Merge pull request #175 from PermutaTriangle/develop

Version 2.1.0

Author: enadeau

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 20.8b0
+    rev: 21.6b0
     hooks:
       - id: black

.zenodo.json

@@ -41,6 +41,10 @@
         },
         {
             "name": "Arnar Bjarni Arnarson"
+        },
+        {
+            "affiliation": "Reykjavik University",
+            "name": "Sigurjón Ingi Jónsson"
         }
     ]
-}
+}

CHANGELOG.md

@@ -6,6 +6,21 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## Unreleased
 
+## 2.1.0 - 2021-06-14
+### Added
+ - Statistic: bounce of a permutation.
+ - Statistic: maximum drop size.
+ - Statistic: number of primes in the column sums.
+ - Statistic: holeyness of a permutation.
+ - Algorithm: `pop stack sort`.
+ - Statistic: count stack sorts.
+ - Statistic: count pop stack sorts.
+ - Statistic: Pinnacle set and number of pinnacles.
+
+### Changed
+  - Functions for ascents and descents now take an optional argument to specify what step size to calculate.
+  - Moved sorting functions from `permuta/bisc/perm_properties.py` to `permuta/patterns/perm.py`.
+
 ## 2.0.3 - 2021-04-28
 ### Added
  - using Github Actions for testing and deployment

README.rst

@@ -16,8 +16,10 @@ permuta
     :alt: Travis
     :target: https://travis-ci.org/PermutaTriangle/Permuta
 .. image:: https://requires.io/github/PermutaTriangle/Permuta/requirements.svg?branch=master
-     :target: https://requires.io/github/PermutaTriangle/Permuta/requirements/?branch=master
-     :alt: Requirements Status
+    :target: https://requires.io/github/PermutaTriangle/Permuta/requirements/?branch=master
+    :alt: Requirements Status
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4725759.svg
+   :target: https://doi.org/10.5281/zenodo.4725759
 
 Permuta is a Python library for working with perms (short for permutations),
 patterns, and mesh patterns.
@@ -235,6 +237,22 @@ and a class (no class will use the set of all permutations).
     [14] Longest increasing subsequence
     [15] Longest decreasing subsequence
     [16] Depth
+    [17] Number of bounces
+    [18] Maximum drop size
+    [19] Number of primes in the column sums
+    [20] Holeyness of a permutation
+    [21] Number of stack-sorts needed
+    [22] Number of pop-stack-sorts needed
+    [23] Number of pinnacles
+    [24] Number of cyclic peaks
+    [25] Number of cyclic valleys
+    [26] Number of double excedance
+    [27] Number of double drops
+    [28] Number of foremaxima
+    [29] Number of afterminima
+    [30] Number of aftermaxima
+    [31] Number of foreminima
+
     >>> depth = PermutationStatistic.get_by_index(16)
     >>> depth.distribution_for_length(5)
     [1, 4, 12, 24, 35, 24, 20]
@@ -251,6 +269,8 @@ Given a bijection as a dictionary, we can check which statistics are preserved w
     ...     print(stat)
     Number of peaks
     Number of valleys
+    Holeyness of a permutation
+    Number of pinnacles
 
 We can find all (predefined) statistics equally distributed over two permutation
 classes with ``equally_distributed``. We also support checks for joint distribution
@@ -272,6 +292,7 @@ of jointly distributed stats with ``jointly_transformed_equally_distributed``.
     Number of right-to-left maximas
     Longest increasing subsequence
     Longest decreasing subsequence
+    Number of pinnacles
 
 The BiSC algorithm
 ==================
@@ -287,20 +308,19 @@ To use the algorithm we first need to import it.
     >>> from permuta.bisc import *
 
 A classic example of a set of permutations described by pattern avoidance are
-the permutations sortable in one pass through a stack. We start by loading a
-function ``stack_sortable`` which returns ``True`` for permutations that
-satisfy this property. The user now has two choices: Run
-``auto_bisc(stack_sortable)`` and let the algorithm run without any more user
-input. It will try to use sensible values, starting by learning small patterns
-from small permutations, and only considering longer patterns when that fails.
-If the user wants to have more control over what happens that is also possible
-and we now walk through that: We input the property into ``bisc`` and ask it to
-search for patterns of length 3.
+the permutations sortable in one pass through a stack. We use the function
+``stack_sortable`` which returns ``True`` for permutations that satisfy this
+property. The user now has two choices: Run
+``auto_bisc(Perm.stack_sortable)`` and let the algorithm run
+without any more user input. It will try to use sensible values, starting by
+learning small patterns from small permutations, and only considering longer
+patterns when that fails. If the user wants to have more control over what
+happens that is also possible and we now walk through that: We input the
+property into ``bisc`` and ask it to search for patterns of length 3.
 
 .. code-block:: python
 
-    >>> from permuta.bisc.perm_properties import stack_sortable
-    >>> bisc(stack_sortable, 3)
+    >>> bisc(Perm.stack_sortable, 3)
     I will use permutations up to length 7
     {3: {Perm((1, 2, 0)): [set()]}}
 
@@ -315,7 +335,7 @@ be considered.
 
 .. code-block:: python
 
-    >>> SG = bisc(stack_sortable, 3, 5)
+    >>> SG = bisc(Perm.stack_sortable, 3, 5)
     >>> show_me(SG)
     There are 1 underlying classical patterns of length 3
     There are 1 different shadings on 120
@@ -341,8 +361,7 @@ patterns, such as the West-2-stack-sortable permutations
 
 .. code-block:: python
 
-    >>> from permuta.bisc.perm_properties import west_2_stack_sortable
-    >>> SG = bisc(west_2_stack_sortable, 5, 7)
+    >>> SG = bisc(Perm.west_2_stack_sortable, 5, 7)
     >>> show_me(SG)
     There are 2 underlying classical patterns of length 4
     There are 1 different shadings on 1230
@@ -394,7 +413,7 @@ which keeps them separated by length.
 
 .. code-block:: python
 
-    >>> A, B = create_bisc_input(7, west_2_stack_sortable)
+    >>> A, B = create_bisc_input(7, Perm.west_2_stack_sortable)
 
 This creates two dictionaries with keys 1, 2, ..., 7 such that ``A[i]`` points
 to the list of permutations of length ``i`` that are West-2-stack-sortable, and
@@ -476,3 +495,13 @@ License
 #######
 
 BSD-3: see the `LICENSE <https://github.com/PermutaTriangle/Permuta/blob/master/LICENSE>`_ file.
+
+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. 
+
+.. _BibTex: https://zenodo.org/record/4725759/export/hx#.YImTibX7SUk
+
+.. _Zenodo: https://doi.org/10.5281/zenodo.4725759

permuta/__init__.py

@@ -1,7 +1,7 @@
 from .patterns import BivincularPatt, CovincularPatt, MeshPatt, Perm, VincularPatt
 from .perm_sets.permset import Av, Basis, MeshBasis
 
-__version__ = "2.0.4"
+__version__ = "2.1.0"
 
 __all__ = [
     "Perm",

permuta/bisc/perm_properties.py

@@ -1,145 +1,10 @@
-from collections import deque
 from itertools import islice
-from typing import Deque, List, Tuple
+from typing import List
 
 from permuta.patterns.meshpatt import MeshPatt
-from permuta.patterns.patt import Patt
 from permuta.patterns.perm import Perm
 from permuta.permutils.groups import dihedral_group
 
-
-def _is_sorted(lis: List[int]) -> bool:
-    #  Return true if w is increasing, i.e., sorted.
-    return all(elem == i for elem, i in zip(lis, range(len(lis))))
-
-
-def _stack_sort(perm_slice: List[int]) -> List[int]:
-    n = len(perm_slice)
-    if n in (0, 1):
-        return perm_slice
-    max_i, max_v = max(enumerate(perm_slice), key=lambda pos_elem: pos_elem[1])
-    # Recursively solve without largest
-    if max_i == 0:
-        n_lis = _stack_sort(perm_slice[1:n])
-    elif max_i == n - 1:
-        n_lis = _stack_sort(perm_slice[0 : n - 1])
-    else:
-        n_lis = _stack_sort(perm_slice[0:max_i])
-        n_lis.extend(_stack_sort(perm_slice[max_i + 1 : n]))
-    n_lis.append(max_v)
-    return n_lis
-
-
-def stack_sortable(perm: Perm) -> bool:
-    """Returns true if perm is stack sortable."""
-    return _is_sorted(_stack_sort(list(perm)))
-
-
-def _bubble_sort(perm_slice: List[int]) -> List[int]:
-    n = len(perm_slice)
-    if n in (0, 1):
-        return perm_slice
-    max_i, max_v = max(enumerate(perm_slice), key=lambda pos_elem: pos_elem[1])
-    # Recursively solve without largest
-    if max_i == 0:
-        n_lis = perm_slice[1:n]
-    elif max_i == n - 1:
-        n_lis = _bubble_sort(perm_slice[0 : n - 1])
-    else:
-        n_lis = _bubble_sort(perm_slice[0:max_i])
-        n_lis.extend(perm_slice[max_i + 1 : n])
-    n_lis.append(max_v)
-    return n_lis
-
-
-def bubble_sortable(perm: Perm) -> bool:
-    """Returns true if perm is stack sortable."""
-    return _is_sorted(_bubble_sort(list(perm)))
-
-
-def _quick_sort(perm_slice: List[int]) -> List[int]:
-    assert not perm_slice or set(perm_slice) == set(
-        range(min(perm_slice), max(perm_slice) + 1)
-    )
-    n = len(perm_slice)
-    if n == 0:
-        return perm_slice
-    maxind = -1
-    # Note that perm does not need standardizing as sfp uses left to right maxima.
-    for maxind in Perm(perm_slice).strong_fixed_points():
-        pass
-    if maxind != -1:
-        lis: List[int] = (
-            _quick_sort(perm_slice[:maxind])
-            + [perm_slice[maxind]]
-            + _quick_sort(perm_slice[maxind + 1 :])
-        )
-    else:
-        firstval = perm_slice[0]
-        lis = (
-            list(filter(lambda x: x < firstval, perm_slice))
-            + [perm_slice[0]]
-            + list(filter(lambda x: x > firstval, perm_slice))
-        )
-    return lis
-
-
-def quick_sortable(perm: Perm) -> bool:
-    """Returns true if perm is quicksort sortable."""
-    return _is_sorted(_quick_sort(list(perm)))
-
-
-_BKV_PATT = Perm((1, 0))
-
-
-def bkv_sortable(perm: Perm, patterns: Tuple[Patt, ...] = ()) -> bool:
-    """Check if a permutation is BKV sortable.
-    See:
-        https://arxiv.org/pdf/1907.08142.pdf
-        https://arxiv.org/pdf/2004.01812.pdf
-    """
-    # See
-    n = len(perm)
-    inp = deque(perm)
-    # the right stack read from top to bottom
-    # the left stack read from top to bottom
-    right_stack: Deque[int] = deque([])
-    left_stack: Deque[int] = deque([])
-    expected = 0
-    while expected < n:
-        if inp:
-            right_stack.appendleft(inp[0])
-            if Perm.to_standard(right_stack).avoids(*patterns):
-                inp.popleft()
-                continue
-            right_stack.popleft()
-
-        if right_stack:
-            left_stack.appendleft(right_stack[0])
-            if Perm.to_standard(left_stack).avoids(_BKV_PATT):
-                right_stack.popleft()
-                continue
-            left_stack.popleft()
-
-        assert left_stack
-        # Normally, we would gather elements from left stack but since we only care
-        # about wether it sorts the permutation, we just compare it against expected.
-        if expected != left_stack.popleft():
-            return False
-        expected += 1
-    return True
-
-
-def west_2_stack_sortable(perm: Perm) -> bool:
-    """Returns true if perm can be sorted by two passes through a stack"""
-    return _is_sorted(_stack_sort(_stack_sort(list(perm))))
-
-
-def west_3_stack_sortable(perm: Perm) -> bool:
-    """Returns true if perm can be sorted by three passes through a stack"""
-    return _is_sorted(_stack_sort(_stack_sort(_stack_sort(list(perm)))))
-
-
 _SMOOTH_PATT = (Perm((0, 2, 1, 3)), Perm((1, 0, 3, 2)))
 
 

permuta/misc/math.py

@@ -0,0 +1,12 @@
+def is_prime(n: int) -> bool:
+    """Primality test using 6k+-1 optimization."""
+    if n <= 3:
+        return n > 1
+    if n % 2 == 0 or n % 3 == 0:
+        return False
+    i = 5
+    while i ** 2 <= n:
+        if n % i == 0 or n % (i + 2) == 0:
+            return False
+        i += 6
+    return True