Removing redundant test summaries, cleanup de tests (#102)

src/grinch/__init__.py

@@ -15,13 +15,6 @@
 from .aliases import ADK, OBS, OBSM, OBSP, UNS, VAR, VARM, VARP, AnnDataKeys
 from .cond_filter import Filter, StackedFilter
 from .conf import BaseConfigurable
-from .de_test_summary import (
-    BimodalTestSummary,
-    DETestSummary,
-    KSTestSummary,
-    PvalTestSummary,
-    TestSummary,
-)
 from .filters import FilterCells, FilterGenes, VarianceFilter
 from .main import instantiate_config
 from .normalizers import Combat, Log1P, NormalizeTotal, Scale
@@ -42,17 +35,12 @@
     'UNS',
     'AnnDataKeys',
     'BaseConfigurable',
-    'BimodalTestSummary',
     'GRPipeline',
     'FilterCells',
     'FilterGenes',
     'VarianceFilter',
     'Report',
     'Reporter',
-    'DETestSummary',
-    'TestSummary',
-    'PvalTestSummary',
-    'KSTestSummary',
     'Filter',
     'StackedFilter',
     'Combat',

src/grinch/aliases.py

@@ -87,6 +87,4 @@ class VARP:
 VARP = AnnDataKeys.VARP
 UNS = AnnDataKeys.UNS
 
-ALLOWED_KEYS = ['obs', 'obsm', 'uns', 'var', 'varm', 'layers', 'obsp', 'varp']
-
 GROUP_SEP = '.'

src/grinch/custom_types.py

@@ -1,9 +1,8 @@
-import inspect
-from operator import attrgetter
 from typing import Annotated, Any, Dict, List, Tuple, TypeAlias
 
 import numpy as np
 import numpy.typing as npt
+import scipy.sparse as sp
 from pydantic import Field
 
 REP_KEY: TypeAlias = str | List[str] | Dict[str, str] | None
@@ -22,41 +21,6 @@
 NP_int = npt.NDArray[np.int_]
 NP_float = npt.NDArray[np.float_]
 
-PercentFraction = Annotated[float, Field(ge=0, le=1)]
-
-
-def optional_staticmethod(klas: str, special_args: Dict[str, str]):
-    """Marks a method as optionally static. If the method is called from an
-    instance of the class, will assume it is not static and will parse any
-    self.keys specified in args. Otherwise will set each to None, and call
-    the method as a staticmethod. This is useful when static behavior is
-    desired if these optional arguments are not always needed.
+NP_SP = np.ndarray | sp.spmatrix
 
-    This mainly exists because of group_label for group processing where
-    optionally we may need to pass group labels. Instead of modifying the
-    set_repr function call for evey derived class, we check if the method
-    was called from an instance of a class and pass group_label through
-    this decorator. This is nice because the derived classes can remain
-    ignorant of any group processing details.
-
-    Parameters
-    __________
-    klas: str
-        This should point to the class name of the object.
-    args: dict
-        Maps a key (member of klas) to a function parameter. These can have
-        multiple dots in the representation. E.g., 'foo.bar.eggs.spam' will
-        try to access self.foo.bar.eggs.spam
-    """
-    def _decorator(f):
-        def _wrapper(*args, **kwargs):
-            bases = inspect.getmro(args[0].__class__)
-            base_qualnames = [base.__qualname__ for base in bases]
-            if len(args) > 0 and klas in base_qualnames:
-                # Assume that this was called from a class instance.
-                for k, v in special_args.items():
-                    kwargs[v] = attrgetter(k)(args[0])
-                args = args[1:]
-            return f(*args, **kwargs)
-        return _wrapper
-    return _decorator
+PercentFraction = Annotated[float, Field(ge=0, le=1)]