Merge pull request #138 from lab-v2/main

upd ai docs branch

Author: ColtonPayne

.pre-commit-config.yaml

@@ -1,56 +1,51 @@
-exclude: 'pyreason/\.cache_status\.yaml'
+exclude: 'pyreason/\.cache_status\.yaml|pyreason/scripts/interpretation/interpretation_parallel\.py'
 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
+        exclude: 'pyreason/scripts/interpretation/interpretation_parallel\.py'
         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
+        entry:  ruff check pyreason/scripts
         language: system
         types: [python]
         pass_filenames: false
         stages: [pre-commit]
-
-      - id: sync-interpretation-parallel
-        name: Sync interpretation_parallel.py from interpretation.py
-        entry: .venv/bin/python sync_interpretation_parallel.py
-        language: system
-        pass_filenames: false
-        files: 'pyreason/scripts/interpretation/interpretation\.py'
-        stages: [pre-commit]
-
+        
       - id: pytest-unit-no-jit
         name: Run JIT-disabled unit tests
-        entry: .venv/bin/python -m pytest tests/unit/disable_jit -m "not slow" --tb=short -q
+        entry:  pytest tests/unit/disable_jit --tb=short -q
         language: system
         pass_filenames: false
         stages: [pre-commit]
+        require_serial: true
 
       - id: pytest-unit-jit
         name: Run JIT-enabled unit tests
-        entry: .venv/bin/python -m pytest tests/unit/dont_disable_jit -m "not slow" --tb=short -q
+        entry: pytest tests/unit/dont_disable_jit --tb=short -q
         language: system
         pass_filenames: false
         stages: [pre-commit]
+        require_serial: true
 
       # --- PUSH STAGE: Complete test suite ---
       - id: pytest-unit-api
         name: Run pyreason api tests
-        entry: .venv/bin/python -m pytest tests/api_tests --tb=short -q
+        entry:  pytest tests/api_tests --tb=short -q
         language: system
         pass_filenames: false
         stages: [pre-push]
 
       - id: pytest-functional-complete
         name: Run functional test suite
-        entry: .venv/bin/python -m pytest tests/functional/ --tb=short -q
+        entry:  pytest tests/functional/ --tb=short -q
         language: system
         pass_filenames: false
-        stages: [pre-push]
+        stages: [pre-push]

Makefile

@@ -85,7 +85,7 @@ test-api: ## Run only API tests (tests/api_tests)
 
 test-jit: ## Run only JIT-disabled tests (tests/unit/disable_jit)
 	@echo "$(BOLD)$(BLUE)Running JIT-disabled tests...$(RESET)"
-	$(RUN_TESTS) --suite don_disable_jit
+	$(RUN_TESTS) --suite dont_disable_jit
 
 test-no-jit: ## Run only JIT-enabled tests (tests/unit/dont_disable_jit)
 	@echo "$(BOLD)$(BLUE)Running JIT-enabled tests...$(RESET)"

README.md

@@ -14,7 +14,7 @@ An explainable inference software supporting annotated, real valued, graph based
 
 [📽️ Video](https://www.youtube.com/watch?v=E1PSl3KQCmo)
 
-[🌐 Website](https://pyreason-staging.sites.syr.edu)
+[🌐 Website](https://pyreason.syracuse.edu/)
 
 [🏋️‍♂️ PyReason Gym](https://github.com/lab-v2/pyreason-gym)
 
@@ -64,7 +64,7 @@ Trademark Permission PyReason™ and PyReason Design Logo <img src="https://raw.
 
 
 ## 6. Contact
-Dyuman Aditya - daditya@syr.edu
+Colton Payne - crpayne@syr.edu
 
 Kaustuv Mukherji - kmukherj@syr.edu
 

examples/closed_world_pred_ex.py

@@ -0,0 +1,57 @@
+import pyreason as pr
+import networkx as nx
+from pprint import pprint
+
+pr.reset()
+pr.reset_rules()
+
+g = nx.DiGraph()
+
+g.add_nodes_from(['cb_1', 'cb_2', 'l1', 'l2'])
+g.add_edge('cb_1', 'cb_2', stepFrom =1)
+g.add_edge('cb_1',  'l1', hasLabel = 1)
+g.add_edge('cb_2',  'l2', hasLabel = 1)
+#g.add_edge('l1','l2', cond=1) # Adding this edge will satisfy hackerControl(cb)
+
+pr.settings.verbose = True
+pr.settings.atom_trace = True
+pr.settings.inconsistency_check = True
+
+pr.load_graph(g)
+
+# hackerControl is a closed-world pred, meaning that it will be grounded as [0,0] if its bounds are [0,1] (or if it is not in the interpretation dict)
+pr.add_closed_world_predicate('hackerControl')
+
+# Initial fact instantiation
+pr.add_fact(pr.Fact('stepFrom(cb_1, cb_2)', 'step_from_fact', 0, 1))
+pr.add_fact(pr.Fact('hackerControl(cb_1)', 'hacker_control_initial_fact', 0, 0))
+
+# Future(Y) will fire for cb_2
+pr.add_rule(pr.Rule('future(Y) <-1 stepFrom(X,Y), hackerControl(X)'))
+
+#This rule will not fire for cb_2, as cond(cb_1, cb_2) is not grounded
+pr.add_rule(pr.Rule('hackerControl(Y) <-1 hackerControl(X), hasLabel(X,L1), hasLabel(Y,L2), cond(L1, L2), stepFrom(X,Y)', 'hacker-control-rule'))
+
+# At timestep 1, hackerControl(cb_1) and hackerControl(cb_2) have no associated bounds, so they are treated as [0,1].
+# Because hackerControl is minimized, its bounds are gounded as [0,0].  Future(cb_2) has bounds [1,1], so inconsistent(cb_2) fires.
+pr.add_rule(pr.Rule('inconsistent(Y) <- future(Y), ~hackerControl(Y), ~hackerControl(X)', 'inconsistent_rule'))
+
+
+interpretation = pr.reason(timesteps=2)
+interp_dict = interpretation.get_dict()
+
+pprint(interp_dict)
+
+# Filter and sort nodes based on hackerControl
+dataframes = pr.filter_and_sort_nodes(interpretation, ['hackerControl'])
+for t, df in enumerate(dataframes):
+    print(f'TIMESTEP - {t}')
+    print(df)
+    print()
+
+# Filter and sort edges based on inconsistent
+edge_dataframes = pr.filter_and_sort_nodes(interpretation, ['inconsistent'])
+for t, df in enumerate(edge_dataframes):
+    print(f'TIMESTEP - {t} (inconsistent nodes)')
+    print(df)
+    print()

…ced_rule_trace_edges_20241119-012153.csv …ced_rule_trace_edges_20241119-012153.csvexamples/csv outputs/advanced_rule_trace_edges_20241119-012153.csv renamed to examples/csv_outputs/advanced_rule_trace_edges_20241119-012153.csv examples/csv outputs/advanced_rule_trace_edges_20241119-012153.csv renamed to examples/csv_outputs/advanced_rule_trace_edges_20241119-012153.csv

@@ -0,0 +1,10 @@
+Time,Fixed-Point-Operation,Edge,Label,Old Bound,New Bound,Occurred Due To,Consistent,Triggered By,Inconsistency Message,Clause-1,Clause-2,Clause-3
+0,0,"('Alice', 'Bob')",close_contact,"[0.0,1.0]","[0.8,1.0]",alice_bob_close_fact,True,Fact,,,,
+0,0,"('Alice', 'Bob')",no_contact,"[0.0,1.0]","[0.0,0.19999999999999996]",IPL: close_contact,True,IPL,,,,
+0,0,"('Bob', 'Carol')",trust,"[0.0,1.0]","[0.9,1.0]",bob_carol_trust_high,True,Fact,,,,
+0,1,"('Bob', 'Carol')",trust,"[0.9,1.0]","[0.0,1.0]",distrust_rule,False,Rule,"Inconsistency occurred. Conflicting bounds for trust(Bob,Carol). Update from [0.900, 1.000] to [0.000, 0.200] is not allowed. Setting bounds to [0,1] and static=True for this timestep.",['Bob'],"[('Bob', 'Carol')]",
+0,1,"('Bob', 'Dave')",trust,"[0.0,1.0]","[0.0,0.2]",distrust_rule,True,Rule,,['Bob'],"[('Bob', 'Dave')]",
+0,1,"('Bob', 'Carol')",risk,"[0.0,1.0]","[0.6,0.8]",risk_rule,True,Rule,,['Bob'],"[('Bob', 'Carol')]",
+0,1,"('Bob', 'Dave')",risk,"[0.0,1.0]","[0.6,0.8]",risk_rule,True,Rule,,['Bob'],"[('Bob', 'Dave')]",
+0,2,"('Bob', 'Dave')",no_contact,"[0.0,1.0]","[0.8,1.0]",quarantine_rule,True,Rule,,['Bob'],['Dave'],"[('Bob', 'Dave')]"
+0,2,"('Bob', 'Dave')",close_contact,"[0.0,1.0]","[0.0,0.19999999999999996]",IPL: no_contact,True,IPL,,,,

…ced_rule_trace_nodes_20241119-012153.csv …ced_rule_trace_nodes_20241119-012153.csvexamples/csv outputs/advanced_rule_trace_nodes_20241119-012153.csv renamed to examples/csv_outputs/advanced_rule_trace_nodes_20241119-012153.csv examples/csv outputs/advanced_rule_trace_nodes_20241119-012153.csv renamed to examples/csv_outputs/advanced_rule_trace_nodes_20241119-012153.csv

@@ -0,0 +1,15 @@
+Time,Fixed-Point-Operation,Node,Label,Old Bound,New Bound,Occurred Due To,Consistent,Triggered By,Inconsistency Message,Clause-1,Clause-2
+0,0,Alice,sick,"[0.0,1.0]","[0.8,1.0]",alice_sick_fact,True,Fact,,,
+0,0,Alice,healthy,"[0.0,1.0]","[0.0,0.19999999999999996]",IPL: sick,True,IPL,,,
+0,0,Alice,healthy,"[0.0,0.19999999999999996]","[0.0,1.0]",alice_healthy_fact,False,Fact,"Inconsistency occurred. Grounding healthy(Alice) conflicts with grounding sick(Alice). Setting bounds to [0,1] and static=True for this timestep.",,
+0,0,Alice,sick,"[0.8,1.0]","[0.0,1.0]",alice_healthy_fact,False,IPL,"Inconsistency occurred. Grounding healthy(Alice) conflicts with grounding sick(Alice). Setting bounds to [0,1] and static=True for this timestep.",,
+0,0,Bob,sick,"[0.0,1.0]","[0.6,0.8]",bob_sick_fact,True,Fact,,,
+0,0,Bob,healthy,"[0.0,1.0]","[0.19999999999999996,0.4]",IPL: sick,True,IPL,,,
+0,0,Carol,healthy,"[0.0,1.0]","[0.9,1.0]",carol_healthy_fact,True,Fact,,,
+0,0,Carol,sick,"[0.0,1.0]","[0.0,0.09999999999999998]",IPL: healthy,True,IPL,,,
+0,0,Bob,tired,"[0.0,1.0]","[0.8,1.0]",bob_tired_fact_1,True,Fact,,,
+0,0,Bob,tired,"[0.8,1.0]","[0.0,1.0]",bob_tired_fact_2,False,Fact,"Inconsistency occurred. Conflicting bounds for tired(Bob). Update from [0.800, 1.000] to [0.000, 0.100] is not allowed. Setting bounds to [0,1] and static=True for this timestep.",,
+0,1,Carol,sick,"[0.0,0.09999999999999998]","[0.0,1.0]",spread_rule,False,Rule,"Inconsistency occurred. Grounding sick(Carol) conflicts with grounding healthy(Carol). Setting bounds to [0,1] and static=True for this timestep.",['Bob'],"[('Bob', 'Carol')]"
+0,1,Carol,healthy,"[0.9,1.0]","[0.0,1.0]",spread_rule,False,IPL,"Inconsistency occurred. Grounding sick(Carol) conflicts with grounding healthy(Carol). Setting bounds to [0,1] and static=True for this timestep.",,
+0,1,Dave,sick,"[0.0,1.0]","[0.5,0.7]",spread_rule,True,Rule,,['Bob'],"[('Bob', 'Dave')]"
+0,1,Dave,healthy,"[0.0,1.0]","[0.30000000000000004,0.5]",IPL: sick,True,IPL,,,