add impute CLI command, complete DA storage args

New `kompot impute` subcommand for single-condition GP smoothing
with all the same options as the Python API (groupby, condition,
genes, sample_col, empirical variance, etc.). Includes YAML config
template.

DA CLI now exposes --store-arrays-on-disk, --disk-storage-dir, and
--max-memory-ratio to match the DE CLI's StorageSettings coverage.

Author: katosh

CHANGELOG.md

@@ -38,7 +38,9 @@ All notable changes to this project will be documented in this file.
  - Consistent parameter naming across plot functions: `background_color_key` → `color`, `de_column` → `direction_column`, `embedding_key` → `basis`.
  - `RunInfo` HTML display now shows parameters hierarchically by Settings group (`gp.sigma`, `fdr.threshold`, …) instead of a flat list.
  - `RunComparison` shows individual changed fields (e.g. `gp.ls_factor: 10.0 → 5.0`) instead of opaque dict diffs.
+ - **`kompot impute` CLI command** for single-condition GP smoothing from the command line, matching the full Python API (condition selection, gene subsetting, empirical variance, sample variance).
  - `--no-progress` flag added to the DA CLI; progress bars can now be fully suppressed in both DA and DE.
+ - DA CLI now exposes `--store-arrays-on-disk`, `--disk-storage-dir`, and `--max-memory-ratio`, matching the DE CLI's StorageSettings coverage.
  - FDR is disabled by default when `sample_col` is provided (not yet calibrated for sample variance). Override with `FDRSettings(null_genes=...)`.
  - Remove `statsmodels` dependency.
 

kompot/cli/da.py

@@ -130,6 +130,25 @@ def add_da_parser(subparsers) -> argparse.ArgumentParser:
         help="Random seed for reproducible landmark selection (default: None)",
     )
 
+    # Memory management
+    parser.add_argument(
+        "--store-arrays-on-disk",
+        action="store_true",
+        help="Store large intermediate arrays on disk instead of RAM",
+    )
+
+    parser.add_argument(
+        "--disk-storage-dir",
+        type=str,
+        help="Directory for disk-backed arrays (default: system temp)",
+    )
+
+    parser.add_argument(
+        "--max-memory-ratio",
+        type=float,
+        help="Fraction of RAM before triggering disk storage (default: 0.8)",
+    )
+
     # Boolean flags
     parser.add_argument(
         "--store-landmarks",
@@ -291,7 +310,14 @@ def run_da(args):
         threshold_kwargs["ptp_threshold"] = params.pop("ptp_threshold")
     threshold = DAThresholdSettings(**threshold_kwargs) if threshold_kwargs else None
 
-    storage_keys = {"result_key", "overwrite", "store_landmarks"}
+    storage_keys = {
+        "result_key",
+        "overwrite",
+        "store_landmarks",
+        "store_arrays_on_disk",
+        "disk_storage_dir",
+        "max_memory_ratio",
+    }
     storage_kwargs = {k: params.pop(k) for k in list(params) if k in storage_keys}
     storage = StorageSettings(**storage_kwargs) if storage_kwargs else None