fieldz-kb 0.1.0__tar.gz

fieldz_kb-0.1.0/.commitlintrc.json

@@ -0,0 +1,5 @@
+{
+  "extends": [
+    "@commitlint/config-conventional"
+  ]
+}

fieldz_kb-0.1.0/.github/workflows/docs.yml

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+name: Deploy documentation
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: ["Release"]
+    types: [completed]
+
+jobs:
+  deploy-docs:
+    name: Deploy documentation
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
+    permissions:
+      contents: write
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        ref: main
+        fetch-depth: 0
+
+    - name: Get latest tag and checkout
+      id: get_tag
+      run: |
+        LATEST_TAG=$(git describe --tags --abbrev=0 --match "v[0-9]*" origin/main)
+        echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+        git checkout $LATEST_TAG
+
+    - name: Configure Git Credentials
+      run: |
+        git config user.name github-actions[bot]
+        git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+    - uses: actions/setup-python@v6
+      with:
+        python-version: 3.x
+    - name: Cache dependencies
+      uses: actions/cache@v5
+      with:
+        key: mkdocs-material-${{ github.run_id }}
+        path: ~/.cache
+        restore-keys: |
+          mkdocs-material-
+    - name: Install MkDocs and dependencies
+      run: pip install mkdocs-material griffe-fieldz mkdocstrings-python griffe-inherited-docstrings
+    - name: Generate changelog
+      uses: orhun/git-cliff-action@v4
+      with:
+        config: cliff.toml
+        args: --verbose
+      env:
+        OUTPUT: docs/CHANGELOG.md
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Deploy documentation
+      run: mkdocs gh-deploy --force

fieldz_kb-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,202 @@
+name: Release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+"
+
+jobs:
+  test:
+    name: Run tests
+    uses: ./.github/workflows/tests.yml
+
+  build:
+    name: Build package
+    needs:
+    - test
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        persist-credentials: false
+        ref: main
+        fetch-depth: 0
+
+    - name: Get latest tag
+      id: get_tag
+      run: |
+        if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+          LATEST_TAG=$(git describe --tags --abbrev=0 --match "v[0-9]*" origin/main)
+          echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+          git checkout $LATEST_TAG
+        else
+          echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+        fi
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.13"
+    - name: Install pypa/build
+      run: python3 -m pip install build --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the packages
+      uses: actions/upload-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  testpypi:
+    name: Publish package to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/fieldz_kb
+
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish package to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  pypi:
+    name: Publish package to PyPI
+    needs:
+    - testpypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fieldz_kb
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  changelog:
+    name: Generate changelog
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        ref: main
+        fetch-depth: 0
+
+    - name: Get tag
+      id: get_tag
+      run: |
+        if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+          LATEST_TAG=$(git describe --tags --abbrev=0 --match "v[0-9]*" origin/main)
+          echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+        else
+          echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Generate changelog for this release
+      uses: orhun/git-cliff-action@v4
+      id: cliff
+      with:
+        config: cliff.toml
+        args: --latest --strip header
+      env:
+        OUTPUT: CHANGELOG_RELEASE.md
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Upload changelog snippet
+      uses: actions/upload-artifact@v5
+      with:
+        name: changelog-snippet
+        path: CHANGELOG_RELEASE.md
+
+  github-release:
+    name: Create GitHub Release
+    needs:
+    - pypi
+    - changelog
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout to get tag info
+      uses: actions/checkout@v5
+      with:
+        ref: main
+        fetch-depth: 0
+
+    - name: Get latest tag
+      id: get_tag
+      run: |
+        if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+          LATEST_TAG=$(git describe --tags --abbrev=0 --match "v[0-9]*" origin/main)
+          echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+        else
+          echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Download dist artifacts
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Download changelog snippet
+      uses: actions/download-artifact@v5
+      with:
+        name: changelog-snippet
+
+    - name: Extract version from tag
+      run: |
+        TAG="${{ steps.get_tag.outputs.tag }}"
+        echo "VERSION=${TAG#v}" >> $GITHUB_ENV
+
+    - name: Build release body
+      run: |
+        cat > RELEASE_BODY.md << 'HEADER'
+        ## What's Changed
+        HEADER
+        cat CHANGELOG_RELEASE.md >> RELEASE_BODY.md
+        cat >> RELEASE_BODY.md << EOF
+
+        ## Installation
+
+        \`\`\`bash
+        pip install fieldz_kb==${{ env.VERSION }}
+        \`\`\`
+
+        ## Links
+
+        - [Documentation](https://adrienrougny.github.io/fieldz_kb/)
+        - [PyPI](https://pypi.org/project/fieldz_kb/${{ env.VERSION }}/)
+        EOF
+
+    - name: Create GitHub Release
+      uses: softprops/action-gh-release@v2
+      with:
+        tag_name: ${{ steps.get_tag.outputs.tag }}
+        files: dist/*
+        body_path: RELEASE_BODY.md

fieldz_kb-0.1.0/.github/workflows/tests.yml

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+name: Tests
+
+on:
+  workflow_call:
+  push:
+    branches:
+      - testing
+      - main
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+    services:
+      neo4j:
+        image: neo4j:5
+        env:
+          NEO4J_AUTH: neo4j/testpassword
+        ports:
+          - 7687:7687
+        options: >-
+          --health-cmd "cypher-shell -u neo4j -p testpassword 'RETURN 1'"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+      falkordb:
+        image: falkordb/falkordb:latest
+        ports:
+          - 6379:6379
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.11'
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+      - name: Install uv and tox
+        run: pip install uv tox tox-uv
+      - name: Run tests with tox
+        env:
+          CI: true
+        run: tox -e py310-min,py311-min,py312-min,py313-min

fieldz_kb-0.1.0/.gitignore

@@ -0,0 +1,168 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+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
+
+# 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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm-project.org/#use-with-ide
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+.venv-sandbox
+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/
+
+
+# opencode plans and artifacts
+.opencode/
+plans/

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

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
+    rev: v9.20.0
+    hooks:
+      - id: commitlint
+        stages: [commit-msg]
+        additional_dependencies: ['@commitlint/config-conventional']

fieldz_kb-0.1.0/AGENTS.md

@@ -0,0 +1 @@
+CLAUDE.md

fieldz_kb-0.1.0/CLAUDE.md

@@ -0,0 +1,89 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+fieldz_kb converts Python dataclass-like objects (via the `fieldz` library) into knowledge base representations: Neo4j graphs, clingo/ASP predicates, and BioCypher-compatible formats.
+
+## Commands
+
+```bash
+# Install with dev dependencies
+uv pip install -e ".[dev]"
+
+# Run all tests (requires a running Neo4j instance, see tests/credentials.py)
+pytest tests/
+
+# Run a single test
+pytest tests/test_typeinfo.py::TestIsFieldzClass::test_returns_true_for_fieldz_class
+
+# Lint and format
+ruff check src/ tests/
+ruff check src/ tests/ --fix
+ruff format src/ tests/
+
+# Multi-version testing
+tox                # all versions (3.10-3.13)
+tox -e py312       # specific version
+```
+
+## Architecture
+
+### Shared layers
+
+- **`typeinfo.py`** — Extracts structured type information from type hints. Returns nested `(type_origin, type_args)` tuples. Handles unions, optionals, generics, and forward references via `typing._eval_type()`.
+
+### LPG backends (`_lpg/`)
+
+All labeled property graph backends follow the **Backend + Session** pattern:
+
+```python
+from fieldz_kb.neo4j import Session, Neo4jBackend
+with Session(Neo4jBackend(hostname="localhost")) as session:
+    session.save_from_object(person)
+    session.execute_query_as_objects("MATCH (n:Person) RETURN n")
+```
+
+- **`_lpg/core.py`** — Plugin system for pylpg: dynamically generates `pylpg.Node` subclasses from Python types. Base types become value nodes, collections become container nodes, dataclasses become node classes with relationship descriptors. Plugin-based extensibility via `PylpgTypePlugin` and `PylpgContext`.
+
+- **`_lpg/session.py`** — Session wrapping `pylpg.Session`. Provides `save_from_object()`, `save_from_objects()`, `make_object_from_node()`, `execute_query()`, `execute_query_as_objects()`, `delete_all()`. Uses batch save for performance.
+
+- **`_lpg/utils.py`** — Shared helpers for type classification, relationship naming, and field introspection.
+
+- **`neo4j/`**, **`falkordb/`**, **`falkordblite/`** — Re-export modules for convenience imports. Each provides `Session` and the corresponding pylpg backend class (e.g., `Neo4jBackend`).
+
+### Other backends
+
+- **`clingo/core.py`** — Generates `clorm.Predicate` classes from types. Each dataclass produces a base predicate plus per-field predicates. Caches in `_type_to_predicate_class` / `_field_key_to_predicate_class`. Key public API: `get_or_make_predicate_classes_from_type()`, `make_facts_from_object()`, `make_ontology_rules_from_type()`.
+
+- **`biocypher/`** — Adapter layer producing `(id, label, properties)` tuples and YAML schema files for BioCypher ingestion.
+
+### Key design patterns
+
+- **Backend + Session** for all LPG backends. Users create a Backend, pass it to Session, and use session methods.
+- **Plugin-based type conversion** via `PylpgTypePlugin` ABC and `PylpgContext` dispatcher.
+- **Global caches** for dynamically generated classes (node classes, predicate classes).
+- **Guard sets** prevent infinite recursion when processing cyclic/self-referential type definitions.
+- **Integration modes** for `save_from_objects()`: `"hash"` (dedup by hash), `"id"` (dedup by Python `id()`).
+- **Relationship naming**: field names are singularized via `inflect` and uppercased (e.g., `employees` → `HAS_EMPLOYEE`).
+- **Custom function registration**: `register_make_nodes_function()` and `register_make_object_function()` allow overriding conversion for specific types.
+
+## Forward References
+
+Dataclasses with forward references (e.g., `List["Employee"]`) **must be defined at module level**, not inside functions or test methods. `get_types_from_type_hint()` resolves forward refs using the module's namespace, so locally-defined classes won't resolve. In test files, define such classes at the top of the file and reference them from test methods.
+
+## Code Style
+
+- Always use **absolute imports** (never relative)
+- Import order: stdlib, third-party, local (separated by blank lines)
+- Type hints on all function signatures; prefer `str | None` over `Optional[str]`
+- Docstrings (triple double quotes) on all public functions with Args/Returns/Raises sections
+- No inline comments — use docstrings
+- Max line length: 88 characters
+
+## Testing
+
+- Neo4j tests require a **real database** — no mocks. Credentials in `tests/credentials.py` (not in git): `URI`, `USERNAME`, `PASSWORD`.
+- Database is cleaned before/after each test via fixtures.
+- Tests grouped in classes; fixtures in `conftest.py`.

fieldz_kb-0.1.0/PKG-INFO

@@ -0,0 +1,46 @@
+Metadata-Version: 2.4
+Name: fieldz_kb
+Version: 0.1.0
+Summary: A library store dataclass-like objects into knowledge bases
+Project-URL: Homepage, https://github.com/adrienrougny/fieldz_kb
+Project-URL: Issues, https://github.com/adrienrougny/fieldz_kb/issues
+Author-email: Adrien Rougny <adrienrougny@gmail.com>
+License: GPL-3.0-or-later
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Requires-Dist: fieldz>=0.1.2
+Requires-Dist: inflect>=7.5.0
+Provides-Extra: all
+Requires-Dist: clorm>=1.6.1; extra == 'all'
+Requires-Dist: frozendict>=2.4.7; extra == 'all'
+Requires-Dist: pylpg>=0.2.0; extra == 'all'
+Requires-Dist: pylpg[falkordb]>=0.2.0; extra == 'all'
+Requires-Dist: pylpg[falkordblite]>=0.2.0; extra == 'all'
+Requires-Dist: pylpg[neo4j]>=0.2.0; extra == 'all'
+Requires-Dist: pyyaml>=6.0; extra == 'all'
+Provides-Extra: biocypher
+Requires-Dist: frozendict>=2.4.7; extra == 'biocypher'
+Requires-Dist: pylpg>=0.2.0; extra == 'biocypher'
+Requires-Dist: pyyaml>=6.0; extra == 'biocypher'
+Provides-Extra: clingo
+Requires-Dist: clorm>=1.6.1; extra == 'clingo'
+Provides-Extra: falkordb
+Requires-Dist: frozendict>=2.4.7; extra == 'falkordb'
+Requires-Dist: pylpg[falkordb]>=0.2.0; extra == 'falkordb'
+Provides-Extra: falkordblite
+Requires-Dist: frozendict>=2.4.7; extra == 'falkordblite'
+Requires-Dist: pylpg[falkordblite]>=0.2.0; extra == 'falkordblite'
+Provides-Extra: neo4j
+Requires-Dist: frozendict>=2.4.7; extra == 'neo4j'
+Requires-Dist: pylpg[neo4j]>=0.2.0; extra == 'neo4j'
+Description-Content-Type: text/markdown
+
+# fieldz_kb
+
+A library to store dataclass-like objects into knowledge bases.

fieldz_kb-0.1.0/README.md

@@ -0,0 +1,3 @@
+# fieldz_kb
+
+A library to store dataclass-like objects into knowledge bases.

fieldz_kb-0.1.0/cliff.toml

@@ -0,0 +1,52 @@
+[changelog]
+header = """# Changelog
+
+All notable changes to fieldz_kb will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/),
+and this project adheres to [Conventional Commits](https://www.conventionalcommits.org/).
+
+"""
+body = """
+{%- macro remote_url() -%}
+  https://github.com/adrienrougny/fieldz_kb
+{%- endmacro -%}
+
+{% if version -%}
+## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
+{% else -%}
+## [Unreleased]
+{% endif -%}
+
+{% for group, commits in commits | group_by(attribute="group") %}
+### {{ group | upper_first }}
+{% for commit in commits %}
+- {{ commit.message | upper_first | trim }}\
+  {% if commit.scope %} *({{ commit.scope }})*{% endif %}\
+  {% if commit.breaking %} **BREAKING**{% endif -%}
+{% endfor %}
+{% endfor %}
+"""
+footer = ""
+trim = true
+
+[git]
+conventional_commits = true
+filter_unconventional = false
+split_commits = false
+commit_parsers = [
+  { message = "^feat", group = "Added" },
+  { message = "^fix", group = "Fixed" },
+  { message = "^perf", group = "Performance" },
+  { message = "^refactor", group = "Changed" },
+  { message = "^doc", group = "Documentation" },
+  { message = "^style", group = "Styling" },
+  { message = "^test", group = "Testing" },
+  { message = "^ci", group = "CI/CD" },
+  { message = "^chore", group = "Miscellaneous" },
+  { message = ".*", group = "Other" },
+]
+protect_breaking_commits = false
+filter_commits = false
+tag_pattern = "v[0-9]+\\.[0-9]+\\.[0-9]+"
+sort_commits = "newest"