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| = Sage 9.3 Release Tour = released May 9, 2021 <<TableOfContents>> == Linear and multilinear algebra == === Bär–Faddeev–LeVerrier algorithm for the Pfaffian of skew-symmetric matrices === According to https://arxiv.org/abs/2008.04247, the Pfaffian of skew-symmetric matrices over commutative torsion-free rings can be computed with a Faddeev–!LeVerrier-like algorithm. This algorithm is now implemented under the weaker assumption of the base ring's fraction field being a `QQ`-algebra ([[https://trac.sagemath.org/ticket/30681|#30681]]). It leads to a significant increase of computational speed in comparison to the definition involving perfect matchings, which has been the only algorithm available in Sage so far. Using the definition of the Pfaffian: {{{ sage: A = matrix([(0, 0, 1, 0, -1, -2, -1, 0, 2, 1), (0, 0, 1, -3/2, 0, -1, 1/2, 3, 3/2, -1/2), (-1, -1, 0, 2, 0, 5/2, 1, 0, -2, 1), (0, 3/2, -2, 0, 5/2, -1, 2, 0, -1, -3/2), (1, 0, 0, -5/2, 0, 0, -1, 1/2, 1, -1), (2, 1, -5/2, 1, 0, 0, 2, 1, 2, 1), (1, -1/2, -1, -2, 1, -2, 0, 0, -3, -1), (0, -3, 0, 0, -1/2, -1, 0, 0, 1/2, 1/2), (-2, -3/2, 2, 1, -1, -2, 3, -1/2, 0, 1), (-1, 1/2, -1, 3/2, 1, -1, 1, -1/2, -1, 0)]) sage: %%time ....: A.pfaffian(algorithm='definition') CPU times: user 18.7 ms, sys: 0 ns, total: 18.7 ms Wall time: 18.6 ms 817/16 }}} With Bär–Faddeev–!LeVerrier: {{{ sage: A = matrix([(0, 0, 1, 0, -1, -2, -1, 0, 2, 1), (0, 0, 1, -3/2, 0, -1, 1/2, 3, 3/2, -1/2), (-1, -1, 0, 2, 0, 5/2, 1, 0, -2, 1), (0, 3/2, -2, 0, 5/2, -1, 2, 0, -1, -3/2), (1, 0, 0, -5/2, 0, 0, -1, 1/2, 1, -1), (2, 1, -5/2, 1, 0, 0, 2, 1, 2, 1), (1, -1/2, -1, -2, 1, -2, 0, 0, -3, -1), (0, -3, 0, 0, -1/2, -1, 0, 0, 1/2, 1/2), (-2, -3/2, 2, 1, -1, -2, 3, -1/2, 0, 1), (-1, 1/2, -1, 3/2, 1, -1, 1, -1/2, -1, 0)]) sage: %%time ....: A.pfaffian(algorithm='bfl') CPU times: user 554 µs, sys: 41 µs, total: 595 µs Wall time: 599 µs 817/16 }}} === Other improvements === * Speedup access items in gf2e dense matrices: [[https://trac.sagemath.org/ticket/29853|29853]] * Speedup conjugation of double dense matrices: [[https://trac.sagemath.org/ticket/31283|31283]] * New Bunch-Kaufman `block_ldlt()` factorization for possibly indefinite matrices: [[https://trac.sagemath.org/ticket/10332|10332]] * New numerically-stable `is_positive_semidefinite()` method for matrices: [[https://trac.sagemath.org/ticket/10332|10332]] == Polyhedral geometry == === New features === The Schlegel diagrams are now repaired (they previously broke convexity). Now, one specifies which facet to use to do the projection [[https://trac.sagemath.org/ticket/30015|30015]]: {{{ #!python sage: fcube = polytopes.hypercube(4) sage: tfcube = fcube.face_truncation(fcube.faces(0)[0]) sage: tfcube.facets()[-1] A 3-dimensional face of a Polyhedron in QQ^4 defined as the convex hull of 8 vertices sage: sp = tfcube.schlegel_projection(tfcube.facets()[-1]) sage: sp.plot() # The proper Schlegel diagram is shown }}} A different values of ``position`` changes the projection: {{{ #!python sage: sp = tfcube.schlegel_projection(tfcube.facets()[4],1/2) sage: sp.plot() Graphics3d Object sage: sp = tfcube.schlegel_projection(tfcube.facets()[4],4) sage: sp.plot() Graphics3d Object }}} New features: * [[https://trac.sagemath.org/ticket/30704|30704]]: Upgrade to Normaliz 3.8.9 and PyNormaliz 2.13 * [[https://trac.sagemath.org/ticket/30946|30946]]: Add "minimal=True" option to affine_hull_projection * [[https://trac.sagemath.org/ticket/30954|30954]]: Implement a proper equality check for polyhedron representation objects === Implementation improvements === The zonotope construction got improved: Before: {{{ sage: from itertools import combinations sage: cu = polytopes.cube() sage: sgmt = [p.vector()-q.vector() for p,q in combinations(cu.vertices(),2)] sage: sgmt2 = set(tuple(x) for x in sgmt) sage: # %time polytopes.zonotope(sgmt) # killed due to memory overflow sage: %time polytopes.zonotope(sgmt2) CPU times: user 2.06 s, sys: 23.9 ms, total: 2.09 s Wall time: 2.09 s A 3-dimensional polyhedron in ZZ^3 defined as the convex hull of 96 vertices }}} With [[https://trac.sagemath.org/ticket/31038|31038]]: {{{ sage: from itertools import combinations sage: cu = polytopes.cube() sage: sgmt = [p.vector()-q.vector() for p,q in combinations(cu.vertices(),2)] sage: sgmt2 = set(tuple(x) for x in sgmt) sage: %time polytopes.zonotope(sgmt) CPU times: user 138 ms, sys: 0 ns, total: 138 ms Wall time: 138 ms A 3-dimensional polyhedron in ZZ^3 defined as the convex hull of 96 vertices sage: %time polytopes.zonotope(sgmt2) CPU times: user 58 ms, sys: 0 ns, total: 58 ms Wall time: 57.6 ms A 3-dimensional polyhedron in ZZ^3 defined as the convex hull of 96 vertices }}} Improvements: * [[https://trac.sagemath.org/ticket/30040|30040]]: Improve face iterator for simple/simplicial polytopes There are also some bug fixes and other improvements. For more details see the [[https://trac.sagemath.org/wiki/SagePolyhedralGeometry#release_9.3|release notes for optimization and polyhedral geometry software interactions in Sage]]. == Graph theory == Major improvements in the backends: * [[https://trac.sagemath.org/ticket/30777|30777]]: Deleting edges * [[https://trac.sagemath.org/ticket/30665|30665]]: Edge iterator and copy * [[https://trac.sagemath.org/ticket/30776|30776]]: Subgraph and equality check * [[https://trac.sagemath.org/ticket/30753|30753]]: Obtaining subgraphs. * [[https://trac.sagemath.org/ticket/31117|31117]], [[https://trac.sagemath.org/ticket/31154|31154]]: Breadth First Search * [[https://trac.sagemath.org/ticket/31129|31129]]: Depth first search * [[https://trac.sagemath.org/ticket/31197|31197]]: Use binary matrix data structure for bitsets. == Algebra == === Power Series Ring === * The method `set_default_prec` is now deprecated since it led to unwanted behavior (see [[https://trac.sagemath.org/ticket/18416|#18416]] for details). If another default precision is needed, a new power series ring must be created: {{{ sage: R.<x> = PowerSeriesRing(QQ, default_prec=10) sage: sin(x) x - 1/6*x^3 + 1/120*x^5 - 1/5040*x^7 + 1/362880*x^9 + O(x^10) sage: R.<x> = PowerSeriesRing(QQ, default_prec=15) sage: sin(x) x - 1/6*x^3 + 1/120*x^5 - 1/5040*x^7 + 1/362880*x^9 - 1/39916800*x^11 + 1/6227020800*x^13 + O(x^15) }}} This change does not affect the behavior of its ring elements. Code that relies on this method needs to be updated. * Inversion of power series ring elements now provides the correct parent: [[https://trac.sagemath.org/ticket/8972|#8972]] === Other additions, improvements, and key bug-fixes === * Implement the symplectic derivation Lie algebra following [[https://arxiv.org/abs/2006.06064]]: {{{ sage: lie_algebras.SymplecticDerivation(QQ, 4) Symplectic derivation Lie algebra of rank 4 over Rational Field }}} * Implement the *-insertion algorithm from [[https://arxiv.org/abs/1911.08732]]: {{{ sage: from sage.combinat.rsk import RuleStar sage: p,q = RuleStar().forward_rule([1,1,2,2,4,4], [1,3,2,4,2,4]) sage: ascii_art(p, q) 1 2 4 1 1 2 1 4 2 4 3 4 sage: line1,line2 = RuleStar().backward_rule(p, q) sage: line1,line2 ([1, 1, 2, 2, 4, 4], [1, 3, 2, 4, 2, 4]) }}} * Speedup iteration of partitions with parts in a specific set: [[https://trac.sagemath.org/ticket/31319|31319]] * Speedup iteration of points in affine and projective space over a finite field: [[https://trac.sagemath.org/ticket/25743|25743]] * We can compute the generators for the homology of a cell complex: [[https://trac.sagemath.org/ticket/30838|30838]] * Actions can now be pickled: [[https://trac.sagemath.org/ticket/29031|29031]] * Fixed bug in tensoring signed with unsigned modules: [[https://trac.sagemath.org/ticket/31266|31266]] * Fix the valuation of Puiseux series: [[https://trac.sagemath.org/ticket/30679|30679]] == Knot theory == Fixed some wrong answers for the unknot: [[https://trac.sagemath.org/ticket/31001|31001]] == Symbolic expressions == The predefined constant `I` in interactive sessions is now an element of the (embedded) number field ℚ[i] rather than a symbolic expression: {{{ sage: I.parent() Number Field in I with defining polynomial x^2 + 1 with I = 1*I }}} This allows it to be used in combination with other Sage objects without the coercion mechanism forcing the result to belong to the symbolic ring. For example, one now has {{{ sage: (1.0 + I).parent() Complex Field with 53 bits of precision }}} Expressions such as {{{ sage: I + pi pi + I }}} still yield symbolic results. The symbolic imaginary unit `I` remains available as `SR(I)` or `SR.I()`, or, for library code, as `sage.symbolic.constants.I`. Importing it from `sage.symbolic` is deprecated. (#18036) == Manifolds == === Spheres added to the manifold catalog === Spheres of arbitrary dimension have been added to the manifold catalog, so that they can be initialized via `manifolds.Sphere(n)` ([[https://trac.sagemath.org/ticket/30804|#30804]]). For instance: {{{ sage: S3 = manifolds.Sphere(3) sage: S3 3-sphere S^3 of radius 1 smoothly embedded in the 4-dimensional Euclidean space E^4 }}} By default, a single chart is initialized: that of spherical coordinates: {{{ sage: S3.atlas() [Chart (A, (chi, theta, phi))] sage: S3.default_chart() is S3.spherical_coordinates() True }}} Note that `A` stands for the domain of spherical coordinates, which is a strict subset of S^3^: {{{ sage: S3.spherical_coordinates().domain() Open subset A of the 3-sphere S^3 of radius 1 smoothly embedded in the 4-dimensional Euclidean space E^4 }}} The sphere S^3^ is considered as an embedded submanifold of the Euclidean space E^4^: {{{ sage: S3.embedding().display() iota: S^3 --> E^4 on A: (chi, theta, phi) |--> (x1, x2, x3, x4) = (cos(phi)*sin(chi)*sin(theta), sin(chi)*sin(phi)*sin(theta), cos(theta)*sin(chi), cos(chi)) }}} S^3^ is a Riemannian manifold, with the metric induced by the Euclidean metric on E^4^: {{{ sage: g = S3.induced_metric() sage: g.display() gamma = dchi*dchi + sin(chi)^2 dtheta*dtheta + sin(chi)^2*sin(theta)^2 dphi*dphi }}} Beside spherical coordinates, stereographic coordinates are available too. Those from the North pole (NP) are obtained by {{{ sage: S3.stereographic_coordinates() Chart (S^3-{NP}, (y1, y2, y3)) }}} The above call has augmented the manifold atlas with various charts and subcharts, corresponding to stereographic coordinates from the North pole and from the South pole: {{{ sage: S3.atlas() [Chart (A, (chi, theta, phi)), Chart (S^3-{NP}, (y1, y2, y3)), Chart (S^3-{SP}, (yp1, yp2, yp3)), Chart (S^3-{NP,SP}, (y1, y2, y3)), Chart (S^3-{NP,SP}, (yp1, yp2, yp3)), Chart (A, (y1, y2, y3)), Chart (A, (yp1, yp2, yp3))] }}} All relevant change-of-coordinate formulas have been initialized. For instance, those relating spherical coordinates to stereographic ones are obtained as follows: {{{ sage: spher = S3.spherical_coordinates() sage: stereo = S3.stereographic_coordinates() sage: A = spher.domain() sage: stereoA = stereo.restrict(A) sage: S3.coord_changes()[(spher, stereoA)].display() y1 = -cos(phi)*sin(chi)*sin(theta)/(cos(chi) - 1) y2 = -sin(chi)*sin(phi)*sin(theta)/(cos(chi) - 1) y3 = -cos(theta)*sin(chi)/(cos(chi) - 1) }}} The change-of-coordinate formulas are automatically invoked to compute the coordinates of a point from previously known ones in a different chart. For instance: {{{ sage: p = S3((pi/2, pi/3, pi/4), chart=spher) sage: p Point on the 3-sphere S^3 of radius 1 smoothly embedded in the 4-dimensional Euclidean space E^4 sage: spher(p) (1/2*pi, 1/3*pi, 1/4*pi) sage: stereo(p) (1/4*sqrt(3)*sqrt(2), 1/4*sqrt(3)*sqrt(2), 1/2) }}} === Use of ambient metric by default for the Hodge dual of a differential form === When asking for the Hodge dual of a differential form on a pseudo-Riemannian manifold without specifying the metric, the manifold's default metric is assumed ([[https://trac.sagemath.org/ticket/31322|#31322]]). For example: {{{ sage: E.<x,y,z> = EuclideanSpace() sage: E.cartesian_coordinates().coframe() Coordinate coframe (E^3, (dx,dy,dz)) sage: dx = E.cartesian_coordinates().coframe()[1] sage: dx 1-form dx on the Euclidean space E^3 sage: dx.hodge_dual() 2-form *dx on the Euclidean space E^3 sage: dx.hodge_dual().display() *dx = dy/\dz }}} === Internal code improvements and bug fixes === Various improvements/refactoring of the code have been performed in this release: * [[https://doc.sagemath.org/html/en/reference/manifolds/manifold.html|topological part]]: [[https://trac.sagemath.org/ticket/30310|#30310]], [[https://trac.sagemath.org/ticket/31243|#31243]] * [[https://doc.sagemath.org/html/en/reference/manifolds/diff_manifold.html|differentiable part]]: [[https://trac.sagemath.org/ticket/30284|#30284]], [[https://trac.sagemath.org/ticket/31215|#31215]], [[https://trac.sagemath.org/ticket/31255|#31255]], [[https://trac.sagemath.org/ticket/31273|#31273]], [[https://trac.sagemath.org/ticket/31323|#31323]]. In addition, various bugs and typos have been fixed: [[https://trac.sagemath.org/ticket/30174|#30174]], [[https://trac.sagemath.org/ticket/30830|#30830]], [[https://trac.sagemath.org/ticket/31202|#31202]]. == Numerics == Automatic conversions from from floating-point numbers and symbolic expressions to real and complex intervals are deprecated and will be removed in the future. Code that relies on the existence of coercions * from `RealField` to `RealIntervalField`, * from `SymbolicRing` to `ComplexIntervalField`, or * from Python `float`s to `ComplexIntervalField`, like {{{ sage: RIF(1/3) + RR(1) }}} or {{{ sage: 1.1*pi*CIF(i) }}} needs to be updated. (Other similar conversions, e.g. from `RealField` to `RealBallField` or from `float` to `RealField`, already need to be performed explicitly.) Beside leading to more consistent behavior, the removal of these coercions will make it easier to use interval arithmetic reliably. ([[https://trac.sagemath.org/ticket/15114|#15114]]) == Graphics == === Three.js viewer === The `thickness` option for lines is now supported on more platforms, including Windows. It can now also be specified for surfaces in conjunction with {{{mesh=True}}} to control the thickness of the wireframe lines: [[https://trac.sagemath.org/ticket/26410|26410]] {{{#!highlight python line = parametric_plot3d([x*cos(x),x*sin(x),x], (x,0,2*pi), thickness=10) surface = dodecahedron(mesh=True, thickness=10) show(line + surface) }}} A dark theme has been implemented for the viewer. Use {{{theme='dark'}}} for the new theme or {{{theme='light'}}} for the default. If you would prefer the dark theme to be the default, edit your [[https://doc.sagemath.org/html/en/reference/repl/startup.html#the-init-sage-script|Sage start-up script]], adding the following: [[https://trac.sagemath.org/ticket/30462|30462]] {{{#!highlight python sage.plot.plot3d.base.SHOW_DEFAULTS['theme'] = 'dark' }}} You may now set the title of the HTML pages generated by the viewer, which can be helpful when having several such tabs open at once: [[https://trac.sagemath.org/ticket/30612|30612]] {{{#!highlight python show(dodecahedron(), page_title="My Favorite Polyhedron") }}} The font and opacity of the axis labels can now be customized similar to what was added in 9.2 for [[https://doc.sagemath.org/html/en/reference/plot3d/sage/plot/plot3d/shapes2.html#sage.plot.plot3d.shapes2.text3d|text3d]]. Pass either a single dictionary of options for all three axes or a list of three dictionaries, one per axis: [[https://trac.sagemath.org/ticket/30628|30628]] {{{#!highlight python style = [dict(color='red', fontweight='bold'), dict(fontsize=20, fontfamily='Times New Roman, Georgia, serif'), dict(fontstyle='italic', opacity=0.5)] show(dodecahedron(), axes_labels_style=style) }}} Fixed clipping issues for plots that are very small or very large. [[https://trac.sagemath.org/ticket/30613|30613]] == Package upgrades, system packages, user packages == === Python === SageMath 9.3 continues to support system Python versions 3.6.x, 3.7.x, 3.8.x, and 3.9.x; support for Python 3.6.x is deprecated and will be removed in the SageMath 9.4 development cycle. If no suitable system Python is found, Sage installs its own copy of Python 3 from source. The version of Python shipped with the Sage distribution has been upgraded from 3.8.5 to 3.9.2. [[https://trac.sagemath.org/ticket/30589|#30589]], [[https://trac.sagemath.org/ticket/31318|#31318]], [[https://trac.sagemath.org/ticket/31419|#31419]] === Other package upgrades === [[https://trac.sagemath.org/query?summary=~update&milestone=sage-9.3&summary=~upgrade&groupdesc=1&group=status&max=1500&col=id&col=summary&col=component&col=time&col=changetime&col=author&col=reviewer&col=keywords&order=component|Upgrade tickets, milestone 9.3]] === SageMath on repology.org === The !SageMath distribution is now [[https://repology.org/repository/sagemath|listed as a repository on repology]]. The [[https://repology.org/projects/?inrepo=sagemath|list of packages]] allows developers to see which packages are in need of updating. === System package information for OpenSUSE === In particular, users of OpenSUSE Tumbleweed will notice the information about system packages that the Sage distribution can use. === Chapter on packages in the Sage reference manual === We have consolidated the information about packages into a single source, [[https://github.com/sagemath/sage/tree/develop/build/pkgs|build/pkgs/]] in the source tree, from which we generate package lists for the reference manual [[https://trac.sagemath.org/ticket/29655|#29655]], to which also the Sage website points. A number of user packages have been added as optional packages: `ore_algebra`, `sage_flatsurf`, `admcycles`, `slabbe`, `snappy`, `surface_dynamics`. Meta-ticket [[https://trac.sagemath.org/ticket/31164|#31164]] tracks the task of adding user packages to `build/pkgs/`. === For developers and packagers: Version constraints for Python packages === For all Python packages in the Sage distribution, `build/pkgs/SPKG/install-requires.txt` now encodes version constraints (such as lower and upper bounds) [[https://trac.sagemath.org/ticket/30719|#30719]]. The constraints are in the format of the `install_requires` key of [[https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html|setup.cfg]] or [[https://packaging.python.org/discussions/install-requires-vs-requirements/#id5|setup.py]]. The files may include comments (starting with `#`) that explain why a particular lower bound is warranted or why we wish to include or reject certain versions. For example: {{{ $ cat build/pkgs/sphinx/package-version.txt 3.1.2.p0 $ cat build/pkgs/sphinx/install-requires.txt # gentoo uses 3.2.1 sphinx >=3, <3.3 }}} The comments may include links to Trac tickets, as in the following example: {{{ $ cat build/pkgs/packaging/install-requires.txt packaging >=18.0 # Trac #30975: packaging 20.5 is known to work but we have to silence "DeprecationWarning: Creating a LegacyVersion" }}} The currently encoded version constraints are merely a starting point. Downstream packagers and developers are invited to refine the version constraints based on their experience and tests. When a package update is made in order to pick up a critical bug fix from a newer version, then the lower bound should be adjusted. In Sage 9.3, the new files are included only for documentation purposes and to facilitate development and packaging. An effort is underway in [[https://trac.sagemath.org/ticket/30913|#30913]] to use the new files to generate dependency metadata for the Sage library. There is no mechanism yet to use system Python packages; see [[https://trac.sagemath.org/ticket/29023|Meta-ticket #29013]] for this task. === For developers: Setting up Python packages from PyPI as Sage packages === Setting up Python packages from PyPI as Sage packages has become easier [[https://trac.sagemath.org/ticket/30974|#30974]]. {{{ $ ./sage -package create scikit_spatial --pypi Downloading tarball to /Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/upstream/scikit-spatial-5.0.0.tar.gz [......................................................................] $ ls build/pkgs/scikit_spatial/ SPKG.rst dependencies package-version.txt type checksums.ini install-requires.txt spkg-install.in $ cat build/pkgs/scikit_spatial/SPKG.rst scikit_spatial: Spatial objects and computations based on NumPy arrays ====================================================================== Description ----------- Spatial objects and computations based on NumPy arrays. License ------- BSD license Upstream Contact ---------------- https://pypi.org/project/scikit-spatial/ }}} Note that this new command does not check the dependencies of the Python package; this still needs to be done manually. The above command creates a [[https://doc.sagemath.org/html/en/developer/packaging.html#package-source-types|"normal" package]] (with tarball information in `checksums.ini`). To create a package as a "pip" package (which will be obtained directly from PyPI on an install), use `./sage -package create scikit_spatial --pypi --source pip` instead. == Cleaning of the Sage codebase to conform to best practices == Major progress has been made since [[https://wiki.sagemath.org/ReleaseTours/sage-9.0|SageMath 9.0]] in a long term effort to clean up the Sage codebase so it conforms to best practices. [[https://wiki.sagemath.org/ReleaseTours/sage-9.2#Testing_and_linting_with_tox|Since SageMath 9.2, various coding style checkers have been available]] via `./sage -tox`. The command `./sage -tox -e pycodestyle-minimal` uses [[https://pypi.org/project/pycodestyle/|pycodestyle]] (formerly known as `pep8`) in a minimal configuration. By passing `--count -qq` we can reduce the output to only show the number of style violation warnings. {{{ $ ./sage -tox -e pycodestyle-minimal -- --count -qq worktree-9.0/src/sage pycodestyle-minimal installed: pycodestyle==2.7.0 pycodestyle-minimal run-test-pre: PYTHONHASHSEED='1305087318' pycodestyle-minimal run-test: commands[0] | pycodestyle --select E401,E701,E702,W605 --count -qq ../worktree-9.0/src/sage 787 $ ./sage -tox -e pycodestyle-minimal -- --count -qq worktree-9.1/src/sage 753 $ ./sage -tox -e pycodestyle-minimal -- --count -qq worktree-9.2/src/sage 547 $ ./sage -tox -e pycodestyle-minimal -- --count -qq worktree-9.3/src/sage 321 }}} The command `./sage -tox -e pycodestyle` runs a more thorough check. {{{ $ ./sage -tox -e pycodestyle -- --count -qq worktree-9.0/src/sage pycodestyle recreate: /Users/mkoeppe/s/sage/sage-rebasing/src/.tox/pycodestyle pycodestyle installdeps: pycodestyle pycodestyle installed: pycodestyle==2.7.0 pycodestyle run-test-pre: PYTHONHASHSEED='906952231' pycodestyle run-test: commands[0] | pycodestyle --count -qq ../worktree-9.0/src/sage 184373 $ ./sage -tox -e pycodestyle -- --count -qq worktree-9.1/src/sage 184731 $ rm -f worktree-9.2/src/tox.ini $ ./sage -tox -e pycodestyle -- --count -qq worktree-9.2/src/sage 186792 $ ./sage -tox -e pycodestyle -- --count -qq worktree-9.3/src/sage 565 E111 indentation is not a multiple of four 202 E114 indentation is not a multiple of four (comment) 70 E115 expected an indented block (comment) 184 E116 unexpected indentation (comment) ... 101486 }}} Finally, there is `./sage -tox -e codespell`, which uses [[https://pypi.org/project/codespell/|codespell]] to find misspelled words. {{{ $ ./sage -tox -e codespell -- --count worktree-9.0/src/sage 2254 $ ./sage -tox -e codespell -- --count worktree-9.1/src/sage 2343 $ ./sage -tox -e codespell -- --count worktree-9.2/src/sage 2648 $ ./sage -tox -e codespell -- --count worktree-9.3/src/sage ../worktree-9.3/src/sage/env.py:270: multible ==> multiple ../worktree-9.3/src/sage/misc/superseded.py:296: supress ==> suppress ../worktree-9.3/src/sage/misc/misc.py:556: occurance ==> occurrence ../worktree-9.3/src/sage/misc/dev_tools.py:285: instanciation ==> instantiation ... 2275 }}} == Modularization and packaging of sagelib == A source tarball of the Sage distribution (or a worktree of the Sage git repository after running the `./bootstrap` script) contains several self-contained source trees of Python distribution packages in `build/pkgs/*/src/`, which can be packaged, built and installed by standard Python procedures: * `setup.py sdist` builds a source distribution (it is invoked by the convenience script `build/pkgs/*/spkg-src`), which can afterwards be installed using `pip`. * `setup.py install` installs the package directly (this is legacy use of `setuptools` and is not recommended). * `setup.py bdist_wheel` builds a wheel, which can afterwards be installed using `pip`. * Note, however, that `pip install .` does not work. In order to keep the monolithic structure of the `SAGE_ROOT/src` tree unchanged (for the convenience of Sage developers), the source trees of the Python distribution packages make use of symlinks. These symlinks are not compatible with `pip install .`. However, `setup.py sdist` follows the symlinks - the resulting source distribution contains ordinary files only and is therefore pip-installable. The following Python distribution packages exist in Sage 9.3: * The Sage library is built from [[https://github.com/sagemath/sage/tree/develop/build/pkgs/sagelib|build/pkgs/sagelib]]`/src`. Since 9.3.beta8, the resulting [[https://pypi.org/project/sagemath-standard/|source distribution sagemath-standard]] is available on PyPI. * The directory [[https://github.com/sagemath/sage/tree/develop/build/pkgs/sage_docbuild|build/pkgs/sage_docbuild]]`/src` contains a distribution that provides the Python package `sage_docbuild`, moved from `sage_setup.docbuild` in [[https://trac.sagemath.org/ticket/30476|#30476]]. Since 9.3.beta9, the resulting [[https://pypi.org/project/sage-docbuild/|source distribution sage-docbuild]] is available on PyPI. * The directory [[https://github.com/sagemath/sage/tree/develop/build/pkgs/sage_sws2rst|build/pkgs/sage_sws2rst]]`/src` contains the source of https://pypi.org/project/sage-sws2rst/ * The directory [[https://github.com/sagemath/sage/tree/develop/build/pkgs/sage_conf|build/pkgs/sage_conf]]`/src` (after running the top-level `configure` script) contains the source of the [[https://trac.sagemath.org/ticket/21707|Sage configuration package]], which provides: * a single Python module, `sage_conf`, providing configuration information to the SageMath library at the time of its installation and at its runtime * a console script `sage-config`, for querying the variables of `sage_conf` from the shell * the sourcable shell script `sage-env-config`, providing additional configuration information in the form of environment variables. In the course of the modularization effort of [[https://trac.sagemath.org/ticket/29705|Meta-ticket #29705]], in the Sage 9.4 series we expect to add many more distribution packages in the same format. * Splitting out `sage_setup` (the build system of the Sage library) as a separate distribution package (currently it is shipped as part of `sagemath-standard`). * Providing alternative implementations of `sage_conf` for different use cases. * Splitting `sagemath-standard` into many namespace packages. == Configuration changes == === Editable ("in-place", "develop") installs of the Sage library === Use `./configure --enable-editable` to configure the Sage distribution to install the Sage library in "develop" ("editable", "in-place") mode instead of using the Sage library's custom incremental build system. [[https://trac.sagemath.org/ticket/31377|#31377]] It has the benefit that to try out changes to Python files, one does not need to run `./sage -b` any more; restarting Sage is enough. It may also have benefits in certain develop environments that get confused by sagelib's custom build system. Note that in an editable install, the source directory will be cluttered with build artifacts (but they are `.gitignore`d). This is normal. === Use of system Jupyter notebook / JupyterLab === The Sage Installation Manual now has instructions on how to run the !SageMath Jupyter kernel in a system Jupyter notebook or !JupyterLab [[https://trac.sagemath.org/ticket/30476|#30476]] * [[https://trac.sagemath.org/ticket/30306|Meta-ticket #30306: Use system Jupyter notebook / JupyterLab]] If you intend to (a) only use Sage in a terminal, or (b) only use the !SageMath kernel with your system Jupyter notebook or !JupyterLab, you can now build Sage without the notebook components, by using `./configure --disable-notebook`. [[https://trac.sagemath.org/ticket/30383|#30383]] [[https://trac.sagemath.org/ticket/31278|#31278]] === Alternative installation methods using pip === There are new installation methods using `pip`. {{{ $ python3 -m pip install sage_conf }}} This will download the [[https://pypi.org/project/sage-conf/|distribution package (sdist) sage_conf from PyPI]], which will build the non-Python components of the Sage distribution in a subdirectory of `$HOME/.sage`. After installation of `sage_conf`, a wheelhouse containing wheels of various Python packages is available; type `ls $(sage-config SAGE_SPKG_WHEELS)` to list them and `python3 -m pip install $(sage-config SAGE_SPKG_WHEELS)/*.whl` to install them. After this, you can install the Sage library, using any of these options: * using `python3 -m pip install sagemath-standard`, which downloads the [[https://pypi.org/project/sagemath-standard/|Sage library from PyPI]] * or, after obtaining the Sage sources from git, `(cd src && python3 -m pip install --editable .)` Also pre-built wheels are available for some platforms. See https://pypi.org/project/sage-conf/ for more information. == Availability of Sage 9.3 and installation help == Sage 9.3 was tagged on 2021-05-09. [[https://github.com/3-manifolds/Sage_macOS/releases|A binary build of release candidate 9.3.rc2 for macOS as a signed and notarized app is available for testing.]] !SageMath 9.3 supports [[https://wiki.sagemath.org/ReleaseTours/sage-9.2#Availability_of_Sage_9.2_and_installation_help|all platforms that were supported by Sage 9.2]]. '''Sage 9.3 adds support for building Sage from source on macOS 11 ("Big Sur").''' Moreover, on macOS, Sage 9.3 no longer refuses to build on systems that have an installation of !MacPorts. [[https://trac.sagemath.org/ticket/31641|#31641]] * See [[https://groups.google.com/forum/#!forum/sage-devel|sage-devel]] for development discussions and [[https://groups.google.com/forum/#!forum/sage-release|sage-release]] for announcements of beta versions and release candidates. == More details == * [[https://www.sagemath.org/changelogs/sage-9.3.txt|Sage 9.3 changelog]] * [[https://trac.sagemath.org/query?milestone=sage-9.3&groupdesc=1&group=status&max=1500&col=id&col=summary&col=author&col=reviewer&col=time&col=changetime&col=component&col=keywords&order=component|Trac tickets with milestone 9.3]] |
