Add unit tests and update api reference to include classifier module

.gitignore

@@ -2,6 +2,8 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.cache_status.yaml
+.DS_STORE
 
 # C extensions
 *.so
@@ -84,6 +86,9 @@ target/
 profile_default/
 ipython_config.py
 
+#VS Code configs
+.vscode/settings.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 +1,18 @@
+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  && open htmlcov/index.html'
+        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]

.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python Debugger: not justMyCode",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": false
+        }
+    ]
+}

contributing.md

@@ -0,0 +1,31 @@
+
+## Setting up Pre-Commit Hooks
+
+To ensure code quality and consistency, set up the pre-commit hooks by running the following command:
+
+```bash
+pre-commit install --hook-type pre-commit --hook-type pre-push
+```
+
+This will configure the necessary hooks to run automatically during commits and pushes.
+
+# Linting
+
+We are working to update the codebase to comply with the `ruff` linting rules.  Run this command to view linting: 
+```bash
+ruff check .
+```
+
+
+## Running Tests
+
+This codebase has a unit and functional test suite.  You can run the unit tests using `pytest` with the following command:
+
+```bash
+pytest tests/unit
+```
+
+```bash
+pytest tests/functional
+```
+

docs/source/api_reference/index.rst

@@ -3,6 +3,11 @@ API Documentation
 
 
 .. automodule:: pyreason
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: classifier
    :members:
    :undoc-members:
    :show-inheritance:

pyreason/.cache_status.yaml

@@ -1 +1 @@
-initialized: false
+initialized: true

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 = min(lower, 1)
+        upper = min(upper, 1)
+        return (lower, upper)
 
 
 @numba.njit

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 my_label in labels:
+            self._world[my_label] = 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 my_label in self._world.keys():
+            result = result + my_label.get_value() + ',' + self._world[my_label].to_str() + '\n'
 
         return result

pyreason/scripts/learning/classification/classifier.py

@@ -51,8 +51,29 @@ def forward(self, x, t1: int = 0, t2: int = 0) -> Tuple[torch.Tensor, torch.Tens
 
         # Convert logits to probabilities assuming a multi-class classification.
         probabilities = F.softmax(output, dim=1).squeeze()
-        opts = self.interface_options
+        print("Probs: ", probabilities)
+
+
+        # Convert bounds to Python floats for fact creation.
+        lower_bounds, upper_bounds = self.calculate_bounds(probabilities)
+        bounds_list = []
+        for i in range(len(self.class_names)):
+            lower = lower_bounds[i].item()
+            upper = upper_bounds[i].item()
+            bounds_list.append([lower, upper])
+
+        # Define time bounds for the facts.
+        facts = []
+        for class_name, bounds in zip(self.class_names, bounds_list):
+            lower, upper = bounds
+            fact_str = f'{class_name}({self.identifier}) : [{lower:.3f}, {upper:.3f}]'
+            fact = Fact(fact_str, name=f'{self.identifier}-{class_name}-fact', start_time=t1, end_time=t2)
+            facts.append(fact)
+        return output, probabilities, facts
+
 
+    def calculate_bounds(self, probabilities):
+        opts = self.interface_options
         # Prepare threshold tensor.
         threshold = torch.tensor(opts.threshold, dtype=probabilities.dtype, device=probabilities.device)
         condition = probabilities > threshold
@@ -72,20 +93,4 @@ def forward(self, x, t1: int = 0, t2: int = 0) -> Tuple[torch.Tensor, torch.Tens
         # For probabilities that pass the threshold, apply the above; else, bounds are fixed to [0,1].
         lower_bounds = torch.where(condition, lower_val, torch.zeros_like(probabilities))
         upper_bounds = torch.where(condition, upper_val, torch.ones_like(probabilities))
-
-        # Convert bounds to Python floats for fact creation.
-        bounds_list = []
-        for i in range(len(self.class_names)):
-            lower = lower_bounds[i].item()
-            upper = upper_bounds[i].item()
-            bounds_list.append([lower, upper])
-
-        # Define time bounds for the facts.
-        facts = []
-        for class_name, bounds in zip(self.class_names, bounds_list):
-            lower, upper = bounds
-            fact_str = f'{class_name}({self.identifier}) : [{lower:.3f}, {upper:.3f}]'
-            fact = Fact(fact_str, name=f'{self.identifier}-{class_name}-fact', start_time=t1, end_time=t2)
-            facts.append(fact)
-        return output, probabilities, facts
-
+        return lower_bounds, upper_bounds

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_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()
     # Modify pyreason settings to make verbose and to save the rule trace to a file
@@ -35,7 +35,7 @@ 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()
     # Modify pyreason settings to make verbose and to save the rule trace to a file
@@ -70,7 +70,7 @@ 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()
     # Modify pyreason settings to make verbose and to save the rule trace to a file
@@ -105,7 +105,7 @@ 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()
     # Modify pyreason settings to make verbose and to save the rule trace to a file

tests/test_classifier.py → tests/functional/test_classifier.py

@@ -27,7 +27,7 @@ def test_classifier_integration():
     )
 
     # Create an instance of LogicIntegratedClassifier.
-    logic_classifier = pr.LogicIntegratedClassifier(model, class_names, model_name="classifier",
+    logic_classifier = pr.LogicIntegratedClassifier(model, class_names, "classifier",
                                                     interface_options=interface_options)
 
     # Create a dummy input tensor with 10 features.

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 +1,7 @@
 # Test if the simple hello world program works
-import pyreason as pr
+#import pyreason as pr
 import faulthandler
+import pyreason.pyreason as pr
 
 
 def test_hello_world():
@@ -10,7 +11,7 @@ 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
@@ -24,6 +25,7 @@ def test_hello_world():
     # Run the program for two timesteps to see the diffusion take place
     faulthandler.enable()
     interpretation = pr.reason(timesteps=2)
+    print("Reasoning")
 
     # Display the changes in the interpretation for each timestep
     dataframes = pr.filter_and_sort_nodes(interpretation, ['popular'])
@@ -48,3 +50,4 @@ 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'
 
+test_hello_world()

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()
     # Modify pyreason settings to make verbose and to save the rule trace to a file

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

tests/unit/disable_jit/conftest.py

@@ -0,0 +1,4 @@
+# # tests/conftest.py
+import os; os.environ["NUMBA_DISABLE_JIT"] = "1"
+import numba; numba.config.DISABLE_JIT = True
+import sys, types; sys.modules.setdefault("pyreason.pyreason", types.ModuleType("pyreason.pyreason"))