feat: Python 3.11–3.14 compatibility, PEP 621 packaging, and uv CI migration

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

@@ -16,23 +16,27 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
+    - name: Cache Numba JIT artifacts
+      uses: actions/cache@v4
+      with:
+        path: pyreason/cache
+        key: numba-${{ matrix.python-version }}-${{ hashFiles('pyreason/scripts/**/*.py') }}
+        restore-keys: |
+          numba-${{ matrix.python-version }}-
     - 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 uv
+      uses: astral-sh/setup-uv@v6
     - 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
+      run: uv pip install --system -e ".[dev,torch]"
     - name: Lint with ruff
-      run: |
-        python -m ruff check pyreason/scripts
+      run: python -m ruff check pyreason/scripts
     - name: Pytest Unit Tests with JIT Disabled
       run: |
         pytest tests/unit/disable_jit --tb=short -q

.github/workflows/python-publish.yml

@@ -21,9 +21,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.readthedocs.yaml

@@ -3,13 +3,16 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.12"
 
 sphinx:
   configuration: docs/source/conf.py
 
 python:
   install:
-    - requirements: requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

pyproject.toml

@@ -1,6 +1,64 @@
 [build-system]
-requires = ['setuptools>=42']
-build-backend = 'setuptools.build_meta'
+requires = ["setuptools>=80", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyreason"
+description = "An explainable inference software supporting annotated, real valued, graph based and temporal logic"
+readme = "README.md"
+license = { text = "BSD 3-Clause" }
+authors = [
+  { name = "Dyuman Aditya", email = "dyuman.aditya@gmail.com" }
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+]
+requires-python = ">=3.10"
+dynamic = ["version"]
+dependencies = [
+    "networkx>=3.1",
+    "pyyaml>=6.0",
+    "pandas>=2.0.0",
+    "numba>=0.65.1",
+    "numpy>=2.1,<2.5",
+]
+
+[project.optional-dependencies]
+torch = ["torch>=2.6.0"]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "pre-commit",
+    "ruff",
+    "memory_profiler",
+]
+docs = [
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinx-autopackagesummary",
+    "sphinx-autoapi",
+]
+
+[project.urls]
+Homepage = "https://github.com/lab-v2/pyreason"
+"Bug Tracker" = "https://github.com/lab-v2/pyreason/issues"
+Repository = "https://github.com/lab-v2/pyreason"
+
+[tool.setuptools_scm]
+fallback_version = "0.0.0"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
 
 [tool.ruff.lint]
 # Ignore ambiguous variable name errors (E741) in interpretation files

pyreason/__init__.py

@@ -1,6 +1,11 @@
 # ruff: noqa: F403 F405 (Ignore Pyreason import * for public api)
 # Set numba environment variable
 import os
+import sys
+
+# Python 3.11+ bytecode generates ~2300 CFG nodes for the large JIT-compiled
+# reasoning functions; Numba's recursive DFS exceeds the default limit of 1000.
+sys.setrecursionlimit(max(sys.getrecursionlimit(), 5000))
 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')
@@ -9,13 +14,11 @@
 
 from pyreason.pyreason import *
 import yaml
-from importlib.metadata import version
-from pkg_resources import get_distribution, DistributionNotFound
+from importlib.metadata import version, PackageNotFoundError
 
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
-    # package is not installed
+    __version__ = version(__name__)
+except PackageNotFoundError:
     pass
 
 

pyreason/pyreason.py

@@ -7,7 +7,12 @@
 import time
 import sys
 import pandas as pd
-import memory_profiler as mp
+try:
+    import memory_profiler as mp
+    _has_memory_profiler = True
+except ImportError:
+    mp = None
+    _has_memory_profiler = False
 import warnings
 from typing import List, Type, Callable, Tuple, Optional
 
@@ -1513,6 +1518,12 @@ def reason(timesteps: int = -1, convergence_threshold: int = -1, convergence_bou
     if settings.output_to_file:
         sys.stdout = open(f"./{settings.output_file_name}_{__timestamp}.txt", "a")
 
+    if settings.memory_profile and not _has_memory_profiler:
+        raise ImportError(
+            "memory_profiler is required for memory profiling. "
+            "Install it with: pip install memory_profiler"
+        )
+
     if not again or __program is None:
         if settings.memory_profile:
             start_mem = mp.memory_usage(max_usage=True)