Upgrade Python Support to 3.13

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

@@ -16,12 +16,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.8", "3.9", "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
@@ -32,7 +32,6 @@ jobs:
         # the last release with the old E4/E7/E9/F default. Unpin only together
         # with an explicit `select` in pyproject.toml and the matching cleanup.
         python -m pip install ruff==0.15.22 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

.readthedocs.yaml

@@ -5,7 +5,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 sphinx:
   configuration: docs/source/conf.py

README.md

@@ -1,7 +1,11 @@
 <img src="https://raw.githubusercontent.com/lab-v2/pyreason/main/media/pyreason_logo.jpg"/>
 
+[![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)](https://www.python.org/downloads/release/python-380/)
 [![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 +47,7 @@ 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 `3.8`, `3.9`, `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 3.8, 3.9, 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 3.8, 3.9, 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

@@ -56,6 +56,45 @@
 edges_to_be_added_type = numba.types.Tuple((numba.types.ListType(node_type), numba.types.ListType(node_type), label.label_type))
 
 
+
+@numba.njit(cache=True)
+def _filter_pending_node_rules(rules_to_be_applied_node, edges_to_be_added_node_rule, rules_to_be_applied_node_trace, rules_to_remove_idx, atom_trace):
+	rules_to_be_applied_node_new = numba.typed.List.empty_list(rules_to_be_applied_node_type)
+	edges_to_be_added_node_rule_new = numba.typed.List.empty_list(edges_to_be_added_type)
+	rules_to_be_applied_node_trace_new = numba.typed.List.empty_list(rules_to_be_applied_trace_type)
+	for keep_idx in range(len(rules_to_be_applied_node)):
+		if keep_idx not in rules_to_remove_idx:
+			rules_to_be_applied_node_new.append(rules_to_be_applied_node[keep_idx])
+			if atom_trace:
+				rules_to_be_applied_node_trace_new.append(rules_to_be_applied_node_trace[keep_idx])
+	# Node rules do not populate the edge list, so it need not match the rule queue.
+	# Preserve independent filtering instead of indexing it for each pending rule.
+	for keep_idx in range(len(edges_to_be_added_node_rule)):
+		if keep_idx not in rules_to_remove_idx:
+			edges_to_be_added_node_rule_new.append(edges_to_be_added_node_rule[keep_idx])
+	rules_to_be_applied_node[:] = rules_to_be_applied_node_new.copy()
+	edges_to_be_added_node_rule[:] = edges_to_be_added_node_rule_new.copy()
+	if atom_trace:
+		rules_to_be_applied_node_trace[:] = rules_to_be_applied_node_trace_new.copy()
+
+
+@numba.njit(cache=True)
+def _filter_pending_edge_rules(rules_to_be_applied_edge, edges_to_be_added_edge_rule, rules_to_be_applied_edge_trace, rules_to_remove_idx, atom_trace):
+	rules_to_be_applied_edge_new = numba.typed.List.empty_list(rules_to_be_applied_edge_type)
+	edges_to_be_added_edge_rule_new = numba.typed.List.empty_list(edges_to_be_added_type)
+	rules_to_be_applied_edge_trace_new = numba.typed.List.empty_list(rules_to_be_applied_trace_type)
+	for keep_idx in range(len(rules_to_be_applied_edge)):
+		if keep_idx not in rules_to_remove_idx:
+			rules_to_be_applied_edge_new.append(rules_to_be_applied_edge[keep_idx])
+			edges_to_be_added_edge_rule_new.append(edges_to_be_added_edge_rule[keep_idx])
+			if atom_trace:
+				rules_to_be_applied_edge_trace_new.append(rules_to_be_applied_edge_trace[keep_idx])
+	rules_to_be_applied_edge[:] = rules_to_be_applied_edge_new.copy()
+	edges_to_be_added_edge_rule[:] = edges_to_be_added_edge_rule_new.copy()
+	if atom_trace:
+		rules_to_be_applied_edge_trace[:] = rules_to_be_applied_edge_trace_new.copy()
+
+
 class Interpretation:
 	specific_node_labels = numba.typed.Dict.empty(key_type=label.label_type, value_type=numba.types.ListType(node_type))
 	specific_edge_labels = numba.typed.Dict.empty(key_type=label.label_type, value_type=numba.types.ListType(edge_type))
@@ -438,9 +477,9 @@ def reason(interpretations_node, interpretations_edge, predicate_map_node, predi
 				# Apply the rules that need to be applied at this timestep
 				# Nodes
 				rules_to_remove_idx.clear()
-				for idx, i in enumerate(rules_to_be_applied_node):
-					if i[0] == t:
-						comp, l, bnd, set_static = i[1], i[2], i[3], i[4]
+				for idx, pending_rule in enumerate(rules_to_be_applied_node):
+					if pending_rule[0] == t:
+						comp, l, bnd, set_static = pending_rule[1], pending_rule[2], pending_rule[3], pending_rule[4]
 						# Check for inconsistencies
 						if check_consistent_node(interpretations_node, comp, (l, bnd)):
 							override = True if update_mode == 'override' else False
@@ -470,16 +509,13 @@ def reason(interpretations_node, interpretations_edge, predicate_map_node, predi
 						rules_to_remove_idx.add(idx)
 
 				# Remove from rules to be applied and edges to be applied lists after coming out from loop
-				rules_to_be_applied_node[:] = numba.typed.List([rules_to_be_applied_node[i] for i in range(len(rules_to_be_applied_node)) if i not in rules_to_remove_idx])
-				edges_to_be_added_node_rule[:] = numba.typed.List([edges_to_be_added_node_rule[i] for i in range(len(edges_to_be_added_node_rule)) if i not in rules_to_remove_idx])
-				if atom_trace:
-					rules_to_be_applied_node_trace[:] = numba.typed.List([rules_to_be_applied_node_trace[i] for i in range(len(rules_to_be_applied_node_trace)) if i not in rules_to_remove_idx])
+				_filter_pending_node_rules(rules_to_be_applied_node, edges_to_be_added_node_rule, rules_to_be_applied_node_trace, rules_to_remove_idx, atom_trace)
 
 				# Edges
 				rules_to_remove_idx.clear()
-				for idx, i in enumerate(rules_to_be_applied_edge):
-					if i[0] == t:
-						comp, l, bnd, set_static = i[1], i[2], i[3], i[4]
+				for idx, pending_rule in enumerate(rules_to_be_applied_edge):
+					if pending_rule[0] == t:
+						comp, l, bnd, set_static = pending_rule[1], pending_rule[2], pending_rule[3], pending_rule[4]
 						sources, targets, edge_l = edges_to_be_added_edge_rule[idx]
 						edges_added, changes = _add_edges(sources, targets, neighbors, reverse_neighbors, nodes, edges, edge_l, interpretations_node, interpretations_edge, predicate_map_edge, num_ga, t)
 						changes_cnt += changes
@@ -544,10 +580,7 @@ def reason(interpretations_node, interpretations_edge, predicate_map_node, predi
 						rules_to_remove_idx.add(idx)
 
 				# Remove from rules to be applied and edges to be applied lists after coming out from loop
-				rules_to_be_applied_edge[:] = numba.typed.List([rules_to_be_applied_edge[i] for i in range(len(rules_to_be_applied_edge)) if i not in rules_to_remove_idx])
-				edges_to_be_added_edge_rule[:] = numba.typed.List([edges_to_be_added_edge_rule[i] for i in range(len(edges_to_be_added_edge_rule)) if i not in rules_to_remove_idx])
-				if atom_trace:
-					rules_to_be_applied_edge_trace[:] = numba.typed.List([rules_to_be_applied_edge_trace[i] for i in range(len(rules_to_be_applied_edge_trace)) if i not in rules_to_remove_idx])
+				_filter_pending_edge_rules(rules_to_be_applied_edge, edges_to_be_added_edge_rule, rules_to_be_applied_edge_trace, rules_to_remove_idx, atom_trace)
 
 				# Fixed point
 				if update:
@@ -1427,15 +1460,15 @@ 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
@@ -1447,8 +1480,9 @@ 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