typedlogic 0.0.0__tar.gz

typedlogic-0.0.0/LICENSE

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+
+The MIT License (MIT)
+
+Copyright (c) 2024 Monarch Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

typedlogic-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: typedlogic
+Version: 0.0.0
+Summary: typedlogic
+License: MIT
+License-File: LICENSE
+Author: Author 1
+Author-email: author@org.org
+Requires-Python: >=3.10
+Classifier: License :: OSI Approved :: MIT License
+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
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: clingo
+Provides-Extra: clorm
+Provides-Extra: dev
+Provides-Extra: gavel-owl
+Provides-Extra: llm
+Provides-Extra: owl
+Provides-Extra: pandas
+Provides-Extra: pandera
+Provides-Extra: problog
+Provides-Extra: pydantic
+Provides-Extra: pyprover
+Provides-Extra: rdflib
+Provides-Extra: snakelog
+Provides-Extra: sympy
+Provides-Extra: tests
+Provides-Extra: z3
+Requires-Dist: black ; extra == "tests"
+Requires-Dist: clingo ; extra == "clingo"
+Requires-Dist: clorm ; extra == "clorm"
+Requires-Dist: gavel-owl ; extra == "gavel-owl"
+Requires-Dist: importlib-metadata (>=8.2.0)
+Requires-Dist: jupyter ; extra == "dev"
+Requires-Dist: llm ; extra == "llm"
+Requires-Dist: mkdocs ; extra == "dev"
+Requires-Dist: mkdocs-click ; extra == "dev"
+Requires-Dist: mkdocs-material ; extra == "dev"
+Requires-Dist: mkdocs-mermaid2-plugin ; extra == "dev"
+Requires-Dist: mkdocs-windmill ; extra == "dev"
+Requires-Dist: mkdocs-with-pdf ; extra == "dev"
+Requires-Dist: mkdocstrings[crystal,python] ; extra == "dev"
+Requires-Dist: mknotebooks (>=0.8.0) ; extra == "dev"
+Requires-Dist: mypy ; extra == "dev"
+Requires-Dist: nbdime ; extra == "dev"
+Requires-Dist: nbformat ; extra == "dev"
+Requires-Dist: pandas ; extra == "pandas"
+Requires-Dist: pandera[mypy] ; extra == "pandera"
+Requires-Dist: papermill ; extra == "dev"
+Requires-Dist: ply ; extra == "gavel-owl"
+Requires-Dist: pre-commit (>=3.3.3) ; extra == "dev"
+Requires-Dist: problog ; extra == "problog"
+Requires-Dist: py-horned-owl (>=1.0.0,!=1.0.1) ; extra == "owl"
+Requires-Dist: pydantic ; extra == "pydantic"
+Requires-Dist: pyprover ; extra == "pyprover"
+Requires-Dist: pytest (>=8.3.2) ; extra == "dev"
+Requires-Dist: rdflib ; extra == "rdflib"
+Requires-Dist: ruff ; extra == "tests"
+Requires-Dist: snakelog ; extra == "snakelog"
+Requires-Dist: sympy ; extra == "sympy"
+Requires-Dist: tox (>=4.16.0) ; extra == "dev"
+Requires-Dist: typer (>=0.12.5)
+Requires-Dist: types-PyYAML ; extra == "dev"
+Requires-Dist: z3-solver ; extra == "z3"
+Description-Content-Type: text/markdown
+
+# py-typedlogic: Pythonic logic for your data models.
+
+Define logical predicates directly in Python as Pydantic, dataclasses, SQLModel, or plain python objects:
+
+```python
+# links.py
+from pydantic import BaseModel
+from typedlogic import FactMixin, Term
+
+ID = str
+
+class Link(BaseModel, FactMixin):
+    """A link between two entities"""
+    source: ID
+    target: ID
+
+class Path(BaseModel, FactMixin):
+    """An N-hop path between two entities, consisting of one or more links"""
+    source: ID
+    target: ID
+    hops: int
+```
+
+This data model has two classes, `Link` and `Path`. These also correspond to *predicate signatures*
+in a logical theory.
+
+You can use this to create objects (ground terms, in logic terms) using normal Python code:
+
+```python
+links = []
+for source, target in [('CA', 'OR'), ('OR', 'WA')]:
+   links.append(link)
+```
+
+Define logical *constraints* or *rules* using Python syntax:
+ 
+```python
+from typedlogic.decorators import axiom
+
+@axiom
+def path_from_link(x: ID, y: ID):
+    """If there is a link from x to y, there is a path from x to y"""
+    if Link(source=x, target=y):
+        assert Path(source=x, target=y, hops=1)
+
+@axiom
+def transitivity(x: ID, y: ID, z: ID, d1: int, d2: int):
+    """Transitivity of paths, plus hop counting"""
+    if Path(source=x, target=y, hops=d1) and Path(source=y, target=z, hops=d2):
+        assert Path(source=x, target=z, hops=d1+d2)
+```
+
+Use a solver to infer new facts:
+
+```python
+from typedlogic.registry import get_solver
+from links import Link
+
+solver = get_solver("clingo")
+solver.load(links) 
+links = [Link(source='CA', target='OR'), Link(source='OR', target='WA')]
+for link in links:
+    solver.add(link)
+model = solver.model()
+for fact in model.iter_retrieve("Path"):
+    print(fact)
+```
+
+prints:
+
+```
+Path(source='CA', target='OR')
+Path(source='OR', target='WA')
+Path(source='CA', target='WA')
+```
+
+## Key Features
+
+- Write logical axioms and rules using [Python syntax](https://py-typedlogic.github.io/py-typedlogic/tutorial/01-first-program/) 
+- Interconvert between different logical formats and formalisms
+    - [Compilers](https://py-typedlogic.github.io/py-typedlogic/conversion/compilers/)
+    - [Parsers](https://py-typedlogic.github.io/py-typedlogic/conversion/parsers/)
+- Benefit from strong typing and mypy validation
+- Integration with multiple [FOL solvers](https://py-typedlogic.github.io/py-typedlogic/integrations/solvers/) and logic programming engines
+- Integration with [OWL-DL](https://py-typedlogic.github.io/py-typedlogic/integrations/frameworks/owldl/)
+- Integration with Python libraries like [Pydantic](https://py-typedlogic.github.io/py-typedlogic/integrations/frameworks/pydantic/)
+- [Command Line](https://py-typedlogic.github.io/py-typedlogic/cli/) and Python interfaces
+
+## Installation
+
+Install TypedLogic using pip:
+
+```bash
+pip install "typedlogic"
+```
+
+## Next Steps
+
+- Consult the [main docs](https://py-typedlogic.github.io/py-typedlogic/) for more information
+
+## Contributing
+
+### Testing with External Dependencies
+
+Some tests require external executables (Prover9, Souffle) that may not be available in all environments. 
+The test suite is designed to automatically skip tests that require unavailable dependencies.
+
+When running in CI environments:
+- Tests for external solvers are automatically skipped if the dependency is not available
+- This allows CI to pass while still testing all available functionality
+
+To install optional dependencies for testing:
+- Prover9: Install from your package manager or from source
+- Souffle: Install from your package manager or from source
+
+Run tests with:
+```bash
+poetry run pytest
+```
+

typedlogic-0.0.0/README.md

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+# py-typedlogic: Pythonic logic for your data models.
+
+Define logical predicates directly in Python as Pydantic, dataclasses, SQLModel, or plain python objects:
+
+```python
+# links.py
+from pydantic import BaseModel
+from typedlogic import FactMixin, Term
+
+ID = str
+
+class Link(BaseModel, FactMixin):
+    """A link between two entities"""
+    source: ID
+    target: ID
+
+class Path(BaseModel, FactMixin):
+    """An N-hop path between two entities, consisting of one or more links"""
+    source: ID
+    target: ID
+    hops: int
+```
+
+This data model has two classes, `Link` and `Path`. These also correspond to *predicate signatures*
+in a logical theory.
+
+You can use this to create objects (ground terms, in logic terms) using normal Python code:
+
+```python
+links = []
+for source, target in [('CA', 'OR'), ('OR', 'WA')]:
+   links.append(link)
+```
+
+Define logical *constraints* or *rules* using Python syntax:
+ 
+```python
+from typedlogic.decorators import axiom
+
+@axiom
+def path_from_link(x: ID, y: ID):
+    """If there is a link from x to y, there is a path from x to y"""
+    if Link(source=x, target=y):
+        assert Path(source=x, target=y, hops=1)
+
+@axiom
+def transitivity(x: ID, y: ID, z: ID, d1: int, d2: int):
+    """Transitivity of paths, plus hop counting"""
+    if Path(source=x, target=y, hops=d1) and Path(source=y, target=z, hops=d2):
+        assert Path(source=x, target=z, hops=d1+d2)
+```
+
+Use a solver to infer new facts:
+
+```python
+from typedlogic.registry import get_solver
+from links import Link
+
+solver = get_solver("clingo")
+solver.load(links) 
+links = [Link(source='CA', target='OR'), Link(source='OR', target='WA')]
+for link in links:
+    solver.add(link)
+model = solver.model()
+for fact in model.iter_retrieve("Path"):
+    print(fact)
+```
+
+prints:
+
+```
+Path(source='CA', target='OR')
+Path(source='OR', target='WA')
+Path(source='CA', target='WA')
+```
+
+## Key Features
+
+- Write logical axioms and rules using [Python syntax](https://py-typedlogic.github.io/py-typedlogic/tutorial/01-first-program/) 
+- Interconvert between different logical formats and formalisms
+    - [Compilers](https://py-typedlogic.github.io/py-typedlogic/conversion/compilers/)
+    - [Parsers](https://py-typedlogic.github.io/py-typedlogic/conversion/parsers/)
+- Benefit from strong typing and mypy validation
+- Integration with multiple [FOL solvers](https://py-typedlogic.github.io/py-typedlogic/integrations/solvers/) and logic programming engines
+- Integration with [OWL-DL](https://py-typedlogic.github.io/py-typedlogic/integrations/frameworks/owldl/)
+- Integration with Python libraries like [Pydantic](https://py-typedlogic.github.io/py-typedlogic/integrations/frameworks/pydantic/)
+- [Command Line](https://py-typedlogic.github.io/py-typedlogic/cli/) and Python interfaces
+
+## Installation
+
+Install TypedLogic using pip:
+
+```bash
+pip install "typedlogic"
+```
+
+## Next Steps
+
+- Consult the [main docs](https://py-typedlogic.github.io/py-typedlogic/) for more information
+
+## Contributing
+
+### Testing with External Dependencies
+
+Some tests require external executables (Prover9, Souffle) that may not be available in all environments. 
+The test suite is designed to automatically skip tests that require unavailable dependencies.
+
+When running in CI environments:
+- Tests for external solvers are automatically skipped if the dependency is not available
+- This allows CI to pass while still testing all available functionality
+
+To install optional dependencies for testing:
+- Prover9: Install from your package manager or from source
+- Souffle: Install from your package manager or from source
+
+Run tests with:
+```bash
+poetry run pytest
+```

typedlogic-0.0.0/pyproject.toml

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+[project]
+name = "typedlogic"
+version = "0.0.0"
+description = "typedlogic"
+authors = [
+    {name = "Author 1", email = "author@org.org"}
+]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "importlib-metadata>=8.2.0",
+    "typer>=0.12.5",
+]
+
+[project.optional-dependencies]
+pydantic = ["pydantic"]
+clingo = ["clingo"]
+z3 = ["z3-solver"]
+pyprover = ["pyprover"]
+snakelog = ["snakelog"]
+problog = ["problog"]
+clorm = ["clorm"]
+rdflib = ["rdflib"]
+sympy = ["sympy"]
+owl = ["py-horned-owl>=1.0.0,!=1.0.1"]
+gavel-owl = ["gavel-owl", "ply"]
+llm = ["llm"]
+pandas = ["pandas"]
+pandera = ["pandera[mypy]"]
+tests = ["black", "ruff"]
+dev = [
+    "pytest>=8.3.2",
+    "tox>=4.16.0",
+    "mypy",
+    "types-PyYAML",
+    "jupyter",
+    "papermill",
+    "nbdime",
+    "nbformat",
+    "pre-commit>=3.3.3",
+    "mkdocs",
+    "mkdocs-mermaid2-plugin",
+    "mkdocstrings[crystal,python]",
+    "mknotebooks>=0.8.0",
+    "mkdocs-windmill",
+    "mkdocs-material",
+    "mkdocs-click",
+    "mkdocs-with-pdf",
+]
+
+[project.scripts]
+typedlogic = "typedlogic.cli:app"
+
+[tool.poetry]
+name = "typedlogic"
+version = "0.2.1"
+description = "typedlogic"
+authors = ["Author 1 <author@org.org>"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.10"
+importlib-metadata = ">=8.2.0"
+pydantic = { version="*",  optional = true }
+clingo = { version="*",  optional = true }
+z3-solver = { version="*",  optional = true }
+pyprover = { version="*",  optional = true }
+snakelog = { version="*",  optional = true }
+problog = { version="*",  optional = true }
+clorm = { version="*",  optional = true }
+rdflib = { version="*",  optional = true }
+sympy = { version="*",  optional = true }
+py-horned-owl = { version="^1.0.0,!=1.0.1", optional = true }  ## https://github.com/ontology-tools/py-horned-owl/issues/34
+llm = { version="*",  optional = true }
+gavel-owl = { version="*",  optional = true }
+ply = { version="*",  optional = true }
+pandas = { version="*",  optional = true }
+pandera = { version="*",  extras = ["mypy"], optional = true }
+typer = "^0.12.5"
+
+[tool.poetry.group.dev.dependencies]
+pytest = {version = ">=8.3.2"}
+tox = {version = ">=4.16.0"}
+mypy = {version = "*"}
+types-PyYAML = {version = "*"}
+jupyter = {version = "*"}
+papermill = {version = "*"}
+nbdime = {version = "*"}
+nbformat = {version = "*"}
+pre-commit = {version = ">=3.3.3"}
+mkdocs = "*"
+mkdocs-mermaid2-plugin = "*"
+mkdocstrings = {extras = ["crystal", "python"], version = "*"}
+mknotebooks = "^0.8.0"
+mkdocs-windmill = "*"
+mkdocs-material = "*"
+mkdocs-click = "*"
+mkdocs-with-pdf = "*"
+
+
+[tool.poetry.extras]
+tests = ["black", "ruff"]
+pydantic = ["pydantic"]
+z3 = ["z3-solver"]
+clingo = ["clingo"]
+pyprover = ["pyprover"]
+snakelog = ["snakelog"]
+problog = ["problog"]
+clorm = ["clorm"]
+rdflib = ["rdflib"]
+owl = ["py-horned-owl"]
+gavel-owl = ["gavel-owl", "ply"]
+pandas = ["pandas"]
+pandera = ["pandera"]
+llm = ["llm"]
+sympy = ["sympy"]
+
+
+[tool.poetry.scripts]
+typedlogic = "typedlogic.cli:app"
+
+[tool.poetry-dynamic-versioning]
+enable = false
+vcs = "git"
+style = "pep440"
+
+[tool.black]
+line-length = 120
+target-version = ["py38", "py39", "py310"]
+
+[tool.ruff]
+lint.extend-ignore = [
+    "D211",  # `no-blank-line-before-class`
+    "D212",  # `multi-line-summary-first-line`
+    "D203",  # `blank-line-before-docstring`
+    ]
+line-length = 120
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+lint.fixable = ["ALL"]
+
+# Select or ignore from https://beta.ruff.rs/docs/rules/
+lint.select = [
+    "B",  # bugbear
+    "D",  # pydocstyle
+    "E",  # pycodestyle errors
+    "F",  # Pyflakes
+    "I",  # isort
+    "S",  # flake8-bandit
+    "W",  # Warning
+]
+
+lint.unfixable = []
+target-version = "py310"
+
+[tool.ruff.lint.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10
+
+[tool.codespell]
+skip = "*.po,*.ts,.git,pyproject.toml,*.ofn,*.owl,*.ttl"
+count = ""
+quiet-level = 3
+ignore-words-list = "fof,te,disjointness,NotIn,EHR"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"
+
+[[tool.mypy.overrides]]
+module = "pyhornedowl.*"
+ignore_errors = true
+follow_imports = "skip"
+
+[tool.mypy]
+exclude = "owl"

typedlogic-0.0.0/src/typedlogic/__init__.py

@@ -0,0 +1,53 @@
+"""typedlogic package."""
+from typedlogic.datamodel import (
+    BooleanSentence,
+    And,
+    Or,
+    Not,
+    Implies,
+    Forall,
+    Exists,
+    Term,
+    NegationAsFailure,
+    not_provable,
+    Xor,
+    Implied,
+    Iff,
+    ExactlyOne,
+    Theory,
+    Sentence,
+    PredicateDefinition,
+    SentenceGroup,
+    Variable,
+)
+from typedlogic.pybridge import FactMixin, Fact
+from typedlogic.generators import gen, gen1, gen2, gen3
+from typedlogic.decorators import axiom, goal
+
+__all__ = [
+    "BooleanSentence",
+    "And",
+    "Or",
+    "Not",
+    "Implies",
+    "Iff",
+    "Forall",
+    "Exists",
+    "Term",
+    "NegationAsFailure",
+    "not_provable",
+    "Xor",
+    "ExactlyOne",
+    "Implied",
+    "Theory",
+    "Sentence",
+    "Variable",
+    "PredicateDefinition",
+    "SentenceGroup",
+    "Fact",
+    "FactMixin",
+    "gen",
+    "gen1",
+    "gen2",
+    "gen3",
+]

typedlogic-0.0.0/src/typedlogic/builtins.py

@@ -0,0 +1,48 @@
+"""
+Mappings for builtin functions and datatypes.
+"""
+import operator as op
+from typing import Callable, Mapping
+
+NUMERIC_BUILTINS: Mapping[str, Callable] = {
+    "ge": op.ge,
+    "gt": op.gt,
+    "le": op.le,
+    "lt": op.lt,
+    "eq": op.eq,
+    "ne": op.ne,
+    "add": op.add,
+    "sub": op.sub,
+    "mul": op.mul,
+    "truediv": op.truediv,
+    "pow": op.pow,
+    "xor": op.xor,
+    "neg": op.neg,
+}
+
+NAME_TO_INFIX_OP: Mapping[str, str] = {
+    "add": "+",
+    "sub": "-",
+    "mul": "*",
+    "truediv": "/",
+    "floordiv": "//",
+    "mod": "%",
+    "pow": "**",
+    "lshift": "<<",
+    "rshift": ">>",
+    "or": "|",
+    "xor": "^",
+    "and": "&",
+    "matmul": "@",
+    # Comparison operators
+    "eq": "==",
+    "ne": "!=",
+    "lt": "<",
+    "le": "<=",
+    "gt": ">",
+    "ge": ">=",
+    "is": "is",
+    "is_not": "is not",
+    "in": "in",
+    "not_in": "not in",
+}