Merge pull request #385 from Jake248Newman/main

SURE - Discovering causal structure

Author: jmafoster1

.gitignore

@@ -67,3 +67,5 @@ temp/
 
 # log files
 *.log
+
+causal_test_results.json

causal_testing/__main__.py

@@ -4,8 +4,12 @@
 import logging
 import os
 import tempfile
+from importlib.metadata import entry_points
 from pathlib import Path
 
+import networkx as nx
+import pandas as pd
+
 from causal_testing.testing.metamorphic_relation import generate_causal_tests
 
 from .main import CausalTestingFramework, CausalTestingPaths, Command, parse_args, setup_logging
@@ -20,74 +24,113 @@ def main() -> None:
 
     # Parse arguments
     args = parse_args()
-
-    if args.command == Command.GENERATE:
-        logging.info("Generating causal tests")
-        generate_causal_tests(
-            args.dag_path,
-            args.output,
-            args.ignore_cycles,
-            args.threads,
-            effect_type=args.effect_type,
-            estimate_type=args.estimate_type,
-            estimator=args.estimator,
-            skip=False,
-        )
-        logging.info("Causal test generation completed successfully")
-        return
-
     # Setup logging
-    setup_logging(args.verbose)
-
-    # Create paths object
-    paths = CausalTestingPaths(
-        dag_path=args.dag_path,
-        data_paths=args.data_paths,
-        test_config_path=args.test_config,
-        output_path=args.output,
-    )
-
-    # Create and setup framework
-    framework = CausalTestingFramework(paths, ignore_cycles=args.ignore_cycles, query=args.query)
-    framework.setup()
-
-    # Load and run tests
-    framework.load_tests()
-
-    if args.batch_size > 0:
-        logging.info(f"Running tests in batches of size {args.batch_size}")
-        with tempfile.TemporaryDirectory() as tmpdir:
-            output_files = []
-            for i, results in enumerate(
-                framework.run_tests_in_batches(
-                    batch_size=args.batch_size,
-                    silent=args.silent,
-                    adequacy=args.adequacy,
-                    bootstrap_size=args.bootstrap_size,
+    setup_logging(args.log_level)
+
+    match args.command:
+        case Command.GENERATE:
+            logging.info("Generating causal tests")
+            generate_causal_tests(
+                args.dag_path,
+                args.output,
+                args.ignore_cycles,
+                args.threads,
+                effect_type=args.effect_type,
+                estimate_type=args.estimate_type,
+                estimator=args.estimator,
+                skip=False,
+            )
+            logging.info("Causal test generation completed successfully.")
+
+        case Command.DISCOVER:
+            discover_map = {ff.name: ff for ff in entry_points(group="discovery")}
+            if args.technique not in discover_map:
+                raise ValueError(
+                    f"Unsupported technique {args.technique}. Supported: {sorted(discover_map)}. "
+                    "If you have implemented a custom technique, you will need to add this to your entrypoints via "
+                    "your pyproject.toml file."
                 )
-            ):
-                temp_file_path = os.path.join(tmpdir, f"output_{i}.json")
-                framework.save_results(results, temp_file_path)
-                output_files.append(temp_file_path)
-                del results
-
-            # Now stitch the results together from the temporary files
-            all_results = []
-            for file_path in output_files:
-                with open(file_path, "r", encoding="utf-8") as f:
-                    all_results.extend(json.load(f))
-
-            output_path = Path(args.output)
-            output_path.parent.mkdir(parents=True, exist_ok=True)
-
-            with open(args.output, "w", encoding="utf-8") as f:
-                json.dump(all_results, f, indent=4)
-    else:
-        logging.info("Running tests in regular mode")
-        results = framework.run_tests(silent=args.silent, adequacy=args.adequacy, bootstrap_size=args.bootstrap_size)
-        framework.save_results(results)
-
-    logging.info("Causal testing completed successfully.")
+            kwargs = {}
+            for argument in args.technique_kwargs:
+                split = argument.split("=")
+                if len(split) != 2:
+                    raise ValueError(f"Malformed argument {argument}. Should be specified as `arg_name=arg_value`")
+                kwargs[split[0]] = split[1]
+
+            logging.info("Discovering causal structure")
+            # Need to reset index to allow for multiple files having the same index (i.e. starting at zero).
+            # Otherwise you end up with duplicate indices, which causes problems further down the line
+            df = pd.concat([pd.read_csv(path) for path in args.data_paths]).reset_index()
+            if args.variables:
+                df = df[args.variables]
+
+            discover_class = discover_map[args.technique].load()
+            discover = discover_class(
+                df=df,
+                exclude_edges=(
+                    list(nx.nx_pydot.read_dot(args.exclude_edges).edges()) if args.exclude_edges is not None else []
+                ),
+                include_edges=(
+                    list(nx.nx_pydot.read_dot(args.include_edges).edges()) if args.include_edges is not None else []
+                ),
+                alpha=args.alpha,
+                **kwargs,
+            )
+            evolved_dag = discover.discover()
+            discover.write_dot(evolved_dag, args.output)
+            logging.info("Causal structure discovery completed successfully.")
+        case Command.TEST:
+            # Create paths object
+            paths = CausalTestingPaths(
+                dag_path=args.dag_path,
+                data_paths=args.data_paths,
+                test_config_path=args.test_config,
+                output_path=args.output,
+            )
+
+            # Create and setup framework
+            framework = CausalTestingFramework(paths, ignore_cycles=args.ignore_cycles, query=args.query)
+            framework.setup()
+
+            # Load and run tests
+            framework.load_tests()
+
+            if args.batch_size > 0:
+                logging.info(f"Running tests in batches of size {args.batch_size}")
+                with tempfile.TemporaryDirectory() as tmpdir:
+                    output_files = []
+                    for i, results in enumerate(
+                        framework.run_tests_in_batches(
+                            batch_size=args.batch_size,
+                            silent=args.silent,
+                            adequacy=args.adequacy,
+                            bootstrap_size=args.bootstrap_size,
+                        )
+                    ):
+                        temp_file_path = os.path.join(tmpdir, f"output_{i}.json")
+                        framework.save_results(results, temp_file_path)
+                        output_files.append(temp_file_path)
+                        del results
+
+                    # Now stitch the results together from the temporary files
+                    all_results = []
+                    for file_path in output_files:
+                        with open(file_path, "r", encoding="utf-8") as f:
+                            all_results.extend(json.load(f))
+
+                    output_path = Path(args.output)
+                    output_path.parent.mkdir(parents=True, exist_ok=True)
+
+                    with open(args.output, "w", encoding="utf-8") as f:
+                        json.dump(all_results, f, indent=4)
+            else:
+                logging.info("Running tests in regular mode")
+                results = framework.run_tests(
+                    silent=args.silent, adequacy=args.adequacy, bootstrap_size=args.bootstrap_size
+                )
+                framework.save_results(results)
+
+            logging.info("Causal testing completed successfully.")
 
 
 if __name__ == "__main__":