Commit graph

2974 commits

Author SHA1 Message Date
jperkin
c7fed90969 Pass through the correct ABI flags as this package calls compilers directly.
Fixes build on Solaris where ABI=32 with 64-bit compilers.
2012-08-09 12:42:16 +00:00
wen
dadc786193 Update to 1.16
Upstream Changes:
1.16    2012-08-06      Florent Angly <florent.angly@gmail.com>
    * Fixed issue introduced in version 1.15 where rand() took no notice of
      argument and irand() did (bug #78200, reported by David Morel)
    * Migration of test suite to Test::More and Test::Number::Delta

1.15    2012-06-04      Florent Angly <florent.angly@gmail.com>
    * Implemented irand() to draw random integers (bug #73298, feature requested
      by crew@cs.stanford.edu)
    * Fixed build failure on Hurd (bug #74165, reported and patched by Salvatore
      Bonaccorso)

1.14    2012-05-27      Florent Angly <florent.angly@gmail.com>
    * Fixed compilation problems with nmake on Windows platforms
      (Florent Angly, bug #74984)
    * Fixed issues with random seed (bug #77343, solution suggested by
      Laurent Dami, fix implemented by Florent Angly)

1.13    2012-01-20      Abhijit Menon-Sen <ams@toroid.org>
    * New seed generation and retrieval mechanism by Florent Angly (bug
      #64640 on rt.cpan.org).
2012-08-06 14:04:08 +00:00
wen
185706b174 + p5-Test-Number-Delta 2012-08-06 13:47:44 +00:00
wen
b7ded4a2ae Import p5-Test-Number-Delta-1.03:
A perl module for compare if the difference between two numbers is within
a specified amount.
2012-08-06 13:44:39 +00:00
marino
2e61fd5808 math/mpcomplex: Update from version 0.9 to 1.0
Changes since version 0.9:
  - First release as a GNU package
  - License change: LGPLv3+ for code, GFDLv1.3+ (with no invariant sections)
    for documentation
  - 100% of all lines are covered by tests
  - Functions renamed:
    mpc_mul_2exp to mpc_mul_2ui, mpc_div_2exp to mpc_div_2ui
  - 0^0, which returned (NaN,NaN) previously, now returns (1,+0)
  - Removed compatibility with K&R compilers, untestable due to lack of
    such compilers
  - New functions: mpc_log10, mpc_mul_2si, mpc_div_2si
  - Speed-ups:
    - mpc_fma
  - Bug fixes:
    - mpc_div and mpc_norm now return a value indicating the effective
      rounding direction, as the other functions
    - mpc_mul, mpc_sqr and mpc_norm now return correct results even if there
      are over- or underflows during the computation
    - mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
      infinite part and equals output variable is corrected
    - mpc_fr_sub: Wrong return value for imaginary part is corrected
2012-08-05 18:24:56 +00:00
obache
b8d6e4640f Bump PKGREVISION for change of PostgreSQL default version to 9.1. 2012-08-05 10:02:09 +00:00
mishka
bc2e21dde7 The R build/install process should seize all relevant environment
variables, and customization should be done via INSTALL_ENV/MAKE_ENV
respectively. This also solves the internationalization issue fixed
in previous commit properly.

Noted by <joerg> on pkgsrc-changes@, many thanks!
2012-08-02 14:35:01 +00:00
jperkin
c599ee4590 Use the correct linker flags on Solaris/GCC.
Fixes Solaris 64-bit build.
2012-08-02 13:52:17 +00:00
drochner
efafd5490e leave DIST_SUBDIR there - as the distribution scheme worked all the time,
patches will be released rather than full new distfiles, and if they crop
up, we'd have to refetch the original distfile otherwise
2012-08-01 19:29:26 +00:00
dholland
1795c39e99 Add patch comment. 2012-07-29 22:24:32 +00:00
wiz
c1a87392c7 Update to 3.1.1:
Changes from version 3.1.0 to version 3.1.1:
- Improved MPFR manual.
- Test coverage: 96.5% lines of code.
- Bug fixes (see <http://www.mpfr.org/mpfr-3.1.0/#fixed> or ChangeLog file).
2012-07-29 20:30:15 +00:00
mishka
50970427cd On internationalized environment some locales may fail wich equals
to error during addons installation phase - force all locales to C.
2012-07-24 21:26:27 +00:00
dholland
b29a551e69 Remove stray commas. 2012-07-22 01:13:29 +00:00
wen
642c4fc4aa Update to 1.7
Release Log
Networkx-1.7
Release date: 4 July 2012

Highlights
New functions for k-clique community finding, flow hierarchy, union, disjoint union, compose, and intersection operators that work on lists of graphs, and creating the biadjacency matrix of a bipartite graph.
New approximation algorithms for dominating set, edge dominating set, independent set, max clique, and min-weighted vertex cover.
Many bug fixes and other improvements.
For full details of the tickets closed for this release (added features and bug fixes) see: https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.7

API Changes
See Version 1.7 notes and API changes
2012-07-13 14:00:32 +00:00
obache
148b967362 Update ruby-spreadsheet to 0.7.3.
=== 0.7.3 / 26.06.2012

* Fix Format borders
* see https://github.com/zdavatz/spreadsheet/pull/6 for full details.
* patches by uraki66@gmail.com
2012-07-13 13:20:52 +00:00
drochner
68822dd5ce for itstool, a BUILD_DEPENDS is sufficient 2012-07-06 14:48:35 +00:00
dholland
8bc5cf4597 Oops, fix thinko in previous. The disturbing part is how much stuff this
baloney *didn't* break.
2012-07-06 05:04:23 +00:00
dholland
828963ef89 Needs textproc/itstool to configure. 2012-07-06 04:30:49 +00:00
asau
8ce0f6c5fa Update to Octave 3.6.2
Summary of important user-visible changes for version 3.6:
---------------------------------------------------------

 ** The PCRE library is now required to build Octave.  If a pre-compiled
    package does not exist for your system, you can find PCRE sources
    at http://www.pcre.org

 ** The ARPACK library is no longer distributed with Octave.
    If you need the eigs or svds functions you must provide an
    external ARPACK through a package manager or by compiling it
    yourself.  If a pre-compiled package does not exist for your system,
    you can find the current ARPACK sources at
    http://forge.scilab.org/index.php/p/arpack-ng

 ** Many of Octave's binary operators (.*, .^, +, -, ...) now perform
    automatic broadcasting for array operations which allows you to use
    operator notation instead of calling bsxfun or expanding arrays (and
    unnecessarily wasting memory) with repmat or similar idioms.  For
    example, to scale the columns of a matrix by the elements of a row
    vector, you may now write

      rv .* M

    In this expression, the number of elements of rv must match the
    number of columns of M.  The following operators are affected:

      plus      +  .+
      minus     -  .-
      times     .*
      rdivide   ./
      ldivide   .\
      power     .^  .**
      lt        <
      le        <=
      eq        ==
      gt        >
      ge        >=
      ne        !=  ~=
      and       &
      or        |
      atan2
      hypot
      max
      min
      mod
      rem
      xor

    additionally, since the A op= B assignment operators are equivalent
    to A = A op B, the following operators are also affected:

      +=  -=  .+=  .-=  .*=  ./=  .\=  .^=  .**=  &=  |=

    See the "Broadcasting" section in the new "Vectorization and Faster
    Code Execution" chapter of the manual for more details.

 ** Octave now features a profiler, thanks to the work of Daniel Kraft
    under the Google Summer of Code mentorship program.  The manual has
    been updated to reflect this addition.  The new user-visible
    functions are profile, profshow, and profexplore.

 ** Overhaul of statistical distribution functions

    Functions now return "single" outputs for inputs of class "single".

    75% reduction in memory usage through use of logical indexing.

    Random sample functions now use the same syntax as rand and accept
    a comma separated list of dimensions or a dimension vector.

    Functions have been made Matlab-compatible with regard to special
    cases (probability on boundaries, probabilities for values outside
    distribution, etc.).  This may cause subtle changes to existing
    scripts.

    negative binomial function has been extended to real, non-integer
    inputs.  The discrete_inv function now returns v(1) for 0 instead of
    NaN.  The nbincdf function has been recoded to use a closed form
    solution with betainc.

 ** strread, textscan, and textread have been completely revamped.

    They now support nearly all Matlab functionality including:

      * Matlab-compatible whitespace and delimiter defaults

      * Matlab-compatible options: 'whitespace', treatasempty', format
        string repeat count, user-specified comment style, uneven-length
        output arrays, %n and %u conversion specifiers (provisionally)

 ** All .m string functions have been modified for better performance or
    greater Matlab compatibility.  Performance gains of 15X-30X have
    been demonstrated.  Operations on cell array of strings no longer pay
    quite as high a penalty as those on 2-D character arrays.

      deblank:  Now requires character or cellstr input.

      strtrim:  Now requires character or cellstr input.
                No longer trims nulls ("\0") from string for Matlab
                compatibility.

      strmatch: Follows documentation precisely and ignores trailing spaces
                in pattern and in string.  Note that this is documented
                Matlab behavior but the implementation apparently does
                not always follow it.

      substr:   Now possible to specify a negative LEN option which
                extracts to within LEN of the end of the string.

      strtok:   Now accepts cellstr input.

      base2dec, bin2dec, hex2dec:
                Now accept cellstr inputs.

      dec2base, dec2bin, dec2hex:
                Now accept cellstr inputs.

      index, rindex:
                Now accept 2-D character array input.

      strsplit: Now accepts 2-D character array input.

 ** Geometry functions derived from Qhull (convhull, delaunay, voronoi)
    have been revamped.  The options passed to the underlying qhull
    command have been changed for better results or for Matlab
    compatibility.

      convhull: Default options are "Qt" for 2D, 3D, 4D inputs
                Default options are "Qt Qx" for 5D and higher

      delaunay: Default options are "Qt Qbb Qc Qz" for 2D and 3D inputs
                Default options are "Qt Qbb Qc Qx" for 4D and higher

      voronoi:  No default arguments

 ** Date/Time functions updated.  Millisecond support with FFF format
    string now supported.

    datestr: Numerical formats 21, 22, 29 changed to match Matlab.
             Now accepts cellstr input.

 ** The following warning IDs have been removed:

      Octave:associativity-change
      Octave:complex-cmp-ops
      Octave:empty-list-elements
      Octave:fortran-indexing
      Octave:precedence-change

 ** The warning ID Octave:string-concat has been renamed to
    Octave:mixed-string-concat.

 ** Octave now includes the following Matlab-compatible preference
    functions:

      addpref  getpref  ispref  rmpref  setpref

 ** The following Matlab-compatible handle graphics functions have been
    added:

      guidata         uipanel        uitoolbar
      guihandles      uipushtool     uiwait
      uicontextmenu   uiresume       waitfor
      uicontrol       uitoggletool

    The uiXXX functions above are experimental.

    Except for uiwait and uiresume, the uiXXX functions are not
    supported with the FLTK+OpenGL graphics toolkit.

    The gnuplot graphics toolkit does not support any of the uiXXX
    functions nor the waitfor function.

 ** New keyword parfor (parallel for loop) is now recognized as a valid
    keyword.  Implementation, however, is still mapped to an ordinary
    for loop.

 ** Other new functions added in 3.6.0:

      bicg                       nthargout                   usejava
      is_dq_string               narginchk                   waitbar
      is_sq_string               python                      zscore
      is_function_handle         register_graphics_toolkit
      loaded_graphics_toolkits   recycle

 ** Deprecated functions.

    The following functions were deprecated in Octave 3.2 and have been
    removed from Octave 3.6.

      create_set          spcholinv    splu
      dmult               spcumprod    spmax
      iscommand           spcumsum     spmin
      israwcommand        spdet        spprod
      lchol               spdiag       spqr
      loadimage           spfind       spsum
      mark_as_command     sphcat       spsumsq
      mark_as_rawcommand  spinv        spvcat
      spatan2             spkron       str2mat
      spchol              splchol      unmark_command
      spchol2inv          split        unmark_rawcommand

    The following functions have been deprecated in Octave 3.6 and will
    be removed from Octave 3.10 (or whatever version is the second major
    release after 3.6):

      cut                is_duplicate_entry
      cor                polyderiv
      corrcoef           shell_cmd
      __error_text__     studentize
      error_text         sylvester_matrix

 ** The following functions have been modified for Matlab compatibility:

      randperm
2012-07-05 19:18:29 +00:00
drochner
33489deaea update to 6.4.2.1
This switches to the gnome-3.4 branch
2012-07-04 20:01:58 +00:00
joerg
3d7227714f Fix main when using C++ test cases 2012-07-03 17:42:48 +00:00
joerg
c14769d27e Fix template usage. 2012-07-03 17:42:05 +00:00
adam
866b730e71 Revbump after updating boost 2012-07-02 13:37:35 +00:00
dholland
49cfd098d9 Add desktopdb.mk and bump PKGREVISION for 118 packages as reported by
pkglint. If any of these are wrong for some reason, please revert/adjust.
2012-07-01 19:05:10 +00:00
asau
b4ba1db240 Update to Mathomatic 16.0.0
CHANGES MADE TO MATHOMATIC 15.8.5 TO BRING IT UP TO THE NEXT VERSION:

Code, documentation, and user interface improvements, corrections,
and cleanup.  Fixed many possible bugs, some where the wrong level global
expression buffers were being used.

05/26/12 - Push command improved with better responses.  Same functionality.

           In the source code, tune-up variable integer_coefficients was
           renamed to "factor_out_all_numeric_gcds", because Mathomatic always
           tries to have integer coefficients this year, but it doesn't always
           factor out all numeric GCDs unless factor_out_all_numeric_gcds
           is true, or the factor command is used.  The default is false,
           for more orderly and revealing coefficients.
           Of course, much of what Mathomatic does is
           try to improve readability and simplicity.
           There is no need to set this variable, just use the factor command.

05/27/12 - Removed C declarations for memmove(3), the defaults in
           /usr/include/string.h are probably better and what's wanted in
           every case.  It would be very odd if this didn't work 100%.

05/28/12 - readline history file renamed to "~/.matho_history" from
           "~/.mathomatic_history".  File name was too long for CygWin.
           Tested thoroughly compiling, installing, and running under
           the latest CygWin.  Works fine, except for rlwrap.  "rlwrap -v"
           returns with error, a successful return is how I test for its
           existence.

           Made output redirection work with the "list primes" command.

06/02/12 - Cleanup of Linux, Mac OS X, and Windows binary distributions.
           The Windows binary distribution now includes m4 scripts, in case
           CygWin is installed, allowing use of m4 Mathomatic in Windows.

           Fixed MinGW version to not output two carriage returns at the
           end of every line of list command output.

06/03/12 - If compiled with -DSHOW_RESOURCES, will give total CPU usage and
           RSS size in the "version status" command.  Requires OS support.
           Some OSes will show even more information.  Uses getrusage(2).

06/04/12 - Allow breaking out of user line-input requests with Control-C.
           Still have to hit the Enter key, but the command will be aborted.

06/05/12 - Added "lib/example.c", the simplest example yet of Symbolic Math
           Library usage.  Compile with "compile.testmain" or practice
           compiling it by hand.

           The simplify command now returns the number of expressions
           simplified, so you can tell if "simplify sign" worked.

           The solve command can now require verification, by using the
           "verifiable" option, instead of the "verify" option.  This causes
           unverifiable solves to return with failure, aborting any reads.

           Fixed missing code in internal C function free_mem().
           I don't think it was used by anyone.  A call to free_mem() is
           now made on exit, if Mathomatic is compiled with -DVALGRIND, to
           check for memory leaks.

06/08/12 - Added polynomial factoring to GCD result of divide command.
           It is always handy to know what the factors are of the GCD.

           Allow comma (,) at the end of most input lines.  A comma now
           terminates an expression instead of giving an error.  Allow
           commas all over the place, where-ever logical, in any
           Mathomatic command-line.  They are used as separators,
           more so than spaces.

06/09/12 - Cleaned up variables command to always allow the count parameter,
           and to line up everything with 8 character wide tabs.

           Added ability to place the definite integration bounds on the
           integrate command-line, just like the nintegrate command.

           Added titles to most help command pages.

06/10/12 - The "factor number" command works much nicer now, and allows comma
           separators and zero.

           Developers should note that to remain the same as past versions,
           HTML mode needs to be "set html all" to output HTML at all times
           in both the application and the symbolic math library, even when
           redirecting output.  Now setting all HTML mode with
           "make pdfsheet".  "set html" only outputs HTML code to standard
           output.

06/13/12 - Added warning in "misc/known_bugs.txt" about LLVM/Clang optimizer
           failure when compiling Mathomatic with LLVM/Clang instead of gcc.
           If you enable any optimization at all, entering (32^.5) and the
           like will hang Mathomatic, putting it in an endless loop.
           So when compiling Mathomatic with LLVM/Clang, always disable
           optimization with "-O0", so that it will then run and pass
           all of the tests in 1 second and not be infinitely slower.
           Mathomatic will hang during "make test"
           if compiled with optimization enabled using LLVM.  Mathomatic is
           not noticeably slower when compiled without any optimization,
           because everything is memmove(3)s and floating point arithmetic.

06/15/12 - Added repeat option to replace command.  A handy feature that
           lets you try plugging different values into an equation.  It
           checks if the result is an identity, too.

06/18/12 - The version command now has a "status" option, which behaves
           as before, displaying all version and status information.
           The version command by itself now only displays the Mathomatic
           version number.  Running "mathomatic -v" is now a good way of
           testing for the existence of Mathomatic on your system, only
           outputting the version number to standard output and exiting
           successfully.

06/19/12 - Removed the parenthesizing of variable names in all messages.

           If the current expression is a non-equation, then prefixing or
           suffixing an expression with "=" will add that expression as
           the other equation side now, conveniently making it an equation
           you can solve.

06/22/12 - Added equation number ranges option to tally command.  Type
           "tally -" to resume if the current equation hasn't changed.  Type
           "tally all" to add together all stored expressions as the starting
           value.  Specifying equation numbers or ranges will silently add
           them, then prompt for the next things to add.  The average option
           now displays the number of entries (count) each time the average
           is displayed.  When you exit by typing an empty line, the current
           total is saved in the next available equation space and made
           current, so it can easily resume with "tally -".  "-" by itself
           always means the current equation.

           gnuplot now works with MS-Windows better.  Tried running a Windows
           gnuplot test from scratch, without Cygwin, and it didn't work.
           It should be mostly fixed now.  So go ahead and try plotting
           in Windows, after downloading and installing gnuplot.  Please
           complain if any problems.

           Fixed a long-running problem with the plot command, by asking the
           user questions, only if needed, so that gnuplot will not give an
           error if you are multi-expression plotting.

06/23/12 - Moved load_rc() out of main.c so that the Mathomatic startup set
           options file can be loaded by the library, if the developer wishes.
           Changed a few things so that "set save" and "set no save" will work
           if load_rc() is called beforehand.

06/25/12 - The simplify command has been fixed for optimal integer coefficient
           factoring results and so "180*(sides-2)" simplification works
           nicely, by keeping the result the same as the start by
           factoring out rational constants greater than 1 (this is new),
           along with less than 1,
           if the coefficients remain or become integers.

           Many things cleaned up and finished, like the official
           documentation, the "code integer" command, and "examples/fact.c".

06/27/12 - Allow an ASCII string after the "set save" command, to save only
           that string in ~/.mathomaticrc, so that string, which should be set
           options, is for every Mathomatic session to start with.
           For example, "set save bold color" will start out Mathomatic in
           bold color mode every time.  Enter "set no save" to remove.
           "set save" by itself saves all of the current set options for every
           future session.

Mathomatic version 16.0.0 released Friday 06/29/12.
2012-07-01 08:02:04 +00:00
dholland
da915af565 This blows up on python25 and it doesn't really seem like it's worth
trying to figure out what's wrong, so just mark it INCOMPATIBLE.
2012-06-16 05:40:05 +00:00
markd
859d12642b Update to KDE SC 4.8.4
Bug fixes.
2012-06-16 04:45:28 +00:00
taca
981936387e Update ruby-spreadsheet to 0.7.2.
=== 0.7.2 / 14.06.2012

* many changes by Mina Naguib <mina.git@naguib.ca>
* see git log for full details
2012-06-15 13:55:09 +00:00
asau
458e616226 Provide TEST_TARGET. 2012-06-14 08:26:14 +00:00
asau
7beedacaa4 The package doesn't install HTML files, remove unneeded patch. 2012-06-14 08:24:14 +00:00
sbd
cdfc7f300d Recursive PKGREVISION bump for libxml2 buildlink addition. 2012-06-14 07:43:06 +00:00
asau
850966c490 PCRE is no longer optional. 2012-06-06 23:14:10 +00:00
obache
06d16c1bda Update py-gmpy to 1.15.
Based on PR 46507 by Wen Heping.
* let to register egg-info.
* all files in distfile are not DOS style EOL oter than Windows related files,
  so remove extract option for ZIP.

GMPY 1.15 is a bug fix release. The following bugs were fixed:
* Reference counting leak in divmod(x,0).
* Fatal crash in remove(x,1).
* Discontinue use of custom memory allocator. (Fixes compatibility with Sage.)
* Allow up to base-62 integer conversion.
2012-06-02 13:52:06 +00:00
obache
acbc041e43 remove buildlink3.mk, this package have no contents to buildlink. 2012-06-02 13:38:56 +00:00
obache
8039ec81d4 Update py-networkx to 1.6.
Based on PR 46506 by Wen Heping.
* let to register egg-info.
* marked as incompatible with python 2.5, as new features in 1.3.
  but not marked as compatible with 3.x, one file will not be compiled well
  both 3.1 and 3.2.

Lease Log:

Networkx-1.6

Release date: 20 November 2011

Highlights

New functions for finding articulation points, generating random bipartite
graphs, constructing adjacency matrix representations, forming graph products,
computing assortativity coefficients, measuring subgraph centrality and
communicability, finding k-clique communities, and writing JSON format output.

New examples for drawing with D3 Javascript library, and ordering matrices with
the Cuthill-McKee algorithm.

More memory efficient implementation of current-flow betweenness and new
approximation algorithms for current-flow betweenness and shortest-path
betweenness.

Simplified handling of "weight" attributes for algorithms that use
weights/costs/values. See Version 1.6 notes and API changes.

Updated all code to work with the PyPy Python implementation http://pypy.org
which produces faster performance on many algorithms.

For full details of the tickets closed for this release (added features and bug
fixes) see: https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.6

API Changes

See Version 1.6 notes and API changes:
	http://networkx.lanl.gov/reference/api_1.6.html

Networkx-1.5

Release date: 4 June 2011

For full details of the tickets closed for this release see: https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.5

Highlights

New features

	* Algorithms for generating and analyzing bipartite graphs
	* Maximal independent set algorithm
	* Erd?s-Gallai graphical degree sequence test
	* Negative edge cycle test
	* More memory efficient Dijkstra path length with cutoff parameter
	* Weighted clustering coefficient
	* Read and write version 1.2 of GEXF reader format
	* Neighbor degree correlation that handle subsets of nodes
	* In-place node relabeling
	* Many `weighted' graph algorithms now take optional parameter to use
	  specified edge attribute (default=`weight') (ticket 509)
	* Test for distance regular graphs
	* Fast directed Erd?s-Renyi graph generator
	* Fast expected degree graph generator
	* Navigable small world generator
	* Waxman model generator
	* Geographical threshold graph generator
	* Karate Club, Florentine Families, and Davis' Women's Club graphs

API Changes
See Version 1.5 notes and API changes
	http://networkx.lanl.gov/reference/api_1.5.html

Bug fixes
	* Fix edge handling for multigraphs in networkx/graphviz interface
	  (ticket 507)
	* Update networkx/pydot interface for new versions of pydot
	  (ticket 506), (ticket 535)
	* Fix negative cycle handling in Bellman-Ford (ticket 502)
	* Write more attributes with GraphML and GML formats (ticket 480)
	* Handle white space better in read_edgelist (ticket 513)
	* Better parsing of Pajek format files (ticket 524) (ticket 542)
	* Isolates functions work with directed graphs (ticket 526)
	* Faster conversion to numpy matrices (ticket 529)
	* Add graph[`name'] and use properties to access Graph.name (ticket 544)
	* Topological sort confused None and 0 (ticket 546)
	* GEXF writer mishandled weight=0 (ticket 550)
	* Speedup in SciPy version of PageRank (ticket 554)
	* Numpy PageRank node order incorrect + speedups (ticket 555)

Networkx-1.4

Release date: 23 January 2011

New features
	* k-shell,k-crust,k-corona
	* read GraphML files from yEd
	* read/write GEXF format files
	* find cycles in a directed graph
	* DFS and BFS algorithms
	* chordal graph functions
	* Prim's algorithm for minimum spanning tree
	* r-ary tree generator
	* rich club coefficient
	* NumPy matrix version of Floyd's algorithm for all-pairs shortest path
	* read GIS shapefiles
	* functions to get and set node and edge attributes
	* and more, see https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.4

API Changes
	* gnp_random_graph() now takes a directed=True|False keyword instead of
	  create_using
	* gnm_random_graph() now takes a directed=True|False keyword instead of
	  create_using

Bug fixes
	* see https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.4

Networkx-1.3

Release date: 28 August 2010

See: https://networkx.lanl.gov/trac/timeline

New features
	* Works with Python versions 2.6, 2.7, 3.1, and 3.2 (but not 2.4 and 2.5).
	* Minimum cost flow algorithms
	* Bellman-Ford shortest paths
	* GraphML reader and writer
	* More exception/error types
	* Updated many tests to unittest style. Run with:
	  "import networkx; networkx.test()" (requires nose testing package)
	* and more, see https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.3

API Changes
	* minimum_spanning_tree() now returns a NetworkX Graph (a tree or forest)

Bug fixes
	* see https://networkx.lanl.gov/trac/query?status=closed&group=milestone&milestone=networkx-1.3
2012-06-02 13:19:17 +00:00
wiz
709b7aa44f Add an option for psiconv support, and turn it off by default.
Fixes PR 46511 by Nouod de Brouwer (using his patch).
2012-06-02 07:11:09 +00:00
wiz
fb06b9e127 Add an option for psiconv support, and turn it off by default.
Fixes PR 46511 by Nouod de Brouwer.

Set LICENSE while here.
2012-06-02 07:10:53 +00:00
wiz
a3645cd4c4 + py-munkres. 2012-05-30 11:05:49 +00:00
wiz
f822ffb023 Initial import of py-munkres-1.0.5.4:
The Munkres module provides an implementation of the Munkres
algorithm (also called the Hungarian algorithm or the Kuhn-Munkres
algorithm), useful for solving the Assignment Problem.

Assignment Problem: Let C be an nxn matrix representing the costs
of each of n workers to perform any of n jobs. The assignment
problem is to assign jobs to workers in a way that minimizes the
total cost. Since each worker can perform only one job and each
job can be assigned to only one worker the assignments represent
an independent set of the matrix C.
2012-05-30 11:05:30 +00:00
cheusov
f84ee98eb0 Remove GNU_PROGRAM_PREFIX variable (discussed in pkgsrc-users@).
All utilities are installed with a prefix 'g'. Symlinks with original
names are created in ${PREFIX}/gnu/bin.

Add LICENSE.

++pkgrevision
2012-05-29 18:33:34 +00:00
asau
c71cb16ea7 + arpack 2012-05-29 16:41:26 +00:00
asau
77f06b302e Import ARPACK 96 as math/arpack.
Contributed to pkgsrc-wip by Jason Bacon.

ARPACK is a collection of Fortran77 subroutines designed to solve large
scale eigenvalue problems.

The package is designed to compute a few eigenvalues and corresponding
eigenvectors of a general n by n matrix A. It is most appropriate for large
sparse or structured matrices A where structured means that a matrix-vector
product w <- Av requires order n rather than the usual order n**2 floating
point operations. This software is based upon an algorithmic variant of the
Arnoldi process called the Implicitly Restarted Arnoldi Method (IRAM). When
the matrix A is symmetric it reduces to a variant of the Lanczos process
called the Implicitly Restarted Lanczos Method (IRLM). These variants may be
viewed as a synthesis of the Arnoldi/Lanczos process with the Implicitly
Shifted QR technique that is suitable for large scale problems. For many
standard problems, a matrix factorization is not required. Only the action
of the matrix on a vector is needed.  ARPACK software is capable of solving
large scale symmetric, nonsymmetric, and generalized eigenproblems from
significant application areas. The software is designed to compute a few (k)
eigenvalues with user specified features such as those of largest real part
or largest magnitude.  Storage requirements are on the order of n*k locations.
No auxiliary storage is required. A set of Schur basis vectors for the desired
k-dimensional eigen-space is computed which is numerically orthogonal to working
precision. Numerically accurate eigenvectors are available on request.

Important Features:

    o  Reverse Communication Interface.
    o  Single and Double Precision Real Arithmetic Versions for Symmetric,
       Non-symmetric, Standard or Generalized Problems.
    o  Single and Double Precision Complex Arithmetic Versions for Standard
       or Generalized Problems.
    o  Routines for Banded Matrices - Standard or Generalized Problems.
    o  Routines for The Singular Value Decomposition.
    o  Example driver routines that may be used as templates to implement
       numerous Shift-Invert strategies for all problem types, data types
       and precision.
2012-05-29 16:38:01 +00:00
wiz
84bced6e89 Update to 2.0.17:
Thiss fixes a compilation issue with aligned_allocator, and a typo
in the ParametrizedLine documentation.
2.0.16:
Fix bug in 3x3 tridiagonlisation (and consequently in 3x3 selfadjoint eigen decomposition).
Fix compilation for new gcc 4.6.
Fix performance regression since 2.0.12: in some matrix-vector product, complex matrix expressions were not pre-evaluated.
Fix documentation of Least-Square.
New feature: support for part<SelfAdjoint>.
Fix bug in SparseLU::setOrderingMethod.
2012-05-29 14:51:42 +00:00
wiz
ec498df47e Update to 3.3.2:
FFTW 3.3.2

* Removed an archaic stack-alignment hack that was failing with
  gcc-4.7/i386.

* Added stack-alignment hack necessary for gcc on Windows/i386.  We
  will regret this in ten years (see previous change).

* Fix incompatibility with Intel icc which pretends to be gcc
  but does not support quad precision.

* make libfftw{threads,mpi} depend upon libfftw when using libtool;
  this is consistent with most other libraries and simplifies the life
  of various distributors of GNU/Linux.

FFTW 3.3.1

* Changes since 3.3.1-beta1:

  - Reduced planning time in estimate mode for sizes with large
    prime factors.

  - Added AVX autodetection under Visual Studio.  Thanks Carsten
    Steger for submitting the necessary code.

  - Modern Fortran interface now uses a separate fftw3l.f03 interface
    file for the long double interface, which is not supported by
    some Fortran compilers.  Provided new fftw3q.f03 interface file
    to access the quadruple-precision FFTW routines with recent
    versions of gcc/gfortran.

* Added support for the NEON extensions to the ARM ISA.  (Note to beta
  users: an ARM cycle counter is not yet implemented; please contact
  fftw@fftw.org if you know how to do it right.)

* MPI code now compiles even if mpicc is a C++ compiler; thanks to
  Kyle Spyksma for the bug report.
2012-05-29 13:53:29 +00:00
wiz
87c8074650 Update to 3.3.2:
FFTW 3.3.2

* Removed an archaic stack-alignment hack that was failing with
  gcc-4.7/i386.

* Added stack-alignment hack necessary for gcc on Windows/i386.  We
  will regret this in ten years (see previous change).

* Fix incompatibility with Intel icc which pretends to be gcc
  but does not support quad precision.

* make libfftw{threads,mpi} depend upon libfftw when using libtool;
  this is consistent with most other libraries and simplifies the life
  of various distributors of GNU/Linux.
2012-05-29 13:40:16 +00:00
asau
34a2ed0a55 Update to Mathomatic 15.8.5
CHANGES MADE TO MATHOMATIC 15.8.4 TO BRING IT UP TO THE NEXT VERSION:

General cleanup.

05/11/12 - Renamed fact(x) function to factorial(x), because Maxima uses
           the function "factorial(x)" and no one uses "fact(x)".  Added
           factorial(x) as a standard function in rmath.  Removed binary
           operator name "mod" from rmath, due to having a different meaning
           in conventional mathematics.  It previously meant the % operator,
           which is a programming language construct and not math.

05/14/12 - Improved user interface of divide command.

05/16/12 - Improved introduction to Mathomatic in "doc/manual.html".

05/17/12 - Made more use of C function !isfinite(double) for better
           reliability.  Checks for infinity and NaN on user input.

05/18/12 - Solve verify now quick simplifies the solve result, so you
           don't have to.  This will result in better verification and
           less chance of oversized expressions.

05/20/12 - Fixed solving bug where it was throwing away absolute values.

           Improved the way Mathomatic looks.

05/21/12 - examples/limits.c is now a highly polished program, LGPL licensed.
           Compile with "./compile.limits".  Tells the integer and float
           C data types, with sizes, characteristics, and verification
           for the current C compiler (cc).

           Display total number of unique solutions stored with
           "simplify sign".

           Fixed several errors in the simplify command documentation in the
           Mathomatic Command Reference.

05/22/12 - Fixed simplify command to simplify (x^2 - 1)^4/(x + 1)^2 properly,
           by factoring repeated factor polynomials at the very end.

           Fixed bug in divide command, wasn't calculating the polynomial GCD
           sometimes, etc, because input was not being expanded.  Broken on
           12/14/11, fixed today.

05/23/12 - Fixed limit command to return the original expression when the
           limit variable is not found or the expression contains no
           variables.  A warning is given, telling that this is the case.
           Thanks to Parag Magunia for indicating that this was a bug.
           Previously these cases only returned with an error message.

           "tests/limits.in" limit command regression tests checked and
           re-added to the main tests.  All still works the same as when
           these limit command regression tests were removed long ago.

05/24/12 - Cleanup, and remove "examples/c", replaced with
           "examples/compile.limits" and "examples/compile.roots".

Mathomatic version 15.8.5 released Friday 05/25/12.

CHANGES MADE TO MATHOMATIC 15.8.3 TO BRING IT UP TO THE NEXT VERSION:

The version command now displays the last main prompt return value, and
the number of allocated equation spaces.

04/29/12 - Added simplifying trig identities to the tests.  Discovered
           "solve 0" doesn't work anymore, use "solve for 0" instead.
           "solve 0" will be fixed and enhanced shortly.

04/30/12 - "solve 0" and "solve verify 0" work now.  "solve verify 0"
           will solve for zero and tell you if the equation is an identity
           or not, while "solve 0" simply solves the current equation for
           zero.  "solve all verify 0" will verify that all entered equations
           are identities.

           With the roots command, the "Inverse check" value is not
           displayed unless debugging is enabled now.

           The iterative calculate command mode now always tells the
           number of completed feedback iterations.
           It was not apparent before.

           Documented and ignore pause command with demo mode now,
           instead of html mode.
           Demo mode is specified with -d, html mode with -x.

05/02/12 - Mathomatic now proudly displays when verifying a solve operation.
           Too many UI improvements to mention, all relatively minor.

05/03/12 - Added "copy select" option to the copy command, which selects
           the first created copy, making it the current equation, rather
           than not updating the current equation.

05/04/12 - Ran valgrind on the symbolic math library executable testmain,
           after running all the tests, no memory
           leaks were found at all!  I was surprised!  Now I get to pat
           myself on the back!  I will make another release soon.

05/05/12 - "display simple" is now allowed, in addition to "display mixed",
           to display simple or mixed fractions as desired, regardless of
           the default.

           "set finance" option removed, replace with "set fixed" option.
           Works similarly, except now you can do "set fixed_point=0" to have
           integer-only output.
           "set no fixed" or "set fixed -1" turns off fixed-point
           mode, returning you to true floating-point mode.

05/06/12 - Added more integer factoring debugging code.  It's a shame that
           Mathomatic only does double precision floating point arithmetic.

           Made "set no autodelete" the default.  Numeric expressions will
           not be deleted.  "set auto" leaves "autodelete" alone now.

05/07/12 - real and imaginary commands now append "_real" or "_imag" to the
           solved for variable name now, if a solved equation.  This is for
           clarification and ease of use.

05/08/12 - Improved "misc/limits.c" and added GNU LGPL license preamble.
           Later moved to directory examples.

           -d demo mode now allows using the calculate command without
           prompting for the values of any of the variables.  This is so the
           calculate command can be used with the online versions of
           Mathomatic.

05/09/12 - Moved all worthy example source code from directory misc to
           directory examples, so they can be included in the binary
           distributions.  Moved and now available are limits.c, roots.c,
           and testprimes.

           Improved/shortened the eliminate command messages and made the
           "using" syntax consistent.

           Need "set debug -2" to suppress everything now, including warnings.
           "set debug -1" only suppresses helpful messages now, warnings will
           get through.  Warnings are usually rather important.

Mathomatic version 15.8.4 released Thursday 05/10/12.

CHANGES MADE TO MATHOMATIC 15.8.2 TO BRING IT UP TO THE NEXT VERSION:

Code cleanup.

03/27/12 - Added simplification of "tests/trig.in" and "tests/hypertrig.in"
           to the regression tests.

04/02/12 - Added ability to create all non-re-entrant code, so that the Apple
           app store won't complain.  The line containing "_REENTRANT" in
           "includes.h" has been commented out, so nothing special needs to be
           done, when compiling for iOS.

04/07/12 - Added ability to make help command text paragraphs all one long
           line, instead of always expecting an 80 column or higher display.
           Useful for 40 column displays for example, as long as the display
           wraps at 40 columns, the output should look OK.  Better than it
           did, anyways.  Tables and such are preserved.  See the beginning
           of "help.c".

04/10/12 - Fixed bug failing to run gnuplot with Mathomatic compiled with
           MINGW. This only affects the MS-Windows version.  So if you have
           downloaded gnuplot under MS-Windows, the plot command should work
           the same as in all other operating systems, now.  Be sure and name
           it gnuplot.exe and have it in an executable directory in your PATH.
           This fixed bug is thanks to Tom Sturgeon for bringing this
           error to my attention.  This gnuplot fix will be included in the
           next release, version 15.8.3, and is now in the development
           version.  The problem was caused by differences between the Unix
           echo command and the Windows echo command.

04/12/12 - Comparing expressions with the compare command will now tell if
           one expression is the negation (times -1) of the other.

04/22/12 - Added the HTML tidy command after rman, so that the HTML errors
           created by rman are all fixed.

           Added and documented matho_clear(3) to Symbolic Math Library,
           replaces clear_all().  Simply rename all occurrences of
           clear_all() in your code that uses the library with
           matho_clear().

04/23/12 - Improved debugging code and error messages.

04/25/12 - The previous autocalc result is erased every time autocalc is
           used, unless "set no autodelete" was done.  This is done in case
           you would like to keep every calculation you made stored in an
           equation space.  The default is the previous behavior:
           "set autodelete", which only keeps one numerical calculation
           in memory.  "autodelete" only means something when "autocalc" is
           on, and since the library has no calculate command, this is not
           available in the symbolic math library.

04/27/12 - Cleanup of equation space selecting, shelling out with !, etc.
           In the Mathomatic application, everything is now flushed before
           user input (with fflush(NULL)).  fflush(NULL) is not used at all
           anymore in the symbolic math library.

Mathomatic version 15.8.3 released Saturday 04/28/12.

CHANGES MADE TO MATHOMATIC 15.8.1 TO BRING IT UP TO THE NEXT VERSION:

Change of 12/18/11 partially undone.  Preventing power collecting
of absolute values doesn't seem necessary anymore, some other
change done recently must have fixed it.
Now power collecting is always done when requested,
fixing a substantial simplification regression that began on 12/18/11.

03/13/12 - Small fix to main makefile.  "mandir" and "docdir" no longer depend
           on "datadir".

03/14/12 - Small fix to simplification.  Any absolute value (such as
           |x*y| = ((x*y)^2)^.5) is now not ever power expanded
           (to (x^2)^.5*(y^2)^.5 or (x*x*y*y)^.5), so some results are
           simpler, like simplifying |x^2-x|.

03/23/12 - A change to the matho script makes GNU m4 no longer quiet
           about any warnings or errors, when running m4 Mathomatic.

Mathomatic version 15.8.2 released Saturday 03/24/12.
2012-05-29 13:23:49 +00:00
marino
9304ece773 math/R-wle: Add gettext-lib buildlink3 2012-05-26 14:38:38 +00:00
marino
2b66ff2518 math/R-circular: Add gettext-lib buildlink3
Yes, it's needed.  During installation on DragonFly:
distance.c: error libintl.h: No such file or directory.
2012-05-21 14:57:31 +00:00
reed
06bec5affe To build it needs at least libgsf 1.14.18
Package revision not bumped since no package with older version possible.0
2012-05-15 03:45:22 +00:00
dholland
94c121a6d3 Build fix for new glib2. 2012-05-10 07:50:11 +00:00