Linting changes

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

@@ -27,16 +27,21 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        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: |
+        python -m ruff check pyreason/scripts
     - name: Pytest Unit Tests with JIT Disabled
       run: |
-        pytest tests/unit/disable_jit
+        pytest tests/unit/disable_jit -m "not slow" --tb=short -q
     - name: Pytest Unit Tests with JIT Enabled
       run: |
-        pytest tests/unit/dont_disable_jit
+        pytest tests/unit/dont_disable_jit -m "not slow" --tb=short -q
+    - name: Pytest API Tests
+      run: |
+        pytest tests/unit/api_tests --tb=short -q
     - name: Pytest Functional Tests
       run: |
-        pytest tests/functional
-
+        pytest tests/functional/ --tb=short

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+"pyreason/.cache_status.yaml
 # Cache status file when initialized
 # Keep the initial false version in repo, ignore when it becomes true
 .DS_STORE
@@ -174,4 +175,3 @@ cython_debug/
 
 # Sphinx Documentation
 /docs/source/_static/css/fonts/
-

.numba_config.yaml

@@ -1,2 +1,2 @@
 disable_jit: 0
-cache_dir: ./pyreason/cache/
+cache_dir: ./pyreason/cache/

.pre-commit-config.yaml

@@ -1,26 +1,40 @@
 exclude: 'pyreason/\.cache_status\.yaml'
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: end-of-file-fixer
+        name: Fix end of files
+        stages: [pre-commit]
+
   - repo: local
     hooks:
       # --- COMMIT STAGE: Fast unit tests only ---
+      - id: ruff-check
+        name: Run ruff linter
+        entry: .venv/bin/python -m ruff check pyreason/scripts
+        language: system
+        types: [python]
+        pass_filenames: false
+        stages: [pre-commit]
+
       - id: pytest-unit-no-jit
-        name: Run JIT-disabled unit tests 
+        name: Run JIT-disabled unit tests
         entry: .venv/bin/python -m pytest tests/unit/disable_jit -m "not slow" --tb=short -q
         language: system
         pass_filenames: false
         stages: [pre-commit]
 
       - id: pytest-unit-jit
-        name: Run JIT-enabled unit tests 
+        name: Run JIT-enabled unit tests
         entry: .venv/bin/python -m pytest tests/unit/dont_disable_jit -m "not slow" --tb=short -q
         language: system
         pass_filenames: false
         stages: [pre-commit]
 
       # --- PUSH STAGE: Complete test suite ---
-
       - id: pytest-unit-api
-        name: Run pyreason api unit tests 
+        name: Run pyreason api unit tests
         entry: .venv/bin/python -m pytest tests/unit/api_tests --tb=short -q
         language: system
         pass_filenames: false

Makefile

@@ -131,10 +131,10 @@ coverage-xml: ## Show path to XML coverage report
 # Development targets
 lint: ## Run linting checks
 	@echo "$(BOLD)$(BLUE)Running linting checks...$(RESET)"
-	@echo "$(YELLOW)Note: Add your preferred linter commands here$(RESET)"
-	# Example: flake8 pyreason tests
-	# Example: black --check pyreason tests
-	# Example: mypy pyreason
+	@echo "Fixing end of files..."
+	@pre-commit run end-of-file-fixer --all-files || true
+	@echo "Running ruff..."
+	./.venv/bin/python -m ruff check pyreason/scripts
 
 check-deps: ## Check if required dependencies are installed
 	@echo "$(BOLD)$(BLUE)Checking dependencies...$(RESET)"
@@ -176,4 +176,4 @@ info: ## Show project and tool versions
 	@echo "Pytest: $$($(PYTHON) -c 'import pytest; print(pytest.__version__)' 2>/dev/null || echo 'Not installed')"
 	@echo "Coverage: $$($(PYTHON) -c 'import coverage; print(coverage.__version__)' 2>/dev/null || echo 'Not installed')"
 	@echo "Working Directory: $$(pwd)"
-	@echo "Test Runner: $$(ls -la run_tests.py 2>/dev/null || echo 'Not found')"
+	@echo "Test Runner: $$(ls -la run_tests.py 2>/dev/null || echo 'Not found')"

contributing.md

@@ -27,7 +27,7 @@ We are working to update the codebase to comply with `ruff` linting rules. Run
 this command to view linting results:
 
 ```bash
-ruff check .
+.venv/bin/python -m ruff check pyreason/scripts
 ```
 
 ## Running Tests

docs/hello-world.md

@@ -131,4 +131,4 @@ After running the python file, the expected output is:
 3. For timestep 2, since Justin has just become popular, John now has one popular friend (Justin) and the same pet as Justin (dog). Therefore `Justin -> popular: [1,1]`
 
 
-We also output two CSV files detailing all the events that took place during reasoning (one for nodes, one for edges)
+We also output two CSV files detailing all the events that took place during reasoning (one for nodes, one for edges)

docs/hello-world.py

@@ -51,4 +51,3 @@
 
 # Get all interpretations in a dictionary
 interpretations_dict = interpretation.get_interpretation_dict()
-

docs/source/api_reference/index.rst

@@ -5,4 +5,4 @@ API Documentation
 .. automodule:: pyreason
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/source/examples_rst/advanced_example.rst

@@ -164,4 +164,3 @@ Advanced Example
     # Display filtered node and edge data
     print(df1)
     print(df2)
-

docs/source/examples_rst/advanced_output_example.rst

@@ -695,4 +695,4 @@ Advanced Example Full Output
         ('customer_6', 'Car_6'): {},
         ('customer_6', 'Pet_4'): {},
         ('customer_6', 'customer_0'): {'same_color_car': (1.0, 1.0)}}}
-
+

docs/source/examples_rst/annF_average_example.rst

@@ -58,4 +58,3 @@ Average Annotation Function Example
         assert interpretation.query('average_function(A, B) : [0.105, 1]'), 'Average function should be [0.105, 1]'
 
     average_annotation_function()
-

docs/source/examples_rst/annF_linear_combination_example.rst

@@ -85,4 +85,4 @@ Linear Combination Annotation Function Example
             assert interpretation.query('linear_combination_function(A, B) : [0.1, 0.4]'), 'Linear combination function should be [0.105, 1]'
 
         # Run the test function
-        linear_combination_annotation_function()
+        linear_combination_annotation_function()

docs/source/examples_rst/index.rst

@@ -13,4 +13,4 @@ Examples
 
     ./*
 
-
+

docs/source/examples_rst/infer_edges_example.rst

@@ -83,4 +83,4 @@ Infer Edges Example
     assert ('Vnukovo_International_Airport', 'Riga_International_Airport') in dataframes[1]['component'].values.tolist() and dataframes[1]['isConnectedTo'].iloc[0] == [1, 1], '(Vnukovo_International_Airport, Riga_International_Airport) should have isConnectedTo bounds [1,1] for t=1 timesteps'
 
     nx.draw(G, with_labels=True, node_color='lightblue', font_weight='bold', node_size=3000)
-    plt.show()
+    plt.show()

docs/source/installation.rst

@@ -20,4 +20,4 @@ You will see a message like this when you import PyReason for the first time:
 
 .. code:: text
 
-    Imported PyReason for the first time. Initializing caches for faster runtimes ... this will take a minute
+    Imported PyReason for the first time. Initializing caches for faster runtimes ... this will take a minute

docs/source/license.rst

@@ -9,4 +9,3 @@ Trademark Permission
    :width: 50
 
 PyReason™ and PyReason Design Logo |logo| ™ are trademarks of the Arizona Board of Regents/Arizona State University. Users of the software are permitted to use PyReason™ in association with the software for any purpose, provided such use is related to the software (e.g., Powered by PyReason™). Additionally, educational institutions are permitted to use the PyReason Design Logo |logo| ™ for non-commercial purposes.
-

docs/source/tutorials/advanced_tutorial.rst

@@ -161,4 +161,4 @@ Below is the expected output at timestep ``0``
       ('customer_6', 'Car_6'): {},
       ('customer_6', 'Pet_4'): {},
       ('customer_6', 'customer_0'): {'same_color_car': (1.0, 1.0)}},
-
+

docs/source/tutorials/index.rst

@@ -16,4 +16,4 @@ Contents
    ./custom_thresholds.rst
    ./infer_edges.rst
    ./annotation_function.rst
-
+

docs/source/tutorials/infer_edges.rst

@@ -146,6 +146,3 @@ The graph after running shows a new connection from ``Vnukovo_International_Airp
 
 .. image:: ../../../media/infer_edges2.png
    :align: center
-
-
-

docs/source/user_guide/3_pyreason_rules.rst

@@ -208,4 +208,4 @@ PyReason's ``Threshold`` class is used to define custom thresholds for a rule. T
 and the second is either ``"total"`` or ``"available"``. ``"total"`` refers to all groundings of the clause, while ``"available"`` refers to the groundings that have the predicate of the clause.
 #. ``thresh`` **(int)**: The value of the threshold
 
-An example usage can be found :ref:`here <custom_thresholds_tutorial>`.
+An example usage can be found :ref:`here <custom_thresholds_tutorial>`.

docs/source/user_guide/4_pyreason_settings.rst

@@ -91,4 +91,4 @@ Notes on Parallelism
 ~~~~~~~~~~~~~~~~~~~~
 PyReason is parallelized over rules, so for large rulesets it is recommended that this setting is used. However, for small rulesets,
 the overhead might be more than the speedup and it is worth checking the performance on your specific use case.
-When possible we recommend using the same number of cores (or a multiple) as the number of rules in the program.
+When possible we recommend using the same number of cores (or a multiple) as the number of rules in the program.

docs/source/user_guide/5_inconsistent_predicate_list.rst

@@ -18,4 +18,4 @@ This can be done by using the following code:
     pr.add_inconsistent_predicate('sick', 'healthy')
 
 This allows PyReason to automatically update the bounds of the predicates in the inconsistent predicate list to the
-negation of a predicate that is updated.
+negation of a predicate that is updated.

docs/source/user_guide/7_jupyter_notebook_usage.rst

@@ -8,4 +8,3 @@ However, if you want to use PyReason in a Jupyter Notebook, make sure you unders
 
 1. When using functions like ``add_rule`` or ``add_fact`` in a Jupyter Notebook, make sure to run the cell only once. Running the cell multiple times will add the same rule/fact multiple times. It is recommended to store all the rules and facts in an array and then add them all at once in one cell towards the end
 2. Functions like ``load_graph`` and ``load_graphml`` which are run multiple times can also have the same issue. Make sure to run them only once.
-

docs/source/user_guide/index.rst

@@ -10,6 +10,3 @@ In this section we demonstrate the functionality of the `pyreason` library and h
     :glob:
 
     ./*
-
-
-

examples/advanced_output.txt

@@ -836,4 +836,4 @@ Filtered Edges:
 6  (customer_4, customer_5)      [0, 1]     [1.0, 1.0]
 7  (customer_5, customer_3)      [0, 1]     [1.0, 1.0]
 8  (customer_5, customer_6)      [0, 1]     [1.0, 1.0]
-9  (customer_6, customer_0)      [0, 1]     [1.0, 1.0]]
+9  (customer_6, customer_0)      [0, 1]     [1.0, 1.0]]

examples/temporal_classifier_integration_ex.py

@@ -77,4 +77,4 @@
 trace = pr.get_rule_trace(interpretation)
 
 print("\n=== Reasoning Rule Trace ===")
-print(trace[0])
+print(trace[0])

initialize.py

@@ -1,4 +1,4 @@
 # Run this script after cloning repository to generate the numba caches. This script runs the hello-world program internally
 print('Initializing PyReason caches')
 import pyreason as pr
-
+

jobs/.gitignore

@@ -1,3 +1,3 @@
 *
 */
-!.gitignore
+!.gitignore

output/.gitignore

@@ -1,3 +1,3 @@
 *
 */
-!.gitignore
+!.gitignore

profiling/.gitignore

@@ -1,3 +1,3 @@
 *
 */
-!.gitignore
+!.gitignore

pyproject.toml

@@ -1,3 +1,8 @@
 [build-system]
 requires = ['setuptools>=42']
 build-backend = 'setuptools.build_meta'
+
+[tool.ruff.lint]
+# Ignore ambiguous variable name errors (E741) in interpretation files
+[tool.ruff.lint.per-file-ignores]
+"pyreason/scripts/interpretation/*.py" = ["E741"]

pyreason/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F403 F405 (Ignore Pyreason import * for public api)
 # Set numba environment variable
 import os
 package_path = os.path.abspath(os.path.dirname(__file__))

pyreason/pyreason.py

@@ -1,4 +1,6 @@
 # This is the file that will be imported when "import pyreason" is called. All content will be run automatically
+# ruff: noqa: F401 (Ignore Pyreason import * for public api)
+import importlib
 import networkx as nx
 import numba
 import time
@@ -25,15 +27,14 @@
 import pyreason.scripts.numba_wrapper.numba_types.fact_edge_type as fact_edge
 import pyreason.scripts.numba_wrapper.numba_types.interval_type as interval
 from pyreason.scripts.utils.reorder_clauses import reorder_clauses
-try:
-    import torch
-except ImportError:
+if importlib.util.find_spec("torch") is not None:
+    from pyreason.scripts.learning.classification.classifier import LogicIntegratedClassifier
+    from pyreason.scripts.learning.utils.model_interface import ModelInterfaceOptions
+else:
     LogicIntegratedClassifier = None
     ModelInterfaceOptions = None
     print('torch is not installed, model integration is disabled')
-else:
-    from pyreason.scripts.learning.classification.classifier import LogicIntegratedClassifier
-    from pyreason.scripts.learning.utils.model_interface import ModelInterfaceOptions
+
 
 
 # USER VARIABLES

pyreason/scripts/annotation_functions/annotation_functions.py

@@ -30,9 +30,9 @@ def _check_bound(lower, upper):
     if lower > upper:
         return (0, 1)
     else:
-        l = min(lower, 1)
-        u = min(upper, 1)
-        return (l, u)
+        lower_bound = min(lower, 1)
+        upper_bound = min(upper, 1)
+        return (lower_bound, upper_bound)
 
 
 @numba.njit
@@ -99,5 +99,3 @@ def minimum(annotations, weights):
     lower, upper = _check_bound(min_lower, min_upper)
 
     return interval.closed(lower, upper)
-
-

pyreason/scripts/components/label.py

@@ -17,4 +17,4 @@ def __hash__(self):
         return hash(str(self))
 
     def __repr__(self):
-        return self.get_value()
+        return self.get_value()

pyreason/scripts/components/world.py

@@ -8,8 +8,8 @@ class World:
     def __init__(self, labels):
         self._labels = labels
         self._world = numba.typed.Dict.empty(key_type=label.label_type, value_type=interval.interval_type)
-        for l in labels:
-            self._world[l] = interval.closed(0.0, 1.0)
+        for lbl in labels:
+            self._world[lbl] = interval.closed(0.0, 1.0)
 
     @property
     def world(self):
@@ -29,9 +29,6 @@ def is_satisfied(self, label, interval):
         return result
 
     def update(self, label, interval):
-        lwanted = None
-        bwanted = None 
-
         current_bnd = self._world[label]
         new_bnd = current_bnd.intersection(interval)
         self._world[label] = new_bnd
@@ -48,7 +45,7 @@ def get_world(self):
 
     def __str__(self):
         result = ''
-        for label in self._world.keys():
-            result = result + label.get_value() + ',' + self._world[label].to_str() + '\n'
+        for lbl in self._world.keys():
+            result = result + lbl.get_value() + ',' + self._world[lbl].to_str() + '\n'
 
         return result