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2018-08-06math/py-scikit-learn: Update to 0.19.2minskim2-8/+7
This release is exclusively in order to support Python 3.7.
2018-07-31Update to 20180729. From the changelog:schmonz3-8/+8
Algorithm Rewrite of the core int32/avx2 implementation for (1) higher speed and (2) reduced memory consumption. Stack allocation is now at most a few kilobytes, even for gigantic arrays. Internally, the sorting algorithm is now mostly bitonic to simplify indexing, although odd-even speedups are still applied when convenient. Lanes are complemented to take the down-up decision out of the inner loops. As in previous djbsort versions, data is sorted first in vector lanes and then transposed for final merges, reducing the overall number of vector permutations. Unlike previous versions, transposition is done in-place. The transposition in this version is bit-reversal on the outer 6 bits (bottom 3 bits and the top 3 bits), but leaves intermediate bits alone. Non-power-of-2 array sizes are handled by an extra, more traditional, merge step. Sizes 2, 3, 4, 5, 6, 7, 8, 16, 32 are now special-cased. Non-power-of-2 sizes below 256 are padded to the next power of 2. Portable implementations: The out-of-place int32/portable1 and int32/portable2 implementations are now gone; the in-place int32/portable3 and int32/portable4 implementations remain. C API float32_sort is now supported. The arithmetic in the reduction from float32 to int32 is int32 31-bit right shift, uint32 1-bit right shift, xor; this is slightly more efficient than the reduction from float32 to uint32 from 2001 Herf. Compiling Tests now have more variation (without much slowdown): the uint32 test cases now deviate from int32 in more than the sign; float32 uses floating-point numbers that aren't integers; int32 does more loops for small cases, and some larger cases. Internals API for 2-input sorting is now MINMAX macro operating on two inputs in place. Better inline assembly from Jason Donenfeld for 2-input sorting: more flexibility in compiler's register allocation. The package version number is now automatically copied to version.c as the implementation version number for implementations that don't provide version.c. Verification minmax now supports more peephole optimizations for complemented bitonic sorting and for padding: xor(s,xor(s,t)) ⇒ t; xor(-1,s) ⇒ invert(s); Reverse(Reverse(s)) ⇒ s; signedmin(invert(s),invert(t)) ⇒ invert(signedmax(s,t)); signedmax(invert(s),invert(t)) ⇒ invert(signedmin(s,t)); invert(s)[high:low] ⇒ invert(s[high:low]); s[bits-1:0] ⇒ s; s[high:low][high2:low2] ⇒ s[high2+low:low2+low]; Concat(...)[high:low] ⇒ ...[high-pos:low-pos] when possible; Reverse(s)[high:low] ⇒ Reverse(s[...]) when possible; eliminate signedmin/signedmax when one input is the minimum or maximum constant. verifymany now includes the implementation version number on verified lines.
2018-07-31Compiler options are also baked into paths, so switch to dynamic PLIST.schmonz3-342/+16
Install with pax, not cp. On deinstall, remove whatever's left in share/djbsort.
2018-07-31From DJB: "For correctness, ./test has to be run on the installationschmonz10-23/+489
machine, not on the machine preparing a binary package." (Also: "The issues are explained in Section 8 of https://pqcrypto.eu.org/deliverables/d2.4.pdf.") For this to work, we install the source tree (with built objects) to ${PREFIX}/share/djbsort. Then we run tests, install to ${PREFIX}/include and ${PREFIX}/lib, and check the installed files against pseudo-PLIST. This means pkg_add(1) will fail if no C compiler is present, which is unusual behavior for pkg_add but perhaps not entirely unreasonable for a C library. Bump PKGREVISION.
2018-07-29Makefile: + djbsortwiz1-1/+2
2018-07-29math/djbsort: import djbsort-20180717wiz5-0/+70
djbsort is a software library for sorting arrays of integers. It provides the following features: - Speed: djbsort holds new speed records for in-memory sorting. - Security: djbsort is designed to be safe for cryptographic contexts. - Verification: djbsort includes tools to automatically verify correctness. These features are not separate options: there is a single sorting function that is simultaneously fast, secure, and verified. Packaged for wip by schmonz@
2018-07-28Add the CRAN archives to R package MASTER_SITES.brook2-4/+4
Distfiles for older R packges are moved on CRAN from contrib/ to contrib/Archive/${R_PKGNAME}/. As a result, they may be inaccessible to 'make fetch'. Add the additional directory to MASTER_SITES in math/R/Makefile.extension so that older distfiles will be retrieved directly from CRAN. In addition, remove the definition of MASTER_SITES from math/R-prob/Makefile, which is the only package directly referring to the distfile archive. At this point all R packages should rely on math/R/Makefile.extension to define MASTER_SITES; they should not be defining MASTER_SITES directly.
2018-07-28Remove MASTER_SITES= from individual R package Makefiles.brook76-152/+76
Each R package should include ../../math/R/Makefile.extension, which also defines MASTER_SITES. Consequently, it is redundant for the individual packages to do the same. Package-specific definitions also prevent redefining MASTER_SITES in a single common place.
2018-07-27math/Makefile: Add stan-mathminskim1-1/+2
2018-07-27math/stan-math: Import version 2.17.1minskim5-0/+1172
The Stan Math Library is a C++, reverse-mode automatic differentiation library designed to be usable, extensive and extensible, efficient, scalable, stable, portable, and redistributable in order to facilitate the construction and utilization of algorithms that utilize derivatives.
2018-07-23math/py-pymc3: Update to 3.5minskim3-11/+23
New features: - Add documentation section on survival analysis and censored data models - Add check_test_point method to pm.Model - Add Ordered Transformation and OrderedLogistic distribution - Add Chain transformation - Improve error message Mass matrix contains zeros on the diagonal. Some derivatives might always be zero during tuning of pm.sample - Improve error message NaN occurred in optimization. during ADVI - Save and load traces without pickle using pm.save_trace and pm.load_trace - Add Kumaraswamy distribution - Add TruncatedNormal distribution - Rewrite parallel sampling of multiple chains on py3. This resolves long standing issues when transferring large traces to the main process, avoids pickling issues on UNIX, and allows us to show a progress bar for all chains. If parallel sampling is interrupted, we now return partial results. - Add sample_prior_predictive which allows for efficient sampling from the unconditioned model. - SMC: remove experimental warning, allow sampling using sample, reduce autocorrelation from final trace. - Add model_to_graphviz (which uses the optional dependency graphviz) to plot a directed graph of a PyMC3 model using plate notation. - Add beta-ELBO variational inference as in beta-VAE model (Christopher P. Burgess et al. NIPS, 2017) - Add __dir__ to SingleGroupApproximation to improve autocompletion in interactive environments
2018-07-20Recursive revbump from textproc/icu-62.1ryoon2-4/+4
2018-07-19Update py-sympy to 1.2prlw13-23/+388
Highlights There are many changes in 1.2 (see below). Some of the highlights are * Python 3.3 is no longer supported. If you require Python 3.3 support, use SymPy 1.1.1. See our [518]policy on dropping support for major Python versions. * Experimental LaTeX parsing with sympy.parsing.latex.parse_latex() has been added, based on the latex2sympy project. This requires antlr-python-runtime to be installed. [519]#13706 * The vector module has been improved to support orthogonal curvilinear coordinate systems ([520]Szymon Mieszczak's GSoC project) * New module sympy.integrals.intpoly for integrating uni/bivariate polynomials over 2-polytopes. ([521]Arif Ahmed's GSoC project) * Improvements to the code generation module. ([522]Bj?rn Dahlgren's GSoC project) * Improvements to the group theory module. See below for more information. ([523]Valeriia Gladkova's GSoC project) * New module sympy.discrete for operating on discrete sequences. polynomials over 2-polytopes. ([521]Arif Ahmed's GSoC project) * Improvements to the code generation module. ([522]Bj?rn Dahlgren's GSoC project) * Improvements to the group theory module. See below for more information. ([523]Valeriia Gladkova's GSoC project) * New module sympy.discrete for operating on discrete sequences. ([524]Sidhant Nagpal's GSoC project) Complete release notes at: https://github.com/sympy/sympy/wiki/release-notes-for-1.2
2018-07-19Recursive revbump associated with the update of lang/ocaml to 4.07.jaapb7-13/+14
2018-07-19py-numexpr: updated to 2.6.6adam2-7/+7
Changes from 2.6.5 to 2.6.6: Fix to the thread barrier that occassionally suffered from spurious wakeups on MacOSX.
2018-07-19R: remove cases for ancient NetBSD versions.maya1-9/+1
2018-07-18Mark packages that require C++03 (or the GNU variants) if they fail withjoerg8-16/+16
C++14 default language.
2018-07-17Revert hard-coded PKGSRC_FORTRAN setting. g95 is perfectly fine here.joerg1-2/+1
2018-07-17octave: force gfortran, g95 is broken is most setups.maya3-3/+19
build fix for newer qt. bump PKGREVISION.
2018-07-13py-lmfit: updated to 0.9.11adam3-14/+11
0.9.11: make exception explicit 0.9.10: add AMPGO and basin-hopping global optimization methods. aborting a fit from the objective function now raises AbortFitException fit statistics are more uniformly calculated. the uncertainties package is now an external dependency, and an out-dated copy is no longer kept in lmfit. more exceptions when import matplotlib are now tolerated. many documentation fixes.
2018-07-09py-pandas: updated to 0.23.3adam3-293/+8
0.23.3: This is a minor bug-fix release in the 0.23.x series and includes a fix for the source distribution on Python 3.7. We recommend that all users upgrade to this version.
2018-07-07Update to 0.6.2wen4-39/+8
Upstream changes: Version 0.6-2 o dbGetQuery do not return NULL. o use registration mechanism to call native routines. Version 0.5-3 o Update the libpq library so that the package can be compiled in new versions of R and macOS. Version 0.5-2 o Support dbBegin() API version 0.5-1 --2014-02-08 o Remove segmentationfault when NULL is passed as host argument. o Conversion routine for raw in R and bytea in PostgreSQL o Use accompanied libpq when either of libpq and header is not found on darwin Version 0.5 -- 2013-10-12 o postgresqlWriteTable: send column names at COPY o System library header search path for OS X 10.9 (Mavericks) o Memory leak was reduced o Close the socket on failure Version 0.4 -- 2013-03-27 o Initial implementation of prepared statement o Use system libpq library when available on OS X (darwin) o Force ISO datestyle for PostgreSQL-R communication by default o Time zone aware Timestamp POSIXct conversion Version 0.3-3 -- 2012-10-05 o Bugfix on dbColumnInfo and others reproducible by gctorture(TRUE) o Do not implicitly make new connections, which interfere with transaction. o Change the notation of the LICENSE
2018-07-07math/Makefile: Add sundialsminskim1-1/+2
2018-07-07math/sundials: Import version 3.1.1minskim5-0/+423
SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. It consists of the following six solvers: CVODE, solves initial value problems for ordinary differential equation (ODE) systems; CVODES, solves ODE systems and includes sensitivity analysis capabilities (forward and adjoint); ARKODE, solves initial value ODE problems with additive Runge-Kutta methods, include support for IMEX methods; IDA, solves initial value problems for differential-algebraic equation (DAE) systems; IDAS, solves DAE systems and includes sensitivity analysis capabilities (forward and adjoint); KINSOL, solves nonlinear algebraic systems.
2018-07-06Recursive revbump from audio/pulseaudioryoon1-2/+2
2018-07-06math/Makefile: Add py-pymc3minskim1-1/+2
2018-07-06math/py-pymc3: Import version 3.4.1minskim4-0/+545
PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.
2018-07-06math/Makefile: Add py-Theanominskim1-1/+2
2018-07-06math/py-Theano: Import version 1.0.2minskim5-0/+1195
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently Packaged by Kamel Ibn Aziz Derouiche for pkgsrc-wip and updated by me.
2018-07-05py-statsmodels: updated to 0.9.0adam3-30/+466
0.9.0: The Highlights -------------- statespace refactoring, Markov Switching Kim smoother 3 Google summer of code (GSOC) projects merged - distributed estimation - VECM and enhancements to VAR (including cointegration test) - new count models: GeneralizedPoisson, zero inflated models Bayesian mixed GLM Gaussian Imputation new multivariate methods: factor analysis, MANOVA, repeated measures within ANOVA GLM var_weights in addition to freq_weights Holt-Winters and Exponential Smoothing
2018-07-05math/py-scipy: Add -headerpad_max_install_names in linking on Darwinminskim1-1/+3
Without the link option, install_name_tool may cause an error.
2018-07-05Update path to math/py-tablesminskim1-2/+2
2018-07-04*: Move SUBST_STAGE from post-patch to pre-configurejperkin3-6/+6
Performing substitutions during post-patch breaks tools such as mkpatches, making it very difficult to regenerate correct patches after making changes, and often leading to substituted string replacements being committed.
2018-07-04py-numexpr: updated to 2.6.5adam2-8/+8
Changes from 2.6.4 to 2.6.5 - The maximum thread count can now be set at import-time by setting the environment variable 'NUMEXPR_MAX_THREADS'. The default number of max threads was lowered from 4096 (which was deemed excessive) to 64. - A number of imports were removed (pkg_resources) or made lazy (cpuinfo) in order to speed load-times for downstream packages (such as pandas, sympy, and tables). Import time has dropped from about 330 ms to 90 ms. Thanks to Jason Sachs for pointing out the source of the slow-down. - Thanks to Alvaro Lopez Ortega for updates to benchmarks to be compatible with Python 3. - Travis and AppVeyor now fail if the test module fails or errors. - Thanks to Mahdi Ben Jelloul for a patch that removed a bug where constants in where calls would raise a ValueError. - Fixed a bug whereby all-constant power operations would lead to infinite recursion.
2018-07-04Update to 3.5.1wen3-9/+11
Upstream changes: CHANGES IN R 3.5.1 BUG FIXES file("stdin") is no longer considered seekable. dput() and dump() are no longer truncating when options(deparse.max.lines = *) is set. Calls with an S3 class are no longer evaluated when printed, fixing part of PR#17398, thanks to a patch from Lionel Henry. Allow file argument of Rscript to include space even when it is first on the command line. callNextMethod() uses the generic from the environment of the calling method. Reported by Hervé Pagès with well documented examples. Compressed file connections are marked as blocking. optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the method), thanks to a suggestion by John Nash. predict(fm, newdata) is now correct also for models where the formula has terms such as splines::ns(..) or stats::poly(..), fixing PR#17414, based on a patch from Duncan Murdoch. simulate.lm(glm(*, gaussian(link = <non-default>))) has been corrected, fixing PR#17415 thanks to Alex Courtiol. unlist(x) no longer fails in some cases of nested empty lists. Reported by Steven Nydick. qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun Ren. The radix sort is robust to vectors with >1 billion elements (but long vectors are still unsupported). Thanks to Matt Dowle for the fix. Terminal connections (e.g., stdin) are no longer buffered. Fixes PR#17432. deparse(x), dput(x) and dump() now respect c()'s argument names recursive and use.names, e.g., for x <- setNames(0, "recursive"), thanks to Suharto Anggono's PR#17427. Unbuffered connections now work with encoding conversion. Reported by Stephen Berman. ‘.Renviron’ on Windows with Rgui is again by default searched for in user documents directory when invoked via the launcher icon. Reported by Jeroen Ooms. printCoefmat() now also works with explicit right=TRUE. print.noquote() now also works with explicit quote=FALSE. The default method for pairs(.., horInd=*, verInd=*) now gets the correct order, thanks to reports by Chris Andrews and Gerrit Eichner. Additionally, when horInd or verInd contain only a subset of variables, all the axes are labeled correctly now. agrep("..|..", .., fixed=FALSE) now matches when it should, thanks to a reminder by Andreas Kolter. str(ch) now works for more invalid multibyte strings.
2018-07-04py-pandas: revbump for py-tablesadam1-2/+3
2018-07-04py-tables: (ex py-pytables) updated to 3.4.4adam6-18/+21
Changes from 3.4.3 to 3.4.4 Improvements Environment variable to control the use of embedded libraries. Include citation in repository. gh-690. Bugs fixed Fixed import error with numexpr 2.6.5.dev0 gh-685. Fixed linter warnings. Fixed for re.split() is version detection. gh-687. Fixed test failures with Python 2.7 and NumPy 1.14.3 gh-688 & gh-689.
2018-07-03extend PYTHON_VERSIONS_ for Python 3.7adam9-18/+18
2018-06-24p5-Alien-GMP: update to 1.11.wiz2-7/+7
1.11 2018-06-07 14:28:04 -0400 - Move to Perl5-Alien org
2018-06-20Added math/p5-Math-Matrix version 0.8 [mef 2018-06-20]mef1-1/+3
Added math/p5-Math-Systems version 0.01 [mef 2018-06-20]
2018-06-20math/p5-Math-Matrix: import p5-Math-Matrix-0.8mef3-0/+42
The following methods are available: new clone size of matrix concat transpose multiply solve multiply_scalar add substract equal slice determinant dot_product absolute normalizing cross_product print
2018-06-20math/p5-Math-Systems: import p5-Math-Systems-0.01mef3-0/+46
Solves systems of equations using Krammer's rule. If you look at the Solve method you'll understand Krammer's rule (I think?) Basically a system of equations is more than one equation/variable your solving. This module REQUIRES you have 1 equation per each coefficent. Try not to use too many equations. 3 equations is probably the limit of reason. But if you don't mind long compilation time, go for as many as you want. This module uses (and ovbiously requires you have) Math::Matrix to do all the Matrix work. Please take a look at that module for details do you can see exactly what is happening. There are no arguements in this module except for the Matrix which will be brought to Math::Matrix. Also, keep in mind, there are no error messenging. I will of course change that someday, but for now I'm satisfied that I can solve systems of equations. Don't allow error-prone things to be written in. But, there are of course times when you won't be able to figure out the stupid answer and this module will absolutly act like it did a great job, and at the same time, fail. So, keep that in mind. BETA means something. It's not good.
2018-06-18py-pandas: updated to 0.23.1adam2-8/+8
pandas 0.23.1 This is a minor release from 0.23.0 and includes a number of bug fixes and performance improvements.
2018-06-18py-numpy: updated to 1.14.5adam3-21/+7
NumPy 1.14.5: This is a bugfix release for bugs reported following the 1.14.4 release. The most significant fixes are: * fixes for compilation errors on alpine and NetBSD
2018-06-17math/Makefile: Add go-unitsminskim1-1/+2
2018-06-17math/go-units: Import version 0.0.20151021minskim5-0/+52
go-units provides helpful unit multipliers and functions in Go. The goal of this package is to have functionality similar to the time package.
2018-06-15z3: Fix broken build system by pretending SunOS is Linux.jperkin2-6/+27
2018-06-14py-scipy: Apply a couple of patches to fix SunOS.jperkin3-5/+32
2018-06-12Revbump all Go packages after lang/go update.bsiegert1-2/+2
2018-06-10Update to 1.14.4wen3-8/+21
Upstream changes: NumPy 1.14.4 Release Notes This is a bugfix release for bugs reported following the 1.14.3 release. The most significant fixes are: fixes for compiler instruction reordering that resulted in NaN's not being properly propagated in np.max and np.min, fixes for bus faults on SPARC and older ARM due to incorrect alignment checks.