Perturbation map build cli

docs/command_line.rst

@@ -133,28 +133,17 @@ Key Features:
    :path: pooled-sbs
 
 
-scallops norm-features
-=======================
+scallops pert-map
+===================
 
-The `scallops norm-features` command is used to normalize features.
+The `scallops pert-map` command provides functionality for perturbation map building.
 
 .. argparse::
    :module: scallops.__main__
    :func: create_parsers
    :prog: scallops
-   :path: rank-features
-
-
-scallops rank-features
-=======================
-
-The `scallops rank-features` command is used to compute significance from the output of `scallops norm-features`.
+   :path: pert-map
 
-.. argparse::
-   :module: scallops.__main__
-   :func: create_parsers
-   :prog: scallops
-   :path: rank-features
 
 
 scallops registration

pyproject.toml

@@ -32,7 +32,7 @@ classifiers = [
 
 dependencies = [
     "adjustText",
-    "anndata>=0.12.4", # https://github.com/scverse/anndata/issues/2166
+    "anndata>=0.13.0",
     "bioio>=3",
     "bioio-nd2",
     "bioio-ome-tiff",

scallops/__init__.py

@@ -1,7 +1,13 @@
 import warnings
 
+import anndata
+
+from scallops.zarr_io import write_basic_dask_dask_dense  # noqa: F401
+
 from .experiment.elements import Experiment  # noqa: F401
 
 warnings.filterwarnings(
-    "ignore", message="unclosed.*", category=ResourceWarning, module="aiohttp"
+    "ignore",
+    message="Unclosed client.* | client_session.*",
 )
+anndata.settings.auto_shard_zarr_v3 = False

scallops/__main__.py

@@ -41,9 +41,8 @@
     features_main,
     find_objects_main,
     illumination_correction_main,
-    norm_features_main,
+    pert_map_main,
     pooled_if_sbs_main,
-    rank_features_main,
     register_main,
     segment_main,
     stitch_main,
@@ -67,8 +66,7 @@ def create_parsers(default_help: bool = False) -> argparse.ArgumentParser:
     segment_main._create_parser(subparsers, default_help)
     illumination_correction_main._create_parser(subparsers, default_help)
     dialout_main._create_parser(subparsers, default_help)
-    norm_features_main._create_parser(subparsers, default_help)
-    rank_features_main._create_parser(subparsers, default_help)
+    pert_map_main._create_parser(subparsers, default_help)
     register_main._create_parser(subparsers, default_help)
     stitch_main._create_stitch_parser(subparsers, default_help)
     stitch_main._create_stitch_preview_parser(subparsers, default_help)

scallops/cli/features.py

@@ -49,7 +49,7 @@
     _to_parquet,
     is_parquet_file,
     pluralize,
-    read_anndata_zarr,
+    read_anndata,
 )
 
 logger = _get_cli_logger()
@@ -79,7 +79,7 @@ def _read_merged_or_objects(
 
     area_column = f"{_label_name_to_prefix[label_name]}_AreaShape_Area"
     if merge_path.lower().endswith(".zarr"):
-        data = read_anndata_zarr(merge_path, dask=True)
+        data = read_anndata(merge_path, dask=True)
         merged_df = data.obs
         columns = {area_column}
         assert area_column in data.var.index