Add Python 3.11-3.13 compatibility

Author: chad

.github/workflows/python-package-version-test.yml

@@ -16,19 +16,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install ruff pytest
-        pip install torch==2.6.0
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with ruff
       run: |

.github/workflows/python-publish.yml

@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

README.md

@@ -1,7 +1,9 @@
 <img src="https://raw.githubusercontent.com/lab-v2/pyreason/main/media/pyreason_logo.jpg"/>
 
-[![Python 3.9](https://img.shields.io/badge/python-3.9-blue.svg)](https://www.python.org/downloads/release/python-390/)
 [![Python 3.10](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/)
+[![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/downloads/release/python-3110/)
+[![Python 3.12](https://img.shields.io/badge/python-3.12-blue.svg)](https://www.python.org/downloads/release/python-3120/)
+[![Python 3.13](https://img.shields.io/badge/python-3.13-blue.svg)](https://www.python.org/downloads/release/python-3130/)
 [![Documentation Status](https://readthedocs.org/projects/pyreason/badge/?version=latest)](https://pyreason.readthedocs.io/en/latest/?badge=latest)
 [![pypi](https://github.com/lab-v2/pyreason/actions/workflows/python-publish.yml/badge.svg)](https://github.com/lab-v2/pyreason/actions/workflows/python-publish.yml)
 [![Tests](https://github.com/lab-v2/pyreason/actions/workflows/python-package-version-test.yml/badge.svg)](https://github.com/lab-v2/pyreason/actions/workflows/python-package-version-test.yml)
@@ -43,7 +45,7 @@ PyReason can be installed as a python library using
 ```bash
 pip install pyreason
 ```
-The Python versions that are currently supported are `3.7`, `3.8`, `3.9`, `3.10`. If you want multi-core parallel support only `3.9` and `3.10` versions work due to limited numba support.
+The Python versions that are currently supported are `3.10`, `3.11`, `3.12`, and `3.13`.
 
 ## 4. Bibtex
 If you used this software in your work please cite our paper

docs/source/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ==========
 
-PyReason is currently compatible with Python 3.9 and 3.10. To install PyReason, you can use pip:
+PyReason is currently compatible with Python 3.10, 3.11, 3.12, and 3.13. To install PyReason, you can use pip:
 
 .. code:: bash
 
@@ -12,7 +12,7 @@ Make sure you're using the correct version of Python. You can create a conda env
 
 .. code:: bash
 
-    conda create -n pyreason-env python=3.10
+    conda create -n pyreason-env python=3.13
 
 PyReason uses a JIT compiler called `Numba <https://numba.pydata.org/>`_ to speed up the reasoning process. This means that
 the first time PyReason is imported it will have to compile certain functions which will result in faster runtimes later on.

docs/source/tutorials/installation.rst

@@ -13,7 +13,7 @@ Prerequisites
 
 .. note::
 
-    Use python version 3.9 or 3.10 .
+    Use Python version 3.10, 3.11, 3.12, or 3.13.
 
 
 Step-by-Step Guide
@@ -50,19 +50,19 @@ Step-by-Step Guide
 
 .. code-block:: bash
 
-  pyenv install 3.8
+  pyenv install 3.13
 
 4. Create a Virtual Environment
 
 .. code-block:: bash
 
-    pyenv virtualenv 3.8 pyreason_venv_3.8
+    pyenv virtualenv 3.13 pyreason_venv_3.13
 
 5. Activate the Virtual Environment
 
 .. code-block:: bash
 
-    pyenv activate pyreason_venv_3.8
+    pyenv activate pyreason_venv_3.13
 
 6. Install pyreason Using `pip`
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ['setuptools>=42']
+requires = ['setuptools>=42', 'setuptools_scm[toml]>=8']
 build-backend = 'setuptools.build_meta'
 
 [tool.ruff.lint]

pyreason/__init__.py

@@ -1,6 +1,7 @@
 # ruff: noqa: F403 F405 (Ignore Pyreason import * for public api)
 # Set numba environment variable
 import os
+import sys
 package_path = os.path.abspath(os.path.dirname(__file__))
 cache_path = os.path.join(package_path, 'cache')
 cache_status_path = os.path.join(package_path, '.cache_status.yaml')
@@ -9,20 +10,21 @@
 
 from pyreason.pyreason import *
 import yaml
-from importlib.metadata import version
-from pkg_resources import get_distribution, DistributionNotFound
+from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+    __version__ = version(__name__)
+except PackageNotFoundError:
     # package is not installed
     pass
 
 
 with open(cache_status_path) as file:
     cache_status = yaml.safe_load(file)
 
-if not cache_status['initialized']:
+running_tests = 'pytest' in sys.modules or 'unittest' in sys.modules
+
+if not cache_status['initialized'] and not running_tests:
     print('Imported PyReason for the first time. Initializing caches for faster runtimes ... this will take a minute')
     graph_path = os.path.join(package_path, 'examples', 'hello-world', 'friends_graph.graphml')
 
@@ -37,9 +39,6 @@
     print('PyReason initialized!')
     print()
 
-    # Update cache status (skip under test runners to keep repo file clean)
-    import sys
-    if 'pytest' not in sys.modules and 'unittest' not in sys.modules:
-        cache_status['initialized'] = True
-        with open(cache_status_path, 'w') as file:
-            yaml.dump(cache_status, file)
+    cache_status['initialized'] = True
+    with open(cache_status_path, 'w') as file:
+        yaml.dump(cache_status, file)

pyreason/scripts/interpretation/interpretation.py

@@ -1376,15 +1376,15 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 	# We replace Y by the sources of Z
 	elif clause_var_1 not in groundings and clause_var_2 in groundings:
 		for n in groundings[clause_var_2]:
-			es = numba.typed.List([(nn, n) for nn in reverse_neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in reverse_neighbors[n]:
+				edge_groundings.append((nn, n))
 
 	# Case 3:
 	# We replace Z by the neighbors of Y
 	elif clause_var_1 in groundings and clause_var_2 not in groundings:
 		for n in groundings[clause_var_1]:
-			es = numba.typed.List([(n, nn) for nn in neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in neighbors[n]:
+				edge_groundings.append((n, nn))
 
 	# Case 4:
 	# We have seen both variables before
@@ -1396,8 +1396,9 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 		else:
 			groundings_clause_var_2_set = set(groundings[clause_var_2])
 			for n in groundings[clause_var_1]:
-				es = numba.typed.List([(n, nn) for nn in neighbors[n] if nn in groundings_clause_var_2_set])
-				edge_groundings.extend(es)
+				for nn in neighbors[n]:
+					if nn in groundings_clause_var_2_set:
+						edge_groundings.append((n, nn))
 
 	return edge_groundings
 

pyreason/scripts/interpretation/interpretation_fp.py

@@ -1496,15 +1496,15 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 	# We replace Y by the sources of Z
 	elif clause_var_1 not in groundings and clause_var_2 in groundings:
 		for n in groundings[clause_var_2]:
-			es = numba.typed.List([(nn, n) for nn in reverse_neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in reverse_neighbors[n]:
+				edge_groundings.append((nn, n))
 
 	# Case 3:
 	# We replace Z by the neighbors of Y
 	elif clause_var_1 in groundings and clause_var_2 not in groundings:
 		for n in groundings[clause_var_1]:
-			es = numba.typed.List([(n, nn) for nn in neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in neighbors[n]:
+				edge_groundings.append((n, nn))
 
 	# Case 4:
 	# We have seen both variables before
@@ -1516,8 +1516,9 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 		else:
 			groundings_clause_var_2_set = set(groundings[clause_var_2])
 			for n in groundings[clause_var_1]:
-				es = numba.typed.List([(n, nn) for nn in neighbors[n] if nn in groundings_clause_var_2_set])
-				edge_groundings.extend(es)
+				for nn in neighbors[n]:
+					if nn in groundings_clause_var_2_set:
+						edge_groundings.append((n, nn))
 
 	return edge_groundings
 

pyreason/scripts/interpretation/interpretation_parallel.py

@@ -1376,15 +1376,15 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 	# We replace Y by the sources of Z
 	elif clause_var_1 not in groundings and clause_var_2 in groundings:
 		for n in groundings[clause_var_2]:
-			es = numba.typed.List([(nn, n) for nn in reverse_neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in reverse_neighbors[n]:
+				edge_groundings.append((nn, n))
 
 	# Case 3:
 	# We replace Z by the neighbors of Y
 	elif clause_var_1 in groundings and clause_var_2 not in groundings:
 		for n in groundings[clause_var_1]:
-			es = numba.typed.List([(n, nn) for nn in neighbors[n]])
-			edge_groundings.extend(es)
+			for nn in neighbors[n]:
+				edge_groundings.append((n, nn))
 
 	# Case 4:
 	# We have seen both variables before
@@ -1396,8 +1396,9 @@ def get_rule_edge_clause_grounding(clause_var_1, clause_var_2, groundings, groun
 		else:
 			groundings_clause_var_2_set = set(groundings[clause_var_2])
 			for n in groundings[clause_var_1]:
-				es = numba.typed.List([(n, nn) for nn in neighbors[n] if nn in groundings_clause_var_2_set])
-				edge_groundings.extend(es)
+				for nn in neighbors[n]:
+					if nn in groundings_clause_var_2_set:
+						edge_groundings.append((n, nn))
 
 	return edge_groundings