Modernize stages -- all

[khoroshevskyi]

Changes:

• Migrates packaging configuration from setup.py/requirements/*.txt/pytest.ini to pyproject.toml (including optional test extras).
• Updates GitHub Actions workflows to build with python -m build and install test deps via pip install ".[test]".
• Modernizes Python code (typing syntax, import ordering, docstring formatting) across core modules and tests.

[Copilot]

Pull request overview

This PR modernizes the project’s packaging/build/test setup (moving to pyproject.toml/hatchling and updating CI), while also updating type hints and docstrings across the peppy, eido, and pephubclient modules.

Changes:

• Migrates packaging configuration from setup.py/requirements/*.txt/pytest.ini to pyproject.toml (including optional test extras).
• Updates GitHub Actions workflows to build with python -m build and install test deps via pip install ".[test]".
• Modernizes Python code (typing syntax, import ordering, docstring formatting) across core modules and tests.

Reviewed changes

Copilot reviewed 55 out of 55 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/peppytests/test_Sample.py	Minor import/spacing normalization for linting/formatting consistency.
tests/peppytests/test_Project.py	Import ordering cleanup (e.g., YAML import placement) for linting/formatting consistency.
tests/eidotests/test_validations.py	Minor import/spacing normalization.
tests/eidotests/test_schema_operations.py	Reorders imports for consistency.
tests/eidotests/conftest.py	Minor import/spacing normalization.
tests/data/peppydata/example_peps-master/subannotation.ipynb	Adds blank lines in example cells (formatting-only).
setup.py	Removed legacy setuptools build configuration (replaced by pyproject.toml).
requirements/requirements-test.txt	Removed legacy test requirements file (replaced by project.optional-dependencies).
requirements/requirements-doc.txt	Removed legacy docs requirements file.
requirements/requirements-all.txt	Removed legacy “all requirements” file (replaced by project.dependencies).
pytest.ini	Removed legacy pytest config (replaced by [tool.pytest.ini_options]).
pyproject.toml	Adds PEP 621 project metadata, deps/extras, build backend, pytest + ruff configuration.
peppy/utils.py	Updates typing imports/annotations and reformats multiple docstrings.
peppy/simple_attr_map.py	Adds type annotations to mapping protocol methods.
peppy/sample.py	Modernizes typing syntax and updates docstrings to Args/Returns style.
peppy/project.py	Broad docstring/type-hint modernization across the main Project API.
peppy/pephubclient/pephubclient.py	Typing/docstring modernization and import ordering adjustments.
peppy/pephubclient/pephub_oauth/pephub_oauth.py	Typing/docstring modernization.
peppy/pephubclient/pephub_oauth/exceptions.py	Docstring cleanup for exceptions.
peppy/pephubclient/modules/view.py	Typing/docstring modernization.
peppy/pephubclient/modules/sample.py	Typing/docstring modernization.
peppy/pephubclient/models.py	Modernizes type hints to `X
peppy/pephubclient/helpers.py	Typing/docstring modernization and more precise annotations.
peppy/pephubclient/files_manager.py	Docstring modernization and minor formatting cleanup.
peppy/pephubclient/exceptions.py	Modernizes exception constructor annotations.
peppy/pephubclient/constants.py	Updates Pydantic model field annotations to `X
peppy/parsers.py	Modernizes container typing (list[...], dict[...]) and docstrings.
peppy/exceptions.py	Updates typing syntax and docstring formatting.
peppy/eido/validation.py	Modernizes typing annotations and docstrings; minor logic readability tweak (not in).
peppy/eido/schema.py	Modernizes typing annotations and docstrings.
peppy/eido/output_formatters.py	Modernizes typing annotations and docstrings.
peppy/eido/inspection.py	Modernizes typing annotations and docstrings.
peppy/eido/exceptions.py	Updates typing annotations for structured error payloads.
peppy/eido/conversion.py	Switches to stdlib importlib.metadata.entry_points and modern typing/docstrings.
peppy/eido/conversion_plugins.py	Modernizes return type annotations and docstrings.
peppy/eido/const.py	Docstring cleanup/normalization.
peppy/eido/cli.py	Modernizes typer option annotations (`X
peppy/cli.py	Switches CLI version reporting to importlib.metadata.version.
peppy/_version.py	Removes static version module (replaced by metadata-driven version).
peppy/init.py	Switches package __version__ to importlib.metadata.version.
MANIFEST.in	Removed legacy MANIFEST (build now controlled by hatchling defaults/config).
docs_jupyter/tutorial.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/feature5_amend.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/feature4_subsample_table.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/feature3_derived.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/feature2_imply.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/feature1_append.ipynb	Deleted legacy notebook documentation artifact.
docs_jupyter/build/.gitignore	Deleted legacy docs build ignore file.
.pre-commit-config.yaml	Removed placeholder/invalid pre-commit config.
.github/workflows/python-publish.yml	Updates publishing workflow to build with python -m build and sets minimal permissions.
.github/workflows/pytest.yml	Updates test workflow to install via extras (pip install ".[test]") and bumps action versions.
.github/workflows/pytest-windows.yml	Updates Windows tests similarly and bumps action versions.
.github/workflows/cli-coverage.yml	Updates coverage workflow to install via extras and bumps Python/action versions.
.github/workflows/black.yml	Replaces Black action usage with ruff lint + ruff format checks.
.flake8	Removed flake8 config (linting now driven by ruff).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.