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Sage 9.7 Release Tour

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Kwankyu Lee edited this page Feb 14, 2023 · 4 revisions

Sage 9.7 was released on September 19, 2022.

A total of 92 people were involved as authors or reviewers of code contributions to Sage 9.7.

Here is an overview of some of the main changes in this version.

Documentation

Sage comes with comprehensive documentation in HTML and PDF formats.

In Sage 9.7, the HTML documentation has been updated to use the Furo theme, which uses a responsive design and offers a choice between dark mode, light mode, and a high-contrast mode. #33601, #33833, #34092, #34252, #34262, #34265, #34267, #34450

Basic arithmetic

  • Sage's Integer has a new .bit_length() method (to increase compatibility with Python's int). #33676
  • The divmod() function now also works for rings which implement % despite not being marked as Euclidean. #33704
  • Finite-field elements now support indexing (and iteration) to access the coefficients of the representing polynomial. #33748
  • The three-argument form of pow() now returns an integer rather than an IntegerMod. #34143

Combinatorics

  • Permutations now enjoy a much faster algorithm to compute the longest_increasing_subsequences as well as a new function that only count them longest_increasing_subsequence_number. #31451, #34218, #34214
  • Cartesian products of infinite enumerated sets now have a working iterator. #34374
  • ImageSets can now be equipped with an inverse function for the purpose of membership testing. #34377

Polyhedral geometry

Triangulations of point configurations (and thus of polyhedra and cones) are now linked to geometric polyhedral complexes. The new methods Triangulation.polyhedral_complex and boundary_polyhedral_complex return a PolyhedralComplex. Also, Triangulation provides a new method boundary_simplicial_complex, which returns an abstract SimplicialComplex. #33586

Abstract SimplicialComplexes now provide a method is_subcomplex, which was previously only available for PolyhedralComplexes. #34294

The new option PolyhedralComplex.plot(explosion_factor=1) plots a 2-dimensional or 3-dimensional polyhedral complex, setting its cells apart proportionally to their distance from a center point. There is also a new option color="rainbow", which assigns a different color to every maximal cell. #33596

The method affine_hull_projection is now available also for unbounded polyhedra, not only polytopes. #34326

RealSets (finite unions of intervals) now have faster intersection, difference, symmetric_difference and are_pairwise_disjoint methods. #32181

Number theory

  • Square roots modulo powers of two are now computed in polynomial time. #33961
  • Definite binary quadratic forms can now be reduced including transformation matrix. #34229
  • Factoring polynomials modulo prime powers is now supported. #34371

Elliptic curves

  • Elliptic curves can now be transformed into a Montgomery model y² = x³ + Ax² + x. #33707, #33708
  • Computing ℓ‑division fields of elliptic curves has been generalized to finite fields. #33939
  • Discrete logarithms on "anomalous" elliptic curves with #E(𝔽ₚ)=p are now computed in polynomial time. #34253
  • Elliptic-curve isogenies can now be computed in square-root time using the √élu algorithm. #34303

Algebra

  • The exterior algebra has changed its indexing set to FrozenBitset for speed #32369 and now has its own ideal class that can compute Gröbner bases over any field #34138.
  • Cubic Hecke algebras are implemented #29717.
  • General implementation of modules over an integral domain #33868.
  • (Graded) Finite free resolutions of modules over multivariate polynomials can be computed via Singular #33950.
sage: from sage.homology.free_resolution import FreeResolution 
sage: R.<x,y,z,w> = QQ[]
sage: I = R.ideal([y*z - x*w, y^3 - x^2*z, x*z^2 - y^2*w, z^3 - y*w^2])
sage: r = FreeResolution(I)
sage: r
S^1 <-- S^4 <-- S^4 <-- S^1 <-- 0
sage: len(r)
3
sage: r.differential(2)
Free module morphism defined as left-multiplication by the matrix
[-z^2 -x*z  y*w -y^2]
[   y    0   -x    0]
[  -w    y    z    x]
[   0    w    0    z]
Domain: Ambient free module of rank 4 over the integral domain Multivariate Polynomial Ring in x, y, z, w over Rational Field
Codomain: Ambient free module of rank 4 over the integral domain Multivariate Polynomial Ring in x, y, z, w over Rational Field
sage: from sage.homology.graded_resolution import GradedFreeResolution
sage: S.<x,y,z,w> = PolynomialRing(QQ)
sage: I = S.ideal([y*w - z^2, -x*w + y*z, x*z - y^2])
sage: r = GradedFreeResolution(I)
sage: r
S(0) <-- S(-2)⊕S(-2)⊕S(-2) <-- S(-3)⊕S(-3) <-- 0
  • The quantum Clifford algebra works for an arbitrary parameter q #34147.
  • Multivariate formal power series that are computed lazily (and exactly) have been implemented #32324.

Knot theory

  • Links-Gould polynomial invariant for links #33798.

Manifolds

Tensor products of free modules of finite rank

Free modules of finite rank, which are used to represent the sets of tensor fields on parallelizable manifolds, have been endowed with a tensor_product method (#31276):

sage: M = Manifold(2, 'M')
sage: X.<x,y> = M.chart()  # makes M parallelizable
sage: XM = M.vector_field_module(); XM
Free module X(M) of vector fields on the 2-dimensional differentiable manifold M
sage: XM.tensor_product(XM)
Free module T^(2,0)(M) of type-(2,0) tensors fields on the 2-dimensional differentiable manifold M
sage: XM.tensor_product(XM) is M.tensor_field_module((2, 0))
True

Vector bases endowed with dictionary methods

Bases of free modules of finite rank now inherit from AbstractFamily, so that they are endowed with methods keys, values and items (#30300). In particular, this regards vector frames on manifolds:

sage: M = Manifold(2, 'M')
sage: X.<x,y> = M.chart()
sage: f = X.frame(); f
Coordinate frame (M, (∂/∂x,∂/∂y))
sage: f.keys()
<generator object FiniteRankFreeModule.irange at 0x7fb2b4b16120>
sage: list(f.keys())
[0, 1]
sage: f.values()
(Vector field ∂/∂x on the 2-dimensional differentiable manifold M,
 Vector field ∂/∂y on the 2-dimensional differentiable manifold M)
sage: f.items()
<zip object at 0x7fb2a1c17fc0>
sage: list(f.items())
[(0, Vector field ∂/∂x on the 2-dimensional differentiable manifold M),
 (1, Vector field ∂/∂y on the 2-dimensional differentiable manifold M)]

Internal code improvements and bug fixes

Various code improvements have been performed: #30235, #34424, #34428, and some bugs have been corrected: #33957, #34158.

See the changelog for more details.

Package upgrades

IPython, providing the interactive shell of Sage, has been upgraded from 7.x to 8.4.0. This upgrade (including upgrades of many of its dependencies) brings many improvements, most notably autosuggestions. #33530

NumPy has been upgraded from 1.21.x to version 1.22.4, see the release notes. #32423

SciPy has been upgraded from 1.7.x to version 1.8.1, see the release notes. #32423

NetworkX, the Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks, has been upgraded to version 2.8.4, see the release notes for 2.7 and 2.8. #32423

The CAS kernel Giac has been upgraded to version 1.9.0-15. #31563

Singular, the CAS for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory, has been upgraded to version 4.3.1p1. #33160

polymake has been upgraded to version 4.7. #34222

The SAT solver cryptominisat has been upgraded to version 5.8.0 (release notes). #25374

SageTeX has been upgraded to version 3.6.1 (making its way to CTAN, too). #32887

The optional FriCAS package has been upgraded to version 1.3.8 #34051.

For a list of all packages and their versions, see

New tools for developers

Visual Studio Code dev containers

The Sage source tree now contains sample devcontainer.json configuration files for several purposes. #33671

  • For using (or trying out) Sage as it is packaged in a distribution, without compiling it: downstream-archlinux-latest, downstream-conda-forge-latest
  • For using (or trying out) Sage as it is provided in a published Docker image: downstream-docker-cocalc, downstream-docker-computop
  • For doing Sage development on top of a published Docker image: develop-docker-computop
  • For portability testing on top of a Docker image prebuilt by our portability suite on GH Actions: portability-ubuntu-jammy-standard

See the two new sections in the developer's guide for more information.

Validating docstring with ./sage -tox -e rst

The new command ./sage -tox -e rst -- FILES-OR-DIRECTORIES-TO-CHECK... checks that docstrings use correct ReST markup. #34157, #30448, #34156, #34158, #34159, #34160, #34161, #34162, #34163, #34164, #34165, #34166, #34168, #34169, #34172, #34288

This is faster than rebuilding the documentation and also checks the docstrings of private functions (functions whose names start with an underscore).

The new check also runs automatically for each ticket as part of the Lint workflow.

Doctesting with sage -t --optional='sage,!FEATURE'

Doctests that are conditional on the presence of a feature using an # optional - FEATURE annotation can now be explicitly disabled. This is useful for checking that # optional annotations are used consistently in a source file. #33823

sage -t now prints some additional information about the build when it starts up. #33967

Debugging on macOS with sage --lldb

Also the Sage doctester can be run under control of the LLDB debugger, using sage -t --lldb. These new commands mirror those for using the GDB debugger on Linux systems, sage --gdb and sage -t --gdb. #33627, #31568

Testing modularized distributions

The new command make pypi-wheels builds wheels for the modularized distribution packages sagemath-objects, sagemath-categories, sagemath-environment, sagemath-repl and runs tests in virtual environments set up using tox. #33817

A build error indicates that a change introduces a modularization regression, which needs to be fixed before the ticket can be merged.

This new check also runs automatically on GitHub Actions as part of the Build&Test workflow.

Gitpod now based on conda-forge, provides a Docker client

We have updated our Gitpod configuration to use conda-forge instead of a large pre-built Docker image. Starting a Gitpod instance is much faster now. It also provides docker now and works correctly in forked repositories. #33739, #34255, #34270

Modularization changes

The work on modularizing the Sage library has continued in Sage 9.7; see Meta-ticket #29705 for all details.

New distribution sagemath-environment

The Sage library contains a runtime feature discovery system in the namespace sage.features.

It is now available as the separately installable, pure Python distribution package sagemath-environment. Also included: sage.env and some modules of sage.misc. #29941

Wheels for modularized distributions

As part of our GH Actions workflows, we now build binary wheels for the distributions sagemath-objects and sagemath-categories, and make them available on PyPI. #34296

Packages sage, sage.rings, ... are now namespaces

As a major modularization milestone, __init__.py files have been removed from the packages sage, sage.arith, sage.categories, sage.ext, sage.graphs, sage.graphs.graph_decompositions, sage.interfaces, sage.libs, sage.matrix, sage.misc, sage.numerical, sage.numerical.backends, sage.rings, sage.sets. They are now PEP 420 implicit namespace packages. #33011, #33754, #34187

This means that several distribution packages ("pip-installable distributions") can now provide portions of these namespaces. The distributions sagemath-objects and sagemath-categories have been changed to do this. #28925

Downstream packages that use Cython and cimport Sage modules need to activate PEP 420 namespace package support in Cython. This is standard in the upcoming Cython 3 (#29863). When using a Cython release from the stable 0.29.x series, use with cython_namespace_package_support(), as is done in https://github.com/sagemath/sage/blob/develop/src/setup.py#L106 for sagelib. Making this change is an opportunity to also check whether your package is compatible with the upcoming Cython 3.

The Sage distribution uses a patched version of Cython 0.29.x with a backport of the Cython 3 namespace package support. #34221

Configuration changes

Editable installation is now the default

By the new default, the Sage library (sagemath-standard) and other distribution packages whose source trees are part of the Sage monorepo (sage-conf, sage-docbuild, sage-setup, sage-sws2rst) are now installed in editable mode. #32406

This means that changes to Python source files take immediate effect after restarting Sage. Running sage -b or make build is only necessary if you make changes (or switch to a branch that makes changes) to Cython sources or external packages.

To go back to the previous default, use ./configure --disable-editable.

If you need wheels for all packages, for example when you want to create a separate venv, you can use the command make wheels. #33817

Support for system Python 3.7 dropped, ensurepip required

It is still possible to build the Sage distribution on systems with older Python versions, but Sage will build its own copy of Python 3.10.5 in this case. #32937, #34090

The Sage distribution now also requires that the system Python includes the standard ensurepip module. On Debian and Ubuntu, it is missing if only python3-minimal is installed; the package python3-venv provides it. #33822

Support for system GCC older than 6.3 dropped

Building Sage from source now requires a system installation of GCC >= 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode CLT installation should be used). An alternative is to use a sufficiently recent version of clang (LLVM). #33316

Users of older Linux distributions (ubuntu-trusty, ubuntu-xenial, linuxmint-17, linuxmint-18, slackware-14.2) should upgrade their systems before attempting to install Sage from source.

Alternatively, users on ubuntu-trusty and ubuntu-xenial can install a modern compiler toolchain using the ubuntu-toolchain-r ppa. On ubuntu-trusty, also the package binutils-2.26 is required; after installing it, make it available using export PATH="/usr/lib/binutils-2.26/bin:$PATH".

Instead of upgrading their distribution, users of centos-7 can install a modern compiler toolchain using Redhat's devtoolset.

On other old distributions, if an upgrade to a newer distribution is not possible, users can try to use ./configure --without-system-gcc. Then Sage will attempt to build its own copy of GCC 11.3.0 using the available system GCC. We no longer test such system configurations, so this may or may not work.

Uninstalling SPKGs using make SPKG-uninstall

This command replaces make SPKG-clean, which is now deprecated. #29097

When an incremental build of the documentation fails, it is once again sufficient to use make doc-clean, followed by make doc-html. To uninstall the entire installation of the documentation, use make doc-uninstall. #33705

Availability of Sage 9.7 and installation help

Sage 9.7 was released on September 19, 2022.

Please read the updated SageMath installation guide. It provides a decision tree that guides users and developers to a type of installation suitable for their system and their needs.

Sources

The Sage source code is available in the sage git repository.

Sage builds successfully on the following platforms:

You can also build Sage on top of conda-forge on Linux and macOS.

Known issues and workarounds:

  • If your system pari package is very new (>= 2.15) but there is no suitable system giac package, then giac will fail to build. Workaround: Use ./configure --without-system-pari. #34586, #34537
  • If your system singular package is very new (>= 4.3.1p3), then sagelib will fail to build. Workaround: Use ./configure --without-system-singular. #34851

Sage 9.7 does not support Cygwin; use Windows Subsystem for Linux instead. Because of unresolved problems with standard packages GIAC (#34269), ECL (#34127), Maxima (#30796), and the rebasing facility (#34223), Sage 9.7 does not support Cygwin. Users on Windows 10 and 11 can migrate to using WSL as described in our installation guide. A convenient way to use such an installation of Sage is via VS Code's WSL remote. #34301, #30484

Binaries

  • The easiest way to install Sage 9.7 on Linux is through a distribution that provides it, see repology.org: sagemath.

Help

See README.md in the source distribution for installation instructions.

Visit sage-support for installation help.

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