added logging statements

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"
@@ -112,7 +112,8 @@ target-version = "py38"
 
 [tool.ruff.per-file-ignores]
 # see https://github.com/charliermarsh/ruff
-"tests/*" = ["FBT003", "INP001", "PLR2004", "S101"]
+"src/*" = ["SLF001", "G004"]
+"tests/*" = ["FBT003", "INP001", "PLR2004", "S101", "SLF001"]
 
 [tool.ruff.pydocstyle]
 convention = "pep257"  # Accepts: "google", "numpy", or "pep257".

src/sensospot_parser/__init__.py

@@ -5,7 +5,7 @@ Parsing the numerical output from Sensovations Sensospot image analysis.
 
 __version__ = "2.0.0"
 
-
+import logging
 import pathlib
 from typing import Union
 
@@ -16,6 +16,9 @@ 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]
@@ -38,6 +41,9 @@ 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)
 
 
@@ -68,14 +74,28 @@ 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):  # noqa: FBT002
+@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=quiet) for source in paths)
     result = (

src/sensospot_parser/csv_parser.py

@@ -3,6 +3,7 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
+import logging
 import pathlib
 import re
 from collections import namedtuple
@@ -13,6 +14,8 @@ 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(
@@ -100,6 +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
@@ -211,12 +215,14 @@ 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
 
     data_frame = add_measurement_parameters(data_frame, folder_path)

src/sensospot_parser/parameters.py

@@ -3,6 +3,7 @@
 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
@@ -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
@@ -65,6 +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)
@@ -84,6 +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

@@ -3,6 +3,7 @@
 Parsing the csv result files from Sensovations Sensospot image analysis.
 """
 
+import logging
 import pathlib
 from datetime import datetime
 from typing import Optional, Union
@@ -12,6 +13,8 @@ from defusedxml import ElementTree
 
 from . import columns, parameters
 
+logger = logging.getLogger("sensospot_parser")
+
 PathLike = Union[str, pathlib.Path]
 
 RESULT_TAG_TYPES = {
@@ -153,9 +156,11 @@ 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)
 
     target = ParserTarget()
@@ -165,11 +170,13 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
         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
 
     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)
 
     return columns._cleanup_data_columns(data_frame)
@@ -191,6 +198,7 @@ def parse_xml_folder(folder: PathLike) -> pandas.DataFrame:
     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)
     data_frame = parse_xml_file(xml_file)
     data_frame = parameters.add_measurement_parameters(data_frame, folder)