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Implement basic multivariate polynomial species #38446

Merged
merged 171 commits into from
Nov 16, 2024
Merged

Implement basic multivariate polynomial species #38446

merged 171 commits into from
Nov 16, 2024

Commits on May 12, 2024

  1. Initial commit

    @Newtech66
    Newtech66 committed May 12, 2024
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Commits on May 14, 2024

  1. Added _add_, _mul_, _element_constructor_ for group action input

    @Newtech66
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  2. Fixed bugs with caching and _mul_

    @Newtech66
    Newtech66 committed May 14, 2024
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Commits on May 15, 2024

  1. Improved repr output and added a way to name conjugacy classes of sub… 

    …groups

Also added various miscellaneous functions
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  2. Merge branch 'develop' into burnside_ring

    @mantepse
    mantepse authored May 15, 2024
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Commits on May 16, 2024

  1. Update src/sage/rings/burnside.py 

    Co-authored-by: Martin Rubey <axiomize@yahoo.de>
    @Newtech66 @mantepse
    Newtech66 and mantepse authored May 16, 2024
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  2. Doctest updates

    @Newtech66
    Newtech66 committed May 16, 2024
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  3. Added ConjugacyClassesOfSubgroups

    @Newtech66
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  4. Burnside ring now inherits from CombinatorialFreeModule 

    Also some fixes to _element_constructor_ ConjugacyClassesOfSubgroups
    @Newtech66
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  5. Changed category of Burnside ring to Algebras(base_ring).Commutative(… 

    …).WithBasis()
    @Newtech66
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Commits on May 17, 2024

  1. Implemented monomial() and one_basis() 

    Added _repr_ for ConjugacyClassesOfSubgroups
I now output B[(gens or name if available)] as _repr_ for generators, for example B[1] + 2*B[(2,3,4)]
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  2. Add rename_gen

    @Newtech66
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  3. Add construct_from_action

    @Newtech66
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  4. Add _from_dict

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Commits on May 18, 2024

  1. Add product_on_basis and monomial_coefficients

    @Newtech66
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  2. Remove ConjugacyClassesOfSubgroups from import

    @Newtech66
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  3. Make indexes for generators use ConjugacyClassesOfSubgroups internall… 

    …y and doctest updates
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  4. Add __eq__ for ConjugacyClassOfSubgroups so we can use it as dict key

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Commits on May 19, 2024

  1. Removed BurnsideRingElement and refactored code

    @Newtech66
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  2. Add __getitem__, minor doctest fix

    @Newtech66
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  3. Add __eq__ and minor fix in _normalize and set_name

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Commits on May 20, 2024

  1. Implemented all suggested changes

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  2. Doctest additions

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Commits on May 21, 2024

  1. Doctest updates

    @Newtech66
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  2. Run doctest fixer

    @Newtech66
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  3. Small change

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Commits on Jun 15, 2024

  1. Draft implementation of PolynomialMolecularDecomposition + other mino… 

    …r changes
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Commits on Jun 16, 2024

  1. Added PolynomialMolecularDecomposition to imports

    @Newtech66
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  2. Fixed __iter__ and added subset in ConjugacyClassesOfSymmetricGroupSu… 

    …bgroups
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Commits on Jun 17, 2024

  1. Refactor conjugacy classes of subgroups of symmetric groups, add spec… 

    …ial case in construct_element
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Commits on Jun 18, 2024

  1. Reworked naming facility + other minor changes

    @Newtech66
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  2. Add default_name for fallback if no name is present

    @Newtech66
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  3. Minor correction

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  4. Remove _repr_ from ConjugacyClassOfSubgroups_SymmetricGroup

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Commits on Jun 22, 2024

  1. Reworked naming system again to use CombinatorialFreeModule's naming … 

    …system
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Commits on Jun 23, 2024

  1. Minor performance improvements

    @Newtech66
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  2. Major performance improvement in PolynomialMolecularDecomposition pro… 

    …duct_on_basis
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Commits on Jun 26, 2024

  1. Much faster implementation of Burnside ring product

    @Newtech66
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Commits on Jun 30, 2024

  1. Improvements and corrections

    @Newtech66
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  2. Doctest fixes

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Commits on Jul 6, 2024

  1. Add most doctests

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Commits on Jul 13, 2024

  1. Doctest fixes

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Commits on Jul 16, 2024

  1. Doctest fix

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Commits on Jul 21, 2024

  1. Rewrite of species decompositions

    @Newtech66
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  2. Doctests

    @Newtech66
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Commits on Jul 22, 2024

  1. Add construct_from_action to PolynomialMolecularDecomposition

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Commits on Jul 24, 2024

  1. Rewrite

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  2. Minor fixes

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  3. More fixes

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Commits on Jul 25, 2024

  1. Add degree_on_basis

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  2. more fixes

    @Newtech66
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  3. Merge branch 'develop' into burnside_ring

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Commits on Jul 29, 2024

  1. Split species into new PR

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  2. grab changes from other PR

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Commits on Jul 31, 2024

  1. Removed dependency on burnside.py (for the time being)

    @Newtech66
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  2. Rewrite

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  3. Normalization fixes

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Commits on Aug 1, 2024

  1. More fixes

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  2. removed __eq__, added _repr_, and doctest fixes

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  3. remove Set, add shortcut element init for AtomicSpecies and Polynomia… 

    …lSpecies
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  4. doctest fixes

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Commits on Aug 2, 2024

  1. improvements (mantepse)

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Commits on Aug 3, 2024

  1. Add __call__ for partitional composition

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Commits on Aug 5, 2024

  1. Highly experimental commit aimed at improving performance, needs a lo… 

    …t of feedback
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  2. Refactoring and bug fixes

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Commits on Aug 7, 2024

  1. Composition works, if there are no coefficients

    @Newtech66
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  2. Added cartesian product

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Commits on Aug 8, 2024

  1. Added addition formula decomposition

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Commits on Aug 9, 2024

  1. Added multiplicity handling

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Commits on Aug 14, 2024

  1. Fixed dompart, caching and construction errors, and equality checking… 

    … for atomic species
    @Newtech66
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  2. revert changes to permgroup.py

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Commits on Aug 17, 2024

  1. Canonicalization fixes, doctest additions

    @Newtech66
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  2. More doctests

    @Newtech66
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  3. Remove current composition and cartesian product framework

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Commits on Aug 19, 2024

  1. Add inner_sum

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  2. Doctest fixes

    @Newtech66
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  3. Move things around and minor fixes

    @Newtech66
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  4. Add renaming patch (thanks mantepse)

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Commits on Aug 20, 2024

  1. Add substitution, element_constructor for molecular species

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Commits on Aug 21, 2024

  1. Add cartesian_product and doctests

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  2. Minor changes

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  3. Minor changes+partial naming changes

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  4. New renaming (thanks mantepse) + construct from group action (wip)

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  5. Construct from group action (complete, added to MolecularSpecies and … 

    …PolynomialSpecies)
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Commits on Aug 22, 2024

  1. Edits to error checking and messages

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  2. More minor changes

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Commits on Aug 24, 2024

  1. Added functorial composition for univariate molecular species

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Commits on Aug 25, 2024

  1. remove functorial_composition and change molecular species grading

    @Newtech66
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  2. Replace tuple with frozenset for dompart

    @Newtech66
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  3. fix doctests

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  4. Add doctests

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  5. run doctest fixer

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Commits on Aug 26, 2024

  1. some more doctests

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  2. run doctest fixer

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  3. pycodestyle fix

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  4. change AtomicSpeciesElement _repr_ and remove multicardinality check … 

    …in MolecularSpecies __call__
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  5. Get rid of some calls to libgap ConjugateGroup without passing domain… 

    … and use gens_small in ConjugacyClassOfSubgroups _canonicalize
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  6. run doctest fixer

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  7. Working composition (thanks mantepse)

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Commits on Aug 27, 2024

  1. use Labelle's powersum species to compute compositions

    @mantepse
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Commits on Aug 30, 2024

  1. Only show dompart for arity >2

    @Newtech66
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  2. Rename _k to _arity globally

    @Newtech66
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  3. fix doctests

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Commits on Sep 9, 2024

  1. Fix in compose_with_singletons

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Commits on Sep 11, 2024

  1. move test for conjugacy to PermutationGroup_generic

    @mantepse
    mantepse committed Sep 11, 2024
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  2. more doctests, fixes for LazySpecies

    @mantepse
    mantepse committed Sep 11, 2024
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  3. make MolecularSpecies accept names as argument, provide graded_compon… 

    …ents
    @mantepse
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Commits on Sep 12, 2024

  1. separate computation of group and domain partition of molecular species

    @mantepse
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Commits on Sep 13, 2024

  1. remove _project and gen

    @mantepse
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  2. fix bugs in _element_constructor_ when creating species from a group … 

    …action
    @mantepse
    mantepse committed Sep 13, 2024
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  3. make indexing of sorts 0-based, be more permissive with input of doma… 

    …in partition
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    mantepse committed Sep 13, 2024
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Commits on Sep 23, 2024

  1. fix domain bug in group_and_partition, add cycle_index

    @mantepse
    mantepse committed Sep 23, 2024
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Commits on Sep 25, 2024

  1. rename and simplify ElementCache by using hash

    @mantepse
    mantepse committed Sep 25, 2024
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  2. remove debugging statement

    @mantepse
    mantepse committed Sep 25, 2024
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  3. simpler and less buggy by using UniqueRepresentation

    @mantepse
    mantepse committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. make homogeneous_degree work if the monomials are not comparable

    @mantepse
    mantepse committed Sep 26, 2024
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  2. beautify

    @mantepse
    mantepse committed Sep 26, 2024
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  3. update references, do not put AtomicSpecies and PolynomialSpecies int… 

    …o global namespace
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    mantepse committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. provide subset (to also get homogeneous_degree_basis) and change_ring

    @mantepse
    mantepse committed Sep 27, 2024
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Commits on Sep 28, 2024

  1. Merge branch 'develop' into simple-species

    @mantepse
    mantepse committed Sep 28, 2024
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  2. Merge branch 'develop' into simple-species

    @mantepse
    mantepse committed Sep 28, 2024
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Commits on Sep 29, 2024

  1. enable user friendly P.<X> = PolynomialSpecies(R), without implementi… 

    …ng gens
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    mantepse committed Sep 29, 2024
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  2. Merge branch 'develop' into simple-species

    @mantepse
    mantepse authored Sep 29, 2024
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  3. mark some doctests as random, run TestSuite also for element classes,… 

    … explain why we are skipping parts of the testsuite
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    mantepse committed Sep 29, 2024
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Commits on Oct 4, 2024

  1. partially fix bug

    @mantepse
    mantepse committed Oct 4, 2024
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  2. fix bug when specifying species via a group action

    @mantepse
    mantepse committed Oct 4, 2024
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Commits on Oct 13, 2024

  1. very minor docstring fixes

    @mantepse
    mantepse committed Oct 13, 2024
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  2. Merge branch 'sagemath:develop' into simple-species

    @mantepse
    mantepse authored Oct 13, 2024
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  3. add factorization of polynomial species

    @mantepse
    mantepse committed Oct 13, 2024
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  4. introduce comparisons and add subset and graded_component for atomic … 

    …species
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    mantepse committed Oct 13, 2024
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Commits on Oct 15, 2024

  1. replace UniqueRepresentation of the Element classes with WithPickling… 

    …ByInitArgs
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    mantepse committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. fix and doctest bug in group_and_partition

    @mantepse
    mantepse committed Oct 16, 2024
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Commits on Oct 21, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Oct 21, 2024
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  2. adapt doctest, improve some docstrings

    @mantepse
    mantepse committed Oct 21, 2024
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  3. test error cases of element constructors

    @mantepse
    mantepse committed Oct 21, 2024
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  4. remove forgotten error in __contains__

    @mantepse
    mantepse committed Oct 21, 2024
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Commits on Oct 22, 2024

  1. restore accidentally deleted caching

    @mantepse
    mantepse committed Oct 22, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Oct 22, 2024
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  3. test that we create every group only once

    @mantepse
    mantepse committed Oct 22, 2024
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  4. Merge branch 'simple-species' of https://github.com/Newtech66/sage-ne… 

    …wtech66 into simple-species
    @mantepse
    mantepse committed Oct 22, 2024
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  5. clarify output of group_and_partition

    @mantepse
    mantepse committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. fix some codecov reports

    @mantepse
    mantepse committed Oct 23, 2024
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  2. implement _richcmp_ instead of __le__ and friends

    @mantepse
    mantepse committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. remove dead code discovered by codecov

    @mantepse
    mantepse committed Oct 24, 2024
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  2. test more errors and remove more dead code discovered by codecov

    @mantepse
    mantepse committed Oct 24, 2024
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Commits on Oct 26, 2024

  1. remove ConjugacyClassOfDirectlyIndecomposableSubgroups and ConjugacyC… 

    …lassesOfDirectlyIndecomposableSubgroups and reorganize AtomicSpeciesElement.__classcall__ for significant performance improvement
    @mantepse
    mantepse committed Oct 26, 2024
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  2. allow to skip checks, make variable names more consistent, avoid unne… 

    …ccessary conversions between gap and sage in AtomicSpeciesElement.__classcall__ for performance
    @mantepse
    mantepse committed Oct 26, 2024
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  3. test sanity of parameters of _compose_with_weighted_singletons

    @mantepse
    mantepse committed Oct 26, 2024
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  4. add doctest, remove dead code discovered by codecov

    @mantepse
    mantepse committed Oct 26, 2024
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  5. rename group_and_partition to permutation_group

    @mantepse
    mantepse committed Oct 26, 2024
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Commits on Oct 27, 2024

  1. add example and test for _compose_with_weighted_singletons for 100% c… 

    …overage
    @mantepse
    mantepse committed Oct 27, 2024
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  2. show construction of table of marks

    @mantepse
    mantepse committed Oct 27, 2024
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  3. remove hash by switching inheritance order, replace richcmp with lt a… 

    …nd le
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    mantepse committed Oct 27, 2024
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Commits on Oct 28, 2024

  1. Merge branch 'develop' into simple-species

    @kwankyu
    kwankyu authored Oct 28, 2024
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Commits on Oct 29, 2024

  1. fix a bug in creating multisort species given an action and fix INPUT… 

    … description
    @mantepse
    mantepse committed Oct 29, 2024
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  2. minor optimization

    @mantepse
    mantepse committed Oct 29, 2024
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Commits on Nov 4, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Nov 4, 2024
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  2. remove unnecessary else spotted by tscrim

    @mantepse
    mantepse committed Nov 4, 2024
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  3. implement _an_element_ instead of caching an_element as spotted by ts… 

    …crim
    @mantepse
    mantepse committed Nov 4, 2024
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  4. adapt doctest

    @mantepse
    mantepse committed Nov 4, 2024
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  5. do not use assert for input checking, spotted by tscrim

    @mantepse
    mantepse committed Nov 4, 2024
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  6. remove superfluous __init__ as spotted by tscrim

    @mantepse
    mantepse committed Nov 4, 2024
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  7. sort cover relations as str

    @mantepse
    mantepse committed Nov 4, 2024
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  8. more replacements of parent == self to parent is self

    @mantepse
    mantepse committed Nov 4, 2024
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Commits on Nov 7, 2024

  1. make MolecularSpecies.__classcall__ sane

    @mantepse
    mantepse committed Nov 7, 2024
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  2. improve documentation

    @mantepse
    mantepse committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. Update src/sage/rings/species.py 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Nov 8, 2024
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  2. Update src/sage/rings/species.py 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Nov 8, 2024
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  3. Apply suggestions from code review 

    Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
    @mantepse @tscrim
    mantepse and tscrim authored Nov 8, 2024
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  4. docfixes

    @mantepse
    mantepse committed Nov 8, 2024
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  5. avoid recursion in _element_constructor_

    @mantepse
    mantepse committed Nov 8, 2024
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