Refactor/codebase

[singjc]

This PR is pretty large, but introduces a few updates, mostly in refactoring the code base.

• Refactored codebase to use dataclass configuration classes (ScoringIOConfig, IPFIOConfig, LevelContextIOConfig) for managing algorithm parameters and simplifying parameter passing across modules.

• Centralized file I/O logic by introducing a unified io.dispatcher module to select the appropriate reader/writer backend based on config.

• Added support for both .osw and .parquet formats throughout the PyProphet, including export, read, and scoring, ipf and level context steps.

• Improved CLI structure using click.Group and shared decorators for consistent global flags and FDR parameters across subcommands.

• Enabled grouped CLI subcommands (e.g., pyprophet levels-context peptide) for cleaner organization of related commands.

• Integrated automatic API and CLI documentation.

• Added internal diagnostics for row mismatches during score application to aid debugging.

• Updated tests to use fixtures for easier re-use

Documentation Enhancements

• General Documentation:
  • Added a new section in README.md with instructions for building the documentation locally using Sphinx. (docs/README.md, docs/README.mdR1-R8)
• API References:
  • Introduced automated API documentation for configuration, IO, CLI commands, and export utilities, including structured sections for scoring, IPF, levels context, and export configurations. (docs/api/config.rst, [1]; docs/api/io.rst, [2]; docs/api/index.rst, [3]
• CLI Documentation:
  • Documented the pyprophet CLI commands, including subcommands for scoring, IPF inference, levels context, and export utilities, with detailed descriptions and usage examples. (docs/cli.rst, docs/cli.rstR1-R156)

Sphinx Configuration

• Added a new conf.py file for Sphinx, enabling automated documentation generation with support for extensions like sphinx.ext.autodoc, sphinx_click, and sphinx_rtd_theme. (docs/conf.py, docs/conf.pyR1-R145)

[Copilot]

Pull Request Overview

This PR refactors the codebase by introducing dataclass-based I/O configurations, centralizing file reading/writing logic, and enhancing the CLI and documentation.

• Introduce BaseIOConfig dataclass and remove legacy classifiers.py
• Update dependencies and Docker/CI to support new I/O and diagnostics
• Add comprehensive Sphinx-based API/CLI/user-guide documentation and fixtures for tests

Reviewed Changes

Copilot reviewed 217 out of 217 changed files in this pull request and generated 4 comments.

File	Description
pyprophet/classifiers.py	Removed obsolete classifier implementations
pyprophet/_base.py	Added BaseIOConfig dataclass for unified I/O config
pyproject.toml	Added new dependencies (loguru, seaborn, etc.)
docs/user_guide/file_conversion.rst	New user guide for file conversion workflows

Comments suppressed due to low confidence (3)

docs/user_guide/file_conversion.rst:8

• Correct the typo 'acheived' to 'achieved'.

… This can be acheived using with pyprophet using the following command:

docs/cli.rst:141

• Fix the typo 'snigle' to 'single'.

… convert the entire *.osw* file to a snigle parquet file …

pyprophet/_base.py:79

• Consider replacing os.path.splitext with pathlib.Path.with_suffix or similar to robustly handle directories and files.

]  # TODO: use pathlib instead to avoid potential cases where the outfile is a directory …

[Copilot]

Replace the repeated '--helphelp' with the correct '--help' flag.

Suggested change

	The :program:`score` command has several advanced options that can be seen using the :option:`--helphelp` flag.
	The :program:`score` command has several advanced options that can be seen using the :option:`--help` flag.

[Copilot]

Exiting the process from a library can be unexpected; consider raising a descriptive exception instead of calling sys.exit.

Suggested change

	sys.exit(1)
	raise FileTypeInferenceError(
	f"Failed to infer file type for: {infile}. Supported formats are: "
	".osw, .sqmass/.sqMass, .parquet, split parquet directories (.oswpq/oswpqd), or .tsv files.\n"
	f" - is_sqlite_file: {is_sqlite_file(infile)}\n"
	f" - endswith .osw: {infile.endswith('.osw')}\n"
	f" - endswith .sqmass/.sqMass: {infile.endswith('.sqmass') or infile.endswith('.sqMass')}\n"
	f" - is_parquet_file: {is_parquet_file(infile)}\n"
	f" - is_valid_single_split_parquet_dir: {is_valid_single_split_parquet_dir(infile)}\n"
	f" - is_valid_multi_split_parquet_dir: {is_valid_multi_split_parquet_dir(infile)}\n"
	f" - is_tsv_file: {is_tsv_file(infile)}"
	)

[Copilot]

Pin dependency versions (e.g., loguru >= 0.x) to ensure reproducible builds.

Suggested change

	"loguru",
	"loguru >= 0.6.0",