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Comment: Summarized #4611, #5088, #3890
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| * Switch to eMPIRe * Switch to ecl * Update Python to 2.5.4 * Ppdate Pari to 2.3.4svn |
* Switch to [[http://www.mpir.org|eMPIRe]] for multi-precision integers and rationals * Switch to [[http://ecls.sourceforge.net|ecl]] for a Common Lisp implementation * Update [[http://www.python.org|Python]] to 2.5.4 * Update [[http://pari.math.u-bordeaux.fr|Pari]] to 2.3.4svn * Switch to [[http://www.flintlib.org|FLINT]] for univariate polynomial arithmetic over {{{Z/nZ}}} |
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| * Improved precision and performance when calculating analytic rank (William Stein) -- When calculating the analytic rank of an elliptic curve, the default is to use Cremona's {{{gp}}} script, where the precision is automatically doubled until it doesn't fail. The precision is started at 16 rather than the previous default precision. The computation is now about 3 times faster usually by starting off using this smaller precision. |
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* {{{ivalue}}} field in {{{integer_mod.pyx}}} is no longer public (Craig Citro) -- The {{{ivalue}}} field for {{{IntegerMod_int}}} is no longer public. This gives about a 1.5 to 2X speedup when multiplying {{{IntegerMod_ints}}}. * Some fixes for {{{is_perfect_power}}} and {{{bessel_J(0,0)}}} (Craig Citro, Robert Bradshaw, Robert Miller) -- A temporary work around for an upstream bug in GMP when using {{{is_perfect_power()}}}. Resolved a Pari interface bug when using {{{bessel_J(0,0)}}}. * Improved performance for generic polynomial rings, and for univariate polynomial arithmetic over {{{Z/nZ[x]}}} (Yann Laigle-Chapuy, Martin Albrecht) -- Improved performance when performing modulo arithmetic between elements of a generic polynomial ring. Univariate polynomial arithmetic over {{{Z/nZ[x]}}} now has considerable speed-up at approximately 20x. * Deprecate the function {{{sqrt_approx()}}} (David Roe) -- To obtain a numerical approximation of the square root of a ring element (integers, polynomials over {{{GF(2^x)}}}, rationals), users are advised to use the function {{{sqrt()}}} with a given number of bits of precision instead. * Use Pohlig-Hellman for generic discrete logarithm (Yann Laigle-Chapuy) -- This results in significant improvement in performance and less memory foot print. * Exact division syntax in finite fields of prime order (David Roe) -- Support the division operator {{{//}}} for finite fields of prime order. |
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| * 64-bit OSX (Michael Abshoff) -- Fixed 64-bit OSX build support for f2c, added 64-bit OSX build support for tachyon, added 64-bit OSX build support for flintqs, and added persistent Sage 64-bit building switch on OSX and Solaris. |
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* LaTeX output (Mike Hansen) -- Added LaTeX output for ceiling, floor, and derivative functions, and LaTaX'ing of powers of negative numbers. * Make {{{bernoulli_polynomial}}} independent of Maxima (Craig Citro) -- A rewrite of {{{bernoulli_polynomial}}} to avoid using Maxima completely in computing Bernoulli polynomials. This gives roughly a factor of 10 speedup. |
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| * Weight distribution for binary codes (Robert Miller) -- A weight distribution algorithm for binary codes using Robert Bradshaw's bitsets. This implementation in [[http://www.cython.org|Cython]] gives a 19 to 20 times performance speed-up over the previous GAP/Guava implementation. |
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* Ring coercion for polynomials over finite fields (William Stein). * Move univariate polynomial rings to new coercion model (Robert Bradshaw). |
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| * Multivariate polynomials over residue fields of number fields (Nick Alexander) -- Fixed an infinite loop bug when working with multivariate polynomials over residue fields of number fields. Previously in hashing "large" characteristic residue fields, the hash method would try to hash an ideal of the residue field itself, which in turn would try to hash its parent, and so on ad infinitum. At no point has a residue field with cardinality a very large prime been created in Sage. * GCD of polynomials over finite fields (Martin Albrecht) -- Previously when using ibsingular to compute the GCD of two (multivariate) polynomials over finite fields, Sage would segfault whenever the base rings are not identical. * Deprecate {{{Ideal.reduced_basis}}} (John Perry) -- The previous name {{{Ideal.reduced_basis}}} is misleading as it suggests that it can be used for computing the reduced Gröbner basis, when in fact it returns the interreduced basis. Thus {{{Ideal.reduced_basis()}}} is now deprecated and users are encouraged to use {{{Ideal.interreduced_basis()}}} instead. |
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| == Doctest == | * GAP configuration file (Matthias Meulien) -- A user's local GAP configuration file is usually named {{{$HOME/.gaprc}}}. When such a file already exists and Sage is compiled from source, using the Sage interface to GAP, e.g. {{{gap._eval_line('1+3;')}}}, can result in gibberish. This is now fixed so that the GAP interface would output a comprehensible message/answer as a result of some GAP calculation. |
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| * Polyhedral improvements (Marshall Hampton) -- Added more built-in Archimedean solids and some new methods such as the Gale transform, bipyramid construction, edge truncation, and perspective projection with (optionally) hidden faces invisible. The Schlegel projection code has also been somewhat refactored to make it more general in the future. |
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* Equality testing in graphs (Robert Miller) -- The "weighted" property or edge label is taken into account when testing for equality in graphs. |
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| * Plotting a region (Arnaud Bergeron) -- Plot a region where a system of equations/inequalities were true. * Consistency in variable range (Mike Hansen, Jason Grout) -- The variable range of {{{parametric_plot}}} is now consistent with that of {{{plot}}}, namely {{{(var, min, max)}}}. * Polar plot syntax (Jason Grout) -- Polar plot now accepts the syntax {{{(t, 0, 2*pi)}}} for the interval. * Added a {{{density_plot()}}} function and improve colour map handling (Arnaud Bergeron) -- The {{{density_plot}}} takes a function of two variables and plots contour lines of the function over two specified ranges. Some improve on how colour map is handled. |
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| == Interact == | * Added an {{{is_cyclic}}} method (David Joyner) -- The {{{is_cyclic}}} method for (finite) groups is currently not as optimized as it should be. Given a finite abelian group, one can test to see whether or not it is cyclic, a test that depends on calculating the elementary divisors of the group. As correctness is the main concern in the current implementation of {{{elementary_divisors()}}}, performance is not taken into account. However, the docstring for {{{elementary_divisors()}}} describes an algorithm communicated by Robert Miller for speeding up this method. |
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| * Magma interface (William Stein) -- Fixed a problem in Sage's interface to Magma so that now the Magma {{{.sig}}} files in {{{extcode}}} are no longer written there by Magma itself. The current behaviour is that the first (and only first) time a Magma interface is started in a given session, files in {{{data/extcode/magma}}} are copied to a temporary directory. * GAP interface (Mike Hansen) -- Ensured that the GAP interface handles keyboard interrupt gracefully, that GAP output would be printed, and that multi-line input and comments are handled as expected. * Sage preparser (Robert Bradshaw) -- Some simplification of the Sage preparser, together with improved handling of literal numbers. |
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| == Memory Leak == | * Multiplication of sparse matrices over finite fields (William Stein, Craig Citro) -- Significant performance improvement when multiplying two sparse matrices over the same finite field. In some cases, performance is about 37 times faster than previously. * Minimum polynomials for {{{GF(p)}}} (Alex Ghitza). * Matrix exponential for general matrices (Jason Grout) -- Added a generic matrix exponential that depends on Maxima's matrix exponentiation function. If the matrix has floating point numbers, these will be rounded automatically to rational numbers during the computation. For numerical approximations to the exponential, one can first convert the matrix to RDF or CDF. * 100% doctest coverage for {{{matrix/constructor.py}}}, {{{matrix/misc.pyx}}}, {{{matrix/matrix_generic_dense.pyx}}} (William Stein) -- Apart from the full doctest coverage, calculating the lift of a matrix is now 20 times faster than previously. * Improved performance for method {{{density()}}} in {{{matrix/matrix_modn_sparse.pyx}}} (Craig Citro). * Added a kernel method for sparse integer matrices (John Palmieri). |
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| == Modular Forms == | * Rewrite of the function {{{__getitem__}}} (Jason Grout, Craig Citro) -- A rewrite of the function {{{__getitem__}}} in {{{matrix/matrix0.pyx}}} to better support slices, negative indices, and improved performance. * Function {{{get_memory_usage()}}} now return a float on all platforms (William Stein). * The function {{{CremonaDatabase().number_of_curves()}}} now works even when the optional Cremona database isn't installed (Alex Ghitza). |
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| * Interact cells in the notebook are not automatically evaluated (Mike Hansen). * Clear browser cache when restarting the worksheet (Mike Hansen). * Update jsmath to version 3.6 (Jason Grout). * In-line WYSIWYG editor for text cells using [[http://tinymce.moxiecode.com|TinyMCE]] (Jason Grout). |
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| == Numerical == | * Number field ideal utilities (John Cremona, Maite Aranes) -- New function {{{invertible_residues()}}} for iterating through only the invertible residues modulo an integral ideal. New function {{{element_1_mod()}}} such that {{{A.element_1_mod(B)}}} returns some {{{a}}} in {{{A}}} such that {{{1 - a}}} is in {{{B}}}. * New function {{{random_element}}} for returning a random element of a number field (Alex Ghitza). * Elliptic curve function {{{integral_points()}}} misses some points (John Cremona) -- Francois Glineur reported that for the elliptic curve {{{20160bg2}}}, the output of {{{integral_points()}}} misses the points {{{x = 168}}} and {{{x = 381}}}. This problem has been narrowed down to the function {{{point_preprocessing()}}}, and the bug is now fixed. |
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| * Modular polynomials database (Alex Ghitza) -- Remove the use of {{{polydict}}} in {{{databases/db_modular_polynomials.py}}}. |
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* Switch gmp to eMPIRe svn1555 (Michael Abshoff) -- The package {{{eMPIRe.spkg}}} is a drop in for the previous package {{{gmp-4.2.1.spkg}}}. * Upgrade [[http://ecm.gforge.inria.fr|GMP-ECM]] to version 6.2.1 (Michael Abshoff). * Move [[http://jquery.com|jquery]] into its own spkg (Jason Grout). * Upgrade [[http://www.selenic.com/mercurial/wiki|Mercurial]] to version 1.1.2 (Mike Hansen). * OS X 64-bit (Michael Abshoff) -- Added 64-bit build support for [[http://sourceforge.net/projects/pynac|PyNaC]], [[http://www.r-project.org|R]], [[http://ghmm.sourceforge.net|GHMM]], and [[http://bdwgc.sourceforge.net|Boehm GC]]. Also added {{{fortran-OSX64-20090120.spkg}}} to the experimental spkg repository. * Upgrade [[http://ipython.scipy.org/moin|IPython]] to version 0.9.1 (Mike Hansen). |
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| * OS X 64-bit (Michael Abshoff) -- Added proper {{{libcsage}}} build support, and [[http://www.singular.uni-kl.de|Singular]] is now built using the flag "{{{--with-malloc=system}}}". |
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* Upgrade libgcrypt to version 1.4.3 and force the function {{{get_memory_usage()}}} to fall back to using {{{top}}} when not on Linux (Michael Abshoff). |
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| * Added a {{{hg_examples}}} Mercurial wrapper for the examples repository (Mike Hansen). |
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* The trac server now displays the comments of a Mercurial diff (Robert Bradshaw). |
Sage 3.3 Release Tour
Sage 3.3 was released on FIXME. For the official, comprehensive release notes, see sage-3.3.txt. In general terms, the following points are some of the foci of this release:
- Clean up various doctest failures from 3.2.3
- Fix some build issues from 3.2.3 on the new set of supported images
- Merge small to medium sized patches ready to go in
Switch to eMPIRe for multi-precision integers and rationals
Switch to ecl for a Common Lisp implementation
Update Python to 2.5.4
Update Pari to 2.3.4svn
Switch to FLINT for univariate polynomial arithmetic over Z/nZ
Here's a summary of features in this release, categorized under various headings.
Algebra
Transitivity for permutation groups (William Stein) -- In the permutation group module permgroup.py, the query function is_transitive() returns whether or not the group is transitive on [1..G.degree()]. A few surrounding docstrings are fixed and doctest coverage for the file sage/groups/perm_gps/permgroup.py is now 100%.
Algebraic Geometry
Improved precision and performance when calculating analytic rank (William Stein) -- When calculating the analytic rank of an elliptic curve, the default is to use Cremona's gp script, where the precision is automatically doubled until it doesn't fail. The precision is started at 16 rather than the previous default precision. The computation is now about 3 times faster usually by starting off using this smaller precision.
Basic Arithmetic
ivalue field in integer_mod.pyx is no longer public (Craig Citro) -- The ivalue field for IntegerMod_int is no longer public. This gives about a 1.5 to 2X speedup when multiplying IntegerMod_ints.
Some fixes for is_perfect_power and bessel_J(0,0) (Craig Citro, Robert Bradshaw, Robert Miller) -- A temporary work around for an upstream bug in GMP when using is_perfect_power(). Resolved a Pari interface bug when using bessel_J(0,0).
Improved performance for generic polynomial rings, and for univariate polynomial arithmetic over Z/nZ[x] (Yann Laigle-Chapuy, Martin Albrecht) -- Improved performance when performing modulo arithmetic between elements of a generic polynomial ring. Univariate polynomial arithmetic over Z/nZ[x] now has considerable speed-up at approximately 20x.
Deprecate the function sqrt_approx() (David Roe) -- To obtain a numerical approximation of the square root of a ring element (integers, polynomials over GF(2^x), rationals), users are advised to use the function sqrt() with a given number of bits of precision instead.
- Use Pohlig-Hellman for generic discrete logarithm (Yann Laigle-Chapuy) -- This results in significant improvement in performance and less memory foot print.
Exact division syntax in finite fields of prime order (David Roe) -- Support the division operator // for finite fields of prime order.
Build
- 64-bit OSX (Michael Abshoff) -- Fixed 64-bit OSX build support for f2c, added 64-bit OSX build support for tachyon, added 64-bit OSX build support for flintqs, and added persistent Sage 64-bit building switch on OSX and Solaris.
Calculus
- LaTeX output (Mike Hansen) -- Added LaTeX output for ceiling, floor, and derivative functions, and LaTaX'ing of powers of negative numbers.
Make bernoulli_polynomial independent of Maxima (Craig Citro) -- A rewrite of bernoulli_polynomial to avoid using Maxima completely in computing Bernoulli polynomials. This gives roughly a factor of 10 speedup.
Coding Theory
Weight distribution for binary codes (Robert Miller) -- A weight distribution algorithm for binary codes using Robert Bradshaw's bitsets. This implementation in Cython gives a 19 to 20 times performance speed-up over the previous GAP/Guava implementation.
Coercion
- Ring coercion for polynomials over finite fields (William Stein).
- Move univariate polynomial rings to new coercion model (Robert Bradshaw).
Combinatorics
Commutative Algebra
- Multivariate polynomials over residue fields of number fields (Nick Alexander) -- Fixed an infinite loop bug when working with multivariate polynomials over residue fields of number fields. Previously in hashing "large" characteristic residue fields, the hash method would try to hash an ideal of the residue field itself, which in turn would try to hash its parent, and so on ad infinitum. At no point has a residue field with cardinality a very large prime been created in Sage.
- GCD of polynomials over finite fields (Martin Albrecht) -- Previously when using ibsingular to compute the GCD of two (multivariate) polynomials over finite fields, Sage would segfault whenever the base rings are not identical.
Deprecate Ideal.reduced_basis (John Perry) -- The previous name Ideal.reduced_basis is misleading as it suggests that it can be used for computing the reduced Gröbner basis, when in fact it returns the interreduced basis. Thus Ideal.reduced_basis() is now deprecated and users are encouraged to use Ideal.interreduced_basis() instead.
Distribution
GAP configuration file (Matthias Meulien) -- A user's local GAP configuration file is usually named $HOME/.gaprc. When such a file already exists and Sage is compiled from source, using the Sage interface to GAP, e.g. gap._eval_line('1+3;'), can result in gibberish. This is now fixed so that the GAP interface would output a comprehensible message/answer as a result of some GAP calculation.
Documentation
Geometry
- Polyhedral improvements (Marshall Hampton) -- Added more built-in Archimedean solids and some new methods such as the Gale transform, bipyramid construction, edge truncation, and perspective projection with (optionally) hidden faces invisible. The Schlegel projection code has also been somewhat refactored to make it more general in the future.
Graph Theory
- Equality testing in graphs (Robert Miller) -- The "weighted" property or edge label is taken into account when testing for equality in graphs.
Graphics
- Plotting a region (Arnaud Bergeron) -- Plot a region where a system of equations/inequalities were true.
Consistency in variable range (Mike Hansen, Jason Grout) -- The variable range of parametric_plot is now consistent with that of plot, namely (var, min, max).
Polar plot syntax (Jason Grout) -- Polar plot now accepts the syntax (t, 0, 2*pi) for the interval.
Added a density_plot() function and improve colour map handling (Arnaud Bergeron) -- The density_plot takes a function of two variables and plots contour lines of the function over two specified ranges. Some improve on how colour map is handled.
Group Theory
Added an is_cyclic method (David Joyner) -- The is_cyclic method for (finite) groups is currently not as optimized as it should be. Given a finite abelian group, one can test to see whether or not it is cyclic, a test that depends on calculating the elementary divisors of the group. As correctness is the main concern in the current implementation of elementary_divisors(), performance is not taken into account. However, the docstring for elementary_divisors() describes an algorithm communicated by Robert Miller for speeding up this method.
Interfaces
Magma interface (William Stein) -- Fixed a problem in Sage's interface to Magma so that now the Magma .sig files in extcode are no longer written there by Magma itself. The current behaviour is that the first (and only first) time a Magma interface is started in a given session, files in data/extcode/magma are copied to a temporary directory.
- GAP interface (Mike Hansen) -- Ensured that the GAP interface handles keyboard interrupt gracefully, that GAP output would be printed, and that multi-line input and comments are handled as expected.
- Sage preparser (Robert Bradshaw) -- Some simplification of the Sage preparser, together with improved handling of literal numbers.
Linear Algebra
- Multiplication of sparse matrices over finite fields (William Stein, Craig Citro) -- Significant performance improvement when multiplying two sparse matrices over the same finite field. In some cases, performance is about 37 times faster than previously.
Minimum polynomials for GF(p) (Alex Ghitza).
- Matrix exponential for general matrices (Jason Grout) -- Added a generic matrix exponential that depends on Maxima's matrix exponentiation function. If the matrix has floating point numbers, these will be rounded automatically to rational numbers during the computation. For numerical approximations to the exponential, one can first convert the matrix to RDF or CDF.
100% doctest coverage for matrix/constructor.py, matrix/misc.pyx, matrix/matrix_generic_dense.pyx (William Stein) -- Apart from the full doctest coverage, calculating the lift of a matrix is now 20 times faster than previously.
Improved performance for method density() in matrix/matrix_modn_sparse.pyx (Craig Citro).
- Added a kernel method for sparse integer matrices (John Palmieri).
Miscellaneous
Rewrite of the function __getitem__ (Jason Grout, Craig Citro) -- A rewrite of the function __getitem__ in matrix/matrix0.pyx to better support slices, negative indices, and improved performance.
Function get_memory_usage() now return a float on all platforms (William Stein).
The function CremonaDatabase().number_of_curves() now works even when the optional Cremona database isn't installed (Alex Ghitza).
Notebook
- Interact cells in the notebook are not automatically evaluated (Mike Hansen).
- Clear browser cache when restarting the worksheet (Mike Hansen).
- Update jsmath to version 3.6 (Jason Grout).
In-line WYSIWYG editor for text cells using TinyMCE (Jason Grout).
Number Theory
Number field ideal utilities (John Cremona, Maite Aranes) -- New function invertible_residues() for iterating through only the invertible residues modulo an integral ideal. New function element_1_mod() such that A.element_1_mod(B) returns some a in A such that 1 - a is in B.
New function random_element for returning a random element of a number field (Alex Ghitza).
Elliptic curve function integral_points() misses some points (John Cremona) -- Francois Glineur reported that for the elliptic curve 20160bg2, the output of integral_points() misses the points x = 168 and x = 381. This problem has been narrowed down to the function point_preprocessing(), and the bug is now fixed.
Optional Packages
Modular polynomials database (Alex Ghitza) -- Remove the use of polydict in databases/db_modular_polynomials.py.
Packages
Switch gmp to eMPIRe svn1555 (Michael Abshoff) -- The package eMPIRe.spkg is a drop in for the previous package gmp-4.2.1.spkg.
Upgrade GMP-ECM to version 6.2.1 (Michael Abshoff).
Move jquery into its own spkg (Jason Grout).
Upgrade Mercurial to version 1.1.2 (Mike Hansen).
OS X 64-bit (Michael Abshoff) -- Added 64-bit build support for PyNaC, R, GHMM, and Boehm GC. Also added fortran-OSX64-20090120.spkg to the experimental spkg repository.
Upgrade IPython to version 0.9.1 (Mike Hansen).
Porting
OS X 64-bit (Michael Abshoff) -- Added proper libcsage build support, and Singular is now built using the flag "--with-malloc=system".
Solaris
Upgrade libgcrypt to version 1.4.3 and force the function get_memory_usage() to fall back to using top when not on Linux (Michael Abshoff).
User Interface
Added a hg_examples Mercurial wrapper for the examples repository (Mike Hansen).
Website/Wiki
- The trac server now displays the comments of a Mercurial diff (Robert Bradshaw).