generate-permutations cli for window_sizes and aggs

pyproject.toml

@@ -22,7 +22,8 @@ meds-tab-tabularize-static = "MEDS_tabular_automl.scripts.tabularize_static:main
 meds-tab-tabularize-time-series = "MEDS_tabular_automl.scripts.tabularize_time_series:main"
 meds-tab-cache-task = "MEDS_tabular_automl.scripts.cache_task:main"
 meds-tab-xgboost = "MEDS_tabular_automl.scripts.launch_xgboost:main"
-meds-tab-xgboost-sweep = "MEDS_tabular_automl.scripts.sweep_xgboost:main"
+generate-permutations = "MEDS_tabular_automl.scripts.generate_permutations:main"
+
 
 [project.optional-dependencies]
 dev = ["pre-commit"]

src/MEDS_tabular_automl/scripts/generate_permutations.py

@@ -0,0 +1,47 @@
+import sys
+from itertools import combinations
+
+
+def format_print(permutations):
+    """
+    Args:
+        permutations: List of all possible permutations of length > 1
+
+    Example:
+    >>> format_print([('2',), ('2', '3'), ('2', '3', '4'), ('2', '4'), ('3',), ('3', '4'), ('4',)])
+    [2],[2,3],[2,3,4],[2,4],[3],[3,4],[4]
+    """
+    out_str = ""
+    for item in permutations:
+        out_str += f"[{','.join(item)}],"
+    out_str = out_str[:-1]
+    print(out_str)
+
+
+def get_permutations(list_of_options):
+    """Generate all possible permutations of a list of options passed as an arg.
+
+    Args:
+    - list_of_options (list): List of options.
+
+    Returns:
+    - list: List of all possible permutations of length > 1
+
+    Example:
+    >>> get_permutations(['2', '3', '4'])
+    [2],[2,3],[2,3,4],[2,4],[3],[3,4],[4]
+    """
+    permutations = []
+    for i in range(1, len(list_of_options) + 1):
+        permutations.extend(list(combinations(list_of_options, r=i)))
+    format_print(sorted(permutations))
+
+
+def main():
+    """Generate all possible permutations of a list of options."""
+    list_of_options = list(sys.argv[1].strip("[]").split(","))
+    get_permutations(list_of_options)
+
+
+if __name__ == "__main__":
+    main()

tests/test_integration.py

@@ -206,7 +206,6 @@ def test_integration():
                 f"Time-Series Data matrix Should have {expected_num_rows}"
                 f" rows but has {ts_matrix.shape[0]}!"
             )
-
         # Step 4: Run the task_specific_caching script
         cache_config = {
             "MEDS_cohort_dir": str(MEDS_cohort_dir.resolve()),
@@ -216,7 +215,7 @@ def test_integration():
             "tqdm": False,
             "loguru_init": True,
             "tabularization.min_code_inclusion_frequency": 1,
-            "tabularization.aggs": "[static/present,static/first,code/count,value/sum]",
+            # "tabularization.aggs": "[static/present,static/first,code/count,value/sum]",
             "tabularization.window_sizes": "[30d,365d,full]",
         }
         with initialize(
@@ -241,50 +240,19 @@ def test_integration():
             out_f.parent.mkdir(parents=True, exist_ok=True)
             df.write_parquet(out_f)
 
-        stderr, stdout = run_command(
-            "meds-tab-cache-task",
-            [],
-            cache_config,
-            "task_specific_caching",
+        stderr, stdout_ws = run_command(
+            "generate-permutations", ["[30d]"], {}, "generate-permutations window_sizes"
         )
-        # Check the files are not empty
-
-        # Step 5: Run the xgboost script
-
-        xgboost_config_kwargs = {
-            "MEDS_cohort_dir": str(MEDS_cohort_dir.resolve()),
-            "do_overwrite": False,
-            "seed": 1,
-            "hydra.verbose": True,
-            "tqdm": False,
-            "loguru_init": True,
-            "tabularization.min_code_inclusion_frequency": 1,
-            "tabularization.aggs": "[static/present,static/first,code/count,value/sum]",
-            "tabularization.window_sizes": "[30d,365d,full]",
-        }
-        with initialize(
-            version_base=None, config_path="../src/MEDS_tabular_automl/configs/"
-        ):  # path to config.yaml
-            overrides = [f"{k}={v}" for k, v in xgboost_config_kwargs.items()]
-            cfg = compose(config_name="launch_xgboost", overrides=overrides)  # config.yaml
-        stderr, stdout = run_command(
-            "meds-tab-xgboost",
-            [],
-            xgboost_config_kwargs,
-            "xgboost",
+        stderr, stdout_agg = run_command(
+            "generate-permutations", ["[static/present,static/first]"], {}, "generate-permutations aggs"
         )
-        output_files = list(Path(cfg.output_dir).parent.glob("**/*.json"))
-        assert len(output_files) == 1
-        # assert output_files[0].stem == '0.6667_model'
 
         stderr, stdout = run_command(
-            "meds-tab-xgboost",
+            "meds-tab-cache-task",
             [
                 "--multirun",
+                f"tabularization.aggs={stdout_agg.strip()}",
             ],
-            xgboost_config_kwargs,
-            "xgboost-sweep",
+            cache_config,
+            "task_specific_caching",
         )
-        output_files = list(Path(cfg.output_dir).parent.glob("**/*.json"))
-        assert len(output_files) == 11
-        # assert output_files[0].stem == "model"

tests/test_tabularize.py

@@ -3,7 +3,7 @@
 root = rootutils.setup_root(__file__, dotenv=True, pythonpath=True, cwd=True)
 
 import json
-import os
+import subprocess
 import tempfile
 from io import StringIO
 from pathlib import Path
@@ -391,3 +391,41 @@ def test_tabularize():
         launch_xgboost.main(cfg)
         output_files = list(Path(cfg.output_dir).glob("**/*.json"))
         assert len(output_files) == 1
+
+
+def run_command(script: str, args: list[str], hydra_kwargs: dict[str, str], test_name: str):
+    command_parts = [script] + args + [f"{k}={v}" for k, v in hydra_kwargs.items()]
+    command_out = subprocess.run(" ".join(command_parts), shell=True, capture_output=True)
+    stderr = command_out.stderr.decode()
+    stdout = command_out.stdout.decode()
+    if command_out.returncode != 0:
+        raise AssertionError(f"{test_name} failed!\nstdout:\n{stdout}\nstderr:\n{stderr}")
+    return stderr, stdout
+
+
+def test_xgboost_config():
+    MEDS_cohort_dir = "blah"
+    stderr, stdout_ws = run_command(
+        "generate-permutations", ["[30d]"], {}, "generate-permutations window_sizes"
+    )
+    stderr, stdout_agg = run_command(
+        "generate-permutations", ["[static/present]"], {}, "generate-permutations aggs"
+    )
+    xgboost_config_kwargs = {
+        "MEDS_cohort_dir": MEDS_cohort_dir,
+        "do_overwrite": False,
+        "seed": 1,
+        "hydra.verbose": True,
+        "tqdm": False,
+        "loguru_init": True,
+        "tabularization.min_code_inclusion_frequency": 1,
+        "tabularization.window_sizes": f"{stdout_ws.strip()}",
+    }
+
+    with initialize(
+        version_base=None, config_path="../src/MEDS_tabular_automl/configs/"
+    ):  # path to config.yaml
+        overrides = [f"{k}={v}" for k, v in xgboost_config_kwargs.items()]
+        cfg = compose(config_name="launch_xgboost", overrides=overrides)  # config.yaml
+    print(cfg.tabularization.window_sizes)
+    assert cfg.tabularization.window_sizes