smftools 0.2.4__py3-none-any.whl → 0.3.0__py3-none-any.whl

smftools/__init__.py

@@ -1,22 +1,52 @@
 """smftools"""
 
+from __future__ import annotations
+
 import logging
 import warnings
-
-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 import import_module
 from importlib.metadata import version
+from typing import TYPE_CHECKING
+
+from .readwrite import adata_to_df, safe_read_h5ad, safe_write_h5ad
 
 package_name = "smftools"
 __version__ = version(package_name)
 
+if TYPE_CHECKING:
+    from smftools import (
+        cli,
+        config,
+        datasets,
+        hmm,
+        informatics,
+        machine_learning,
+        plotting,
+        preprocessing,
+        tools,
+    )
+
+_LAZY_MODULES = {
+    "cli": "smftools.cli",
+    "config": "smftools.config",
+    "datasets": "smftools.datasets",
+    "hmm": "smftools.hmm",
+    "inform": "smftools.informatics",
+    "ml": "smftools.machine_learning",
+    "pl": "smftools.plotting",
+    "pp": "smftools.preprocessing",
+    "tl": "smftools.tools",
+}
+
+
+def __getattr__(name: str):
+    if name in _LAZY_MODULES:
+        module = import_module(_LAZY_MODULES[name])
+        globals()[name] = module
+        return module
+    raise AttributeError(f"module '{__name__}' has no attribute '{name}'")
+
+
 __all__ = [
     "adata_to_df",
     "inform",
@@ -24,7 +54,7 @@ __all__ = [
     "pp",
     "tl",
     "pl",
-    "datasets"
+    "datasets",
     "safe_write_h5ad",
-    "safe_read_h5ad"
-]
+    "safe_read_h5ad",
+]

smftools/_settings.py

@@ -1,20 +1,20 @@
+from __future__ import annotations
+
 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 +1,3 @@
-__version__ = "0.2.4"
+from __future__ import annotations
+
+__version__ = "0.3.0"

smftools/cli/__init__.py

@@ -0,0 +1 @@
+from __future__ import annotations

smftools/cli/archived/cli_flows.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 def flow_I(config_path):
     """
     High-level function to call for converting raw sequencing data to an adata object. 

smftools/cli/helpers.py

@@ -1,8 +1,14 @@
+from __future__ import annotations
+
 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
@@ -41,8 +47,10 @@ def get_adata_paths(cfg) -> AdataPaths:
         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)
-    return path
+    write_runtime_schema_yaml(adata, path, step_name="runtime")
+    return path