Fix Pyflakes F403 errors

lib/bx/align/sitemask/__init__.py

@@ -3,4 +3,9 @@
 example masking CpG sites or sites with low sequence quality.
 """
 
-from bx.align.sitemask.core import *  # noqa: F40
+from bx.align.sitemask.core import (
+    Masker,
+    MaskPipeline,
+)
+
+__all__ = ["Masker", "MaskPipeline"]

lib/bx/align/sitemask/core.py

@@ -43,5 +43,5 @@ def __call__(self, block):
             try:
                 masker.__call__
             except AttributeError:
-                raise Exception('Masker in pipeline does not implement "filter( self, block )".')
+                raise Exception('Masker in pipeline does not implement "filter(self, block)".')
             masker(block)

lib/bx/align/tools/__init__.py

@@ -2,7 +2,24 @@
 Various utilities for working with `bx.align.Alignment` objects.
 """
 
-from .chop import *  # noqa: F40
-from .fuse import *  # noqa: F40
-from .thread import *  # noqa: F40
-from .tile import *  # noqa: F40
+from .chop import chop_list
+from .fuse import (
+    fuse,
+    fuse_list,
+    FusingAlignmentWriter,
+)
+from .thread import get_components_for_species
+from .tile import (
+    intervals_from_mask,
+    tile_interval,
+)
+
+__all__ = [
+    "chop_list",
+    "fuse",
+    "fuse_list",
+    "FusingAlignmentWriter",
+    "get_components_for_species",
+    "intervals_from_mask",
+    "tile_interval",
+]

lib/bx/intervals/__init__.py

@@ -4,4 +4,11 @@
 """
 
 # For compatiblity with existing stuff
-from bx.intervals.intersection import *  # noqa: F40
+from bx.intervals.intersection import (
+    Intersecter,
+    Interval,
+    IntervalNode,
+    IntervalTree,
+)
+
+__all__ = ["Intersecter", "Interval", "IntervalNode", "IntervalTree"]

lib/bx/seq/__init__.py

@@ -4,4 +4,12 @@
 formats.
 """
 
-from bx.seq.core import *  # noqa: F40
+from bx.seq.core import (
+    infer_format,
+    reverse_complement,
+    seq_file,
+    seq_reader,
+    seq_writer,
+)
+
+__all__ = ["infer_format", "reverse_complement", "seq_file", "seq_reader", "seq_writer"]

pyproject.toml

@@ -83,7 +83,7 @@ target-version = "py38"
 # flake8-comprehensions (C4), flake8-logging-format (G),
 # flake8-implicit-str-concat (ISC) and pyupgrade (UP)
 #select = ["E", "F", "B", "C4", "G", "ISC", "NPY", "UP"]
-select = ["E", "ISC"]
+select = ["E", "F", "ISC"]
 # Exceptions:
 # B9 flake8-bugbear opinionated warnings
 # E501 is line length (delegated to black)