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reiniscirponsjames-d-mitchellJoseph-Edwards
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Add support for Sims for v1 release, version 2.0, now with better branch name! (#220)
* Start adding python bindings for Sims * Fix some issues with Sims1 * Make Sims1, Sims2 more easily importable, add tests * Add more sims constructs * Add pruners to sims * Try adding more stuff * Fix bug in chainable setters, add test markers, port over more tests. * Add functions from sims namespace * Start adding docs for Sims * Start fixin doc * First pass formatting changes to docs * More d o c u m e n t a t i o n improvements * Add more tests * Fixes after recent changes in libsemigroups * Reorg doc * Doc tweaks * Review return value policy * Linting + formatting * Fix spelling * Uncomment sims tests * Add missing asserts --------- Co-authored-by: James D. Mitchell <jdm3@st-andrews.ac.uk> Co-authored-by: Joseph Edwards <josephdavidedwards@gmail.com>
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‎docs/source/conf.py

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@@ -56,7 +56,9 @@ def doc_only_run(self):
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docstring = list(node.findall(condition=desc_content))
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if not docstring:
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logger.warning(f"The docstring for {self.arguments[0]} cannot be found.")
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logger.warning(
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f"The docstring for {self.arguments[0]} cannot be found."
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)
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return []
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return docstring
@@ -102,7 +104,9 @@ def no_doc_run(self):
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source_suffix = ".rst"
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master_doc = "index"
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project = "libsemigroups_pybind11"
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copyright = "2021-2024, Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
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copyright = (
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"2021-2024, Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
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)
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author = "Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
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version = "1.0.0"
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release = "1.0.0"
@@ -160,7 +164,17 @@ def no_doc_run(self):
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r"libsemigroups::DynamicMatrix<libsemigroups::IntegerPlus<long long>, "
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r"libsemigroups::IntegerProd<long long>, libsemigroups::IntegerZero"
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r"<long long>, libsemigroups::IntegerOne<long long>, long long>"
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): "Matrix",
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): r"Matrix",
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r"libsemigroups::SimsStats": r"SimsStats",
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r"libsemigroups::Sims1": r"Sims1",
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r"libsemigroups::Sims2": r"Sims2",
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r"libsemigroups::RepOrc": r"RepOrc",
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r"libsemigroups::MinimalRepOrc": r"MinimalRepOrc",
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(
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r"libsemigroups::DynamicMatrix<libsemigroups::BooleanPlus, "
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r"libsemigroups::BooleanProd, libsemigroups::BooleanZero, "
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r"libsemigroups::BooleanOne, int>"
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): r"Matrix",
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}
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# This dictionary should be of the form class_name -> (pattern, repl), where
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],
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"FroidurePinPBR": [(r"\bPBR\b", "Element")],
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"SchreierSimsPerm1": [(r"\bPerm1\b", "Element")],
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"Sims1": [("SubclassType", "Sims1"), ("SimsSettingsSims1", "Sims1")],
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"Sims2": [("SubclassType", "Sims2"), ("SimsSettingsSims2", "Sims2")],
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"MinimalRepOrc": [
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("SubclassType", "MinimalRepOrc"),
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("SimsSettingsMinimalRepOrc", "MinimalRepOrc"),
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(r"\bRepOrc\b", "MinimalRepOrc"),
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],
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"RepOrc": [
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("SubclassType", "RepOrc"),
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("SimsSettingsRepOrc", "RepOrc"),
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],
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}
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# This is what sphinx considers to be a signature

‎docs/source/index.rst

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main-algorithms/kambites/index
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main-algorithms/knuth-bendix/index
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main-algorithms/konieczny/index
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main-algorithms/low-index/index
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main-algorithms/radoszewski-rytter/index
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main-algorithms/schreier-sims/index
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main-algorithms/sims/index
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main-algorithms/stephen/index
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main-algorithms/todd-coxeter/index
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‎docs/source/main-algorithms/low-index/classes/index.rst

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.. Copyright (c) 2024 R. Cirpons
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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Classes for low-index congruences
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=================================
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On this page we describe the functionality relating to the Sims's
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low-index congruence algorithm for semigroups and monoids that is available in
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``libsemigroups_pybind11``.
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.. doctest::
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>>> from libsemigroups_pybind11 import Sims1, Presentation, presentation
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>>> p = Presentation([0, 1])
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>>> presentation.add_rule(p, [0, 1], [1, 0])
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>>> sims = Sims1(p)
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>>> sims.number_of_congruences(4)
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117
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.. toctree::
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:maxdepth: 1
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minimalreporc
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reporc
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sims1
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sims2
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simsrefinerfaithful
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simsrefinerideals
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simsstats

‎docs/source/main-algorithms/low-index/classes/minimalreporc.rst

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.. Copyright (c) 2025 J. D. Mitchell
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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The MinimalRepOrc class
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=======================
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.. autoclass:: MinimalRepOrc
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:doc-only:
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:class-doc-from: class
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Contents
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--------
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.. autosummary::
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:nosignatures:
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~MinimalRepOrc
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MinimalRepOrc.__init__
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MinimalRepOrc.add_excluded_pair
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MinimalRepOrc.add_included_pair
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MinimalRepOrc.add_pruner
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MinimalRepOrc.clear_excluded_pairs
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MinimalRepOrc.clear_included_pairs
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MinimalRepOrc.clear_long_rules
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MinimalRepOrc.clear_pruners
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MinimalRepOrc.excluded_pairs
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MinimalRepOrc.first_long_rule_position
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MinimalRepOrc.idle_thread_restarts
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MinimalRepOrc.included_pairs
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MinimalRepOrc.init
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MinimalRepOrc.long_rule_length
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MinimalRepOrc.long_rules
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MinimalRepOrc.number_of_long_rules
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MinimalRepOrc.number_of_threads
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MinimalRepOrc.presentation
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MinimalRepOrc.pruners
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MinimalRepOrc.stats
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Full API
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--------
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.. autoclass:: MinimalRepOrc
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:no-doc:
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:class-doc-from: class
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:members:
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:inherited-members:
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:special-members: __init__
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‎docs/source/main-algorithms/low-index/classes/reporc.rst

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.. Copyright (c) 2025 J. D. Mitchell
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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The RepOrc class
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=======================
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.. autoclass:: RepOrc
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:doc-only:
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:class-doc-from: class
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Contents
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--------
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.. autosummary::
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:nosignatures:
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~RepOrc
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RepOrc.__init__
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RepOrc.add_excluded_pair
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RepOrc.add_included_pair
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RepOrc.add_pruner
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RepOrc.clear_excluded_pairs
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RepOrc.clear_included_pairs
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RepOrc.clear_long_rules
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RepOrc.clear_pruners
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RepOrc.excluded_pairs
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RepOrc.first_long_rule_position
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RepOrc.idle_thread_restarts
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RepOrc.included_pairs
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RepOrc.init
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RepOrc.long_rule_length
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RepOrc.long_rules
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RepOrc.number_of_long_rules
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RepOrc.number_of_threads
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RepOrc.presentation
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RepOrc.pruners
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RepOrc.stats
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Full API
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--------
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.. autoclass:: RepOrc
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:no-doc:
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:class-doc-from: class
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:members:
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:inherited-members:
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:special-members: __init__
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‎docs/source/main-algorithms/low-index/classes/sims1.rst

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.. Copyright (c) 2025 J. D. Mitchell
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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The Sims1 class
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===============
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.. autoclass:: Sims1
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:doc-only:
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:class-doc-from: class
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Contents
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--------
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.. autosummary::
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:nosignatures:
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~Sims1
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Sims1.add_excluded_pair
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Sims1.add_included_pair
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Sims1.add_pruner
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Sims1.clear_excluded_pairs
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Sims1.clear_included_pairs
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Sims1.clear_long_rules
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Sims1.clear_pruners
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Sims1.copy
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Sims1.excluded_pairs
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Sims1.find_if
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Sims1.first_long_rule_position
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Sims1.for_each
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Sims1.idle_thread_restarts
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Sims1.included_pairs
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Sims1.init
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Sims1.iterator
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Sims1.long_rule_length
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Sims1.long_rules
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Sims1.number_of_congruences
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Sims1.number_of_long_rules
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Sims1.number_of_threads
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Sims1.presentation
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Sims1.pruners
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Sims1.stats
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Full API
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--------
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.. TODO(0) document __init__ directly, the same trick that works for RepOrc +
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MinimalRepOrc doesn't work here for some reason.
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.. autoclass:: Sims1
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:class-doc-from: init
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:members:
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:inherited-members:

‎docs/source/main-algorithms/low-index/classes/sims2.rst

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.. Copyright (c) 2025 J. D. Mitchell
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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The Sims2 class
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===============
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.. autoclass:: Sims2
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:doc-only:
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:class-doc-from: class
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Contents
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--------
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.. autosummary::
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:nosignatures:
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~Sims2
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Sims2.add_excluded_pair
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Sims2.add_included_pair
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Sims2.add_pruner
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Sims2.clear_excluded_pairs
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Sims2.clear_included_pairs
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Sims2.clear_long_rules
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Sims2.clear_pruners
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Sims2.copy
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Sims2.excluded_pairs
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Sims2.find_if
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Sims2.first_long_rule_position
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Sims2.for_each
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Sims2.idle_thread_restarts
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Sims2.included_pairs
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Sims2.init
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Sims2.iterator
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Sims2.long_rule_length
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Sims2.long_rules
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Sims2.number_of_congruences
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Sims2.number_of_long_rules
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Sims2.number_of_threads
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Sims2.presentation
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Sims2.pruners
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Sims2.stats
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Full API
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--------
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.. TODO(0) document __init__ directly, the same trick that works for RepOrc +
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MinimalRepOrc doesn't work here for some reason.
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.. autoclass:: Sims2
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:class-doc-from: init
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:members:
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:inherited-members:

‎docs/source/main-algorithms/low-index/classes/simsrefinerfaithful.rst

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.. Copyright (c) 2025 J. D. Mitchell
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Distributed under the terms of the GPL license version 3.
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The full license is in the file LICENSE, distributed with this software.
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.. currentmodule:: _libsemigroups_pybind11
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The SimsRefinerFaithful class
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=============================
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.. autoclass:: SimsRefinerFaithful
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:doc-only:
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:class-doc-from: class
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Contents
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--------
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.. autosummary::
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:nosignatures:
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~SimsRefinerFaithful
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SimsRefinerFaithful.__init__
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SimsRefinerFaithful.__call__
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SimsRefinerFaithful.forbid
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SimsRefinerFaithful.init
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Full API
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--------
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.. autoclass:: SimsRefinerFaithful
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:no-doc:
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:class-doc-from: class
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:members:
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:inherited-members:
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:special-members: __call__, __init__

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