smftools 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

smftools/__init__.py

@@ -2,17 +2,15 @@
 
 import logging
 import warnings
+from importlib.metadata import version
 
+from . import cli, config, datasets, hmm
 from . import informatics as inform
 from . import machine_learning as ml
 from . import plotting as pl
 from . import preprocessing as pp
 from . import tools as tl
-
-from . import cli, config, datasets, hmm
-from .readwrite import adata_to_df, safe_write_h5ad, safe_read_h5ad, merge_barcoded_anndatas_core
-
-from importlib.metadata import version
+from .readwrite import adata_to_df, merge_barcoded_anndatas_core, safe_read_h5ad, safe_write_h5ad
 
 package_name = "smftools"
 __version__ = version(package_name)
@@ -24,7 +22,7 @@ __all__ = [
     "pp",
     "tl",
     "pl",
-    "datasets"
+    "datasets",
     "safe_write_h5ad",
-    "safe_read_h5ad"
-]
+    "safe_read_h5ad",
+]

smftools/_settings.py

@@ -1,20 +1,18 @@
 from pathlib import Path
 from typing import Union
 
+
 class SMFConfig:
     """\
     Config for smftools.
     """
 
-    def __init__(
-        self,
-        *,
-        datasetdir: Union[Path, str] = "./datasets/"
-    ):
+    def __init__(self, *, datasetdir: Union[Path, str] = "./datasets/"):
         self._datasetdir = Path(datasetdir) if isinstance(datasetdir, str) else datasetdir
 
     @property
     def datasetdir(self) -> Path:
         return self._datasetdir
 
-settings = SMFConfig()
+
+settings = SMFConfig()

smftools/_version.py

@@ -1 +1 @@
-__version__ = "0.2.3"
+__version__ = "0.2.5"

smftools/cli/helpers.py

@@ -0,0 +1,54 @@
+from dataclasses import dataclass
+from pathlib import Path
+
+import anndata as ad
+
+from ..metadata import write_runtime_schema_yaml
+from ..readwrite import safe_write_h5ad
+
+
+@dataclass
+class AdataPaths:
+    raw: Path
+    pp: Path
+    pp_dedup: Path
+    spatial: Path
+    hmm: Path
+
+
+def get_adata_paths(cfg) -> AdataPaths:
+    """
+    Central helper: given cfg, compute all standard AnnData paths.
+    """
+    h5_dir = Path(cfg.output_directory) / "h5ads"
+
+    raw = h5_dir / f"{cfg.experiment_name}.h5ad.gz"
+
+    pp = h5_dir / f"{cfg.experiment_name}_preprocessed.h5ad.gz"
+
+    if cfg.smf_modality == "direct":
+        # direct SMF: duplicate-removed path is just preprocessed path
+        pp_dedup = pp
+    else:
+        pp_dedup = h5_dir / f"{cfg.experiment_name}_preprocessed_duplicates_removed.h5ad.gz"
+
+    pp_dedup_base = pp_dedup.name.removesuffix(".h5ad.gz")
+
+    spatial = h5_dir / f"{pp_dedup_base}_spatial.h5ad.gz"
+    hmm = h5_dir / f"{pp_dedup_base}_spatial_hmm.h5ad.gz"
+
+    return AdataPaths(
+        raw=raw,
+        pp=pp,
+        pp_dedup=pp_dedup,
+        spatial=spatial,
+        hmm=hmm,
+    )
+
+
+def write_gz_h5ad(adata: ad.AnnData, path: Path) -> Path:
+    if path.suffix != ".gz":
+        path = path.with_name(path.name + ".gz")
+    safe_write_h5ad(adata, path, compression="gzip", backup=True)
+    write_runtime_schema_yaml(adata, path, step_name="runtime")
+    return path