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Backports for Oscar 1.0-rc #3378

Merged
merged 29 commits into from
Feb 23, 2024
Merged

Backports for Oscar 1.0-rc #3378

merged 29 commits into from
Feb 23, 2024

Commits on Feb 16, 2024

  1. Change some things from British to American spelling (#3367)

    * `factorisations` -> `factorizations`
    
    * comment and docu fixes
    
    * Add `centraliser` -> `centralizer` deprecation
    
    * `neighbour` -> `neighbor`
    lgoettgens authored and benlorenz committed Feb 16, 2024
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  3. Performance improvements for PointVector, RayVector, SubObjectIterator (

    #3369)
    
    Add type assertions to their getindex methods to improve type stability.
    Similarly ensure that the return value of `size` is recognized as Tuple{Int}.
    
    Silly microbenchmark, before:
    
        julia> v = PointVector{ZZRingElem}(matrix(ZZ, [1 2 3 ; ]));
    
        julia> @Btime prod(v)
          1.217 μs (21 allocations: 336 bytes)
    
    After:
    
        julia> @Btime prod(v);
          288.449 ns (5 allocations: 80 bytes)
    fingolfin authored and benlorenz committed Feb 16, 2024
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Commits on Feb 17, 2024

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  2. Adv/upgrade regression fix (#3325)

    * some debuggging
    
    * add fix to upgrade tests, and fix code regression
    
    * updates johnson matrices, and always adds the refs to s.refs
    antonydellavecchia authored and benlorenz committed Feb 17, 2024
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  4. Make partitions and (semi)standard_tableaux return iterators (#3365)

    ... the quick and dirty way to have a stable API
    joschmitt authored and benlorenz committed Feb 17, 2024
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  5. Bugfix from running book code run.

    (cherry picked from commit d0aad4e)
    
    from PR #3298
    HechtiDerLachs authored and benlorenz committed Feb 17, 2024
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Commits on Feb 18, 2024

  1. Remove deprecated functions (#3366)

    * Remove deprecated use of `Frac`
    
    * Remove deprecated use of `chi`
    
    * Remove deprecated use of `MPolyElem`
    joschmitt authored and benlorenz committed Feb 18, 2024
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  2. New linear solving interface + bump dependencies (#3350)

    * feat: Use new linear algebra functionality
    
    * Adjust to deleted deprecations/aliases Hecke edition
    joschmitt authored and benlorenz committed Feb 18, 2024
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Commits on Feb 19, 2024

  1. Fix Grassmann Pluecker (#3382)

    * fixed
    
    * fix for symmetric intersections test
    
    * back to the roots
    
    * revert
    
    * Apply suggestions from code review
    
    Co-authored-by: Benjamin Lorenz <benlorenz@users.noreply.github.com>
    
    ---------
    
    Co-authored-by: Tommy Hofmann <thofma@gmail.com>
    Co-authored-by: Benjamin Lorenz <benlorenz@users.noreply.github.com>
    (cherry picked from commit 7433548)
    antonydellavecchia authored and benlorenz committed Feb 19, 2024
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  2. Fix show for RelativeBrauerGroupElem (#3373)

    - fix error because `Indent` was undefined
    - remove extra newline at end
    - add a missing `Lowercase`
    - simplify the code
    - make output order less random
    
    (cherry picked from commit aefcd0a)
    fingolfin authored and aaruni96 committed Feb 19, 2024
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Commits on Feb 21, 2024

  1. Enable edit and show source buttons in docs (#3381)

    * Typos
    * Make the "show source" buttons in the docs work again
    * Enable the "Edit page on GitHub" buttons
    
    (cherry picked from commit 56b8182)
    lgoettgens authored and benlorenz committed Feb 21, 2024
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  2. galois_group: fix is_normal call after removed deprecations (#3385)

    * fix is_normal call after removed deprecations
    
    * galois_group: add test from the book
    
    (cherry picked from commit a73b844)
    benlorenz committed Feb 21, 2024
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  3. Rename vec for AbstractAlgebra matrices to _vec (#3387)

    * Rename `vec` for AbstractAlgebra matrices to `_vec`
    
    * Move `_vec` to src
    
    * Adapt callsites
    
    (cherry picked from commit 0b282fb)
    lgoettgens authored and benlorenz committed Feb 21, 2024
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  4. add map_entries for matrix groups (#3341)

    (cherry picked from commit eb7bbdf)
    ThomasBreuer authored and benlorenz committed Feb 21, 2024
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  5. Remove unneeded GAP package sla (#3398)

    (cherry picked from commit 0bc8558)
    lgoettgens authored and benlorenz committed Feb 21, 2024
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  6. Make is_exterior_power (and friends) internal (#3346)

    * Rename `is_exterior_power` to `is_exterior_power_with_data` (and friends)
    
    * Revert "Rename `is_exterior_power` to `is_exterior_power_with_data` (and friends)"
    
    This reverts commit b19369b.
    
    * Make `is_exterior_power` internal
    
    * the same for similar functions
    
    (cherry picked from commit 9d88a8f)
    lgoettgens authored and benlorenz committed Feb 21, 2024
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  7. Make equality check less expensive (#3399)

    (cherry picked from commit 6408748)
    joschmitt authored and benlorenz committed Feb 21, 2024
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Commits on Feb 22, 2024

  1. Fixes for phylogenetic adjacency tree (#3406)

    * fixers for phylogenetic adjacency tree
    
    * get rid of whitespace
    
    * fix for tests
    
    (cherry picked from commit c65cb77)
    antonydellavecchia authored and benlorenz committed Feb 22, 2024
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  2. Draft - InvRing for SLn (#2823)

    * added cayley-omega.jl
    
    * made omegap a separate function
    
    * updates reynolds__ - need to fix det denominator
    
    * First attempt for SLn
    
    * fixed the bug
    
    * Added direct product and tensor
    
    * removed a loop from generators
    
    * small fix - reduce_gens_
    
    * deleted cayley omega
    
    * coefficient bug fixed
    
    * Created object Reductive Groups in file InvariantRings_ReductiveGroups
    
    * small fixes in InvariantRings_ReductiveGroups.jl
    
    * callable derksen_ideal and hilbert_ideal in InvariantRings_ReductiveGroups
    
    * export functions in InvariantRings_ReductiveGroups
    
    * printing of direct sum of vector stpaces in InvariantRings_ReductiveGroups
    
    * mu_star, reynolds_operator added to Inv Rings Red Grps
    
    * added file InvariantRings_ReductiveGroups
    
    * deleted redundant folder
    
    * Some tweaks
    
    * edits to make the code more efficient in InvariantTheory.jl
    
    * minor edits in InvariantTheory.jl
    
    * fixed coefficient problem in InvariantTheory.jl
    
    * added comments and minor edits. Lazy computation of InvariantRing in InvariantTheory.jl
    
    * minor edits to InvariantTheory.jl
    
    * added export functions in InvariantTheory.jl
    
    * typo in InvariantTheory.jl
    
    * minor edits in InvaraintTheory.jl, few tests in tests.jl
    
    * finished tests.jl for invariant theory of SLm
    
    * removed factorise in InvariantTheory.jl
    
    * more efficient rep_mat_ function in InvariantTheory.jl
    
    * chenged degree_basis function
    
    * pretty(io) in InvariantTheory.jl
    
    * minor change in reductive group constructor
    
    * evaluate func in generators func in InvariantTheory.jl
    
    * started with adding Torus to reductive groups
    
    * incorporating tori with fast algorithm to InvariantTheory.jl
    
    * removed show functions, added test in invariant theory
    
    * field error for reductive groups
    
    * minor type changes
    
    * added test for invariants of tori
    
    * direct product and tensor for representations
    
    * tests for direct sum, tensor of representaions, minor fix in construction function of reductive groups
    
    * minor modification
    
    * minor edits in InvariantTheory.jl
    
    * Update experimental/InvariantTheory/src/InvariantTheory.jl
    
    Co-authored-by: Max Horn <max@quendi.de>
    
    * Update experimental/InvariantTheory/src/InvariantTheory.jl
    
    Co-authored-by: Max Horn <max@quendi.de>
    
    * minor changes discussed in pull request
    
    * removed goto in torus invariants function
    
    * removed import statement
    
    * changed name of representation_from_forms
    
    * torus of rank
    
    * minor changes from pull request
    
    * minor edits from pr comments
    
    * minor changes in show commands
    
    * started file for torus fast
    
    * shifted torus to new file TorusInvariantsFast
    
    * minor change in fundtion degree basis
    
    * fixed typo
    
    * added comments, removed extra output of generators(..)
    
    * renamed InvariantRing to RedGrpInvRing
    
    * minor changes
    
    * fixed all texts except torus
    
    * no internal constructor needed
    
    * fixed tests, changed names
    
    * print field for LinearlyReductiveGroup
    
    * changed RedGrpInvRing to attributes. Other minor changes
    
    * added error messages for @Req, fixed typo
    
    * added export functions to torus groups
    
    * fixed export functions in InvariantTheory.jl
    
    * minor changes suggested in pr implemented
    
    * fixed test
    
    * exported direct_sum, tensor
    
    * included file TorusInvariantsFast.jl
    
    ---------
    
    Co-authored-by: Max Horn <max@quendi.de>
    (cherry picked from commit 7da4224)
    Lax202 authored and benlorenz committed Feb 22, 2024
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  3. Fixes for the degree function (#3298)

    * Remove :task from sub methods for modules.
    
    * Introduce new function submodule.
    
    * Remove all deprecated uses of sub.
    
    * Export submodule.
    
    * Fix tests.
    
    * Fix tests again.
    
    * Register morphisms in general.
    
    * Rebase network of natural maps on WeakKeyIdDicts.
    
    * Clean up the morphisms network and dont store the actual morphisms.
    
    * Some small fix for Wolfram.
    
    * Some fixes and marking the test as broken again.
    
    * Fix documentation.
    
    * Another small fix for Wolfram.
    
    * Fix the fix.
    
    * Fix method selection.
    
    * Introduce kw argument for caching morphisms.
    
    * Redirect previous usages.
    
    * Adjust tests.
    
    * submodule -> sub_object.
    
    * Fix docstrings and signatures for quo.
    
    * Fix methods for quo.
    
    * Adjust documentation.
    
    * Fix up usages of quo.
    
    * Export new functions.
    
    * Some fixes.
    
    * Fix tests.
    
    * Fix tests.
    
    * Fix tests.
    
    * Fix tests.
    
    * Fix tests.
    
    * Fix tests.
    
    * Squashed changes.
    
    * Fix tests.
    
    * Fix up the truncation.
    
    * New rebase.
    
    * Fix tests.
    
    * WIP with debug messages.
    
    * Progress in debugging.
    
    * WIP on debugging.
    
    * Write truely generic presentation and kernel methods [no ci].
    
    * Repair graded_map to accept zero entries.
    
    * Add tensor decomposition function to return value.
    
    * Add some assertions.
    
    * Repair kernel routine.
    
    * Rewrite hom methods for modules.
    
    * Add generic method for simplification of SubquoModuleElems.
    
    * Add missing check argument.
    
    * Fix or disable brittle tests.
    
    * Fix faulty merge.
    
    * Go back to old hom.
    
    * Switch tests to old hom.
    
    * Clean up some deprecated assertions.
    
    * Repair truncate.
    
    * Disable internal checks.
    
    * Update docs/src/CommutativeAlgebra/ModulesOverMultivariateRings/free_modules.md
    
    * Revert "Go back to old hom."
    
    This reverts commit a6b7c15.
    
    * Revert "Switch tests to old hom."
    
    This reverts commit 178eaf3.
    
    * Disable duplicate method.
    
    * Adjust printing.
    
    * Fix tests.
    
    * Fix keyword argument for duals.
    
    * Fix doctests.
    
    * Fix tests.
    
    * Fix doctests.
    
    * Delete some falsely added files.
    
    * Remove deprecated code.
    
    * Another round of disabling internal checks.
    
    * Disable various internal checks.
    
    * Disable further internal checks.
    
    * Set random seeds in tests.
    
    * Adjust use of keyword argument.
    
    * Fix more random seeds.
    
    * Fix the generic simplify method for SubquoModuleElems.
    
    * Revert "Remove deprecated code."
    
    This reverts commit 190256b.
    
    * Repair revert to old hom.
    
    * Repair preimage function.
    
    * Repair degree function.
    
    * Adjust tests to use of repaired old hom.
    
    * Add dummy simplify function for FreeModuleElems.
    
    * Fix doctests.
    
    * Repair simplify.
    
    * Fix documentation.
    
    * Fix doctests.
    
    * Some tuning.
    
    * Fix tests.
    
    * Bugfix from running book code run.
    
    * Remove some debugging artifacts.
    
    * Fix faulty merge.
    
    * Restrict signature.
    
    * Update flattenings of modules over towers of polynomial rings to make the tests run again.
    
    * Small fix.
    
    * Disable the superfluous kernel routine.
    
    * Restrict some further signatures to cases Singular can handle.
    
    * Add tests for flattenings of modules.
    
    * Readd methods which are not superfluous, yet.
    
    ---------
    
    Co-authored-by: Lars Göttgens <lars.goettgens@rwth-aachen.de>
    Co-authored-by: Lars Göttgens <lars.goettgens@gmail.com>
    (cherry picked from commit cfb3413)
    HechtiDerLachs authored and benlorenz committed Feb 22, 2024
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  4. Bump dependencies (#3374)

    * `ordering` -> `internal_ordering` for polynomial rings
    * Adjust to unexported symbols from Hecke
    * `find_name` now lives in `PrettyPrinting`
    
    (cherry picked from commit d32efdd)
    joschmitt authored and benlorenz committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. Corrected defn of deg(ideal); correction from W Decker (#3412)

    * Corrected defn of deg(ideal); correction from W Decker
    
    * Removed spaces at end of lines (to force GitHub to try again)
    
    (cherry picked from commit 290734f)
    JohnAAbbott authored and benlorenz committed Feb 23, 2024
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  2. Serialize Polyhedral Objects over Oscar fields (#3386)

    * some progress on serializing dicts
    
    * saving
    
    * serialization: add helpers to deconstruct polymake bigobject to dict
    
    currently with a few warnings that might be removed later
    
    * updates
    
    * starting on load
    
    * fix type string for saving
    
    * adds work around for vector{Int}
    
    * use new qualified bigobject name
    
    * serialize dicts
    
    * still need to work out loading
    
    * can load polyhedral object over different fields
    
    * some updates
    
    * add helpers for conversion from oscar graphs back to polymake
    
    * tiny improvement
    
    * fix inner types, store coeff only once
    
    * polymake: improve matrix conversion helpers, allow float in some places
    
    * adds serialzation for sets
    
    * adds test for dicts
    
    * adds test for sets
    
    * replace johnson matrices with Johnson solids
    
    * replace johnson matrices with solids
    
    * pretty print the rest of the Johnson Solids
    
    * pretty print
    
    * padding, + file extension and not pretty printed
    
    * fixes polyhedral test
    
    * update file version tag
    
    * file version tag + add extension for surface files
    
    * fix surface loading
    
    * fix typo
    
    * adds fix for polyhedron of floats and adds test
    
    * fix typo
    
    * better padding implementation
    
    * adds catch for unsupported loading types
    
    * remove Nothing type for coeff inputs, and fixed vector collect
    
    * adds tests for serializing polyhdral objects over oscar fields
    
    * fixes to MILP
    
    * MILP: add missing specialization for QQ to avoid saving other fields for now
    
    * polymake: change warnings to debug when saving unsupported polymake properties
    
    * polyhedral: add missing field for loading milp
    
    * fix for polyhedron with floats
    
    * serialization: fix load distinction between different fields, fix loading float polytopes
    
    * Update test/Serialization/PolyhedralGeometry.jl
    
    * Apply suggestions from code review
    
    Co-authored-by: Lars Kastner <lkastner@users.noreply.github.com>
    
    ---------
    
    Co-authored-by: Benjamin Lorenz <lorenz@math.tu-berlin.de>
    Co-authored-by: Benjamin Lorenz <benlorenz@users.noreply.github.com>
    Co-authored-by: Lars Kastner <lkastner@users.noreply.github.com>
    (cherry picked from commit 52c1236)
    antonydellavecchia authored and benlorenz committed Feb 23, 2024
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  3. QuadFormAndIsom: fixes and a new feature (#3394)

    (cherry picked from commit 376b3f0)
    StevellM authored and benlorenz committed Feb 23, 2024
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  4. Tweak exterior_algebra tests (#3415)

    Do not just verify that certain `exterior_algebra` invocations don't error
    out; also check that the returned values satisfy certain properties.
    
    Also disable two `@test_broken` tests for now, because (a) the underlying
    issue is fixed in a Singular PR, but this causes OscarCI failures there.. (b)
    even if the underlying issue is fixed, those test were wrong, because
    `exterior_algebra` doesn't return a boolean, but the return value was used in
    a context where it must be boolean (namely as "argument" for `@test_broken`).
    fingolfin authored and benlorenz committed Feb 23, 2024
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  5. Eliminate more spelling differences between American and British Engl…

    …ish (#3392)
    
    * `behaviour` -> `behavior`
    
    * `labelled` -> `labeled`
    
    * `modelled` -> `modeled`
    
    * `cancelled` -> `canceled`
    
    * `cancellation` -> `cancelation`
    
    * `regocnise` -> `recognize`
    
    * More `-ise-` -> `-ize-`
    
    * `-re` -> `-er`
    
    (cherry picked from commit 898f41a)
    lgoettgens authored and benlorenz committed Feb 23, 2024
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  6. Adapt interface for orthogonal and symplectic Lie algebras (#3391)

    * Small docs improvements
    
    * Adapt so interface
    
    * Add sp Lie algebra
    
    * Adapt to `vec` renaming
    
    * Don't assume anything about the kernel structure
    
    * Apply suggestions from code review
    
    Co-authored-by: Max Horn <max@quendi.de>
    
    ---------
    
    Co-authored-by: Max Horn <max@quendi.de>
    (cherry picked from commit db3dc1f)
    lgoettgens authored and benlorenz committed Feb 23, 2024
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