agglovar 0.0.1.dev15__tar.gz → 0.0.1.dev17__tar.gz

{agglovar-0.0.1.dev15/src/agglovar.egg-info → agglovar-0.0.1.dev17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: agglovar
-Version: 0.0.1.dev15
+Version: 0.0.1.dev17
 Summary: Toolkit for fast genomic variant transformations and intersects
 License-Expression: MIT
 Requires-Python: >=3.12

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/__init__.py

@@ -1,6 +1,6 @@
 """Agglovar: A toolkit for fast genomic variant transformations and intersects."""
 
-__version__ = '0.0.1.dev15'
+__version__ = '0.0.1.dev17'
 
 __all__ = [
     'align',
@@ -29,3 +29,9 @@ from . import schema
 from . import seqmatch
 from . import vcf
 from . import util
+
+
+# Configure logging
+
+import logging
+logging.getLogger(__name__).addHandler(logging.NullHandler())

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/align/op.py

@@ -42,10 +42,14 @@ __all__ = [
 ]
 
 
-import numpy as np
+import logging
 from types import MappingProxyType
 from typing import Mapping
 
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
 INT_STR_SET: frozenset[str] = frozenset({'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', })
 """Set of valid integer character strings representing operation codes."""
 

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/align/score.py

@@ -12,13 +12,24 @@ __all__ = [
     'get_affine_by_params',
 ]
 
-from abc import ABC, abstractmethod
-import numpy as np
+from abc import (
+    ABC,
+    abstractmethod,
+)
+import logging
 import re
-from typing import Any, Iterable, Self
+from typing import (
+    Any,
+    Iterable,
+    Self,
+)
+
+import numpy as np
 
 from . import op
 
+logger = logging.getLogger(__name__)
+
 AFFINE_SCORE_MATCH = 2.0
 """Default match score."""
 

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/bed/col.py

@@ -7,13 +7,23 @@ __all__ = [
     'standardize',
 ]
 
-from collections.abc import Iterable, Container
+from collections.abc import (
+    Iterable,
+    Container,
+)
 from dataclasses import dataclass
+import logging
 import re
-from typing import Optional, Self, Any
+from typing import (
+    Optional,
+    Self,
+    Any,
+)
 
 import polars as pl
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass(frozen=True)
 class CoordColExpr(Iterable[pl.Expr]):

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/bed/intersect.py

@@ -1,19 +1,31 @@
 """Table intersects."""
 
+import logging
 from pathlib import Path
-from typing import Iterable, Optional
+from typing import (
+    Iterable,
+    Optional,
+)
 
 import polars as pl
 
-from .join import pairwise_join, pairwise_join_iter
+from .col import (
+    CoordCol,
+    get_coord_cols,
+)
+from .join import (
+    pairwise_join,
+    pairwise_join_iter,
+)
 from .merge import merge_depth
-from .col import CoordCol, get_coord_cols
 
 __all__ = [
     'as_bool',
     'as_proportion',
 ]
 
+logger = logging.getLogger(__name__)
+
 
 def as_bool(
         df_a: pl.LazyFrame | pl.DataFrame,

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/bed/join.py

@@ -5,14 +5,25 @@ __all__ = [
     'pairwise_join_iter',
 ]
 
+import logging
 from pathlib import Path
-from typing import Iterable, Iterator, Optional
+from typing import (
+    Iterable,
+    Iterator,
+    Optional,
+)
 
 import polars as pl
 
-from .col import CoordCol, get_coord_cols
 from ..util.lazy import materialize_pair
 
+from .col import (
+    CoordCol,
+    get_coord_cols,
+)
+
+logger = logging.getLogger(__name__)
+
 CHUNK_SIZE: int = 2_500
 """Default size of join chunks. Breaks up tables into batches of this size or less."""
 

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/bed/merge.py

@@ -4,11 +4,21 @@ __all__ = [
     'merge_depth',
 ]
 
-from typing import Optional, Iterable
+import logging
+from typing import (
+    Optional,
+    Iterable,
+)
 
 import polars as pl
 
-from .col import CoordCol, get_coord_cols, make_unique_col
+from .col import (
+    CoordCol,
+    get_coord_cols,
+    make_unique_col,
+)
+
+logger = logging.getLogger(__name__)
 
 
 def merge_depth(

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/dev/imports.py

@@ -11,14 +11,24 @@ __all__ = [
 
 import ast
 from collections.abc import Iterable
-from dataclasses import dataclass, field
+from dataclasses import (
+    dataclass,
+    field,
+)
 from graphlib import TopologicalSorter
 import importlib
 import inspect
+import logging
 import re
 import sys
 from types import ModuleType
-from typing import Any, Generator, Optional
+from typing import (
+    Any,
+    Generator,
+    Optional,
+)
+
+logger = logging.getLogger(__name__)
 
 
 @dataclass(frozen=True)

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/expr/variant.py

@@ -9,10 +9,13 @@ __all__ = [
     'lead_src_expr',
 ]
 
+import logging
 from typing import Optional
 
 import polars as pl
 
+logger = logging.getLogger(__name__)
+
 id_snv_expr = (
     pl.concat_str(
         pl.col('chrom'),

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/fa.py

@@ -6,14 +6,20 @@ __all__ = [
 ]
 
 import hashlib
+import logging
 from pathlib import Path
-from typing import Iterable, Optional
+from typing import (
+    Iterable,
+    Optional,
+)
 
 import Bio.SeqIO
 import polars as pl
 
 from . import io
 
+logger = logging.getLogger(__name__)
+
 
 def read_fai(
         fai_file_name: str | Path,

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/io.py

@@ -4,10 +4,19 @@ __all__ = [
     'PlainOrGzReader',
 ]
 
-from dataclasses import dataclass, field
+from dataclasses import (
+    dataclass,
+    field,
+)
 import gzip
+import logging
 from pathlib import Path
-from typing import Any, Optional
+from typing import (
+    Any,
+    Optional,
+)
+
+logger = logging.getLogger(__name__)
 
 
 @dataclass

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/kmer/plot.py

@@ -5,9 +5,11 @@ __all__ = [
 ]
 
 import collections
-import numpy as np
+import logging
 from typing import Any
 
+import numpy as np
+
 from . import util as kmer_util
 
 # Get type hints for optional matplotlib objects
@@ -22,6 +24,8 @@ try:
 except ImportError:
     pass
 
+logger = logging.getLogger(__name__)
+
 
 def dotplot(
         seq_x: str,

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/kmer/util.py

@@ -12,12 +12,20 @@ __all__ = [
     'stream_index',
 ]
 
+import logging
 import math
 from types import MappingProxyType
-from typing import Self, Optional, Iterator, Mapping
+from typing import (
+    Self,
+    Optional,
+    Iterator,
+    Mapping,
+)
 
 import numpy as np
 
+logger = logging.getLogger(__name__)
+
 # Integer to base
 INT_TO_BASE: list[str] = ['A', 'C', 'G', 'T']
 """Maps 2-bit integer to base string."""

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/merge/base.py

@@ -1,7 +1,4 @@
-"""Base class for callset intersects.
-
-
-"""
+"""Base class for callset intersects."""
 
 __all__ = [
     'CallsetDef',
@@ -9,9 +6,16 @@ __all__ = [
     'CallsetDefInputType',
 ]
 
-from abc import ABC, abstractmethod
-from collections.abc import Container, Iterable
+from abc import (
+    ABC,
+    abstractmethod,
+)
+from collections.abc import (
+    Container,
+    Iterable,
+)
 import json
+import logging
 from pathlib import Path
 from typing import (
     Any,
@@ -25,6 +29,8 @@ import polars as pl
 from ..meta.decorators import lockable
 from ..util.str import collision_rename
 
+logger = logging.getLogger(__name__)
+
 
 class CallsetDef(NamedTuple):
     """Callset definition.
@@ -33,27 +39,31 @@ class CallsetDef(NamedTuple):
     :ivar name: The name of the callset within a collection of callsets.
     :ivar metadata: The metadata of the callset or None if no metadata is provided.
     """
+
     table: pl.LazyFrame
     name: str
     metadata: Optional[str]
 
     def __str__(self) -> str:
+        """Return a string representation of the callset definition."""
         return self.name
 
     def __repr__(self) -> str:
+        """Return a string representation of the callset definition."""
         return f'CallsetDef(table={self.table!r}, name={self.name}, metadata={self.metadata})'
 
+
 CallsetDefInputType: TypeAlias = (
     pl.DataFrame
     | pl.LazyFrame
     | tuple[
         pl.DataFrame | pl.LazyFrame,
     ]
-    | tuple [
+    | tuple[
         pl.DataFrame | pl.LazyFrame,
         Optional[str],
     ]
-    | tuple [
+    | tuple[
         pl.DataFrame | pl.LazyFrame,
         Optional[str],
         Optional[str | dict],
@@ -81,7 +91,6 @@ def _get_definition(
 
     :return: A callset definition.
     """
-
     # Get callset table and name
     callset_name = None
     callset_meta = None
@@ -100,8 +109,8 @@ def _get_definition(
     elif isinstance(callset_def, tuple):
         if len(callset_def) < 1:
             raise ValueError(
-                f'Callset must be a Polars table or an iterable '
-                f'of callset definition elements (table, name, metadata): Received an empty iterable'
+                'Callset must be a Polars table or an iterable '
+                'of callset definition elements (table, name, metadata): Received an empty iterable'
             )
 
         if isinstance(callset_def[0], pl.LazyFrame):
@@ -161,8 +170,10 @@ def _get_definition(
             )
             .cast(pl.String)
             .fill_null(
-                pl.concat_str(pl.lit('var'),
-                pl.col('_mg_src_index')),
+                pl.concat_str(
+                    pl.lit('var'),
+                    pl.col('_mg_src_index')
+                ),
             )
             .alias('id')
         )
@@ -177,8 +188,7 @@ def _get_definition(
         table=callset_table,
         name=callset_name,
         metadata=callset_meta,
-   )
-
+    )
 
 
 @lockable
@@ -244,7 +254,6 @@ class MergeBase(ABC):
         :return: A list of :class:`CallsetDef`, one per input source, in input order.
         """
         name_set = set()
-        callset_table: pl.LazyFrame
 
         callset_tuple_list: list[CallsetDef] = []
 
@@ -290,7 +299,7 @@ def _get_name(
     :returns: A name for this input source.
     """
     if name is None:
-        name = f'source.1'
+        name = 'source.1'
 
     name = collision_rename(str(name), '.', *args)
 

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/merge/config/parser.py

@@ -9,10 +9,13 @@ __all__ = [
     'IntersectConfigParser',
 ]
 
+import logging
+from typing import Any
+
 import ply.lex
 import ply.yacc
 
-from typing import Any
+logger = logging.getLogger(__name__)
 
 
 class IntersectConfigLexer(object):

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/merge/config/stage.py

@@ -19,8 +19,14 @@ __all__ = [
 
 from abc import ABCMeta
 from dataclasses import dataclass
+import logging
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, Optional, Mapping
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Optional,
+    Mapping,
+)
 
 from ...align import score
 from ...seqmatch import MatchScoreModel
@@ -29,6 +35,9 @@ if TYPE_CHECKING:
     from .strategy import IntersectStrategy
 
 
+logger = logging.getLogger(__name__)
+
+
 RESERVED_PARAM_NAMES: frozenset[str] = frozenset({
     'spec_type',
     'arg_list',

{agglovar-0.0.1.dev15 → agglovar-0.0.1.dev17}/src/agglovar/merge/config/strategy.py

@@ -11,11 +11,20 @@ __all__ = [
 # IntersectConfig (full configuration specification)
 #
 
+import logging
 import re
 from typing import Optional
 
 from .parser import IntersectConfigParser
-from .stage import IntersectStage, IntersectStageMatch, IntersectStageRo, IntersectStageDistance, IntersectStageExact
+from .stage import (
+    IntersectStage,
+    IntersectStageMatch,
+    IntersectStageRo,
+    IntersectStageDistance,
+    IntersectStageExact,
+)
+
+logger = logging.getLogger(__name__)
 
 
 class IntersectStrategy(object):