Added 'flit' to dev dependencies

Installing a project in development mode was changed to using pip directly. This removed flit from the installed packages - but it's needed to publish to pypi.

.gitignore

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

.pre-commit-config.yaml

@@ -11,33 +11,18 @@ 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: black
+        name: Autoformatting code with "black"
         entry: black src tests
         language: system
         pass_filenames: false
-    -   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
+    -   id: ruff
+        name: Linting code with "ruff"
+        entry: ruff src tests
         language: system
         pass_filenames: false
     -   id: pytest
-        name: pytest
+        name: Testing the project with "pytest"
         entry: pytest tests
-        pass_filenames: false
         language: system
+        pass_filenames: false

CHANGES.md

@@ -1,3 +1,18 @@
+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 tox
+.PHONY: clean coverage coverall docs devenv install lint prepareenv repo serve-docs test testall testfunctional nox tox
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -54,11 +54,8 @@ 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
-	flake8 --ignore E231,W503,E402 src
-	flake8 --ignore S101,W503 tests
+	ruff src tests
 
 test: lint ## run tests quickly, stop on first error
 	pytest tests -x -l --last-failed --disable-warnings -m "not functional"
@@ -79,8 +76,11 @@ coverall: lint ## full test suite, check code coverage and open coverage report
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
-tox:  ## run fully isolated tests with tox
-	tox
+nox:  ## run fully isolated tests with nox
+	nox
+
+tox:  ## old habits die hard: typo-squatting to use nox
+	nox
 
 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 with flint
-	flit install --pth-file
+install:  ## install updated project.toml
+	.venv/bin/pip3 install -e ".[docs,dev,test]"
 
 prepareenv: ## setup virtual environment and install packages
+	rm -fr .venv/
 	python3 -m venv --prompt sensospot .venv
-	.venv/bin/pip3 install --upgrade pip
-	.venv/bin/pip3 install "flit>3.2"
-	.venv/bin/flit install --pth-file
+	.venv/bin/pip3 install --upgrade pip wheel
+	.venv/bin/pip3 install -e ".[docs,dev,test]"
 
 devenv: prepareenv ## setup development environment including precommit hooks
 	.venv/bin/pre-commit install --install-hooks
@@ -107,5 +107,4 @@ 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

@@ -43,6 +43,11 @@ 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()`
@@ -88,3 +93,4 @@ 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

@@ -0,0 +1,8 @@
+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 = [
-    "pandas >=1.0.0",
+    "click",
     "defusedxml >=0.6.0",
+    "pandas >=1.0.0",
     "tables >=3.6.1",
-    "click",
 ]
 [project.urls]
 Source = "https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_parser.git"
@@ -39,26 +39,34 @@ 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",
-    "flake8",
-    "flake8-comprehensions",
-    "flake8-bandit",
-    "isort >= 5.0.0",
+    "flit",
     "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
@@ -74,16 +82,39 @@ extend-exclude = '''
 ^/.dist
 '''
 
-[tool.isort]
-line_length=79
-multi_line_output=3
-length_sort="True"
-include_trailing_comma="True"
+[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",
 
-[tool.pytest.ini_options]
-markers = [
-    "functional: marks tests as functional (deselect with '-m \"not functional\"')",
-]
-addopts = [
-    "--strict-markers",
+    # ignored, "black" will handle this
+    # flake8-commas
+    "COM",
+
+    # ignored, due to Windows / WSL2 setup
+    # flake8-executable
+    "EXE",
+
+    # project specific ignores
+    # flake8-import-conventions
+    "ICN",
 ]
+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__ = "2.0.0"
-
+__version__ = "2.0.2"
 
+import logging
 import pathlib
 from typing import Union
 
@@ -16,12 +16,15 @@ 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
@@ -38,7 +41,10 @@ def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
         return parse_xml_folder(source)
     except ValueError:
         pass
-    return parse_csv_folder(source, quiet)
+    logger.info(
+        "Could not parse xml results file, using fall-back csv parsing"
+    )
+    return parse_csv_folder(source, quiet=quiet)
 
 
 @click.command()
@@ -68,16 +74,30 @@ 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):
+@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
     """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.
-    I this doesn't work, the fallback is to parse the csv files.
+    If 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) 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

@@ -3,16 +3,19 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
-import re
+import logging
 import pathlib
-from typing import Union, TextIO, Optional, Sequence
+import re
 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(
@@ -74,10 +77,11 @@ 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)
@@ -99,6 +103,7 @@ 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
@@ -143,7 +148,8 @@ 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 +192,8 @@ 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 +201,7 @@ 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
 
@@ -210,12 +215,15 @@ 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:
-        raise ValueError(f"No sensospot data found in folder '{folder}'")
+    except ValueError as e:
+        msg = f"No sensospot data found in folder '{folder}'"
+        logger.warning(msg)
+        raise ValueError(msg) from e
 
     data_frame = add_measurement_parameters(data_frame, folder_path)
 

src/sensospot_parser/parameters.py

@@ -3,9 +3,10 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
+import logging
 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
@@ -15,6 +16,8 @@ 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
@@ -30,10 +33,7 @@ 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 +45,9 @@ 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
@@ -68,6 +68,7 @@ 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)
@@ -87,6 +88,7 @@ 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

@@ -3,15 +3,18 @@
 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 = {
@@ -76,7 +79,9 @@ 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 +113,6 @@ 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]:
@@ -152,9 +156,12 @@ 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():
-        raise ValueError("Xml file does not exist")
+        msg = "Xml file does not exist"
+        logger.debug(f"{msg}: {xml_file}")
+        raise ValueError(msg)
 
     target = ParserTarget()
     parser = ElementTree.DefusedXMLParser(target=target)
@@ -162,11 +169,15 @@ 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"
+        logger.warning(f"{msg} {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"
+        logger.warning(f"{msg} {xml_file}")
+        raise ValueError(msg)
 
     return columns._cleanup_data_columns(data_frame)
 
@@ -186,7 +197,9 @@ 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"
+        logger.debug(f"{msg} in folder {folder}")
+        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
@@ -26,13 +27,14 @@ 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),
@@ -40,7 +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)

tox.ini

@@ -1,14 +0,0 @@
-[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