Merge pull request #186 from PermutaTriangle/develop

christianbean · web-flow · commit 1fb948af715d · 2021-10-21T11:12:32.000Z
Version 2.2.0
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -31,6 +31,9 @@ jobs:
           - python: 3.9
             toxenv: py39
             os: ubuntu-latest
+          - python: "3.10"
+            toxenv: py310
+            os: ubuntu-latest
           - python: pypy-3.7
             toxenv: pypy37
             os: ubuntu-latest
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+dfa_db/*
 .mypy_cache
 # Mac stuff
 *.DS_Store
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 21.6b0
+    rev: 21.9b0
     hooks:
       - id: black
diff --git a/.pylintrc b/.pylintrc
@@ -3,14 +3,15 @@
 [MASTER]
 ignore-patterns=test_.*?py,
                 # TODO: REMOVE
-                bisc.py, 
+                bisc.py,
                 bisc_subfunctions.py
 ignore= tests
 init-hook="from pylint.config import find_pylintrc; import os, sys; sys.path.append(os.path.dirname(find_pylintrc())+'/permuta')"
-disable=bad-continuation, 
+disable=bad-continuation,
         missing-module-docstring,
         fixme,
-        unsubscriptable-object
+        unsubscriptable-object,
+        unspecified-encoding
 good-names=i,j,n,k,x,y,_
 
 [SIMILARITIES]
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,50 +1,51 @@
 {
     "upload_type": "software",
+    "title": "Permuta: A Python Library for Permutations and Patterns",
     "creators": [
         {
             "name": "Ragnar Pall Ardal"
         },
         {
-            "name": "Tomas Ken Magnusson"
+            "name": "Arnar Bjarni Arnarson"
         },
         {
             "affiliation": "Reykjavik University",
-            "name": "Émile Nadeau"
-        },
-        {
-            "name": "Bjarni Jens Kristinsson"
+            "name": "Christian Bean"
         },
         {
-            "name": "Bjarki Agust Gudmundsson"
+            "name": "Alfur Birkir Bjarnason"
         },
         {
             "affiliation": "Reykjavik University",
-            "name": "Christian Bean"
+            "name": "Jon Steinn Eliasson"
         },
         {
-            "affiliation": "Reykjavik University",
-            "name": "Henning Ulfarsson"
+            "name": "Bjarki Agust Gudmundsson"
         },
         {
             "affiliation": "Reykjavik University",
-            "name": "Jon Steinn Eliasson"
+            "name": "Sigurjón Ingi Jónsson"
+        }
+        {
+            "name": "Bjarni Jens Kristinsson"
         },
         {
-            "name": "Murray Tannock"
+            "name": "Tomas Ken Magnusson"
         },
         {
-            "name": "Alfur Birkir Bjarnason"
+            "affiliation": "Reykjavik University",
+            "name": "Émile Nadeau"
         },
         {
             "affiliation": "Marquette University",
             "name": "Jay Pantone"
         },
         {
-            "name": "Arnar Bjarni Arnarson"
+            "name": "Murray Tannock"
         },
         {
             "affiliation": "Reykjavik University",
-            "name": "Sigurjón Ingi Jónsson"
-        }
+            "name": "Henning Ulfarsson"
+        },
     ]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## Unreleased
 
+## 2.2.0 - 2021-10-21
+### Added
+ - Bijection class for known bijection.
+ - An implementation of the Simion and Schmidt bijection.
+ - Enumeration strategy to check whether a class has finitely many simple permutations
+
+### Changed
+ - Perm.to_standard now uses an lru cache
+
 ## 2.1.0 - 2021-06-14
 ### Added
  - Statistic: bounce of a permutation.
diff --git a/README.rst b/README.rst
@@ -24,6 +24,10 @@ permuta
 Permuta is a Python library for working with perms (short for permutations),
 patterns, and mesh patterns.
 
+If this code is useful to you in your work, please consider citing it. To generate a
+BibTeX entry (or another format), click the "DOI" badge above and locate the "Cite As"
+section.
+
 If you need support, you can join us in our `Discord support server`_.
 
 .. _Discord support server: https://discord.gg/ngPZVT5
@@ -259,7 +263,7 @@ and a class (no class will use the set of all permutations).
     >>> depth.distribution_up_to(4, Av.from_string("123"))
     [[1], [1], [1, 1], [0, 2, 3], [0, 0, 3, 7, 4]]
 
-Given a bijection as a dictionary, we can check which statistics are preserved with 
+Given a bijection as a dictionary, we can check which statistics are preserved with
 ``check_all_preservations`` and which are transformed with ``check_all_transformed``
 
 .. code-block:: python
@@ -499,9 +503,9 @@ BSD-3: see the `LICENSE <https://github.com/PermutaTriangle/Permuta/blob/master/
 Citing
 ######
 
-If you found this library helpful with your research and would like to cite us, 
-you can use the following `BibTeX`_ or go to `Zenodo`_ for alternative formats. 
+If you found this library helpful with your research and would like to cite us,
+you can use the following `BibTeX`_ or go to `Zenodo`_ for alternative formats.
 
 .. _BibTex: https://zenodo.org/record/4725759/export/hx#.YImTibX7SUk
 
-.. _Zenodo: https://doi.org/10.5281/zenodo.4725759
+.. _Zenodo: https://doi.org/10.5281/zenodo.4725759
diff --git a/mypy.ini b/mypy.ini
@@ -2,4 +2,7 @@
 warn_return_any = True
 warn_unused_configs = True
 warn_no_return = False
-files = permuta/**/*.py
+files = permuta/**/*.py
+
+[mypy-automata.*]
+ignore_missing_imports = True
diff --git a/permuta/__init__.py b/permuta/__init__.py
@@ -1,7 +1,7 @@
 from .patterns import BivincularPatt, CovincularPatt, MeshPatt, Perm, VincularPatt
 from .perm_sets.permset import Av, Basis, MeshBasis
 
-__version__ = "2.1.0"
+__version__ = "2.2.0"
 
 __all__ = [
     "Perm",
diff --git a/permuta/enumeration_strategies/__init__.py b/permuta/enumeration_strategies/__init__.py
@@ -4,14 +4,17 @@
 
 from .abstract_strategy import EnumerationStrategy
 from .core_strategies import core_strategies
+from .finitely_many_simples import FinitelyManySimplesStrategy
 from .insertion_encodable import InsertionEncodingStrategy
 
 fast_enumeration_strategies: List[Type[EnumerationStrategy]] = [
     InsertionEncodingStrategy
 ]
 fast_enumeration_strategies.extend(core_strategies)
 
-long_enumeration_strategies: List[Type[EnumerationStrategy]] = []
+long_enumeration_strategies: List[Type[EnumerationStrategy]] = [
+    FinitelyManySimplesStrategy
+]
 
 all_enumeration_strategies: List[Type[EnumerationStrategy]] = (
     fast_enumeration_strategies + long_enumeration_strategies
diff --git a/permuta/enumeration_strategies/core_strategies.py b/permuta/enumeration_strategies/core_strategies.py
@@ -1,4 +1,4 @@
-from abc import abstractmethod, abstractproperty
+from abc import abstractmethod
 from typing import ClassVar, FrozenSet, List, Type
 
 from permuta import Av, MeshPatt, Perm
@@ -13,7 +13,8 @@ class CoreStrategy(EnumerationStrategyWithSymmetry):
     # https://arxiv.org/pdf/1912.07503.pdf
     # See this paper for corr_number
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def patterns_needed(self) -> FrozenSet[Perm]:
         """Return the set of patterns that are needed for the strategy to be useful."""
 
diff --git a/permuta/enumeration_strategies/finitely_many_simples.py b/permuta/enumeration_strategies/finitely_many_simples.py
@@ -0,0 +1,14 @@
+from permuta.enumeration_strategies.abstract_strategy import EnumerationStrategy
+from permuta.permutils.pin_words import PinWords
+
+
+class FinitelyManySimplesStrategy(EnumerationStrategy):
+    """Enumeration strategies related to the class having finitely many simple
+    permutations."""
+
+    def applies(self) -> bool:
+        return PinWords.has_finite_simples(self.basis)
+
+    @classmethod
+    def reference(cls) -> str:
+        return "The class contains only finitely many simple permutations"
diff --git a/permuta/patterns/perm.py b/permuta/patterns/perm.py
@@ -4,6 +4,7 @@
 
 import bisect
 import collections
+import functools
 import itertools
 import math
 import numbers
@@ -12,7 +13,6 @@
 from typing import (
     TYPE_CHECKING,
     Callable,
-    ClassVar,
     Deque,
     Dict,
     Iterable,
@@ -43,8 +43,6 @@
 class Perm(TupleType, Patt):
     """A perm class."""
 
-    _TO_STANDARD_CACHE: ClassVar[Dict[Tuple, "Perm"]] = {}
-
     def __new__(cls, iterable: Iterable[int] = ()) -> "Perm":
         """Return a Perm instance.
 
@@ -60,11 +58,6 @@ def __init__(self, _iterable: Iterable[int] = ()) -> None:
         # Cache for data used when finding occurrences of self in a perm
         self._cached_pattern_details: Optional[List[Tuple[int, int, int, int]]] = None
 
-    @classmethod
-    def clear_cache(cls):
-        """Clears to_standardize cache."""
-        cls._TO_STANDARD_CACHE = {}
-
     @classmethod
     def to_standard(cls, iterable: Iterable) -> "Perm":
         """Return the perm corresponding to iterable. Duplicate elements
@@ -76,13 +69,15 @@ def to_standard(cls, iterable: Iterable) -> "Perm":
             >>> Perm.to_standard("caaba")
             Perm((4, 0, 1, 3, 2))
         """
-        iterable = tuple(iterable)
-        if iterable not in cls._TO_STANDARD_CACHE:
-            cls._TO_STANDARD_CACHE[iterable] = cls(
-                idx
-                for (idx, _) in sorted(enumerate(iterable), key=operator.itemgetter(1))
-            ).inverse()
-        return cls._TO_STANDARD_CACHE[iterable]
+        return cls._to_standard(tuple(iterable))
+
+    @classmethod
+    @functools.lru_cache(maxsize=10000)
+    def _to_standard(cls, iterable: Tuple) -> "Perm":
+        """A cached function that standardise a tuple."""
+        return cls(
+            idx for (idx, _) in sorted(enumerate(iterable), key=operator.itemgetter(1))
+        ).inverse()
 
     standardize = to_standard
     from_iterable = to_standard
@@ -2134,7 +2129,7 @@ def rank(self) -> int:
         fact = [1]
         for i in range(n):
             fact.append(fact[i] * (i + 1))
-        vals: List[int] = list()
+        vals: List[int] = []
         for idx, val in enumerate(self):
             ordered_pos = bisect.bisect_left(vals, val)
             res += (val - ordered_pos) * fact[n - idx - 1] + fact[n - idx - 1]
diff --git a/permuta/perm_sets/permset.py b/permuta/perm_sets/permset.py
@@ -138,7 +138,7 @@ def _ensure_level_classical_pattern_basis(self, level_number: int) -> None:
         max_size = max(lengths)
         for nplusone in range(len(self.cache), level_number + 1):
             n = nplusone - 1
-            new_level: Dict[Perm, Optional[List[int]]] = dict()
+            new_level: Dict[Perm, Optional[List[int]]] = {}
             last_level = self.cache[-1]
             check_length = nplusone in lengths
             smaller_elems = {b for b in self.basis if len(b) == nplusone}
diff --git a/permuta/permutils/bijections.py b/permuta/permutils/bijections.py
@@ -0,0 +1,47 @@
+import itertools
+
+from permuta import Perm
+
+
+class Bijections:
+    """A collection of known bijections."""
+
+    # pylint: disable=too-few-public-methods
+
+    @staticmethod
+    def simion_and_schmidt(perm: Perm, inverse: bool = False) -> Perm:
+        """The bijection from `Restricted permutations` by R. Simion and F. Schmidt
+        between Av(123) and Av(132).
+        """
+        n = len(perm)
+        if n == 0:
+            return Perm()
+        if inverse:
+            if perm.contains(Perm((0, 2, 1))):
+                raise ValueError("Map only works for 132 avoiding permutations")
+            return Bijections._simion_and_schmidt_inv(perm, n)
+        if perm.contains(Perm((0, 1, 2))):
+            raise ValueError("Map only works for 123 avoiding permutations")
+        return Bijections._simion_and_schmidt(perm, n)
+
+    @staticmethod
+    def _simion_and_schmidt(perm: Perm, n: int) -> Perm:
+        used, img, min_val = {perm[0]}, [perm[0]] * n, perm[0]
+        for idx, val in itertools.islice(enumerate(perm), 1, None):
+            if min_val > val:  # val is L2R minima
+                img[idx], min_val = val, val
+            else:
+                img[idx] = next(k for k in range(min_val + 1, n) if k not in used)
+            used.add(img[idx])
+        return Perm(img)
+
+    @staticmethod
+    def _simion_and_schmidt_inv(perm: Perm, n: int) -> Perm:
+        used, img, min_val = {perm[0]}, [perm[0]] * n, perm[0]
+        for idx, val in itertools.islice(enumerate(perm), 1, None):
+            if min_val > val:  # val is L2R minima
+                img[idx], min_val = val, val
+            else:
+                img[idx] = next(k for k in range(n - 1, -1, -1) if k not in used)
+            used.add(img[idx])
+        return Perm(img)
diff --git a/permuta/permutils/insertion_encodable.py b/permuta/permutils/insertion_encodable.py
@@ -10,7 +10,7 @@ class InsertionEncodablePerms:
     """
 
     _ALL_PROPERTIES: ClassVar[int] = 15
-    _CACHE: ClassVar[Dict[Tuple, int]] = dict()
+    _CACHE: ClassVar[Dict[Tuple, int]] = {}
 
     @staticmethod
     def _is_incr_next_incr(perm: Perm) -> bool:
diff --git a/permuta/permutils/pin_words.py b/permuta/permutils/pin_words.py
diff --git a/permuta/permutils/pinword_util.py b/permuta/permutils/pinword_util.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/setup.py b/setup.py
diff --git a/tests/enumeration_strategies/test_enumeration_strategies.py b/tests/enumeration_strategies/test_enumeration_strategies.py
diff --git a/tests/permutils/test_bijections.py b/tests/permutils/test_bijections.py
diff --git a/tests/permutils/test_pinwords.py b/tests/permutils/test_pinwords.py
diff --git a/tox.ini b/tox.ini

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+dfa_db/*`
`1`	`2`	`.mypy_cache`
`2`	`3`	`# Mac stuff`
`3`	`4`	`*.DS_Store`
Original file line number	Diff line number	Diff line change
`@@ -1,50 +1,51 @@`
`1`	`1`	`{`
`2`	`2`	`"upload_type": "software",`
	`3`	`+ "title": "Permuta: A Python Library for Permutations and Patterns",`
`3`	`4`	`"creators": [`
`4`	`5`	`{`
`5`	`6`	`"name": "Ragnar Pall Ardal"`
`6`	`7`	`},`
`7`	`8`	`{`
`8`		`- "name": "Tomas Ken Magnusson"`
	`9`	`+ "name": "Arnar Bjarni Arnarson"`
`9`	`10`	`},`
`10`	`11`	`{`
`11`	`12`	`"affiliation": "Reykjavik University",`
`12`		`- "name": "Émile Nadeau"`
`13`		`- },`
`14`		`- {`
`15`		`- "name": "Bjarni Jens Kristinsson"`
	`13`	`+ "name": "Christian Bean"`
`16`	`14`	`},`
`17`	`15`	`{`
`18`		`- "name": "Bjarki Agust Gudmundsson"`
	`16`	`+ "name": "Alfur Birkir Bjarnason"`
`19`	`17`	`},`
`20`	`18`	`{`
`21`	`19`	`"affiliation": "Reykjavik University",`
`22`		`- "name": "Christian Bean"`
	`20`	`+ "name": "Jon Steinn Eliasson"`
`23`	`21`	`},`
`24`	`22`	`{`
`25`		`- "affiliation": "Reykjavik University",`
`26`		`- "name": "Henning Ulfarsson"`
	`23`	`+ "name": "Bjarki Agust Gudmundsson"`
`27`	`24`	`},`
`28`	`25`	`{`
`29`	`26`	`"affiliation": "Reykjavik University",`
`30`		`- "name": "Jon Steinn Eliasson"`
	`27`	`+ "name": "Sigurjón Ingi Jónsson"`
	`28`	`+ }`
	`29`	`+ {`
	`30`	`+ "name": "Bjarni Jens Kristinsson"`
`31`	`31`	`},`
`32`	`32`	`{`
`33`		`- "name": "Murray Tannock"`
	`33`	`+ "name": "Tomas Ken Magnusson"`
`34`	`34`	`},`
`35`	`35`	`{`
`36`		`- "name": "Alfur Birkir Bjarnason"`
	`36`	`+ "affiliation": "Reykjavik University",`
	`37`	`+ "name": "Émile Nadeau"`
`37`	`38`	`},`
`38`	`39`	`{`
`39`	`40`	`"affiliation": "Marquette University",`
`40`	`41`	`"name": "Jay Pantone"`
`41`	`42`	`},`
`42`	`43`	`{`
`43`		`- "name": "Arnar Bjarni Arnarson"`
	`44`	`+ "name": "Murray Tannock"`
`44`	`45`	`},`
`45`	`46`	`{`
`46`	`47`	`"affiliation": "Reykjavik University",`
`47`		`- "name": "Sigurjón Ingi Jónsson"`
`48`		`- }`
	`48`	`+ "name": "Henning Ulfarsson"`
	`49`	`+ },`
`49`	`50`	`]`
`50`	`51`	`}`