osa-py 0.1.0__tar.gz

osa_py-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+      - uses: taiki-e/install-action@just
+      - run: uv sync --frozen --dev
+      - run: just lint
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+      - uses: taiki-e/install-action@just
+      - run: uv sync --frozen --dev
+      - run: just test

osa_py-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+      - run: uv build
+      - run: uv publish

osa_py-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.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/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+# Docker
+.docker/
+
+# Environment
+.env
+!.env.example

osa_py-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.10
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty type check
+        entry: uv run ty check osa
+        language: system
+        types: [python]
+        pass_filenames: false
+
+      - id: unit-tests
+        name: unit tests
+        entry: uv run pytest tests/ -q --tb=short
+        language: system
+        types: [python]
+        pass_filenames: false
+        stages: [pre-commit]

osa_py-0.1.0/Justfile

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+default:
+    @just --list
+
+# Run all checks (lint, typecheck, test)
+check: lint test
+
+# Run tests
+test *args:
+    uv run pytest tests/ -v --tb=short {{ args }}
+
+# Run tests with coverage
+coverage:
+    uv run pytest tests/ --cov=osa --cov-report=term-missing
+
+# Lint and format check
+lint:
+    uv run ruff check osa/ tests/
+    uv run ruff format --check osa/ tests/
+    uv run ty check osa
+
+# Auto-fix lint errors and format
+fix:
+    uv run ruff check osa/ tests/ --fix
+    uv run ruff format osa/ tests/
+
+# Build the package
+build:
+    uv build
+
+# Clean build artifacts
+clean:
+    rm -rf dist/ build/ *.egg-info
+    find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+
+# Install in development mode
+dev:
+    uv sync

osa_py-0.1.0/LICENSE

@@ -0,0 +1,190 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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osa_py-0.1.0/PKG-INFO

@@ -0,0 +1,124 @@
+Metadata-Version: 2.4
+Name: osa-py
+Version: 0.1.0
+Summary: OSA Python SDK — validators and transforms for the Open Scientific Archive
+Project-URL: Homepage, https://github.com/opensciencearchive/osa-py
+Project-URL: Repository, https://github.com/opensciencearchive/osa-py
+Project-URL: Issues, https://github.com/opensciencearchive/osa-py/issues
+Author-email: Rory Byrne <rory@rory.bio>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: archive,metadata,oci,scientific-data,validation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.13
+Requires-Dist: httpx>=0.27
+Requires-Dist: pydantic>=2
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: typer>=0.23.1
+Description-Content-Type: text/markdown
+
+<img src="https://opensciencearchive.org/osa_logo.svg" alt="OSA" width="64" />
+
+# OSA Python SDK
+
+The developer toolkit for the [Open Science Archive](https://github.com/opensciencearchive/server) — define metadata schemas, write validation hooks, build ingesters, and deploy conventions.
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue?style=flat-square)](LICENSE)
+[![Python](https://img.shields.io/badge/python-≥3.13-blue?style=flat-square)](https://python.org)
+
+> **Pre-release** — APIs will change without notice.
+
+---
+
+## Install
+
+```bash
+pip install osa
+```
+
+## Quickstart
+
+Define a schema, write a hook, register a convention:
+
+```python
+from osa import Schema, Field, Record, Reject, hook, convention
+
+class Crystal(Schema, id="crystal-structure"):
+    pdb_id: str
+    resolution: float = Field(unit="Å")
+    method: str
+
+@hook
+def resolution_check(record: Record[Crystal]) -> None:
+    if record.metadata.resolution > 3.5:
+        raise Reject("Resolution too low for inclusion")
+
+convention(
+    title="Crystal Structures",
+    schema=Crystal,
+    hooks=[resolution_check],
+    files={"extensions": [".cif"], "min_count": 1},
+)
+```
+
+## Testing
+
+Test hooks in-process without Docker:
+
+```python
+from osa.testing import run_hook
+
+run_hook(resolution_check, meta={"pdb_id": "1ABC", "resolution": 2.1, "method": "X-ray"})
+```
+
+## Deploy
+
+```bash
+osa link --server https://my-archive.org
+osa login
+osa deploy
+```
+
+## CLI reference
+
+| Command | Description |
+|---|---|
+| `osa link --server <url>` | Link project to an archive server |
+| `osa login` | Authenticate via device flow |
+| `osa logout` | Remove stored credentials |
+| `osa deploy` | Build OCI images and register conventions |
+| `osa meta` | Print the convention manifest |
+| `osa ingestion start` | Trigger an ingestion run |
+
+## Concepts
+
+**Schema** — a Pydantic model defining typed metadata fields for a convention.
+
+**Hook** — a pure function decorated with `@hook` that receives a `Record[T]` and returns structured results. Hooks run as OCI containers with a filesystem I/O contract.
+
+**Convention** — a bundle of a schema, hooks, file requirements, and an optional ingester.
+
+**Ingester** — an async generator that pulls records from external systems into the archive on a schedule.
+
+**Record\[T\]** — generic container binding a schema type to its metadata, files, and SRN.
+
+## Project structure
+
+```
+osa/
+├── __init__.py              # Public API
+├── authoring/               # @hook, convention(), Reject, Ingester
+├── types/                   # Schema, Record, Field, File
+├── runtime/                 # OCI entrypoints (osa-run-hook, osa-run-ingester)
+├── testing/                 # run_hook() test harness
+└── cli/                     # osa command (login, deploy, link, ...)
+```
+
+## License
+
+[Apache 2.0](LICENSE)