kasm-pkg 0.1.0__py3-none-any.whl

kasm/__init__.py

@@ -0,0 +1,70 @@
+"""kasm — kernel allelic series model."""
+
+from kasm import covar
+from kasm._logging import configure_logging, logger
+from kasm.api import (
+    RandomFit,
+    combine_mixed_effects,
+    combine_random_hsq,
+    fit_fixed_effects,
+    fit_random_effects,
+)
+from kasm.covar import (
+    CovarResult,
+    compute_random_covar,
+)
+from kasm.dataset import (
+    Dataset,
+    parse_variant_ids,
+    sort_variant_df,
+)
+from kasm.enrichment import EnrichResult, pool_enrichment
+from kasm.fixed_effects import FixedFit
+from kasm.fitting import jackknife_se
+from kasm.kernels import KernelId, KernelLayout, KernelOptions
+from kasm.ldm import LDM, LDMLoader
+from kasm.model import Model
+from kasm.simulation import (
+    simulate_burden_effects,
+    simulate_sumstats,
+)
+from kasm.suffstats import (
+    ExtraEnrichCols,
+    ExtSuffStats,
+    JKSuffStats,
+    SuffStats,
+    compute_jk_suffstats,
+)
+
+__all__ = [
+    "LDM",
+    "CovarResult",
+    "Dataset",
+    "EnrichResult",
+    "ExtSuffStats",
+    "ExtraEnrichCols",
+    "FixedFit",
+    "JKSuffStats",
+    "KernelId",
+    "KernelLayout",
+    "KernelOptions",
+    "LDMLoader",
+    "Model",
+    "RandomFit",
+    "SuffStats",
+    "combine_mixed_effects",
+    "combine_random_hsq",
+    "covar",
+    "configure_logging",
+    "compute_jk_suffstats",
+    "compute_random_covar",
+    "fit_fixed_effects",
+    "fit_random_effects",
+    "jackknife_se",
+    "logger",
+    "parse_variant_ids",
+    "pool_enrichment",
+    "simulate_burden_effects",
+    "simulate_sumstats",
+    "sort_variant_df",
+]

kasm/_logging.py

@@ -0,0 +1,42 @@
+"""Logging configuration for kasm workflows."""
+
+from __future__ import annotations
+
+import logging
+from pathlib import Path
+
+logger = logging.getLogger("kasm")
+
+
+def configure_logging(
+    level: int | str = "INFO", *, filename: str | Path | None = None
+) -> None:
+    """Configure console logging, and optionally file logging, for ``kasm.*``.
+
+    Only handlers previously installed by this function are replaced. This
+    leaves application-owned handlers and the root logger untouched.
+    """
+    resolved_level = (
+        logging._nameToLevel.get(level.upper()) if isinstance(level, str) else level
+    )
+    if not isinstance(resolved_level, int):
+        raise ValueError(f"unknown logging level {level!r}")
+    formatter = logging.Formatter(
+        "%(asctime)s %(module)s %(levelname)s %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    for handler in tuple(logger.handlers):
+        if getattr(handler, "_kasm_managed", False):
+            logger.removeHandler(handler)
+            handler.close()
+    handlers: list[logging.Handler] = [logging.StreamHandler()]
+    if filename is not None:
+        path = Path(filename)
+        path.parent.mkdir(parents=True, exist_ok=True)
+        handlers.append(logging.FileHandler(path, mode="a"))
+    for handler in handlers:
+        handler.setFormatter(formatter)
+        handler._kasm_managed = True
+        logger.addHandler(handler)
+    logger.setLevel(resolved_level)
+    logger.propagate = False