Based on PR#43282 by Wen Heping.
2.7.9 --> 2.7.10
----------------
Bug fixes:
- Removed all occurrences of "as" as a variable name for compatibility
with Python 2.6.
- Installation without the netCDF module did not work.
Improvements:
- Vector.dyadicProduct() was replaced by a more efficient implementation.
- Scientific.IO.PDB: Atom objects now have a parent attribute whose
value is the containing group.
2.7.8 --> 2.7.9
---------------
License change: ScientificPython is now distributed under the
CeCILL-C license, which is an adaptation of the LGPL to French
law. The previously used CeCILL license, similar to the GPL, was
considered too restrictive.
Bug fixes:
- MPI interfaces did not work correctly with NumPy and/or Python 2.5.
Improvements:
- Compilation script for mpipython works around a Python configuration
bug under MacOS X.
- Docstrings have been cleaned up.
2.7.7 --> 2.7.8
---------------
Bug fixes:
- Due to a typo in Scientific.IO.PDBSpaceGroups, some space group
names were not found in the space group table.
Improvements:
- Vector objects can now be multiplied with NumPy scalar objects
(which is what you get when extracting numbers from NumPy
arrays). Due to the way NumPy scalars handle multiplication, the
result used to be an array rather than a Vector, which caused
various applications to crash.
- The build procedure under Windows has been improved. It can
generate a binary installer that includes the netCDF DLL,
making ScientificPython independent of a netCDF installation.
2.7.6 --> 2.7.7
---------------
Bug fixes:
- Installation on Windows didn't work because the Unix maths libraries
don't exist there.
Improvements:
- InterpolatingFunction and TensorField objects can represent
periodic functions/fields.
- DistributedComputing: the watchdog period of slave processes is now
a user-definable parameter.
- PDBSpaceGroups was simplified, making it shorter and faster to load.
- Scientific.N contains the array type object in the variable array_type.
This makes it possible to write Pyrex modules using arrays in such a
way that they always use the numeric module for which ScientificPython
was compiled.
2.7.5 --> 2.7.6
---------------
Bug fixes:
- NumPy compatibility fixes.
- Pyro 3.6 compatibility fix in DistributedComputing.MasterSlave
2.7.4 --> 2.7.5
---------------
New features:
- Scaling, inversion, and shear transformations added to
Geometry.Transformations
Improvements:
- PDB parser handles CRYST1, SCALEn and MTRIXn records
- Better identification of the Numerics package that is being used
Bug fixes:
- Scientific_affinitypropagation.c compiles with NumPy
2.7.3 --> 2.7.4
---------------
New features:
- New module Clustering.AffinityPropagation.
- New class BSP.ParRootSequence.
Bug fixes:
- Replaced float equality test in Functions.InterpolatingFunction
- Removed exception for order > 1 in Derivatives.DerivVar.__init__
- Fixed reading of non-string attributes from netCDF files.
Improvements:
- New methods getBinIndices and getBinCount in Statistics.Histogram.Histogram
- Physics.PhysicalQuantities: unit definitions added to doc string
2.7.2 --> 2.7.3
---------------
Improvements:
- Added multi-module setup for master-slave computations.
- More information available through task_manager.
- task_manager can start slave processes.
2.7.1 --> 2.7.2
---------------
Bug fixes:
- Scientific_netcdf would not compile with NumPy under Python 2.4
because NumPy also defined Py_ssize_t.
2.7 --> 2.7.1
-------------
Improvements:
- NumPy compatibility. Scientific_netcdf was revised by hand.
The Python code was run through numpy.oldnumeric.alter_code1 to
identify the critical sections, which were then all handled in
some way. It is possible that there are still incompatibilities
of the kind that numpy.oldnumeric.alter_code1 cannot detect
2.5.12hg --> 2.7
----------------
New features:
- Subpackage Scientific.DistributedComputing for easy parallelization
of independent tasks.
2.5.11 --> 2.5.12hg
-------------------
Bug fixes:
- VRML2 output would crash for scenes containing Line objects
- Pyrex implmentation of vector objects could crash instead of raising
an exception in divide operations.
- Pyrex implmentation of vector objects would raise exceptions incorrectly
under Python 2.5
Improvements:
- builds Macintosh packages with documentation and examples
2.5.10 --> 2.5.11
-----------------
Bug fixes:
- Pyrex implementation of vector objects raised exceptions in comparisons
- Pyrex implementation of vector objects did not accept negative indices
- Some object deletions during conversion to epydoc had to be reversed
Improvements:
- Two test suites
2.5.9 --> 2.5.10
----------------
Bug fixes:
- Fixed netCDF error handling
Improvements:
- Support for NumPy (not very well tested yet)
- Scientific.NumberDict more efficient
2.5.8 --> 2.5.9
---------------
Improvements:
- Scientifc.IO.NetCDF supports the new 64-bit data structures in Python 2.5
(not yet tested on a 64-bit machine)
- Docstrings modified for use with Epydoc.
2.5.7 --> 2.5.8
---------------
Bug fixes:
- Syntax error in Scientific.IO.PDB
- Attribute deletion in netCDF file and variable objects caused a crash.
2.5.6 --> 2.5.7
----------------
Bug fixes:
- Tensor-vector multiplication was incorrect with the Pyrex implementation
of vector objects.
2.5.5 --> 2.5.6
----------------
Bug fixes:
- Scientific.BSP.ParClass did not pass on __call__ and __getitem__
to local class
- Scientific.BSP.ParClass: Class wrappers did not always return the right
global object.
2.5.4 --> 2.5.5
----------------
Bug fixes:
- Scientific.IO.NetCDF.NetCDFVariable.assignValue() had incomplete error
reporting. Some errors would not raise exceptions as required.
2.5.3 --> 2.5.4
----------------
Improvements:
- A "test" method on MPI request objects permits to check if data
is available (thanks to Jakob Schiotz for this addition).
Bug fixes:
- The new Pyrex vector objects could not be pickled.
2.5.1 --> 2.5.3
----------------
Improvements:
- The class Scientific.Geometry.Vector has been reimplemented in Pyrex,
yielding much faster vector operations. There is, however, the restriction
that the vector elements must be of type "float". For the rare applications
where this condition is not fulfilled (such as
Scientific.Functions.Derivatives.DerivVector), the Python implementation
remains accessible as Scientific.Geometry.VectorModule.Vector.
2.4.9 --> 2.5.1
----------------
Improvements:
- Vector and Tensor objects permit comparison with other types
of objects (which always return False)
- Numarray can be used instead of Numeric as far as possible
(see README for details)
2.4.7 --> 2.4.9:
----------------
Bug fixes:
- Integer array attributes caused a TypeError with recent versions of
Numeric (that don't do silent casts from Long to Int any more).
Additions:
- Method "threeAngles" in Geometry.Transformation.Rotation.
2.4.6 --> 2.4.7:
----------------
Bug fixes:
- Scientific.BSP: alltrue() and anytrue() sometimes returned wrong results.
Additions:
- Scientific.Visualization.VMD can now correctly launch VMD under Windows
* This is a maintainer release.
* `configure.ac' was changed to allow building the package under
Mac OS and Darwin with ODBC support.
* The SQL table driver was improved to process NULL data.
* Some bugs were fixed in the LP/MIP preprocessor.
Changes 4.42:
* The new API routines were added.
* The new command-line options were added to the stand-alone solver glpsol.
TinySVM is an implementation of Support Vector Machines (SVMs) [Vapnik 95],
[Vapnik 98] for the problem of pattern recognition. Support Vector Machines is a
new generation learning algorithms based on recent advances in statistical
learning theory, and applied to large number of real-world applications, such as
text categorization, hand-written character recognition.
* To compile fityk, Boost (only headers) and xylib must be installed first.
Fityk tarball does not contain a copy of boost and xylib now.
* user-defined functions: split functions can be defined in this way:
SplitG(h, c, w1, w2) = x < c ? Gaussian(h, c, w1) : Gaussian(h, c, w2)
* added info-numeric-format option
* a couple of bug fixes
Changes 0.9.1:
* added cfityk to Windows installer
* Unix only: fitting can be interrupted by the INT signal
* changed output of "info errors", see the manual for details
* GUI: "plot in @n" changes selected datasets (useful in scripts)
* many bugs fixed
Changes 0.9.0:
* GUI: Data > Editor dialog was replaced with two dialogs: Data > Table
and Data > Edit Transformations
* added Lua bindings (configure option --enable-lua)
* a syntax to execute output from external program: command ! program [args...]
* xyConvert (which requires wx 2.9) is built by default.
Added flag --disable-xyconvert, which must be used with wx 2.8.
* parsing of info command was rewritten, but functionality is almost the same
* bug fixes
* fixed reading of Bruker v3 files
* changes in API, added C API
Changes 0.5:
* added support for compressed files \*.gz (requires zlib) and \*.bz2 (bzlib)
New items in core:
* plot3d: multiple surfaces; built-in spherical transformation
Other revisions:
* revision of hypergeometic functions
* extension of Bessel functions
* extension of abs_defint function
* extension of Riemann zeta function
* limits of signum functions
* package draw: new graphic object 'tube'
Bug fixes:
2979579: plot3d with format xmaxima does not work in Xmaxima
2976744: postscript terminal requires manual reset of default termina
2976657: Usage of gammagreek and %gammagreek
2974616: mat_cond
2969599: integrate bug?
2968344: gamma_incomplete(1.0, 4.368265444147715e+19) fails
2968174: Integration of hypergeometric bug
2965201: run_testsuite() causes Lisp error
2965115: 2*%e,numer -> single float precision
2962943: simplifya gives Lisp error for a cons
2961822: sinh(0.0b0) causes Maxima to abort
2957758: plotting gamma_incomplete_regularized incorrect
2954141: Kummer reflection
2953369: Definite Integration of 1/(a-b*cos(x)) wrong
2949677: hypergeometric floating point
2948800: integrate((1-cos(2*x)^2)^2/x^4,x,0,inf) wrong
2945609: incomplete/misleading documentation of coeff
2943581: Grind omits empty strings
2943400: 'linel' command can crash 'maxima'
2938716: too much evaluation in translated code
2938177: simplify_sum(sum(k^n,k,1,m)) -> stack overflow
2938078: Crash on attached input
2937837: find_root_error documentation incorrect
2935631: bfloat(log(n)) can be different from log(bfloat(n))
2933996: abs_integrate bug
2933440: sqrt(-z^2) simplifies to %i*sqrt(z^2) for z complex
2932096: allroots fails for real polynomial.
2927502: abs() or cabs() are much slower than just sqrt(re^2+im^2)
2924831: file_type is wrong for ccl on mac os x
2921946: Expansion of bessel_k(1/2,x) with radexpand:false
2920190: non-integer value for maxposex
2919296: binomial sums
2914376: implicit_plot error
2914296: Limit gets Maxima stuck
2914176: Conversion of rational to bfloat is inaccurate
2913614: LAPACK: dgesvd is broken
2911891: gcfac gives Lisp error
2910437: non-repeatable beta_incomplete(1b0,1,z)
2910001: optimization of bfloat input
2909980: optimization for log of bfloats
2909917: documentation type -- jornan
2907952: diff of a taylor series
2907815: sold variable in diag(x) (package diag) should be local
2907727: Incorrect Integral with option integrate_use_rootsof
2892710: Allow easier library access
2880797: bad answer in integrate(sqrt(sin(t)^2+cos(t)^2),t,0,2*%pi)
2875784: fourier integral incorrect
2859856: csign(log(x)) --> pnz
2852992: sqrt(-1/x)-%i/sqrt(x) not zero
2843621: GosperSum error
2808861: list function arguments with mode_declare in translate
2786017: realonly in algsys.lisp
2607007: legend does not work
1869296: hgfred([1,2],[6],1) bogus
1857562: hgfred([a,b],[c], 0) -/--> 1
1633149: sum bug that never happens
1620165: assoc needs to check argument, was: Strange error
1531688: hgfred([ ], [ ], 0)
1440286: documentation for 'listofvars'
1440069: euler numbers & zerobern
1376392: limit(x/(2+sin(1/x)), x, 0); wrong result
1372264: no user doc for 'numer_pbranch'
1219846: properties of translated functions
1106912: limit(x/sin(x)^2,x,inf)
1010768: sqrt(1/z) - 1/sqrt(z) => 0
932095: ode2 redundant asksign
910270: 1/+3*x parses as 1/(+3*x)
903166: assume works for real values only
900860: Simplifications involving abs
893633: depends(a,[b,b,b])
856209: inconsistency between facts() and facts(v)
840848: trigreduce doesn't enter unknown functions
811522: redundant question in limit
781657: binomial(x,x) => 1, but binomial(-1,-1) => 0
777564: subtraction \"-\"(a,b) should work/FIX
776441: orderlessp not transitive
767556: Distributing operations over =
767528: op(box(a)) bogus
752417: KEEPFLOAT:TRUE ignored by SOLVE
719968: No SIMP function
710307: orderlessp of bfloat, %e, and inf
660876: taylor and keepfloat ERR
655270: Incomplete integration
643254: orderlessp([rat(x)], [rat(x)])
593351: limit/sin(inf)etc. should give 0, not IND
* Packages must have been installed under R >= 2.10.0, as the
current help system is the only one now supported.
* A port to 64-bit Windows is now available as well as binary package
repositiories: see the 'R Administration and Installation Manual'.
* Argument matching for primitive functions is now done in the same way
as for interpreted functions except for the deliberate exceptions
call switch .C .Fortran .Call .External
all of which use positional matching for their first argument,
and also some internal-use-only primitives.
* The default device for command-line R at the console on Mac OS X
is now quartz() and not X11().
New features
* The 'open' modes for connections are now interpreted more consistently.
* R CMD INSTALL now uses the internal untar() in package utils.
* help(try.all.packages = TRUE) is much faster.
* R CMD check has a new option '--timings' to record per-example timings
in file <pkg>.Rcheck/<pkg>-Ex.timings.
* The TRE library has been updated to version 0.8.0 (minor bugfixes).
More...
besides being portable and extensible, for instance three dimensional
tables and iterative expressions.
The most important feature is the funktional addressing of cells,
unlike the traditional approach like A0, C5, etc. which is probably
inherited from VisiCalc.
From Wen Heping in PR pkg/43204.
This minor release removes datetime support, which fixes the binary
incompatibility issues with SciPy and other packages. It also includes several
bug fixes. No new features are introduced.
Bugs fixed
----------
- #1336: Fix for 1299 exposes Bus error on Sparc
- #1379: CPU ID not set correctly on PARISC
- #1388: frombuffer calls PyErr_Format without throwing an error
- log1p
- kaiser for M=1
- paver execution on Windows 7 for Python 2.6
- several fixes to Chebyshev and Polynomial
changes:
-General build updates and bug fixes
-Bug fix for segfaults with some uses of integrate()
-New Simplified Chinese translation
-Fix crash with unsupported operator in RPN syntax
-Fix reduction of vector size
Mon Mar 22 23:54:07 MDT 2010
* GSL-1.14 support
* Added GSL::Multiset class
* Added GSL::Function#glfixed(a, b table)
Sun Aug 16 19:01:31 BOT 2009
* Added Non-negative Matrix Factorization (NMF) support (by Roman Shterenzon)
Sat Aug 8 22:36:24 BOT 2009
* Added GSL-1.13 features:
* Added GSL::Monte::Miser#params_get, GSL::Monte::Vegas#params_get
* Added GSL::BSpline::greville_abscissa(i)
* Added GSL::Poly#eval_derivs(x)
* Added a new minimization algorithm "quad_golden"
* Added a new multimin algorithm "nmsimplex2rand"
Tue Jun 9 10:42:30 JST 2009
* Fixed bug in linalg.c (bug [#25842])
Thu Feb 2 12:16:38 JST 2009
* Fixed a bug in GSL::Histogram.alloc_uniform() (bug [#23040])
* Fixed a bug in GSL::Vector#/ (bug [#23334])
Thu Nov 6 17:34:18 JST 2008
* Match with the tensor extension version 0.99
* now not compatible for the versions older than tensor-0.97.
Sat Jul 26 08:23:45 JST 2008
* GSL::Poly.eval now handles complex numbers (GSL-1.11)
* Added new quasi-random generators "halton" and "reversehalton"
* Added a module function GSL::MultiFit::linear_residuals() (GSL-1.11)
* Fixed a bug in ODE solver
Mon Jun 30 22:07:24 JST 2008
* Fixed GSL::Vector#normalize (#20865)
Mon May 26 19:21:15 JST 2008
* Fixed a bug in GSL::Matrix::to_v (#19757)
* Fixed a bug in GSL::Vector::Int multiplication (#19924)
pkgsrc changes:
- Adjust dependencies
Upstream changes:
0.39 Tue 16 Mar 2010
- Doc fix (RT#54507, Patrick Cronin)
- Upped Copyright notices to 2010
- Drop YAML version to 1.0
C++ library of mathematical, signal processing and communication
routines
Its main use is in simulation of communication systems and for
performing research in the area of communications. The kernel of the
library consists of generic vector and matrix classes, and a set of
accompanying routines. Such a kernel makes IT++ similar to MATLAB or
GNU Octave.
* What is new in gsl-1.14:
** Upgraded to latest libtool, autoconf and automake (libtool-2.2.6b,
autoconf-2.65, automake-1.11.1). Fixes security hole in 'make
dist' (see Automake CVE-2009-4029).
** Added support for "multisets", which are similar to permutations
and combinations. A multiset is an array of k integers in the
range 0 to n-1 where each value may occur more than once. Multisets
can be used to iterate over the indices of a k-th order symmetric
tensor in n-space. (Rhys Ulerich)
** Added gsl_integrate_glfixed routines for performing fixed order
Gauss-Legendre integration
(Pavel Holoborodko, Konstantin Holoborodko, Rhys Ulerich)
** In the LMDER multi-dimensional fitting routines, the return code
GSL_ENOPROG is now used instead of GSL_CONTINUE for the case where
10 or more attempts to find a suitable trial step have been made
without success. [bug #25383]
** The confluent hypergeometric function gsl_sf_hyperg_U (a,b,x) has
been extended to support x < 0 for cases not involving
singularities in 1F1(a,b,x). [bug #27859]
** The F-distribution gsl_ran_fdist_pdf now avoids unnecessary
underflow and overflow and handles cases where n > 248. [bug
#28500]
** The SVD routines now use a scaled version of the implicit QR method
and compute the shift more reliably for values at the limit of
double precision, avoiding potential NaNs. [bug #28767]
** A compile time error is emitted if the configuration stage prevents
the functions gsl_isnan and gsl_finite from being defined.
** Added missing dereference in GSL_VECTOR_COMPLEX when not using
GSL_RANGE_CHECK [bug #28017]
** Improved the range of gsl_sf_hyperg1F1(a,b,x) when a<0,b>0. [bug
#28718]
** Added macros GSL_MAJOR_VERSION and GSL_MINOR_VERSION in
<gsl/gsl_version.h>
** Improved gsl_eigen_symmv and gsl_eigen_symm to avoid a potential
infinite loop when the tridiagonalised matrix contains very small
values. [bug #28096]
** Added functions gsl_multifit_linear_usvd and
gsl_multifit_wlinear_usvd for multilinear fitting without
column-scaling of the fit matrix.
is rendered and installed. Disabling the option is helpful e.g. for
web servers supporting OpenID logins, where X and TeX aren't present.
Bump PKGREVISION.
pkgsrc changes:
- Add license definition
- Adjust dependencies
Upstream changes:
0.05 Mon. Feb 22, 2010
- updates copyright on all files
* Test::Excel::Template::Plus
- Fixing some test failures because of an
internals change in Spreadsheet::ParseExcel
- thanks to Chris Travers
pkgsrc changes:
- Adjust patch which allows to use math/pari
Upstream changes:
2.01080604
Add (missing in 2.1.*) declaration for pari_init().
Minor miscount in docs.
Math::PariBuild: detecting `patch --binary' missed -p1; same for inc_h.diff
Work around bug in XSUB.h (at least up to 5.11.2) with puts.
Get GPDATADIR from gp, if present.
Make self-documentation for switching to 2.3.* more explicit.
kmx patch for mingw 32-bit Win-build:
include windows.h (early!) in Pari.xs and highlvl.c
enable assembler for this build
x86_64 assembler detection after 2.2.7; thanks to Alexander Haeckel
Based on PR#42834 by Wen Heping.
Update MASTER_SITES, set LICENSE=modified-bsd, 3-caulse BSD.
======================================================================
Networkx-1.0.1
Release date: 11 Jan 2010
See: https://networkx.lanl.gov/trac/timeline
Bug fix release for missing setup.py in manifest.
======================================================================
Networkx-1.0
Release date: 8 Jan 2010
See: https://networkx.lanl.gov/trac/timeline
New features
This release has sigificant changes to parts of the graph API to allow graph, node, and edge attributes. See http://networkx.lanl.gov//reference/api_changes.html
* Update Graph, DiGraph, and MultiGraph classes to allow attributes.
* Default edge data is now an empty dictionary (was the integer 1)
* Difference and intersection operators
* Average shortest path
* A* (A-Star) algorithm
* PageRank, HITS, and eigenvector centrality
* Read Pajek files
* Line graphs
* Minimum spanning tree (Kruskal¡Çs algorithm)
* Dense and sparse Fruchterman-Reingold layout
* Random clustered graph generator
* Directed scale-free graph generator
* Faster random regular graph generator
* Improved edge color and label drawing with Matplotlib
* and much more, see https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.0
Examples
* Update to work with networkx-1.0 API
* Graph subclass example
======================================================================
Networkx-0.99
Release date: 18 November 2008
See: https://networkx.lanl.gov/trac/timeline
New features¢ù
This release has sigificant changes to parts of the graph API. See http://networkx.lanl.gov//reference/api_changes.html
* Update Graph and DiGraph classes to use weighted graphs as default Change in API for performance and code simplicity.
* New MultiGraph and MultiDiGraph classes (replace XGraph and XDiGraph)
* Update to use Sphinx documentation system http://networkx.lanl.gov/
* Developer site at https://networkx.lanl.gov/trac/
* Experimental LabeledGraph and LabeledDiGraph
* Moved package and file layout to subdirectories.
Bug fixes
* handle root= option to draw_graphviz correctly
Examples
* Update to work with networkx-0.99 API
* Drawing examples now use matplotlib.pyplot interface
* Improved drawings in many examples
* New examples - see http://networkx.lanl.gov/examples/
Upstream changes:
2.37 February 2 2010 - Minor
+ Added set_chartarea() and set_plotarea() methods to set
chart and plot background colours and border lines.
! Fixed bug where embedded charts gave "Data may be lost"
warning. Reported by Andreas Strobitzer.
! Fixed issue where set_properties() didn't work with ::Big.
Marked ::Big as deprecated in the docs in favour of using
Spreadsheet::WriteExcel directly. Removed WorkbookBig.pm.
