Merge pull request #195 from PermutaTriangle/develop

Version 2.3.0

Author: christianbean

.github/workflows/build-and-deploy.yml

@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: "3.10"
     - name: install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test.yml

@@ -9,22 +9,19 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python: 3.8
+          - python: "3.11"
             toxenv: flake8
             os: ubuntu-latest
-          - python: 3.8
+          - python: "3.11"
             toxenv: mypy
             os: ubuntu-latest
-          - python: 3.8
+          - python: "3.11"
             toxenv: pylint
             os: ubuntu-latest
-          - python: 3.8
+          - python: "3.11"
             toxenv: black
             os: ubuntu-latest
 
-          - python: 3.7
-            toxenv: py37
-            os: ubuntu-latest
           - python: 3.8
             toxenv: py38
             os: ubuntu-latest
@@ -34,25 +31,31 @@ jobs:
           - python: "3.10"
             toxenv: py310
             os: ubuntu-latest
-          - python: pypy-3.7
-            toxenv: pypy37
+          - python: "3.11"
+            toxenv: py311
+            os: ubuntu-latest
+          - python: "3.12"
+            toxenv: py312
+            os: ubuntu-latest
+          - python: 'pypy3.9'
+            toxenv: pypy39
             os: ubuntu-latest
 
-          - python: 3.8
-            toxenv: py38
+          - python: "3.11"
+            toxenv: py311
             os: macos-latest
-          - python: 3.8
-            toxenv: py38
+          - python: "3.11"
+            toxenv: py311
             os: windows-latest
 
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{  matrix.python }}
       - name: install dependencies
-        run: python -m pip install --upgrade pip tox
+        run: python -m pip install --upgrade pip tox setuptools wheel
       - name: run
         env:
           TOXENV: ${{ matrix.toxenv }}

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 21.9b0
+    rev: 22.10.0
     hooks:
       - id: black

.pylintrc

@@ -7,8 +7,7 @@ ignore-patterns=test_.*?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,
-        missing-module-docstring,
+disable=missing-module-docstring,
         fixme,
         unsubscriptable-object,
         unspecified-encoding

CHANGELOG.md

@@ -4,7 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## Unreleased 
+
+## 2.3.0 - 2024-04-03
+### Changed
+ - Updated dependency on automata-lib to version 7.0.1
+ - Perm.avoids/contains will raise a TypeError if input is not an iterable of Patt
+
+### Added
+ - Now testing on Python 3.11
+ - 'simple' to the permtool command for checking if finitely many simples in a class
+
+### Fixed
+ - bug in autobisc during setup
 
 ## 2.2.0 - 2021-10-21
 ### Added
@@ -29,6 +41,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### 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`.
+  - If you pass an iterable (that is not a perm) to a contains method, then it will now raise an error. 
+  These should be passed with the splat '*'. 
 
 ## 2.0.3 - 2021-04-28
 ### Added

README.rst

@@ -18,8 +18,8 @@ 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
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4725759.svg
-   :target: https://doi.org/10.5281/zenodo.4725759
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4725758.svg
+   :target: https://doi.org/10.5281/zenodo.4725758
 
 Permuta is a Python library for working with perms (short for permutations),
 patterns, and mesh patterns.
@@ -114,6 +114,21 @@ Printing perms gives zero-based strings.
     >>> print(Perm((6, 2, 10, 9, 3, 8, 0, 1, 5, 11, 4, 7)))
     (6)(2)(10)(9)(3)(8)(0)(1)(5)(11)(4)(7)
 
+To get an iterator of all permutations of a certain length you can use
+
+.. code-block:: python
+
+    >>> Perms4 = Perm.of_length(4)
+
+You can run a for-loop over this iterator if you need to do something with all
+the permutations of this size. If you just want a specific permutation of this
+size you might be better off using the unrank function.
+
+.. code-block:: python
+
+    >>> Perm.unrank(23,4)
+    Perm((3, 2, 1, 0))
+
 The avoids, contains, and occurrence methods enable working with patterns:
 
 .. code-block:: python
@@ -206,6 +221,11 @@ given class.
     >>> for strat in find_strategies(basis):
     ...     print(strat.reference())
     Enumeration of Permutation Classes and Weighted Labelled Independent Sets: Corollary 4.3
+    >>> basis = [Perm((1, 3, 0, 2)), Perm((2, 0, 3, 1))]
+    >>> for strat in find_strategies(basis):
+    ...     print(strat.reference())
+    Enumeration of Permutation Classes and Weighted Labelled Independent Sets: Corollary 4.6
+    The class contains only finitely many simple permutations
 
 Permutation statistics
 ######################
@@ -506,6 +526,6 @@ 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
+.. _BibTex: https://zenodo.org/record/4945792/export/hx#.YImTibX7SUk
 
-.. _Zenodo: https://doi.org/10.5281/zenodo.4725759
+.. _Zenodo: https://doi.org/10.5281/zenodo.4725758

mypy.ini

@@ -1,4 +1,5 @@
 [mypy]
+check_untyped_defs = True
 warn_return_any = True
 warn_unused_configs = True
 warn_no_return = False

permuta/__init__.py

@@ -1,7 +1,7 @@
 from .patterns import BivincularPatt, CovincularPatt, MeshPatt, Perm, VincularPatt
 from .perm_sets.permset import Av, Basis, MeshBasis
 
-__version__ = "2.2.0"
+__version__ = "2.3.0"
 
 __all__ = [
     "Perm",

permuta/bisc/__init__.py

@@ -1,3 +1,5 @@
+# type: ignore
+
 from .bisc import auto_bisc, bisc, create_bisc_input, read_bisc_file, write_bisc_files
 from .bisc_subfunctions import (
     patterns_suffice_for_bad,

permuta/bisc/bisc.py

@@ -1,3 +1,5 @@
+# type: ignore
+
 import json
 import os
 import types
@@ -17,7 +19,6 @@
 
 
 def bisc(A, m, n=None, report=False):
-
     if isinstance(A, list):
         D = defaultdict(list)
         for perm in A:
@@ -54,7 +55,6 @@ def bisc(A, m, n=None, report=False):
 
 
 def auto_bisc(prop):
-
     L = 8  # Want to sanity check on at least S8, and one above n
     n = 4
     m = 2
@@ -69,10 +69,10 @@ def auto_bisc(prop):
         if L not in A.keys():
             print("You should have permutations up to length at least 8")
             return
-        for i in range(L + 1):
-            for perm in Perm.of_length(i):
-                if perm not in A[i]:
-                    B[i].append(perm)
+        for i in range(max(L + 1, max(A.keys()) + 1)):
+            if i > 7:
+                print("Populating the dictionary of bad perms of length ", i)
+            B[i] = [perm for perm in Perm.of_length(i) if perm not in A[i]]
 
     elif isinstance(prop, types.FunctionType):
         # If a property is passed in then we use it to populate both
@@ -212,7 +212,7 @@ def auto_bisc(prop):
         oldL = L
         if L < n + 1:
             L = n + 1
-            if isinstance(prop, list) and L > max(A.keys):
+            if isinstance(prop, list) and L > max(A.keys()):
                 print("You need to input a longer list of permutations")
                 return
 
@@ -272,7 +272,6 @@ def create_bisc_input(N, prop):
     A, B = {}, {}
 
     for n in range(N + 1):
-
         An, Bn = [], []
 
         for perm in Perm.of_length(n):