Refactor import behaviour

pyproject.toml

@@ -136,10 +136,9 @@ line-length = 100
 
 [tool.ruff.lint]
 ignore = [
-    "E111",   # indentation-with-invalid-multiple 
-    "E114",   # indentation-with-invalid-multiple-comment 
-    "E117",   # over-indented 
-    "F401",   # unused-import
+    "E111",   # indentation-with-invalid-multiple
+    "E114",   # indentation-with-invalid-multiple-comment
+    "E117",   # over-indented
     "SIM108", # use-ternary-operator
 ]
 select = [
@@ -156,12 +155,14 @@ select = [
 "setup.py" = [
     "E402", # module-import-not-at-top-of-file
 ]
+"src/libsemigroups_pybind11/__init__.py" = ["F403"]
 "src/libsemigroups_pybind11/presentation/examples.py" = [
     "E501", # line-too-long
 ]
 "tests/test_constants.py" = ["SIM"]
 
 [tool.ruff.lint.isort]
+classes                 = ["PBR"]                     # This tells ruff PBR is a class, not a constant
 combine-as-imports      = true
 known-first-party       = ["_libsemigroups_pybind11"]
 split-on-trailing-comma = false

src/libsemigroups_pybind11/__init__.py

@@ -6,32 +6,43 @@
 
 """This package provides the user-facing python part of libsemigroups_pybind11"""
 
-import libsemigroups_pybind11.aho_corasick
-import libsemigroups_pybind11.bipartition
-import libsemigroups_pybind11.blocks
-import libsemigroups_pybind11.bmat8
-import libsemigroups_pybind11.congruence
-import libsemigroups_pybind11.forest
-import libsemigroups_pybind11.froidure_pin
-import libsemigroups_pybind11.hpcombi
-import libsemigroups_pybind11.kambites
-import libsemigroups_pybind11.knuth_bendix
-import libsemigroups_pybind11.matrix
-import libsemigroups_pybind11.paths
-import libsemigroups_pybind11.pbr
-import libsemigroups_pybind11.sims
-import libsemigroups_pybind11.stephen
-import libsemigroups_pybind11.todd_coxeter
-import libsemigroups_pybind11.ukkonen
-import libsemigroups_pybind11.word_graph
-import libsemigroups_pybind11.words
-
-from ._version import version as __version__
+from . import (
+    action,
+    adapters,
+    aho_corasick,
+    bipartition,
+    blocks,
+    bmat8,
+    congruence,
+    forest,
+    froidure_pin,
+    hpcombi,
+    kambites,
+    knuth_bendix,
+    konieczny,
+    matrix,
+    paths,
+    pbr,
+    presentation,
+    schreier_sims,
+    sims,
+    stephen,
+    todd_coxeter,
+    transf,
+    ukkonen,
+    word_graph,
+    words,
+)
+from ._version import __version__
 from .action import Action, LeftAction, RightAction
 from .adapters import ImageLeftAction, ImageRightAction
+from .bipartition import Bipartition
+from .blocks import Blocks
 from .congruence import Congruence
-from .detail.dot import _Dot as Dot
+from .detail.dot import Dot
+from .forest import PathsFromRoots, PathsToRoots
 from .froidure_pin import FroidurePin
+from .hpcombi import LIBSEMIGROUPS_HPCOMBI_ENABLED
 from .is_obviously_infinite import is_obviously_infinite
 from .kambites import Kambites
 from .knuth_bendix import KnuthBendix
@@ -45,7 +56,11 @@
 from .todd_coxeter import ToddCoxeter
 from .transf import Perm, PPerm, Transf
 
-DISCLAIMER = (
+if LIBSEMIGROUPS_HPCOMBI_ENABLED:
+    from .hpcombi import Perm16, PPerm16, PTransf16, Transf16, Vect16
+
+
+_DISCLAIMER = (
     "(You should not see this message unless you are installing libsemigroups_pybind11 from its "
     "sources. If you are not installing from the sources, please raise an issue at "
     "https://github.com/libsemigroups/libsemigroups_pybind11)"
@@ -54,17 +69,12 @@
 try:
     from _libsemigroups_pybind11 import (
         LIBSEMIGROUPS_EIGEN_ENABLED,
-        LIBSEMIGROUPS_HPCOMBI_ENABLED,
         LIMIT_MAX,
         NEGATIVE_INFINITY,
-        PBR,
         POSITIVE_INFINITY,
         UNDEFINED,
         AhoCorasick,
-        Bipartition,
-        Blocks,
         BMat8,
-        Dot,
         Forest,
         Gabow,
         Joiner,
@@ -74,6 +84,7 @@
         NegativeInfinity,
         Order,
         Paths,
+        PBR,
         PositiveInfinity,
         Reporter,
         ReportGuard,
@@ -103,12 +114,120 @@
 except ModuleNotFoundError as e:
     raise ModuleNotFoundError(
         f'{e.msg}, did you forget to run "pip install ." in the libsemigroups_pybind11 '
-        f"directory? {DISCLAIMER}"
+        f"directory? {_DISCLAIMER}"
     ) from e
 
-# The following fools sphinx into thinking that MatrixKind + Matrix are not
-# aliases.
-Matrix.__module__ = __name__
-Matrix.__name__ = "Matrix"
-MatrixKind.__module__ = __name__
-MatrixKind.__name__ = "MatrixKind"
+
+__all__ = [
+    "__version__",
+    # Constants from _libsemigruops_pybind11
+    "LIBSEMIGROUPS_EIGEN_ENABLED",
+    "LIMIT_MAX",
+    "NEGATIVE_INFINITY",
+    "POSITIVE_INFINITY",
+    "UNDEFINED",
+    # Classes from _libsemigroups_pybind11
+    "AhoCorasick",
+    "BMat8",
+    "Forest",
+    "Gabow",
+    "Joiner",
+    "LibsemigroupsError",
+    "LimitMax",
+    "Meeter",
+    "NegativeInfinity",
+    "Order",
+    "Paths",
+    "PBR",
+    "PositiveInfinity",
+    "Reporter",
+    "ReportGuard",
+    "Runner",
+    "SimsStats",
+    "StringRange",
+    "ToString",
+    "ToWord",
+    "Ukkonen",
+    "Undefined",
+    "WordGraph",
+    "WordRange",
+    # Free functions from _libsemigroups_pybind11
+    "congruence_kind",
+    "delta",
+    "error_message_with_prefix",
+    "freeband_equal_to",
+    "lexicographical_compare",
+    "number_of_words",
+    "random_string",
+    "random_strings",
+    "random_word",
+    "recursive_path_compare",
+    "shortlex_compare",
+    "side",
+    "tril",
+    # Submodules
+    "action",
+    "adapters",
+    "aho_corasick",
+    "bipartition",
+    "blocks",
+    "bmat8",
+    "congruence",
+    "forest",
+    "froidure_pin",
+    "hpcombi",
+    "kambites",
+    "knuth_bendix",
+    "konieczny",
+    "matrix",
+    "paths",
+    "pbr",
+    "presentation",
+    "schreier_sims",
+    "sims",
+    "stephen",
+    "todd_coxeter",
+    "transf",
+    "ukkonen",
+    "word_graph",
+    "words",
+    # Classes defined in submodules
+    "Action",
+    "Bipartition",
+    "Blocks",
+    "Congruence",
+    "Dot",
+    "FroidurePin",
+    "ImageLeftAction",
+    "ImageRightAction",
+    "InversePresentation",
+    "Kambites",
+    "KnuthBendix",
+    "Konieczny",
+    "LeftAction",
+    "LIBSEMIGROUPS_HPCOMBI_ENABLED",
+    "Matrix",
+    "MatrixKind",
+    "MinimalRepOrc",
+    "PathsFromRoots",
+    "PathsToRoots",
+    "Perm",
+    "PPerm",
+    "Presentation",
+    "RepOrc",
+    "RightAction",
+    "SchreierSims",
+    "Sims1",
+    "Sims2",
+    "SimsRefinerFaithful",
+    "SimsRefinerIdeals",
+    "Stephen",
+    "ToddCoxeter",
+    "Transf",
+    # Free functions from submodules
+    "to",
+    "is_obviously_infinite",
+]
+
+if LIBSEMIGROUPS_HPCOMBI_ENABLED:
+    __all__ += ["Perm16", "PPerm16", "PTransf16", "Transf16", "Vect16"]

src/libsemigroups_pybind11/action.py

@@ -50,7 +50,6 @@
     to_py as _to_py,
 )
 from .detail.decorators import copydoc as _copydoc
-from .transf import PPerm as _PPerm, Transf as _Transf
 
 ########################################################################
 # Action python class
@@ -267,3 +266,6 @@ def __init__(self: _Self, *args, generators=None, seeds=None) -> None:
         .. include:: ../../_static/runner_non_inherit.rst
         """
         super().__init__(generators=generators, seeds=seeds, side=_side.left, func=_ImageLeftAction)
+
+
+__all__ = ["Action", "LeftAction", "RightAction"]

src/libsemigroups_pybind11/adapters.py

@@ -141,3 +141,6 @@ class ImageLeftAction(_ImageAction):
     @_copydoc(_ImageLeftActionPPerm1PPerm1.__call__)
     def __call__(self: _Self, pt: Point, x: Element) -> Point:
         return _to_py(_to_cxx(self)(_to_cxx(pt), _to_cxx(x)))
+
+
+__all__ = ["ImageLeftAction", "ImageRightAction"]

src/libsemigroups_pybind11/aho_corasick.py

@@ -11,9 +11,11 @@
 as free functions instead.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import (
     aho_corasick_add_word as add_word,
     aho_corasick_dot as dot,
     aho_corasick_rm_word as rm_word,
     aho_corasick_traverse_word as traverse_word,
 )
+
+__all__ = ["add_word", "dot", "rm_word", "traverse_word"]

src/libsemigroups_pybind11/bipartition.py

@@ -8,10 +8,12 @@
 contains helper functions for the :any:`Bipartition` class.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import (
     Bipartition,
     bipartition_one as one,
     bipartition_random as random,
     bipartition_underlying_partition as underlying_partition,
     bipartition_uniform_random as uniform_random,
 )
+
+__all__ = ["Bipartition", "one", "random", "underlying_partition", "uniform_random"]

src/libsemigroups_pybind11/blocks.py

@@ -8,7 +8,6 @@
 contains helper functions for the :any:`Blocks` class.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
-    Blocks,
-    blocks_underlying_partition as underlying_partition,
-)
+from _libsemigroups_pybind11 import Blocks, blocks_underlying_partition as underlying_partition
+
+__all__ = ["Blocks", "underlying_partition"]

src/libsemigroups_pybind11/bmat8.py

@@ -8,7 +8,7 @@
 ``libsemigroups_pybind11.bmat8``.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import (
     bmat8_col_space_basis as col_space_basis,
     bmat8_col_space_size as col_space_size,
     bmat8_is_regular_element as is_regular_element,
@@ -22,3 +22,18 @@
     bmat8_rows as rows,
     bmat8_transpose as transpose,
 )
+
+__all__ = [
+    "col_space_basis",
+    "col_space_size",
+    "is_regular_element",
+    "minimum_dim",
+    "number_of_cols",
+    "number_of_rows",
+    "one",
+    "random",
+    "row_space_basis",
+    "row_space_size",
+    "rows",
+    "transpose",
+]

src/libsemigroups_pybind11/congruence.py

@@ -128,3 +128,5 @@ def has(self: _Self, t: type) -> bool:
 
 partition = _wrap_cxx_free_fn(_congruence_partition)
 non_trivial_classes = _wrap_cxx_free_fn(_congruence_non_trivial_classes)
+
+__all__ = ["Congruence", "partition", "non_trivial_classes"]

src/libsemigroups_pybind11/detail/congruence_common.py

@@ -11,7 +11,6 @@
 from typing_extensions import Self
 
 from _libsemigroups_pybind11 import congruence_kind as _congruence_kind
-from libsemigroups_pybind11.presentation import Presentation as _Presentation
 
 from .cxx_wrapper import CxxWrapper as _CxxWrapper, to_cxx as _to_cxx
 

src/libsemigroups_pybind11/detail/dot.py

@@ -11,7 +11,7 @@
 
 from graphviz import Source as _Source
 
-from _libsemigroups_pybind11 import Dot as _Dot
+from _libsemigroups_pybind11 import Dot
 
 
 def _view(  # pylint: disable=too-many-arguments, too-many-positional-arguments
@@ -39,4 +39,4 @@ def _view(  # pylint: disable=too-many-arguments, too-many-positional-arguments
     s.view()
 
 
-_Dot.view = _view
+Dot.view = _view