-"src/*" = ["SLF001", "G004"]
-"tests/*" = ["FBT003", "INP001", "PLR2004", "S101", "SLF001"]
-
-[tool.ruff.pydocstyle]
-convention = "pep257"  # Accepts: "google", "numpy", or "pep257".

src/sensospot_parser/__init__.py

@@ -3,9 +3,9 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-__version__ = "2.0.2"
+__version__ = "2.0.0"
+
 
-import logging
 import pathlib
 from typing import Union
 
@@ -16,15 +16,12 @@ from . import columns  # noqa: F401
 from .csv_parser import parse_csv_folder
 from .xml_parser import parse_xml_folder
 
-logging.basicConfig(level=logging.DEBUG)
-logger = logging.getLogger("sensospot_parser")
-
 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
@@ -41,10 +38,7 @@ def parse_folder(source: PathLike, *, quiet: bool = False) -> pandas.DataFrame:
         return parse_xml_folder(source)
     except ValueError:
         pass
-    logger.info(
-        "Could not parse xml results file, using fall-back csv parsing"
-    )
-    return parse_csv_folder(source, quiet=quiet)
+    return parse_csv_folder(source, quiet)
 
 
 @click.command()
@@ -74,30 +68,16 @@ def parse_folder(source: PathLike, *, quiet: bool = False) -> pandas.DataFrame:
     default=False,
     help="Ignore sanity check for csv file parsing",
 )
-@click.option(
-    "-v",
-    "--verbose",
-    help="Set verbosity of log, add multiple -vv for more verbose logging",
-    count=True,
-)
-def main(sources, output, verbose, quiet=False):  # noqa: FBT002
+def main(sources, output, quiet=False):
     """Parses the measurement results of the Sensospot reader
 
     The resulting output is either echoed to stdout or saved to a file.
 
     At first parsing the assay result xml file is tried.
-    If this doesn't work, the fallback is to parse the csv files.
+    I this doesn't work, the fallback is to parse the csv files.
     """
-
-    if verbose == 0:
-        logging.disable()
-    elif verbose == 1:
-        logging.disable(level=logging.DEBUG)
-    else:
-        logging.disable(level=logging.NOTSET)
-
     paths = (pathlib.Path(source) for source in sources)
-    collection = (parse_folder(source, quiet=quiet) for source in paths)
+    collection = (parse_folder(source, quiet) for source in paths)
     result = (
         pandas.concat(collection, ignore_index=True)
         .reset_index()

src/sensospot_parser/csv_parser.py

@@ -3,19 +3,16 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
-import logging
-import pathlib
 import re
+import pathlib
+from typing import Union, TextIO, Optional, Sequence
 from collections import namedtuple
-from typing import Optional, Sequence, TextIO, Union
 
 import pandas
 
 from . import columns
 from .parameters import add_measurement_parameters
 
-logger = logging.getLogger("sensospot_parser")
-
 PathLike = Union[str, pathlib.Path]
 
 REGEX_WELL = re.compile(
@@ -77,11 +74,10 @@ 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)
+    *rest, well, exposure = data_path.stem.rsplit("_", 2)  # noqa: F841
     matched = REGEX_WELL.match(well)
     if matched is None:
-        msg = f"not a valid well: '{well}'"
-        raise ValueError(msg)
+        raise ValueError(f"not a valid well: '{well}'")
     row = matched["row"].upper()
     column = int(matched["column"])
     exposure = int(exposure)
@@ -103,7 +99,6 @@ def parse_csv_file(data_file: PathLike) -> pandas.DataFrame:
         ValueError: if metadata could not be extracted
     """
     data_path = pathlib.Path(data_file).resolve()
-    logger.debug(f"Parsing csv file {data_path}")
     measurement_info = _extract_measurement_info(data_path)
     data_frame = _parse_csv(data_path)
     # normalized well name
@@ -148,8 +143,7 @@ def parse_multiple_csv_files(
         pandas data frame with all parsed data combined
     """
     if not file_list:
-        msg = "Empty file list provided"
-        raise ValueError(msg)
+        raise ValueError("Empty file list provided")
     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()
@@ -192,8 +186,9 @@ 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):
-        msg = f"Measurements are missing: {expected_rows} != {len(data_frame)}"
-        raise ValueError(msg)
+        raise ValueError(
+            f"Measurements are missing: {expected_rows} != {len(data_frame)}"
+        )
     # 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])
@@ -201,7 +196,7 @@ 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
 
@@ -215,15 +210,12 @@ def parse_csv_folder(
     Returns:
         a pandas data frame with parsed data
     """
-    logger.info(f"Parsing csv files in folder {folder}")
     folder_path = pathlib.Path(folder)
     file_list = find_csv_files(folder_path)
     try:
         data_frame = parse_multiple_csv_files(file_list)
-    except ValueError as e:
-        msg = f"No sensospot data found in folder '{folder}'"
-        logger.warning(msg)
-        raise ValueError(msg) from e
+    except ValueError:
+        raise ValueError(f"No sensospot data found in folder '{folder}'")
 
     data_frame = add_measurement_parameters(data_frame, folder_path)
 

src/sensospot_parser/parameters.py

@@ -3,10 +3,9 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-import logging
 import pathlib
-from typing import Any, Dict, Optional, Union
-from xml.etree.ElementTree import Element as ElementType
+from typing import Any, Dict, Union, Optional
+from xml.etree.ElementTree import Element as ElementType  # noqa: S405
 
 import numpy
 import pandas
@@ -16,8 +15,6 @@ from . import columns
 
 PathLike = Union[str, pathlib.Path]
 
-logger = logging.getLogger("sensospot_parser")
-
 
 def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
     """searches for a exposure settings file in a folder
@@ -33,7 +30,10 @@ def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
     if not params_folder.is_dir():
         return None
     param_files = list(params_folder.glob("**/*.svexp"))
-    return param_files[0] if len(param_files) == 1 else None
+    if len(param_files) == 1:
+        return param_files[0]
+    else:
+        return None
 
 
 def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
@@ -45,9 +45,9 @@ def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
     Returns:
         dict with the information
     """
-    # Example "ChannelConfig1"
+    # child.tag == "ChannelConfig1"
     exposure_id = int(channel_node.tag[-1])
-    # Example "Cy3 Green"
+    # channel_description == "[Cy3|Cy5] Green"
     description = channel_node.attrib["Description"]
     exposure_channel = description.rsplit(" ", 1)[-1]
     # floats can be used for exposure times, not only ints
@@ -68,7 +68,6 @@ def _parse_measurement_params(params_file: PathLike) -> pandas.DataFrame:
     Returns:
         pandas data frame with the parsed information
     """
-    logger.debug(f"Parsing parameters file {params_file}")
     file_path = pathlib.Path(params_file)
     with file_path.open("r") as file_handle:
         tree = ElementTree.parse(file_handle)
@@ -88,7 +87,6 @@ def get_measurement_params(folder: PathLike) -> Optional[pandas.DataFrame]:
     params_file = _search_params_file(folder)
     if params_file is not None:
         return _parse_measurement_params(params_file)
-    logger.debug(f"Could not locate parameters file in folder {folder}")
     return None
 
 

src/sensospot_parser/xml_parser.py

@@ -3,18 +3,15 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
-import logging
 import pathlib
+from typing import Union, Optional
 from datetime import datetime
-from typing import Optional, Union
 
 import pandas
 from defusedxml import ElementTree
 
 from . import columns, parameters
 
-logger = logging.getLogger("sensospot_parser")
-
 PathLike = Union[str, pathlib.Path]
 
 RESULT_TAG_TYPES = {
@@ -79,9 +76,7 @@ class ParserTarget:
 
     def _data_timestamp_parser(self, data: str) -> None:
         """parses the data section of a "Timestamp" tag"""
-        timestamp = datetime.strptime(  # noqa: DTZ007
-            data.strip(), DATETIME_XML_FORMAT
-        )
+        timestamp = datetime.strptime(data.strip(), DATETIME_XML_FORMAT)
         self._current[columns.ANALYSIS_DATETIME] = timestamp
 
     def _data_image_name_parser(self, data: str) -> None:
@@ -113,6 +108,7 @@ 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]:
@@ -156,12 +152,9 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
     Raises:
         ValueError if the xml file could not be parsed
     """
-    logger.info(f"Parsing xml results file {xml_file}")
     xml_file = pathlib.Path(xml_file)
     if not xml_file.is_file():
-        msg = "Xml file does not exist"
-        logger.debug(f"{msg}: {xml_file}")
-        raise ValueError(msg)
+        raise ValueError("Xml file does not exist")
 
     target = ParserTarget()
     parser = ElementTree.DefusedXMLParser(target=target)
@@ -169,15 +162,11 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
     try:
         parser.feed(xml_file.read_text())
     except (IndexError, KeyError, ValueError, TypeError) as e:
-        msg = "Malformed data in xml file"
-        logger.warning(f"{msg} {xml_file}")
-        raise ValueError(msg) from e
+        raise ValueError("Malformed data in xml file") from e
 
     data_frame = pandas.DataFrame(data=target.collected).reset_index()
     if data_frame.empty:
-        msg = "Could not parse assay results xml file"
-        logger.warning(f"{msg} {xml_file}")
-        raise ValueError(msg)
+        raise ValueError("Could not parse assay results xml file")
 
     return columns._cleanup_data_columns(data_frame)
 
@@ -197,9 +186,7 @@ def parse_xml_folder(folder: PathLike) -> pandas.DataFrame:
     folder = pathlib.Path(folder)
     xml_file = _find_result_xml_file(folder)
     if xml_file is None:
-        msg = "Could not find assay results xml file"
-        logger.debug(f"{msg} in folder {folder}")
-        raise ValueError(msg)
+        raise ValueError("Could not find assay results xml file")
     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)
-    return root_dir / "example_data"
+    yield root_dir / "example_data"
 
 
-@pytest.fixture()
+@pytest.fixture
 def example_file(example_dir):
     data_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS
-    return data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"
+    yield data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"
 
 
-@pytest.fixture()
+@pytest.fixture
 def exposure_df():
     from pandas import DataFrame
 
-    return DataFrame(data={"Exposure.Id": [1, 2, 3]})
+    yield 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:
+    for value_column in RAW_DATA_NORMALIZATION_MAP.keys():
         data_frame[value_column] = data_frame["Value"]
 
-    return data_frame
+    yield 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

@@ -1,5 +1,6 @@
 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_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
+from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS
 
 
 @pytest.mark.parametrize(
-    ("sub_dir", "file_name"),
+    "sub_dir, file_name",
     [
         (
             EXAMPLE_DIR_CSV_WO_PARAMS,
@@ -65,15 +65,14 @@ def test_parse_csv_no_array(example_dir):
 
 
 @pytest.mark.parametrize(
-    ("provided", "expected"),
-    [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")],
+    "input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")]
 )
-def test_guess_decimal_separator_returns_correct_separator(provided, expected):
+def test_guess_decimal_separator_returns_correct_separator(input, expected):
     from io import StringIO
 
     from sensospot_parser.csv_parser import _guess_decimal_separator
 
-    handle = StringIO(f"header\n{provided}\n")
+    handle = StringIO(f"header\n{input}\n")
     result = _guess_decimal_separator(handle)
 
     assert result == expected
@@ -99,17 +98,17 @@ def test_well_regex_ok():
     assert result["column"] == "123"
 
 
-@pytest.mark.parametrize("provided", ["", "A", "1", "1A", "-1", "A-"])
-def test_well_regex_no_match(provided):
+@pytest.mark.parametrize("input", ["", "A", "1", "1A", "-1", "A-"])
+def test_well_regex_no_match(input):
     from sensospot_parser.csv_parser import REGEX_WELL
 
-    result = REGEX_WELL.match(provided)
+    result = REGEX_WELL.match(input)
 
     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):
@@ -124,7 +123,7 @@ 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):  # noqa: PT011
+    with pytest.raises(ValueError):
         _extract_measurement_info(filename)
 
 
@@ -179,7 +178,7 @@ def test_parse_file_raises_error(example_dir):
         / "should_raise_value_error.csv"
     )
 
-    with pytest.raises(ValueError):  # noqa: PT011
+    with pytest.raises(ValueError):
         parse_csv_file(csv_file)
 
 
@@ -224,6 +223,7 @@ 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):  # noqa: PT011
+    with pytest.raises(ValueError):
         parse_multiple_csv_files([])
 
 
@@ -242,6 +242,7 @@ 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
 
@@ -305,5 +306,5 @@ 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):  # noqa: PT011
+    with pytest.raises(ValueError):
         _sanity_check(data_frame)

tests/test_parameters.py

@@ -1,6 +1,6 @@
 import pandas
 
-from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
+from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_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 (
-        _parse_measurement_params,
         _search_params_file,
+        _parse_measurement_params,
     )
 
     params = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)

tests/test_sensospot_data.py

@@ -5,17 +5,16 @@ from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
 
 
 def test_import_api():
-    from sensospot_parser import (
-        columns,  # noqa: F401
-        main,  # noqa: F401
-        parse_csv_folder,  # noqa: F401
-        parse_folder,  # noqa: F401
-        parse_xml_folder,  # noqa: F401
-    )
+    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
 
 
 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
@@ -27,14 +26,13 @@ def test_compare_xml_to_csv(example_dir):
     assert isinstance(xml_df, pandas.DataFrame)
 
     assert len(csv_df) == len(xml_df)
-    assert set(csv_df.columns) == set(xml_df.columns)
     assert set(csv_df["Well.Name"]) == set(xml_df["Well.Name"])
     assert set(csv_df["Exposure.Id"]) == set(xml_df["Exposure.Id"])
     assert set(csv_df["Spot.Diameter"]) == set(xml_df["Spot.Diameter"])
 
 
 @pytest.mark.parametrize(
-    ("folder", "length", "hasnans"),
+    "folder, length, hasnans",
     [
         (EXAMPLE_DIR_XML_WO_PARAMS, 6400, False),
         (EXAMPLE_DIR_CSV_WO_PARAMS, 28800, True),
@@ -42,6 +40,7 @@ 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_WITH_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
+from .conftest import EXAMPLE_DIR_XML_WO_PARAMS, EXAMPLE_DIR_XML_WITH_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),
@@ -108,40 +108,16 @@ 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),  # 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
-        ),
+        ("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)),
     ],
 )
 def test_parser_target_data_timestamp_parser(value, expected):
@@ -227,6 +203,8 @@ 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
@@ -279,6 +257,8 @@ 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
@@ -286,9 +266,10 @@ 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 (
-        _find_result_xml_file,
         parse_xml_file,
+        _find_result_xml_file,
     )
 
     folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@@ -307,10 +288,10 @@ 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"),
-        ("defect.xml", "Could not parse assay results xml file"),
+        ("incomplete.xml", "Could not parse assay results xml file"),
         ("malformed_data.xml", "Malformed data in xml file"),
     ],
 )
@@ -319,14 +300,14 @@ def test_parse_xml_file_raies_error(file_name, message, example_dir):
 
     xml_file = example_dir / file_name
 
-    with pytest.raises(ValueError) as e:  # noqa: PT011
+    with pytest.raises(ValueError) as e:
         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
@@ -340,6 +321,7 @@ 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
@@ -354,7 +336,6 @@ 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:  # noqa: PT011
+    with pytest.raises(ValueError) as e:
         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)

tox.ini

@@ -0,0 +1,14 @@
+[tox]
+envlist = py39, py310
+isolated_build = True
+
+[testenv]
+deps =
+    pytest
+    pytest-cov
+    pytest-mock
+    setuptools>=41.2.0
+    pip>=20.0.2
+
+changedir = {toxinidir}/tests
+commands = pytest --cov=sensovation_parser