Sage 9.5 Release Tour
release candidate (2022)
Contents
Symbolics
Changes to symbolic expressions
symbolic_expression is now able to create vectors and matrices of symbolic expressions for more general inputs. #16761
- For example, if the input is a list or tuple of lists/tuples/vectors:
sage: M = symbolic_expression([[1, x, x^2], (x, x^2, x^3), vector([x^2, x^3, x^4])]); M [ 1 x x^2] [ x x^2 x^3] [x^2 x^3 x^4] sage: M.parent() Full MatrixSpace of 3 by 3 dense matrices over Symbolic Ring
- For example, if the input is a list or tuple of lists/tuples/vectors:
Symbolic expressions can no longer be called with positional arguments. #14270
This was deprecated since Sage 4.0, although a bug prevented the deprecation warning from being issued in Sage versions 8.4 to 9.3. #32319
Instead of (x+1)(2), write either (x+1)(x=2), or (x+1).subs(x=2), or ((x+1).function(x))(2).
Interface to Mathics, a free implementation of the Wolfram language
Sage now has an optional package providing Mathics, a free (open-source) general-purpose computer algebra system featuring Mathematica-compatible syntax and functions, and an interface to it.#31778
Linear Algebra
The Cholesky decomposition for sparse RDF/CDF matrices now uses a specialized fast algorithm when cvxopt is available. #13674
The is_hermitian() method for sparse RDF/CDF matrices now uses a small tolerance by default to mitigate numerical issues. This brings it to parity with its dense counterpart. #33031
Manifolds
The full list of changes is available in this changelog.
De Rham cohomology and characteristic classes
The de Rham cohomology has been made an algebra (#32270).
The algorithm for characteristic forms has been replaced by a faster one and characteristic cohomology classes have been implemented as a sub-ring of the de Rham cohomology ring (#29581).
Automatic coordinate change in curve plots
The method plot of curves is now allowed to perform a coordinate change to make the plot in terms of the coordinates specified via the argument chart, in case the curve is not known in these coordinates (#32578). For example, a cardioid is defined in terms of polar coordinates:
sage: E.<r, phi> = EuclideanSpace(coordinates='polar') sage: c = E.curve((1 + cos(phi), phi), (phi, 0, 2*pi)) sage: c.display() (0, 2*pi) → E^2 phi ↦ (r, phi) = (cos(phi) + 1, phi)
and its plot in terms of Cartesian coordinates can now be obtained simply by
sage: c.plot(chart=E.cartesian_coordinates(), aspect_ratio=1)
The above command has triggered the computation of the curve's expression in terms of Cartesian coordinates:
sage: c.display() (0, 2*pi) → E^2 phi ↦ (r, phi) = (cos(phi) + 1, phi) phi ↦ (x, y) = (cos(phi)^2 + cos(phi), (cos(phi) + 1)*sin(phi))
Internal code improvements and bug fixes
Various improvements have been performed in the internal code, some of them in view of SageMath modularization:
faster generation of non-redundant indices (#32318)
unnecessary uses of symbolic functions removed from sage.tensor.modules (#32415)
doctests involving SR marked optional in sage.tensor.modules (#32712)
sage.tensor.modules made independent from sage.manifolds (#32708).
Some bugs have been fixed: #31781, #32457, #32355, #32929.
Number theory
Logarithms modulo composite integers are now dramatically faster in some important cases (such as prime-power moduli). #32375
Logarithms in binary finite fields now use index calculus instead of generic-group algorithms when appropriate (via PARI's fflog()). #32842
Binary quadratic forms' .solve_integer() method now uses PARI's qfbsolve() instead of a brute-force search, which is often exponentially faster. #32782
Prime counting and related functions, in particular prime_pi, are now implemented using external libraries, primecount and primesieve. This improved performance and fixed a long-standing bug #24960
Elliptic curves and isogenies
Composite isogenies of elliptic curves have been added as an experimental feature. This includes support for compact smooth-degree isogenies. #32744
Isomorphisms of elliptic curves now expose the same interface as other isogenies. #32502
The .abelian_group() method for elliptic curves over finite fields is now much faster (with an exponential speedup in some cases). #32312
Mutability of elliptic-curve isogenies is now deprecated. #32388
(This affects the methods .switch_sign(), .set_pre_isomorphism(), and .set_post_isomorphism().)
Bugfixes:
The .multiplication_by_m_isogeny() method used to be correct only up to isomorphism. #32490
Computing isomorphisms between elliptic curves in characteristic 2 used to fail in some cases. #32632
Modular and quasimodular forms
David Ayotte's project in the 2021 Google Summer of Code has brought major new features and improvements to modular forms:
The class ModularFormsRing (now in sage.modular.modform.ring) now follows the Parent/Element structure. #31559.
Rings of quasimodular forms for a given congruence subgroups are now implemented. #31512
One can now convert a modular form ring element and a quasimodular form ring element to a polynomial in the generator of the ring. #32135, #32336
It is now possible to take derivatives of modular forms and quasimodular forms. #32343, #32357
Also a conversion bug between spaces of modular forms was fixed. See Meta-ticket #31560 for an overview of tickets.
Algebra
The Lie algebras e7 and e8 now have implementations as matrix Lie algebras.
New lazy Laurent series backend
The lazy Laurent series has been nearly completely rewritten using a new backend coefficient stream with a cache has both sparse and dense formatted input. This has been designed to increase speed and be very flexible. This has also been extensively doctested to make sure the code is robust. This constituted Tejavsi Chebrolu's 2021 GSoC project (metaticket). This is meant to be the eventual replacement of the coefficient streams used in the species code (including for lazy power series), which is known to be buggy (see, e.g., #15673). This also extends the functionality to include:
- formal power series defined by functional equations;
special functions such as sin(f);
- dense and sparse implementations;
- more robust checks for equality.
Lazy Dirichlet series
As a demonstration of the flexibility for the coefficient stream framework for lazy Laurent series, we also implement lazy Dirichlet series. We also give this a structure of a valuation ring by using the log of degree of the lowest nonzero coefficient.
Deprecated and removed functionality
The package sage.finance is now deprecated. (The module sage.finance.time_series is now available as sage.stats.time_series.) #32427
The module sage.interfaces.primecount is now deprecated. The functionality should now be imported from primecountpy, provided by the new standard package primecountpy. #32412, #32894
The package sage.media is now deprecated. #12673
The module sage.stats.basic_stats is now deprecated. #29662
In the deprecation messages, we point users to suitable numpy, and scipy.stats, and pandas functions. (Python 3 also comes with a basic built-in stats module, but much of its functionality is unfortunately incompatible with SageMath's number types, #28234.)
Many is_... functions are now deprecated.
Use isinstance with the new abstract base classes instead (see below).
Package upgrades
Sage 9.5 continues to support system installations of Python 3.7.x, 3.8.x, and 3.9.x. New in Sage 9.5 is experimental support for system Python 3.10.x. If no suitable system Python is found, Sage builds its own copy from source; the SPKG has been upgraded to version 3.9.9. #30766, #32853
lcalc has been upgraded to the new 2.x series maintained by the Sage team (Release notes). #32037, #33043
NumPy has been upgraded from 1.20.3 to the 1.21 series, see the release notes.
SciPy has been upgraded from 1.6.3 to the 1.7 series, see the release notes.
Matplotlib has been upgraded from 3.3.4 to the 3.5 series. #31580, #33040
NetworkX has been upgraded from 2.5.1 to the 2.6 series, bringing various new features and improvements, see the changelog.
SymPy has been upgraded from 1.8 to 1.9, see the release notes.
polymake has been upgraded from 4.4 to 4.5, see the release notes. On macOS, Sage is now also able to use a polymake installation made via Homebrew.
IPython and Jupyter packages have been upgraded. In particular, notebook has been upgraded from 6.1.1 to the 6.4 series, see the changelog. #31280, #32930, #33020
For a list of all packages and their versions, see
Configuration changes
Separate virtual environment for Python packages
In non-incremental builds from source, Sage now defaults to setting up the virtual environment for the Python packages in a directory separate from SAGE_ROOT/local. #32442
At the end of a run of ./configure, you will see messages like the following:
config.status: executing links commands config.status: creating convenience symlink prefix -> local config.status: creating convenience symlink venv -> local/var/lib/sage/venv-python3.9
The symbolic link SAGE_ROOT/venv points to the location of the virtual environment. It depends on the version of Python that is in use. The symbolic link is not needed for build or runtime; it is only provided for convenience.
The previous behavior can be restored by using ./configure --without-sage-venv.
Thanks to this new default, it has become easier for developers to work with several Python versions: There is no need to run make distclean or similar if you want to switch to a different Python version; just reconfigure using ./configure --with-python3=..... The SageMath distribution keeps the installation records for Python packages separately for each venv.
New default: configure --with-system-gcc=force
The Sage distribution no longer attempts to build its own gcc if no suitable C/C++ compilers can be found. Instead, configure will exit with an error in this situation. #32060
The previous behavior can be restored by using ./configure --with-system-gcc=yes; alternatively, you can use ./configure --with-system-gcc=no.
New option: configure --disable-doc
If you do not intend to build the Sage documentation from source, you can now use ./configure --disable-doc. It suppresses the installation of several packages that are only needed for docbuilding and makes make (or make all) equivalent to make build. #32759
Packages atlas and mpir removed
The package atlas, which could be used as an alternative to openblas, and the corresponding configure options have been removed. #30350
The package mpir, which could be used as an alternative to gmp, and the corresponding configure options have been removed. #32549, #32727
psutil package removed
The psutil (memory management) python package has been removed. The version within sage was heavily patched and no longer feasible to maintain, and the upstream version is incompatible with one of our supported platforms. #32656
System singular detection
Sage is now able to use a suitable version of the Singular package from the system if one is detected by the ./configure script. #29024
For developers and packagers: Modularization and packaging changes
Sage 9.5 contains many changes that were made as part of the modularization project described in #29705 and in the new section of the developer's guide, Packaging the Sage Library.
New distribution package on PyPI: sage-setup
The build system of the Sage library, sage_setup, is now provided by a separate distribution package sage-setup. The source tree is the subdirectory pkgs/sage-setup/ of the Sage git repository. #29847
Since 9.5.rc0, the distribution packages sage-conf, sage-docbuild, sage-setup, sage-sws2rst, and sagemath-standard are uploaded automatically to PyPI on each release tag by a GitHub Actions workflow. #32062
Pynac merged into the Sage library
The core of the symbolic expressions subsystem of Sage, an adaptation of the GiNaC library to Python known as Pynac, has been merged into the Sage library source code as src/sage/symbolic/ginac/; all future development of Pynac is intended to happen here. #32386, #32387
This removes an obstacle to Python packaging: Pynac was a shared library with a dependency on the Python C API but not an extension module, and it could not be installed using standard Python tools. Now the shared library is gone; all of Pynac (about 60kLOC of C++ code spread over 100 *.h and *.cpp files) is put in a single extension module sage.symbolic.expression. All other extension modules that used to link to libpynac (sage.libs.pynac.pynac, sage.symbolic.function, sage.symbolic.series etc.) have either been merged into sage.symbolic.expression, or the dependency has been resolved through refactoring. The integration of Pynac into the Sage source tree will also make it easier for Sage developers to make changes to symbolics.
Doctest annotation "# optional - FEATURE" for portions of the Sage library
In the Sage doctesting framework, a line of tests can be conditionalized on the presence of a feature, such as an installed optional package, using a comment of the form # optional - FEATURE.
In Sage 9.5, doctests can also be conditionalized on the presence of certain parts of the Sage library. #32614
For example, doctests that depend on the Symbolic Ring can be marked # optional - sage.symbolic, and doctests that need number fields can be marked # optional - sage.rings.number_field.
Also various runtime tests for external programs have been rewritten as Features. #27744, #32174, #32649, #32650, #32866, #32926
Module-level annotation "# sage.doctest: optional - FEATURE"
Moreover, Sage 9.5 extends this mechanism by allowing developers to mark all doctests in a Python file as conditional on a feature. #30778
These module-level directives go to the top of the source file and take the form
# sage.doctest: optional - FEATURE
Abstract base classes for "isinstance" testing
The new module sage.rings.abc defines a number of abstract base classes that can be used for isinstance testing with parent classes instead of importing is_... functions from various implementation modules. #32566, #32600, #32606, #32610, #32612, #32660, #32665, #32719, #32742, #32750
In a similar way, sage.geometry.abc defines abstract base classes Polyhedron, ConvexRationalPolyhedralCone, etc. #32637
Likewise, sage.structure.element now defines an abstract base class Expression that can be used for isinstance testing, instead of importing is_Expression or the implementation class Expression from sage.symbolic.expression. #32638, #32730
See also Meta-ticket #32414.
Availability of Sage 9.5 and installation help
Sources
The first beta release in the 9.5 development series was tagged on 2021-08-31. The first release candidate was tagged 2022-01-09; the current release candidate is 9.5.rc3, tagged 2022-01-18.
SageMath 9.5 supports most platforms that were supported by Sage 9.4 and adds support for building on recent Linux distributions that use glibc ≥ 2.34 (fedora-35, ubuntu-impish, ubuntu-jammy, archlinux-latest, etc.) #32756
Sage 9.5 has dropped support for debian-jessie with the default compiler, GCC 4.9.x. This has allowed us to upgrade the package primecount to the latest version, which has stricter requirements for C++ 11, and to make it a standard package. (Sage 9.5 still supports distributions with compilers from the GCC 4.8.x series, such as ubuntu-trusty.) #25009
Here is a summary of the platforms on which Sage 9.5 is known to build from source. (On platforms marked with the superscript ⁺, installing optional packages is not supported unless you upgrade the toolchain (gcc, binutils).)
Linux 64-bit (x86_64)
Linux 32-bit (i386/i686)
- ubuntu-bionic
- debian-buster
centos-7⁺ (but docbuild is broken, #32768)
macOS (Intel) (x86_64) - with Homebrew or without
- macOS 10.15 (Catalina)
- macOS 11.x (Big Sur)
macOS 12.x (Monterey) #32855
macOS (Apple Silicon, M1) #30592
Building Sage 9.5 from source on Apple Silicon (M1) requires the use of Homebrew (recommended) or conda-forge, which package versions of gfortran with necessary changes for this platform that are not in a released upstream version of GCC. (The gfortran package that comes with Sage is not suitable for the M1.)
Make sure that /usr/local does not contain an old copy of homebrew (or other software) for x86_64 that you may have copied from an old machine. Homebrew for the M1 is installed in /opt/homebrew, not /usr/local.
Be sure to follow the README and the instructions that the ./configure command issues regarding the installation of system packages from Homebrew or conda.
Cygwin (x86_64)
use with system Python 3.9 needs Cygwin test package python39 3.9.9-3, see #33078
Since 9.5.rc0, Sage has experimental support for system Python 3.10.x. It continues to support Python 3.7.x, 3.8.x, 3.9.x. #30766
Binaries
Binary package for 9.5.rc1 on macOS from the 3-manifolds project
- separate disk images for Intel (x86_64) and Apple Silicon (M1, arm64)
- also includes many optional Sage packages
Help
See sage-devel for development discussions and sage-release for announcements of beta versions and release candidates.