Interpretation tests and pipeline updates

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

@@ -30,12 +30,13 @@ jobs:
         python -m pip install flake8 pytest
         pip install torch==2.6.0
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
+    - name: Pytest Unit Tests with JIT Disabled
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+        pytest tests/unit/disable_jit
+    - name: Pytest Unit Tests with JIT Enabled
       run: |
-        pytest
+        pytest tests/unit/dont_disable_jit
+    - name: Pytest Functional Tests
+      run: |
+        pytest tests/functional
+

.gitignore

@@ -2,6 +2,8 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.cache_status.yaml
+.DS_STORE
 
 # C extensions
 *.so
@@ -84,6 +86,12 @@ target/
 profile_default/
 ipython_config.py
 
+#VS Code configs
+.vscode/settings.json
+.vscode/tasks.json
+.vscode/launch.json
+.vscode/extensions.json
+
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+  - repo: local
+    hooks:
+      # --- Unit tests ---
+      - id: pytest-unit-with-coverage
+        name: Run unit tests with coverage and open report
+        entry: bash -c 'pytest tests/unit/disable_jit --cov pyreason   --cov-report=html  && ( (command -v xdg-open >/dev/null && xdg-open htmlcov/index.html) || (command -v open >/dev/null && open htmlcov/index.html) || (command -v start >/dev/null && start htmlcov/index.html) )'
+        language: system
+        pass_filenames: false
+
+      - id: pytest-unit-jit
+        name: Run JIT-enabled unit tests
+        entry: bash -c 'pytest tests/unit/dont_disable_jit'
+        language: system
+        pass_filenames: false
+
+      # --- Functional tests ---
+      - id: pytest-functional
+        name: Run functional tests
+        entry: bash -c 'pytest tests/functional'
+        language: system
+        pass_filenames: false
+        # Only run manually, not on every commit
+        stages: [pre-push]

contributing.md

@@ -0,0 +1,47 @@
+
+## Getting Started
+
+Install the project requirements and the pre-commit framework:
+
+```bash
+pip install -r requirements.txt
+pip install pre-commit
+```
+
+## Setting up Pre-Commit Hooks
+
+To ensure code quality and consistency, enable the pre-commit hooks:
+
+```bash
+pre-commit install --hook-type pre-commit --hook-type pre-push
+```
+
+On every commit, the hooks will run the unit tests located in
+`tests/unit/disable_jit` and `tests/unit/dont_disable_jit`. Functional tests in
+`tests/functional` execute on every push. You can trigger all checks manually
+with `pre-commit run --all-files`.
+
+## Linting
+
+We are working to update the codebase to comply with `ruff` linting rules. Run
+this command to view linting results:
+
+```bash
+ruff check .
+```
+
+## Running Tests Manually
+
+The automated hooks cover most scenarios, but you can invoke the test suites
+directly:
+
+```bash
+pytest tests/unit
+```
+
+```bash
+pytest tests/functional
+```
+
+Running tests locally before committing or pushing helps catch issues early and
+speeds up code review.

pyreason/scripts/learning/classification/classifier.py

@@ -88,4 +88,3 @@ def forward(self, x, t1: int = 0, t2: int = 0) -> Tuple[torch.Tensor, torch.Tens
             fact = Fact(fact_str, name=f'{self.identifier}-{class_name}-fact', start_time=t1, end_time=t2)
             facts.append(fact)
         return output, probabilities, facts
-

requirements.txt

@@ -5,7 +5,10 @@ numba==0.59.1
 numpy==1.26.4
 memory_profiler
 pytest
+torch
 setuptools_scm
+pytest-cov
+pre-commit
 
 sphinx_rtd_theme
 sphinx

tests/test_annotation_function.py → tests/functional/test_annotation_function.py

@@ -2,6 +2,7 @@
 import pyreason as pr
 import numba
 import numpy as np
+from pyreason.scripts.numba_wrapper.numba_types.interval_type import closed
 
 
 @numba.njit
@@ -13,6 +14,17 @@ def probability_func(annotations, weights):
     return union_prob, 1
 
 
+def test_probability_func_consistency():
+    """Ensure annotation function behaves the same with and without JIT."""
+    annotations = numba.typed.List()
+    annotations.append(numba.typed.List([closed(0.01, 1.0)]))
+    annotations.append(numba.typed.List([closed(0.2, 1.0)]))
+    weights = numba.typed.List([1.0, 1.0])
+    jit_res = probability_func(annotations, weights)
+    py_res = probability_func.py_func(annotations, weights)
+    assert jit_res == py_res
+
+
 def test_annotation_function():
     # Reset PyReason
     pr.reset()

tests/test_anyBurl_infer_edges_rules.py → tests/functional/test_anyBurl_infer_edges_rules.py

@@ -2,7 +2,7 @@
 
 
 def test_anyBurl_rule_1():
-    graph_path = './tests/knowledge_graph_test_subset.graphml'
+    graph_path = './tests/functional/knowledge_graph_test_subset.graphml'
     pr.reset()
     pr.reset_rules()
     pr.reset_settings()
@@ -36,7 +36,7 @@ def test_anyBurl_rule_1():
 
 
 def test_anyBurl_rule_2():
-    graph_path = './tests/knowledge_graph_test_subset.graphml'
+    graph_path = './tests/functional/knowledge_graph_test_subset.graphml'
     pr.reset()
     pr.reset_rules()
     pr.reset_settings()
@@ -72,7 +72,7 @@ def test_anyBurl_rule_2():
 
 
 def test_anyBurl_rule_3():
-    graph_path = './tests/knowledge_graph_test_subset.graphml'
+    graph_path = './tests/functional/knowledge_graph_test_subset.graphml'
     pr.reset()
     pr.reset_rules()
     pr.reset_settings()
@@ -108,7 +108,7 @@ def test_anyBurl_rule_3():
 
 
 def test_anyBurl_rule_4():
-    graph_path = './tests/knowledge_graph_test_subset.graphml'
+    graph_path = './tests/functional/knowledge_graph_test_subset.graphml'
     pr.reset()
     pr.reset_rules()
     pr.reset_settings()

tests/test_custom_thresholds.py → tests/functional/test_custom_thresholds.py

@@ -9,7 +9,7 @@ def test_custom_thresholds():
     pr.reset_rules()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = "./tests/group_chat_graph.graphml"
+    graph_path = "./tests/functional/group_chat_graph.graphml"
 
     # Modify pyreason settings to make verbose
     pr.reset_settings()

tests/test_hello_world.py → tests/functional/test_hello_world.py

@@ -1,6 +1,13 @@
 # Test if the simple hello world program works
 import pyreason as pr
 import faulthandler
+import json
+import os
+import subprocess
+import sys
+import textwrap
+
+# import pyreason.pyreason as pr
 
 
 def test_hello_world():
@@ -10,7 +17,7 @@ def test_hello_world():
     pr.reset_settings()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = './tests/friends_graph.graphml'
+    graph_path = './tests/functional/friends_graph.graphml'
 
     # Modify pyreason settings to make verbose
     pr.settings.verbose = True     # Print info to screen
@@ -47,3 +54,35 @@ def test_hello_world():
 
     # John should be popular in timestep 3
     assert 'John' in dataframes[2]['component'].values and dataframes[2].iloc[1].popular == [1, 1], 'John should have popular bounds [1,1] for t=2 timesteps'
+
+def test_hello_world_consistency():
+    """Ensure hello world output matches when using JIT vs pure Python interval constructors."""
+
+    import pyreason.scripts.numba_wrapper.numba_types.interval_type as interval_type
+
+    def run():
+        pr.reset()
+        pr.reset_rules()
+        pr.reset_settings()
+        pr.settings.verbose = False
+        pr.load_graphml('./tests/functional/friends_graph.graphml')
+        pr.add_rule(pr.Rule('popular(x) <-1 popular(y), Friends(x,y), owns(y,z), owns(x,z)', 'popular_rule'))
+        pr.add_fact(pr.Fact('popular(Mary)', 'popular_fact', 0, 2))
+        interpretation = pr.reason(timesteps=2)
+        dataframes = pr.filter_and_sort_nodes(interpretation, ['popular'])
+        return [df[['component', 'popular']].to_dict('records') for df in dataframes]
+
+    original_closed = interval_type.closed
+    jit_res = run()
+    try:
+        from pyreason.scripts.interval.interval import Interval
+
+        def py_closed(lower, upper, static=False):
+            return Interval(float(lower), float(upper), static)
+
+        interval_type.closed = py_closed
+        py_res = run()
+    finally:
+        interval_type.closed = original_closed
+
+    assert jit_res == py_res

tests/test_hello_world_parallel.py → tests/functional/test_hello_world_parallel.py

@@ -8,7 +8,7 @@ def test_hello_world_parallel():
     pr.reset_rules()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = './tests/friends_graph.graphml'
+    graph_path = './tests/functional/friends_graph.graphml'
 
     # Modify pyreason settings to make verbose
     pr.reset_settings()

tests/test_num_ga.py → tests/functional/test_num_ga.py

@@ -3,7 +3,7 @@
 
 
 def test_num_ga():
-    graph_path = './tests/knowledge_graph_test_subset.graphml'
+    graph_path = './tests/functional/knowledge_graph_test_subset.graphml'
     pr.reset()
     pr.reset_rules()
     pr.reset_settings()

tests/test_reason_again.py → tests/functional/test_reason_again.py

@@ -10,7 +10,7 @@ def test_reason_again():
     pr.reset_settings()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = './tests/friends_graph.graphml'
+    graph_path = './tests/functional/friends_graph.graphml'
 
     # Modify pyreason settings to make verbose
     pr.settings.verbose = True     # Print info to screen

tests/test_reorder_clauses.py → tests/functional/test_reorder_clauses.py

@@ -9,7 +9,7 @@ def test_reorder_clauses():
     pr.reset_settings()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = './tests/friends_graph.graphml'
+    graph_path = './tests/functional/friends_graph.graphml'
 
     # Modify pyreason settings to make verbose
     pr.settings.verbose = True     # Print info to screen

tests/test_rule_filtering.py → tests/functional/test_rule_filtering.py

@@ -8,7 +8,7 @@ def test_rule_filtering():
     pr.reset_settings()
 
     # Modify the paths based on where you've stored the files we made above
-    graph_path = './tests/friends_graph.graphml'
+    graph_path = './tests/functional/friends_graph.graphml'
 
     # Modify pyreason settings to make verbose
     pr.settings.verbose = True     # Print info to screen