added mkdocs for documentation

.gitignore

@@ -1,4 +1,4 @@
-# ---> Python
+j# ---> Python
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -53,8 +53,9 @@ coverage.xml
 # Django stuff:
 *.log
 
-# Sphinx documentation
+# documentation
 docs/_build/
+site/
 
 # PyBuilder
 target/
@@ -66,4 +67,4 @@ target/
 *.h5
 
 # Editors
-.vscode/
+.vscode/

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean coverage coverall devenv install lint prepareenv repo test testall testfunctional tox
+.PHONY: clean coverage coverall docs devenv install lint prepareenv repo serve-docs test testall testfunctional tox
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -29,7 +29,7 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+clean: clean-build clean-docs clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
 
 clean-build: ## remove build artifacts
 	rm -fr build/
@@ -38,6 +38,9 @@ clean-build: ## remove build artifacts
 	find . -name '*.egg-info' -exec rm -fr {} +
 	find . -name '*.egg' -exec rm -f {} +
 
+clean-docs: ## remove documentation artifacts
+	rm -fr site/
+
 clean-pyc: ## remove Python file artifacts
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
@@ -79,6 +82,12 @@ coverall: lint ## full test suite, check code coverage and open coverage report
 tox:  ## run fully isolated tests with tox
 	tox
 
+docs:  ## build the documentation using mkdocs
+	mkdocs build
+
+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
 

docs/explanation.md

@@ -0,0 +1,18 @@
+# Explanation
+
+This part of the project documentation focuses on a
+**learning-oriented** approach. You'll learn how to
+get started with the code in this project.
+
+> **Note:** Expand this section by considering the
+> following points:
+
+- Help newcomers with getting started
+- Teach readers about your library by making them
+    write code
+- Inspire confidence through examples that work for
+    everyone, repeatably
+- Give readers an immediate sense of achievement
+- Show concrete examples, no abstractions
+- Provide the minimum necessary explanation
+- Avoid any distractions

docs/how-to-guides.md

@@ -0,0 +1,6 @@
+# How-To Guides
+
+This part of the project documentation focuses on a
+**problem-oriented** approach. You'll tackle common
+tasks that you might have, with the help of the code
+provided in this project.

docs/index.md

@@ -0,0 +1,20 @@
+# SensoSpot Parser Documentation
+
+This site contains the project documentation for the
+`sensospot_parser` project.
+
+
+## Table Of Contents
+
+The documentation follows the best practice for
+project documentation as described by Daniele Procida
+in the [Diátaxis documentation framework](https://diataxis.fr/)
+and consists of four separate parts:
+
+1. [Tutorials](tutorials.md)
+2. [How-To Guides](how-to-guides.md)
+3. [Reference](reference.md)
+4. [Explanation](explanation.md)
+
+Quickly find what you're looking for depending on
+your use case by looking at the different pages.

docs/reference.md

@@ -0,0 +1,9 @@
+# Reference
+
+This part of the project documentation focuses on
+an **information-oriented** approach. Use it as a
+reference for the technical implementation of the
+`sensospot_tools` project code.
+
+
+::: sensospot_parser.parser

docs/tutorials.md

@@ -0,0 +1,17 @@
+# Tutorials
+
+This part of the project documentation focuses on an
+**understanding-oriented** approach. You'll get a
+chance to read about the background of the project,
+as well as reasoning about how it was implemented.
+
+> **Note:** Expand this section by considering the
+> following points:
+
+- Give context and background on your library
+- Explain why you created it
+- Provide multiple examples and approaches of how
+    to work with it
+- Help the reader make connections
+- Avoid writing instructions or technical descriptions
+    here

mkdocs.yml

@@ -0,0 +1,17 @@
+site_name: Sensospot Parser Docs
+
+nav:
+  - Introduction: index.md
+  - Tutorials: tutorials.md
+  - How-To Guides: how-to-guides.md
+  - Reference: reference.md
+  - Explanation: explanation.md
+
+repo_url: https://github.com/example/repository/
+
+theme:
+    name: readthedocs
+    highlightjs: true
+
+plugins:
+  - mkdocstrings

pyproject.toml

@@ -53,6 +53,10 @@ dev = [
     "keyring",
     "pre-commit",
 ]
+docs = [
+    "mkdocs",
+    "mkdocstrings[python]",
+]
 
 [tool.black]
 line-length = 79

src/sensospot_parser/parameters.py

@@ -19,8 +19,11 @@ PathLike = Union[str, pathlib.Path]
 def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
     """searches for a exposure settings file in a folder
 
-    folder:  directory to search
-    returns: the path to the settings file or None
+    Args:
+        folder:  directory to search
+
+    Returns:
+        the path to the settings file or None
     """
     folder_path = pathlib.Path(folder)
     params_folder = folder_path / "Parameters"
@@ -36,8 +39,11 @@ def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
 def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
     """parses the information from an xml node of the channel settings
 
-    channel_node:   the xml node of the channel settings
-    returns:        dict with the information
+    Args:
+        channel_node:   the xml node of the channel settings
+
+    Returns:
+        dict with the information
     """
     # child.tag == "ChannelConfig1"
     exposure_id = int(channel_node.tag[-1])
@@ -56,8 +62,11 @@ def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
 def _parse_measurement_params(params_file: PathLike) -> pandas.DataFrame:
     """parses the cannel informations from a settings file
 
-    params_file: path to the settings file
-    returns:     pandas DataFrame with the parsed information
+    Args:
+        params_file: path to the settings file
+
+    Returns:
+        pandas data frame with the parsed information
     """
     file_path = pathlib.Path(params_file)
     with file_path.open("r") as file_handle:
@@ -69,8 +78,11 @@ def _parse_measurement_params(params_file: PathLike) -> pandas.DataFrame:
 def get_measurement_params(folder: PathLike) -> Optional[pandas.DataFrame]:
     """searches the settings file and returns the parameters
 
-    folder: path to the folder with the measurement data
-    returns: pandas DataFrame with the parsed parameters or None
+    Args:
+        folder: path to the folder with the measurement data
+
+    Returns:
+        pandas data frame with the parsed parameters or None
     """
     params_file = _search_params_file(folder)
     if params_file is not None:
@@ -89,8 +101,11 @@ def add_measurement_parameters(
     If the parameters could not be found, parsed or do not match up with the
     measurement data, the additional collumns will contain NaN.
 
-    measurement: the parsed measurement data
-    returns:     the measurement data with parameters added
+    Args:
+        measurement: the parsed measurement data
+
+    Returns:
+        the measurement data with parameters added
     """
     params = get_measurement_params(folder)
     if params is not None:

src/sensospot_parser/parser.py

@@ -32,8 +32,11 @@ def _guess_decimal_separator(file_handle: TextIO) -> str:
     This is a very crude method, but depending on the language setting,
     different decimal separators may be used.
 
-    file_handle:  a file handle to an opened csv file
-    returns: either '.' or ',' as a decimal separator
+    Args:
+        file_handle:  a file handle to an opened csv file
+
+    Returns:
+        either '.' or ',' as a decimal separator
     """
     file_handle.seek(0)
     headers = next(file_handle)  # noqa: F841
@@ -48,8 +51,11 @@ def _parse_csv(data_file: PathLike) -> pandas.DataFrame:
 
     Tries to guess the decimal separator from the file contents
 
-    data_file: path to the csv file
-    returns:   pandas DataFrame with the parsed data
+    Args:
+        data_file: path to the csv file
+
+    Returns:
+        pandas data frame with the parsed data
     """
     data_path = pathlib.Path(data_file)
     with data_path.open("r") as handle:
@@ -61,8 +67,11 @@ def _parse_csv(data_file: PathLike) -> pandas.DataFrame:
 def _extract_measurement_info(data_file: PathLike) -> FileInfo:
     """extract measurement meta data from a file name
 
-    data_file:  path to the csv data file
-    returns:    named tuple FileInfo with parsed metadata
+    Args:
+        data_file:  path to the csv data file
+
+    Returns:
+        named tuple FileInfo with parsed metadata
     """
     data_path = pathlib.Path(data_file)
     *rest, well, exposure = data_path.stem.rsplit("_", 2)  # noqa: F841
@@ -78,8 +87,11 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo:
 def _cleanup_data_columns(data_frame: pandas.DataFrame) -> pandas.DataFrame:
     """renames some data columns for consistency and drops unused columns
 
-    data_frame: pandas DataFrame with parsed measurement data
-    returns:    pandas DataFrame, column names cleaned up
+    Args:
+        data_frame: pandas DataFrame with parsed measurement data
+
+    Returns:
+        pandas DataFrame, column names cleaned up
     """
     renamed = data_frame.rename(columns=columns.CSV_RENAME_MAP)
     surplus_columns = set(renamed.columns) - columns.PARSED_DATA_COLUMN_SET
@@ -91,9 +103,14 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame:
 
     will race a ValueError, if metadata could not be extracted
 
-    data_file: path to the csv data file
-    raises:    ValueError if metadata could not be extracted
-    returns:   pandas DataFrame with the parsed data
+    Args:
+        data_file: path to the csv data file
+
+    Returns:
+        pandas data frame with the parsed data
+
+    Raises:
+        ValueError: if metadata could not be extracted
     """
     data_path = pathlib.Path(data_file).resolve()
     measurement_info = _extract_measurement_info(data_path)
@@ -112,8 +129,13 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame:
 def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]:
     """parses one data file and adds metadata
 
-    data_file: path to the csv data file
-    returns: pandas DataFrame with the parsed data or None on error
+    Safety checks are supressed
+
+    Args:
+        data_file: path to the csv data file
+
+    Returns:
+        pandas data frame with the parsed data or None on error
     """
     try:
         return parse_file(data_file)
@@ -124,8 +146,10 @@ def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]:
 def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame:
     """parses a list of file paths to one combined data frame
 
-    file_list: collection of paths to csv data files
-    returns:   pandas DataFrame with all parsed data combined
+    Args:
+        file_list: collection of paths to csv data files
+    Returns:
+        pandas data frame with all parsed data combined
     """
     if not file_list:
         raise ValueError("Empty file list provided")
@@ -141,8 +165,11 @@ def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame:
 def find_csv_files(folder: PathLike) -> Sequence[pathlib.Path]:
     """returns all csv files in a folder
 
-    folder:  path to the folder to search for csv files
-    returns: iterator with the found csv files
+    Args:
+        folder:  path to the folder to search for csv files
+
+    Returns:
+        iterator with the found csv files
     """
     folder_path = pathlib.Path(folder)
     files = (item for item in folder_path.iterdir() if item.is_file())
@@ -153,9 +180,14 @@ def find_csv_files(folder: PathLike) -> Sequence[pathlib.Path]:
 def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
     """checks some basic constrains of a combined data frame
 
-    data_frame: measurement data
-    raises:     ValueError if basic constrains are not met
-    returns:    pandas DataFrame
+    Args:
+        data_frame: measurement data
+
+    Returns:
+        a pandas DataFrame
+
+    Raises:
+        ValueError: if basic constrains are not met
     """
     field_rows = len(data_frame[columns.WELL_ROW].unique())
     field_cols = len(data_frame[columns.WELL_COLUMN].unique())
@@ -178,9 +210,12 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame:
     Will raise an ValueError, if no sensospot data could be found in
     the folder
 
-    folder:  path of folder containing data files
-    quiet:   skip sanity check, defaults to False
-    returns: pandas dataframe with parsed data
+    Args:
+        folder:  path of folder containing data files
+        quiet:   skip sanity check, defaults to False
+
+    Returns:
+        a pandas data frame with parsed data
     """
     folder_path = pathlib.Path(folder)
     file_list = find_csv_files(folder_path)