diff --git a/pyproject.toml b/pyproject.toml
index d68f317f..f25aba8f 100644
--- a/pyproject.toml
+++ b/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
diff --git a/src/libsemigroups_pybind11/__init__.py b/src/libsemigroups_pybind11/__init__.py
index 25bd333f..132396e2 100644
--- a/src/libsemigroups_pybind11/__init__.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/action.py b/src/libsemigroups_pybind11/action.py
index 4287daa5..238d5359 100644
--- a/src/libsemigroups_pybind11/action.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/adapters.py b/src/libsemigroups_pybind11/adapters.py
index fe094c1e..203b8d24 100644
--- a/src/libsemigroups_pybind11/adapters.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/aho_corasick.py b/src/libsemigroups_pybind11/aho_corasick.py
index 3a932b7b..906ac6da 100644
--- a/src/libsemigroups_pybind11/aho_corasick.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/bipartition.py b/src/libsemigroups_pybind11/bipartition.py
index c66b10a9..9aa2ee40 100644
--- a/src/libsemigroups_pybind11/bipartition.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/blocks.py b/src/libsemigroups_pybind11/blocks.py
index f4342d48..b065fa1f 100644
--- a/src/libsemigroups_pybind11/blocks.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/bmat8.py b/src/libsemigroups_pybind11/bmat8.py
index 782270a9..9cc82e77 100644
--- a/src/libsemigroups_pybind11/bmat8.py
+++ b/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",
+]
diff --git a/src/libsemigroups_pybind11/congruence.py b/src/libsemigroups_pybind11/congruence.py
index d2d66bc0..d9300f58 100644
--- a/src/libsemigroups_pybind11/congruence.py
+++ b/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"]
diff --git a/src/libsemigroups_pybind11/detail/congruence_common.py b/src/libsemigroups_pybind11/detail/congruence_common.py
index 0db45479..20213262 100644
--- a/src/libsemigroups_pybind11/detail/congruence_common.py
+++ b/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
 
diff --git a/src/libsemigroups_pybind11/detail/dot.py b/src/libsemigroups_pybind11/detail/dot.py
index e584805a..a763a9f0 100644
--- a/src/libsemigroups_pybind11/detail/dot.py
+++ b/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
diff --git a/src/libsemigroups_pybind11/forest.py b/src/libsemigroups_pybind11/forest.py
index e77b8b8a..e12d7ecc 100644
--- a/src/libsemigroups_pybind11/forest.py
+++ b/src/libsemigroups_pybind11/forest.py
@@ -9,9 +9,7 @@
 contained in the submodule ``forest``.
 """
 
-from typing_extensions import Self as _Self
-
-from _libsemigroups_pybind11 import (  # pylint: disable= unused-import
+from _libsemigroups_pybind11 import (
     forest_depth as depth,
     forest_dot as dot,
     forest_is_root as is_root,
@@ -23,8 +21,19 @@
 )
 
 # The following fools sphinx into thinking that PathsToRoots is not an
-# aliases.
+# alias.
 PathsFromRoots.__module__ = __name__
 PathsFromRoots.__name__ = "PathsFromRoots"
 PathsToRoots.__module__ = __name__
 PathsToRoots.__name__ = "PathsToRoots"
+
+__all__ = [
+    "PathsFromRoots",
+    "PathsToRoots",
+    "depth",
+    "dot",
+    "is_root",
+    "max_label",
+    "path_from_root",
+    "path_to_root",
+]
diff --git a/src/libsemigroups_pybind11/froidure_pin.py b/src/libsemigroups_pybind11/froidure_pin.py
index b77740ba..dd88ba11 100644
--- a/src/libsemigroups_pybind11/froidure_pin.py
+++ b/src/libsemigroups_pybind11/froidure_pin.py
@@ -19,7 +19,6 @@
 
 from _libsemigroups_pybind11 import (
     LIBSEMIGROUPS_HPCOMBI_ENABLED as _LIBSEMIGROUPS_HPCOMBI_ENABLED,
-    PBR as _PBR,
     Bipartition as _Bipartition,
     BMat as _BMat,
     BMat8 as _BMat8,
@@ -61,6 +60,7 @@
     MinPlusMat as _MinPlusMat,
     MinPlusTruncMat as _MinPlusTruncMat,
     NTPMat as _NTPMat,
+    PBR as _PBR,
     Perm1 as _Perm1,
     Perm2 as _Perm2,
     Perm4 as _Perm4,
@@ -273,3 +273,19 @@ def sorted_elements(  # pylint: disable=missing-function-docstring
 product_by_reduction = _wrap_cxx_free_fn(_froidure_pin_product_by_reduction)
 rules = _wrap_cxx_free_fn(_froidure_pin_rules)
 to_element = _wrap_cxx_free_fn(_froidure_pin_to_element)
+
+__all__ = [
+    "FroidurePin",
+    "current_minimal_factorisation",
+    "current_normal_forms",
+    "current_position",
+    "current_rules",
+    "equal_to",
+    "factorisation",
+    "minimal_factorisation",
+    "normal_forms",
+    "position",
+    "product_by_reduction",
+    "rules",
+    "to_element",
+]
diff --git a/src/libsemigroups_pybind11/hpcombi.py b/src/libsemigroups_pybind11/hpcombi.py
index 990d18b5..8793ad9c 100644
--- a/src/libsemigroups_pybind11/hpcombi.py
+++ b/src/libsemigroups_pybind11/hpcombi.py
@@ -10,6 +10,8 @@
 
 from _libsemigroups_pybind11 import LIBSEMIGROUPS_HPCOMBI_ENABLED
 
+__all__ = ["LIBSEMIGROUPS_HPCOMBI_ENABLED"]
+
 if LIBSEMIGROUPS_HPCOMBI_ENABLED:
     from _libsemigroups_pybind11 import (  # pylint: disable=no-name-in-module
         hpcombi_Perm16 as Perm16,
@@ -32,3 +34,5 @@
     Transf16.__name__ = "Transf16"
     Vect16.__module__ = __name__
     Vect16.__name__ = "Vect16"
+
+    __all__ += ["Perm16", "PPerm16", "PTransf16", "Transf16", "Vect16"]
diff --git a/src/libsemigroups_pybind11/is_obviously_infinite.py b/src/libsemigroups_pybind11/is_obviously_infinite.py
index fde937cc..75d765b2 100644
--- a/src/libsemigroups_pybind11/is_obviously_infinite.py
+++ b/src/libsemigroups_pybind11/is_obviously_infinite.py
@@ -14,3 +14,5 @@
 from .detail.cxx_wrapper import wrap_cxx_free_fn as _wrap_cxx_free_fn
 
 is_obviously_infinite = _wrap_cxx_free_fn(_is_obviously_infinite)
+
+__all__ = ["is_obviously_infinite"]
diff --git a/src/libsemigroups_pybind11/kambites.py b/src/libsemigroups_pybind11/kambites.py
index 47d07da1..2855befc 100644
--- a/src/libsemigroups_pybind11/kambites.py
+++ b/src/libsemigroups_pybind11/kambites.py
@@ -14,7 +14,6 @@
     KambitesMultiViewString as _KambitesMultiViewString,
     KambitesString as _KambitesString,
     KambitesWord as _KambitesWord,
-    congruence_kind as _congruence_kind,
     kambites_non_trivial_classes as _kambites_non_trivial_classes,
     kambites_normal_forms as _kambites_normal_forms,
     kambites_partition as _kambites_partition,
@@ -70,6 +69,8 @@ def __init__(self: _Self, *args, **kwargs) -> None:
 _register_cxx_wrapped_type(_KambitesMultiViewString, Kambites)
 _register_cxx_wrapped_type(_KambitesString, Kambites)
 
-partition = _wrap_cxx_free_fn(_kambites_partition)
 non_trivial_classes = _wrap_cxx_free_fn(_kambites_non_trivial_classes)
 normal_forms = _wrap_cxx_free_fn(_kambites_normal_forms)
+partition = _wrap_cxx_free_fn(_kambites_partition)
+
+__all__ = ["Kambites", "non_trivial_classes", "normal_forms", "partition"]
diff --git a/src/libsemigroups_pybind11/knuth_bendix.py b/src/libsemigroups_pybind11/knuth_bendix.py
index 3cd5e7a8..ac2410d4 100644
--- a/src/libsemigroups_pybind11/knuth_bendix.py
+++ b/src/libsemigroups_pybind11/knuth_bendix.py
@@ -14,7 +14,6 @@
     KnuthBendixStringRewriteTrie as _KnuthBendixStringRewriteTrie,
     KnuthBendixWordRewriteFromLeft as _KnuthBendixWordRewriteFromLeft,
     KnuthBendixWordRewriteTrie as _KnuthBendixWordRewriteTrie,
-    congruence_kind as _congruence_kind,
     knuth_bendix_by_overlap_length as _knuth_bendix_by_overlap_length,
     knuth_bendix_is_reduced as _knuth_bendix_is_reduced,
     knuth_bendix_non_trivial_classes as _knuth_bendix_non_trivial_classes,
@@ -110,3 +109,13 @@ def __init__(self, *args, rewriter="RewriteTrie", **kwargs) -> None:
 normal_forms = _wrap_cxx_free_fn(_knuth_bendix_normal_forms)
 partition = _wrap_cxx_free_fn(_knuth_bendix_partition)
 redundant_rule = _wrap_cxx_free_fn(_knuth_bendix_redundant_rule)
+
+__all__ = [
+    "KnuthBendix",
+    "by_overlap_length",
+    "is_reduced",
+    "non_trivial_classes",
+    "normal_forms",
+    "partition",
+    "redundant_rule",
+]
diff --git a/src/libsemigroups_pybind11/konieczny.py b/src/libsemigroups_pybind11/konieczny.py
index 19960730..8321659f 100644
--- a/src/libsemigroups_pybind11/konieczny.py
+++ b/src/libsemigroups_pybind11/konieczny.py
@@ -212,3 +212,5 @@ def D_classes(self: _Self) -> _Iterator[DClass]:
     Konieczny.DClass._py_template_params_to_cxx_type.values()  # pylint: disable=protected-access
 ):
     _register_cxx_wrapped_type(_type, Konieczny.DClass)
+
+__all__ = ["Konieczny"]
diff --git a/src/libsemigroups_pybind11/matrix.py b/src/libsemigroups_pybind11/matrix.py
index 6f681aa6..717ae5a9 100644
--- a/src/libsemigroups_pybind11/matrix.py
+++ b/src/libsemigroups_pybind11/matrix.py
@@ -184,13 +184,22 @@ def __hash__(self: _Self) -> int:
         return _to_cxx(self).__hash__()
 
 
+# The following fools sphinx into thinking that MatrixKind + Matrix are not
+# aliases.
+Matrix.__module__ = __name__
+Matrix.__name__ = "Matrix"
+MatrixKind.__module__ = __name__
+MatrixKind.__name__ = "MatrixKind"
+
 _copy_cxx_mem_fns(_NTPMat, Matrix)
 
 ########################################################################
 # Helper functions
 ########################################################################
 
-row_space_size = _wrap_cxx_free_fn(_row_space_size)
 period = _wrap_cxx_free_fn(_period)
 row_basis = _wrap_cxx_free_fn(_row_basis)
+row_space_size = _wrap_cxx_free_fn(_row_space_size)
 threshold = _wrap_cxx_free_fn(_threshold)
+
+__all__ = ["MatrixKind", "Matrix", "period", "row_basis", "row_space_size", "threshold"]
diff --git a/src/libsemigroups_pybind11/paths.py b/src/libsemigroups_pybind11/paths.py
index a4e9230a..20dc4178 100644
--- a/src/libsemigroups_pybind11/paths.py
+++ b/src/libsemigroups_pybind11/paths.py
@@ -8,7 +8,7 @@
 contains helper functions for the :any:`Paths` class.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=no-name-in-module,unused-import
+from _libsemigroups_pybind11 import (
     paths_algorithm as algorithm,
     paths_number_of_paths as number_of_paths,
     paths_number_of_paths_algorithm as number_of_paths_algorithm,
@@ -18,3 +18,5 @@
 # alias.
 algorithm.__module__ = __name__
 algorithm.__name__ = "algorithm"
+
+__all__ = ["algorithm", "number_of_paths", "number_of_paths_algorithm"]
diff --git a/src/libsemigroups_pybind11/pbr.py b/src/libsemigroups_pybind11/pbr.py
index 292e8d90..df5e3598 100644
--- a/src/libsemigroups_pybind11/pbr.py
+++ b/src/libsemigroups_pybind11/pbr.py
@@ -8,4 +8,6 @@
 contains helper functions for the :any:`PBR` class.
 """
 
-from _libsemigroups_pybind11 import pbr_one as one  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import pbr_one as one
+
+__all__ = ["one"]
diff --git a/src/libsemigroups_pybind11/presentation/__init__.py b/src/libsemigroups_pybind11/presentation/__init__.py
index 78232d8d..ab3cac38 100644
--- a/src/libsemigroups_pybind11/presentation/__init__.py
+++ b/src/libsemigroups_pybind11/presentation/__init__.py
@@ -56,14 +56,16 @@
     presentation_to_gap_string as _to_gap_string,
     presentation_try_detect_inverses as _try_detect_inverses,
 )
-from libsemigroups_pybind11.detail.cxx_wrapper import (
+
+from ..detail.cxx_wrapper import (
     CxxWrapper as _CxxWrapper,
     copy_cxx_mem_fns as _copy_cxx_mem_fns,
     register_cxx_wrapped_type as _register_cxx_wrapped_type,
     to_cxx as _to_cxx,
     wrap_cxx_free_fn as _wrap_cxx_free_fn,
 )
-from libsemigroups_pybind11.detail.decorators import copydoc as _copydoc
+from ..detail.decorators import copydoc as _copydoc
+from . import examples
 
 ########################################################################
 # Presentation
@@ -271,3 +273,51 @@ def __init__(self: _Self, *args, **kwargs) -> None:
 is_normalized = _wrap_cxx_free_fn(_is_normalized)
 is_rule = _wrap_cxx_free_fn(_is_rule)
 try_detect_inverses = _wrap_cxx_free_fn(_try_detect_inverses)
+
+__all__ = [
+    "Presentation",
+    "InversePresentation",
+    "add_commutator_rule",
+    "add_identity_rules",
+    "add_inverse_rules",
+    "add_rule",
+    "add_rules",
+    "add_zero_rules",
+    "are_rules_sorted",
+    "change_alphabet",
+    "commutator",
+    "contains_rule",
+    "first_unused_letter",
+    "greedy_reduce_length",
+    "greedy_reduce_length_and_number_of_gens",
+    "is_strongly_compressible",
+    "length",
+    "longest_rule",
+    "longest_rule_length",
+    "longest_subword_reducing_length",
+    "make_semigroup",
+    "normalize_alphabet",
+    "reduce_complements",
+    "reduce_to_2_generators",
+    "remove_duplicate_rules",
+    "remove_redundant_generators",
+    "remove_trivial_rules",
+    "replace_subword",
+    "replace_word",
+    "replace_word_with_new_generator",
+    "reverse",
+    "shortest_rule",
+    "shortest_rule_length",
+    "sort_each_rule",
+    "sort_rules",
+    "strongly_compress",
+    "throw_if_bad_inverses",
+    "to_gap_string",
+    "balance",
+    "add_cyclic_conjugates",
+    "index_rule",
+    "is_normalized",
+    "is_rule",
+    "try_detect_inverses",
+    "examples",
+]
diff --git a/src/libsemigroups_pybind11/presentation/examples.py b/src/libsemigroups_pybind11/presentation/examples.py
index 9f7ca960..f7863553 100644
--- a/src/libsemigroups_pybind11/presentation/examples.py
+++ b/src/libsemigroups_pybind11/presentation/examples.py
@@ -191,3 +191,89 @@
 uniform_block_bijection_monoid_Fit03 = _wrap_cxx_free_fn(_uniform_block_bijection_monoid_Fit03)
 zero_rook_monoid = _wrap_cxx_free_fn(_zero_rook_monoid)
 zero_rook_monoid_Gay18 = _wrap_cxx_free_fn(_zero_rook_monoid_Gay18)
+
+__all__ = [
+    "abacus_jones_monoid",
+    "abacus_jones_monoid_AJP25",
+    "alternating_group",
+    "alternating_group_Moo97",
+    "brauer_monoid",
+    "braid_group",
+    "brauer_monoid_KM07",
+    "chinese_monoid",
+    "chinese_monoid_CEKNH01",
+    "cyclic_inverse_monoid",
+    "cyclic_inverse_monoid_Fer22_a",
+    "cyclic_inverse_monoid_Fer22_b",
+    "dual_symmetric_inverse_monoid",
+    "dual_symmetric_inverse_monoid_EEF07",
+    "fibonacci_semigroup",
+    "fibonacci_semigroup_CRRT94",
+    "full_transformation_monoid",
+    "full_transformation_monoid_Aiz58",
+    "full_transformation_monoid_II74",
+    "full_transformation_monoid_MW24_a",
+    "full_transformation_monoid_MW24_b",
+    "hypo_plactic_monoid",
+    "hypo_plactic_monoid_Nov00",
+    "monogenic_semigroup",
+    "motzkin_monoid",
+    "motzkin_monoid_PHL13",
+    "not_renner_type_B_monoid",
+    "not_renner_type_B_monoid_Gay18",
+    "not_renner_type_D_monoid",
+    "not_renner_type_D_monoid_God09",
+    "not_symmetric_group",
+    "not_symmetric_group_GKKL08",
+    "order_preserving_cyclic_inverse_monoid",
+    "order_preserving_cyclic_inverse_monoid_Fer22",
+    "order_preserving_monoid",
+    "order_preserving_monoid_AR00",
+    "orientation_preserving_monoid",
+    "orientation_preserving_monoid_AR00",
+    "orientation_preserving_reversing_monoid",
+    "orientation_preserving_reversing_monoid_AR00",
+    "partial_brauer_monoid",
+    "partial_brauer_monoid_KM07",
+    "partial_isometries_cycle_graph_monoid",
+    "partial_isometries_cycle_graph_monoid_FP22",
+    "partial_transformation_monoid",
+    "partial_transformation_monoid_MW24",
+    "partial_transformation_monoid_Shu60",
+    "partition_monoid",
+    "partition_monoid_Eas11",
+    "partition_monoid_HR05",
+    "plactic_monoid",
+    "plactic_monoid_Knu70",
+    "rectangular_band",
+    "rectangular_band_ACOR00",
+    "renner_type_B_monoid",
+    "renner_type_B_monoid_Gay18",
+    "renner_type_D_monoid",
+    "renner_type_D_monoid_Gay18",
+    "sigma_plactic_monoid",
+    "sigma_plactic_monoid_AHMNT24",
+    "singular_brauer_monoid",
+    "singular_brauer_monoid_MM07",
+    "special_linear_group_2",
+    "special_linear_group_2_CR80",
+    "stellar_monoid",
+    "stellar_monoid_GH19",
+    "stylic_monoid",
+    "stylic_monoid_AR22",
+    "symmetric_group",
+    "symmetric_group_Bur12",
+    "symmetric_group_Car56",
+    "symmetric_group_Moo97_a",
+    "symmetric_group_Moo97_b",
+    "symmetric_inverse_monoid",
+    "symmetric_inverse_monoid_Sol04",
+    "symmetric_inverse_monoid_MW24",
+    "symmetric_inverse_monoid_Shu60",
+    "temperley_lieb_monoid",
+    "temperley_lieb_monoid_Eas21",
+    "uniform_block_bijection_monoid",
+    "uniform_block_bijection_monoid_Fit03",
+    "zero_rook_monoid",
+    "zero_rook_monoid_Gay18",
+]
diff --git a/src/libsemigroups_pybind11/schreier_sims.py b/src/libsemigroups_pybind11/schreier_sims.py
index dd10de6c..907b3462 100644
--- a/src/libsemigroups_pybind11/schreier_sims.py
+++ b/src/libsemigroups_pybind11/schreier_sims.py
@@ -108,3 +108,5 @@ def __init__(self: _Self, *args) -> None:
 
 
 intersection = _wrap_cxx_free_fn(_schreier_sims_intersection)
+
+__all__ = ["SchreierSims", "intersection"]
diff --git a/src/libsemigroups_pybind11/sims.py b/src/libsemigroups_pybind11/sims.py
index 37a811eb..acc722d2 100644
--- a/src/libsemigroups_pybind11/sims.py
+++ b/src/libsemigroups_pybind11/sims.py
@@ -286,10 +286,26 @@ def __call__(self: _Self, *args, **kwargs) -> bool:
 # Helper functions
 ########################################################################
 
-right_generating_pairs = _wrap_cxx_free_fn(_right_generating_pairs)
-two_sided_generating_pairs = _wrap_cxx_free_fn(_two_sided_generating_pairs)
+is_maximal_right_congruence = _wrap_cxx_free_fn(_is_maximal_right_congruence)
 is_right_congruence = _wrap_cxx_free_fn(_is_right_congruence)
 is_right_congruence_of_dual = _wrap_cxx_free_fn(_is_right_congruence_of_dual)
 is_two_sided_congruence = _wrap_cxx_free_fn(_is_two_sided_congruence)
-is_maximal_right_congruence = _wrap_cxx_free_fn(_is_maximal_right_congruence)
 poset = _wrap_cxx_free_fn(_poset)
+right_generating_pairs = _wrap_cxx_free_fn(_right_generating_pairs)
+two_sided_generating_pairs = _wrap_cxx_free_fn(_two_sided_generating_pairs)
+
+__all__ = [
+    "MinimalRepOrc",
+    "RepOrc",
+    "Sims1",
+    "Sims2",
+    "SimsRefinerFaithful",
+    "SimsRefinerIdeals",
+    "is_maximal_right_congruence",
+    "is_right_congruence_of_dual",
+    "is_right_congruence",
+    "is_two_sided_congruence",
+    "poset",
+    "right_generating_pairs",
+    "two_sided_generating_pairs",
+]
diff --git a/src/libsemigroups_pybind11/stephen.py b/src/libsemigroups_pybind11/stephen.py
index 592db98e..5598cce4 100644
--- a/src/libsemigroups_pybind11/stephen.py
+++ b/src/libsemigroups_pybind11/stephen.py
@@ -103,3 +103,14 @@ def __imul__(self: _Self, other: _Self) -> _Self:
 number_of_left_factors = _wrap_cxx_free_fn(_stephen_number_of_left_factors)
 number_of_words_accepted = _wrap_cxx_free_fn(_stephen_number_of_words_accepted)
 words_accepted = _wrap_cxx_free_fn(_stephen_words_accepted)
+
+__all__ = [
+    "Stephen",
+    "accepts",
+    "dot",
+    "is_left_factor",
+    "left_factors",
+    "number_of_left_factors",
+    "number_of_words_accepted",
+    "words_accepted",
+]
diff --git a/src/libsemigroups_pybind11/to.py b/src/libsemigroups_pybind11/to.py
index 5fcbf96e..b60915d5 100644
--- a/src/libsemigroups_pybind11/to.py
+++ b/src/libsemigroups_pybind11/to.py
@@ -147,3 +147,6 @@ def to(*args, rtype: tuple):
         )
     constructor = rtype[0]
     return constructor(_RETURN_TYPE_TO_CONVERTER_FUNCTION[rtype](*cxx_args))
+
+
+__all__ = ["to"]
diff --git a/src/libsemigroups_pybind11/todd_coxeter.py b/src/libsemigroups_pybind11/todd_coxeter.py
index 110c86b8..7eb2c55f 100644
--- a/src/libsemigroups_pybind11/todd_coxeter.py
+++ b/src/libsemigroups_pybind11/todd_coxeter.py
@@ -88,6 +88,18 @@ def __init__(self: _Self, *args, **kwargs) -> None:
 perform_lookbehind = _wrap_cxx_free_fn(_todd_coxeter_perform_lookbehind)
 redundant_rule = _wrap_cxx_free_fn(_todd_coxeter_redundant_rule)
 
+__all__ = [
+    "ToddCoxeter",
+    "class_by_index",
+    "class_of",
+    "is_non_trivial",
+    "non_trivial_classes",
+    "normal_forms",
+    "partition",
+    "perform_lookbehind",
+    "redundant_rule",
+]
+
 ########################################################################
 # Helper functions
 ########################################################################
diff --git a/src/libsemigroups_pybind11/transf.py b/src/libsemigroups_pybind11/transf.py
index 80075ebd..e0d68202 100644
--- a/src/libsemigroups_pybind11/transf.py
+++ b/src/libsemigroups_pybind11/transf.py
@@ -10,7 +10,6 @@
 """
 
 import abc
-from typing import Any as _Any
 
 from typing_extensions import Self
 
@@ -352,9 +351,11 @@ def one(n: int) -> Self:
 # Helper functions
 ########################################################################
 
-one = _wrap_cxx_free_fn(_transf_one)
+domain = _wrap_cxx_free_fn(_transf_domain)
+image = _wrap_cxx_free_fn(_transf_image)
 inverse = _wrap_cxx_free_fn(_transf_inverse)
-right_one = _wrap_cxx_free_fn(_transf_right_one)
 left_one = _wrap_cxx_free_fn(_transf_left_one)
-image = _wrap_cxx_free_fn(_transf_image)
-domain = _wrap_cxx_free_fn(_transf_domain)
+one = _wrap_cxx_free_fn(_transf_one)
+right_one = _wrap_cxx_free_fn(_transf_right_one)
+
+__all__ = ["Perm", "PPerm", "Transf", "domain", "image", "inverse", "left_one", "one", "right_one"]
diff --git a/src/libsemigroups_pybind11/ukkonen.py b/src/libsemigroups_pybind11/ukkonen.py
index 1312bc42..70b67419 100644
--- a/src/libsemigroups_pybind11/ukkonen.py
+++ b/src/libsemigroups_pybind11/ukkonen.py
@@ -8,7 +8,7 @@
 contains helper functions for the :any:`Ukkonen` class.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import (
     ukkonen_add_word as add_word,
     ukkonen_add_words as add_words,
     ukkonen_dot as dot,
@@ -24,3 +24,20 @@
     ukkonen_pieces as pieces,
     ukkonen_traverse as traverse,
 )
+
+__all__ = [
+    "add_word",
+    "add_words",
+    "dot",
+    "is_piece",
+    "is_subword",
+    "is_suffix",
+    "length_maximal_piece_prefix",
+    "length_maximal_piece_suffix",
+    "maximal_piece_prefix",
+    "maximal_piece_suffix",
+    "number_of_distinct_subwords",
+    "number_of_pieces",
+    "pieces",
+    "traverse",
+]
diff --git a/src/libsemigroups_pybind11/word_graph.py b/src/libsemigroups_pybind11/word_graph.py
index d6d42770..a94a6020 100644
--- a/src/libsemigroups_pybind11/word_graph.py
+++ b/src/libsemigroups_pybind11/word_graph.py
@@ -10,7 +10,7 @@
 are contained in the subpackage ``word_graph``.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import
+from _libsemigroups_pybind11 import (
     word_graph_add_cycle as add_cycle,
     word_graph_adjacency_matrix as adjacency_matrix,
     word_graph_dot as dot,
@@ -30,3 +30,24 @@
     word_graph_standardize as standardize,
     word_graph_topological_sort as topological_sort,
 )
+
+__all__ = [
+    "add_cycle",
+    "adjacency_matrix",
+    "dot",
+    "equal_to",
+    "follow_path",
+    "is_acyclic",
+    "is_compatible",
+    "is_complete",
+    "is_connected",
+    "is_reachable",
+    "is_strictly_cyclic",
+    "last_node_on_path",
+    "nodes_reachable_from",
+    "number_of_nodes_reachable_from",
+    "random_acyclic",
+    "spanning_tree",
+    "standardize",
+    "topological_sort",
+]
diff --git a/src/libsemigroups_pybind11/words.py b/src/libsemigroups_pybind11/words.py
index 1c0f126f..4b3f0893 100644
--- a/src/libsemigroups_pybind11/words.py
+++ b/src/libsemigroups_pybind11/words.py
@@ -9,10 +9,12 @@
 contains helper functions related to words.
 """
 
-from _libsemigroups_pybind11 import (  # pylint: disable=unused-import,redefined-builtin
+from _libsemigroups_pybind11 import (  # pylint: disable=redefined-builtin
     words_human_readable_index as human_readable_index,
     words_human_readable_letter as human_readable_letter,
     words_parse_relations as parse_relations,
     words_pow as pow,
     words_prod as prod,
 )
+
+__all__ = ["human_readable_index", "human_readable_letter", "parse_relations", "pow", "prod"]
diff --git a/tests/test_froidure_pin.py b/tests/test_froidure_pin.py
index eea7d86f..5c751ada 100644
--- a/tests/test_froidure_pin.py
+++ b/tests/test_froidure_pin.py
@@ -14,7 +14,6 @@
 import pytest
 
 from libsemigroups_pybind11 import (
-    PBR,
     UNDEFINED,
     Bipartition,
     BMat8,
@@ -23,6 +22,7 @@
     LibsemigroupsError,
     Matrix,
     MatrixKind,
+    PBR,
     Perm,
     PPerm,
     Presentation,