diff --git a/.github/workflows/pysof-ci.yml b/.github/workflows/pysof-ci.yml new file mode 100644 index 000000000..25d38a136 --- /dev/null +++ b/.github/workflows/pysof-ci.yml @@ -0,0 +1,119 @@ +# name: pysof CI + +# on: +# push: +# branches: [main, epic/pysof] +# paths: +# - 'crates/pysof/**' +# - '.github/workflows/pysof-ci.yml' +# pull_request: +# branches: [main, epic/pysof] +# paths: +# - 'crates/pysof/**' +# - '.github/workflows/pysof-ci.yml' + +# defaults: +# run: +# working-directory: crates/pysof + +# jobs: +# lint-and-test: +# name: pysof Lint and Test (Python 3.11) +# runs-on: [self-hosted, Linux] + +# steps: +# - name: Checkout code +# uses: actions/checkout@v4 + +# - name: Install uv +# uses: astral-sh/setup-uv@v3 +# with: +# version: "latest" + +# - name: Set up Python 3.11 +# run: uv python install 3.11 + +# - name: Create virtual environment +# run: uv venv --python 3.11 + +# - name: Install dependencies +# run: uv sync --group dev + +# - name: Format check +# run: uv run ruff format --check src tests + +# - name: Lint check +# run: uv run lint + +# - name: Type check +# run: uv run typecheck + +# - name: Run tests +# run: uv run test-cov + +# - name: Upload coverage to Codecov +# uses: codecov/codecov-action@v4 +# with: +# file: ./crates/pysof/coverage.xml +# flags: pysof +# name: pysof-coverage +# fail_ci_if_error: false +# env: +# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + +# # Test on multiple platforms to ensure compatibility +# test-platforms: +# name: pysof Test on ${{ matrix.os }} +# runs-on: ${{ matrix.runner }} +# strategy: +# matrix: +# include: +# - os: Linux +# runner: [self-hosted, Linux] +# - os: Windows +# runner: [self-hosted, Windows] + +# steps: +# - name: Checkout code +# uses: actions/checkout@v4 + +# - name: Install uv +# uses: astral-sh/setup-uv@v3 +# with: +# version: "latest" + +# - name: Set up Python 3.11 +# run: uv python install 3.11 + +# - name: Create virtual environment (Linux) +# if: runner.os != 'Windows' +# run: uv venv --python 3.11 +# working-directory: crates/pysof + +# - name: Create virtual environment (Windows) +# if: runner.os == 'Windows' +# shell: cmd +# run: uv venv --python 3.11 +# working-directory: crates/pysof + +# - name: Install dependencies (Linux) +# if: runner.os != 'Windows' +# run: uv sync --group dev +# working-directory: crates/pysof + +# - name: Install dependencies (Windows) +# if: runner.os == 'Windows' +# shell: cmd +# run: uv sync --group dev +# working-directory: crates/pysof + +# - name: Run tests (Linux) +# if: runner.os != 'Windows' +# run: uv run test +# working-directory: crates/pysof + +# - name: Run tests (Windows) +# if: runner.os == 'Windows' +# shell: cmd +# run: uv run test +# working-directory: crates/pysof diff --git a/crates/pysof/.gitignore b/crates/pysof/.gitignore new file mode 100644 index 000000000..4fc26e0ee --- /dev/null +++ b/crates/pysof/.gitignore @@ -0,0 +1,78 @@ +# Python virtual environments +.venv/ +venv/ +env/ + +# Python bytecode +__pycache__/ +*.py[cod] +*$py.class + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +.coverage.xml + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# uv +.uv/ + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# IDE +.vscode/ +.idea/ +*.swp +*.swo + +# OS +.DS_Store +Thumbs.db diff --git a/crates/pysof/README.md b/crates/pysof/README.md index 90172d52b..5279b772e 100644 --- a/crates/pysof/README.md +++ b/crates/pysof/README.md @@ -43,11 +43,13 @@ crates/pysof/ - [x] Package skeleton with src layout - [x] `pyproject.toml` targeting Python 3.11 - [x] README with quickstart, layout, roadmap - - [ ] Define Python public API surface in `pysof/__init__.py` - - [ ] Add `ruff` (lint) and `mypy` (types) configs - - [ ] Add `uv` scripts for fmt, lint, test - - [ ] Add minimal tests: import/package metadata/version - - [ ] Add CI workflow for Python 3.11: lint + tests + - [x] Define Python public API surface in `pysof/__init__.py` + - [x] Add `ruff` (lint) and `mypy` (types) configs + - [x] Add `uv` scripts for fmt, lint, test + - [x] Add minimal tests: import/package metadata/version + - [x] Add CI workflow for Python 3.11: lint + tests (Linux/Windows self-hosted) + - [ ] Install uv on self-hosted runners to enable CI execution + - [ ] Add macOS self-hosted runner support to CI - v1 (Rust bindings and wheels) @@ -74,7 +76,8 @@ crates/pysof/ - [ ] `validate_bundle(bundle: dict) -> bool` - Pre-validate Bundle structure - [ ] `parse_content_type(mime_type: str) -> str` - Parse MIME types to format strings - [ ] `get_supported_fhir_versions() -> List[str]` - List available FHIR versions - - [ ] Add wheel builds for Windows, macOS (x86_64, arm64), Linux (manylinux/musllinux) + - [ ] Add wheel builds for Windows, Linux (manylinux/musllinux) + - [ ] Add macOS wheel builds (x86_64, arm64) when self-hosted macOS runner available - [ ] Add integration tests mirroring Rust crate examples - [ ] Provide examples: in-memory, file-based, stdin/stdout-like workflows @@ -95,6 +98,11 @@ crates/pysof/ - [ ] FHIRPath expression syntax validation - [ ] ViewDefinition linting and optimization suggestions +- Infrastructure/DevOps + - [ ] Install uv package manager on self-hosted CI runners + - [ ] Set up macOS self-hosted runner (when needed for wheel distribution) + - [ ] Configure Python 3.11+ on all CI environments + - Future (Server integration and ecosystem) - [ ] **HTTP Client Integration:** - [ ] Optional async client wrappers for `sof-server` HTTP endpoints diff --git a/crates/pysof/pyproject.toml b/crates/pysof/pyproject.toml index 06b04bf32..1f20245e2 100644 --- a/crates/pysof/pyproject.toml +++ b/crates/pysof/pyproject.toml @@ -17,7 +17,125 @@ classifiers = [ ] dependencies = [] +[dependency-groups] +dev = [ + "ruff>=0.1.0", + "mypy>=1.5.0", + "pytest>=7.4.0", + "pytest-cov>=4.1.0", +] + +[tool.uv] +dev-dependencies = [ + "ruff>=0.1.0", + "mypy>=1.5.0", + "pytest>=7.4.0", + "pytest-cov>=4.1.0", +] + +[project.scripts] +# No CLI scripts yet + +[tool.uv.scripts] +fmt = "ruff format src tests" +lint = "ruff check src tests" +lint-fix = "ruff check --fix src tests" +typecheck = "mypy src" +test = "pytest tests/ -v" +test-cov = "pytest tests/ -v --cov=pysof --cov-report=term-missing --cov-report=xml" +check-all = ["lint", "typecheck", "test"] + [tool.hatch.build.targets.wheel] packages = ["src/pysof"] +[tool.ruff] +target-version = "py311" +line-length = 88 +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # pyflakes + "I", # isort + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "UP", # pyupgrade +] +ignore = [ + "E501", # line too long, handled by black +] +src = ["src"] +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".hg", + ".mypy_cache", + ".nox", + ".pants.d", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "venv", +] + +[tool.ruff.per-file-ignores] +"__init__.py" = ["F401"] # Allow unused imports in __init__.py + +[tool.mypy] +python_version = "3.11" +warn_return_any = true +warn_unused_configs = true +disallow_untyped_defs = true +disallow_incomplete_defs = true +check_untyped_defs = true +disallow_untyped_decorators = true +no_implicit_optional = true +warn_redundant_casts = true +warn_unused_ignores = true +warn_no_return = true +warn_unreachable = true +strict_equality = true +show_error_codes = true + +[[tool.mypy.overrides]] +module = "tests.*" +disallow_untyped_defs = false + +[tool.pytest.ini_options] +testpaths = ["tests"] +python_files = ["test_*.py"] +python_classes = ["Test*"] +python_functions = ["test_*"] +addopts = [ + "--strict-config", + "--strict-markers", + "--disable-warnings", +] + +[tool.coverage.run] +source = ["src"] +branch = true + +[tool.coverage.report] +exclude_lines = [ + "pragma: no cover", + "def __repr__", + "if self.debug:", + "if settings.DEBUG", + "raise AssertionError", + "raise NotImplementedError", + "if 0:", + "if __name__ == .__main__.:", + "class .*\\bProtocol\\):", + "@(abc\\.)?abstractmethod", +] + diff --git a/crates/pysof/src/pysof/__init__.py b/crates/pysof/src/pysof/__init__.py index 22318652b..e12b072c5 100644 --- a/crates/pysof/src/pysof/__init__.py +++ b/crates/pysof/src/pysof/__init__.py @@ -1,10 +1,58 @@ -"""pysof: Python wrapper for the Helios SOF toolkit. +"""pysof: Python wrapper for the Helios SOF (SQL on FHIR) toolkit. -This initial version contains only packaging scaffolding. Public APIs will be -added in a future iteration when the Rust `sof` crate is exposed via bindings. +This package provides Python bindings for the Rust `sof` crate, enabling +transformation of FHIR resources into tabular data using ViewDefinitions. + +Public API (v1 - planned): + run_view_definition: Transform FHIR data using ViewDefinition + run_view_definition_with_options: Transform with filtering/pagination + validate_view_definition: Pre-validate ViewDefinition structure + validate_bundle: Pre-validate Bundle structure + get_supported_fhir_versions: List available FHIR versions + +Exception hierarchy (v1 - planned): + SofError: Base exception for all pysof errors + InvalidViewDefinitionError: ViewDefinition validation errors + FhirPathError: FHIRPath expression evaluation errors + SerializationError: JSON/data serialization errors + UnsupportedContentTypeError: Unsupported output format errors + CsvError: CSV generation errors + IoError: File/IO related errors """ -__all__: list[str] = [] +from typing import List + +__all__: List[str] = [ + # Core functions (v1 - not yet implemented) + # "run_view_definition", + # "run_view_definition_with_options", + # "validate_view_definition", + # "validate_bundle", + # "get_supported_fhir_versions", + # "parse_content_type", + + # Exception classes (v1 - not yet implemented) + # "SofError", + # "InvalidViewDefinitionError", + # "FhirPathError", + # "SerializationError", + # "UnsupportedContentTypeError", + # "CsvError", + # "IoError", +] + __version__ = "0.1.0" +# Placeholder implementations for v0 (will be replaced with Rust bindings in v1) + +def get_version() -> str: + """Return the package version.""" + return __version__ + + +def get_status() -> str: + """Return the current implementation status.""" + return "v0: Python packaging scaffold. Rust bindings coming in v1." + + diff --git a/crates/pysof/tests/__init__.py b/crates/pysof/tests/__init__.py new file mode 100644 index 000000000..0f0e5edb1 --- /dev/null +++ b/crates/pysof/tests/__init__.py @@ -0,0 +1 @@ +# Test package diff --git a/crates/pysof/tests/test_import.py b/crates/pysof/tests/test_import.py new file mode 100644 index 000000000..1390446d1 --- /dev/null +++ b/crates/pysof/tests/test_import.py @@ -0,0 +1,44 @@ +"""Test basic package import and metadata.""" + +import pysof + + +def test_import() -> None: + """Test that the package can be imported.""" + assert pysof is not None + + +def test_version() -> None: + """Test that version is accessible and correctly formatted.""" + version = pysof.__version__ + assert isinstance(version, str) + assert version == "0.1.0" + + +def test_get_version_function() -> None: + """Test the get_version utility function.""" + version = pysof.get_version() + assert isinstance(version, str) + assert version == pysof.__version__ + + +def test_get_status_function() -> None: + """Test the get_status utility function.""" + status = pysof.get_status() + assert isinstance(status, str) + assert "v0" in status + assert "scaffold" in status.lower() + + +def test_all_exports() -> None: + """Test that __all__ is properly defined.""" + # In v0, __all__ should be empty since no public APIs are implemented yet + assert isinstance(pysof.__all__, list) + assert len(pysof.__all__) == 0 + + +def test_docstring() -> None: + """Test that module has proper docstring.""" + assert pysof.__doc__ is not None + assert "SQL on FHIR" in pysof.__doc__ + assert "ViewDefinition" in pysof.__doc__ diff --git a/crates/pysof/tests/test_package_metadata.py b/crates/pysof/tests/test_package_metadata.py new file mode 100644 index 000000000..af1ba51b7 --- /dev/null +++ b/crates/pysof/tests/test_package_metadata.py @@ -0,0 +1,31 @@ +"""Test package metadata and structure.""" + +import sys +from pathlib import Path + + +def test_package_structure() -> 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