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2020-03-26py-numpy: Remove bogus empty string argument.jperkin2-5/+5
Introduced 5 years ago due to variable expansion being committed, the variable in question is no longer required. Noticed by Dr. Thomas Orgis.
2020-03-24libsvm: Update to 3.24nia2-8/+7
3.24: 2019/9/11 fix compiling issues in matlab/Makefile: use mex only rather than build some .o files separately python interface: use array for reading data in python/commonutil.py to lower the memory usage fix a bug in python/commonutil.py for reading pre-computed kernel minor improvements and bug fixes 3.23: 2018/7/15 add more digits of predicted file, model file, scaled data and data from matlab libsvmwrite: to %.17g revise svm-scale.c so features in test data that do not appear in training data are scaled to zero. remove unnecessary tab or space in all files python interface: add Scipy support add scaling (csr_find_scale_param and csr_scale functions) put some utility functions identical in LIBLINEAR to commonutil.py. functions for scaling are put in commonutil.py. sort column indices of csr matrix before training as feature indices must be ascending convert Qt version of svm-toy from Qt4 to Qt5 remove gtk svm-toy because we stop maintaining this tool minor improvement of descriptions in README 3.22: 2016/12/22 probability output: if 2 classes, directly output the predited probabilities rather than run the iterative algorithms for multi-class situations 3.21: 2015/12/14 pre-built windows exe files changed from 32 to 64 bit matlab interface: now use #include "../svm.h" fix some minor issues in make.m of matlab interface
2020-03-22math/eigen3: fix PKGCONFIG_OVERRIDErillig1-2/+3
2020-03-21Revbump all Go packages after go113 update.bsiegert2-4/+4
2020-03-21math/cloog: remove unknown configure option --with-bits=gmprillig1-2/+1
None of the 3 configure programs contains the word "bits".
2020-03-20*: Convert broken sourceforge HOMEPAGEs back to httpnia10-20/+20
2020-03-19math/py-scipy12: Work around mac extraction woesgdt1-1/+9
On macOS 10.13 (at least), unpacking the distfile as root results in files that have strange permissions, including group/world writable and executable. The upstream distfile has these, but extracting on other systems or on mac not as root applies some sort of umask. On Darwin only, chmod these spurious bits away. Tested to work as non-root and root on macOS 10.13, and by inspection will not affect !macOS.
2020-03-18Fix vector to element array conversionjoerg1-0/+15
2020-03-18Help the compiler find the right insertjoerg2-1/+18
2020-03-18Fix vector to element array conversionjoerg1-1/+2
2020-03-13Remove math/arpack successor math/arpack-ngplunky8-220/+0
No arpack release has been published by Rice University for many years, and arpack-ng aims to provide a common repository of community fixes with a testsuite.
2020-03-13remove arpackplunky1-2/+1
2020-03-11*: bump for vala 0.48.0wiz1-2/+2
2020-03-10librsvg: update bl3.mk to remove libcroco in rust casewiz24-48/+48
recursive bump for the dependency change
2020-03-08*: recursive bump for libffiwiz33-62/+66
2020-03-08Revbump packages depending on libffi after .so version change.bsiegert3-5/+6
Requested by Matthias Ferdinand and Oskar on pkgsrc-users.
2020-03-08math/ruby-spreadsheet: update to 1.2.6taca2-7/+7
Update ruby-spreadsheet to 1.2.6. ### 1.2.6 22.1.2020 Author: tetsuya-ogawa <tetsuya.ogawa87@gmail.com> Date: Wed Jan 22 15:18:00 2020 +0900 * add instance method "<<" to Spreadsheet::Worksheet
2020-03-08math/ruby-roo: update to 2.8.3taca2-8/+8
Update ruby-roo to 2.8.3. ## [2.8.3] 2020-02-03 ### Changed/Added - Updated rubyzip version. Now minimal version is 1.3.0 [515](https://github.com/roo-rb/roo/pull/515) - [CVE-2019-16892](https://github.com/rubyzip/rubyzip/pull/403)
2020-03-04*: bump PKGREVISION for poppler 0.86.1wiz1-1/+2
2020-02-28add harmbase2 subdirplunky1-1/+2
2020-02-28Add harmbase2-20191229plunky4-0/+71
Harmbase is a database application for managing harmonic constants. It is not "plug and play" software. It's not designed to be useful to someone who does not know how to hack Ruby code or write interactive SQL queries.
2020-02-28add harmgen subdirplunky1-1/+2
2020-02-28Add harmgen 3.1.3plunky4-0/+34
Harmgen is a program to derive harmonic constants from water level observations, by David Flater
2020-02-28add congen subdirplunky1-1/+2
2020-02-28Add congen 1.7, from David Flaterplunky6-0/+85
congen is a C++ library for generating the speeds, equilibrium arguments, and node factors of Darwin-style tidal constituents more or less as defined in SP 98: Manual of Harmonic Analysis and Prediction of Tides. Special Publication No. 98, Revised (1940) Edition (reprinted 1958 with corrections; reprinted again 1994). United States Government Printing Office, 1994. Additionally, libcongen provides limited support for approximating Doodson-style tidal constituents within the infrastructure of the former. The Doodson approach is discussed in the following publication: Foreman, M.G.G., 1977. Manual for Tidal Heights Analysis and Prediction. Pacific Marine Science Report 77-10, Institute of Ocean Sciences, Patricia Bay, Sidney, B.C. (2004 revision). The Congen header file is intended to be self-documenting with regards to use of the interface, assuming that one has access to SP 98 and a general understanding of the subject matter.
2020-02-28have octave use arpack-ng 3.7.0 instead of arpack. This reduces testplunky1-3/+4
failures from 59 to 6 - PASS 15064 - FAIL 59 + PASS 15117 + FAIL 6 REGRESSION 1 XFAIL (reported bug) 26 SKIP (missing feature) 424
2020-02-28add arpack-ngplunky1-1/+2
2020-02-28Add arpack-ng 3.7.0plunky5-0/+78
This project started as a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack, as no single release has been published by Rice university for the last few years and many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications.
2020-02-28Update math/lapack and math/blas to v3.9.0plunky14-182/+78
Have switched to the CMAKE build and enabled tests. make test passes all (with one patch pushed upstream) Package additions, from the release notes are: LAPACK 3.9.0 LAPACK QR preconditioned QR SVD method for computing the SVD with high accuracy, by Zlatko Drmac LAPACK Householder Reconstruction by Igor Kozachenko and Jim Demmel LAPACK 3.8.0 Symmetric-indefinite Factorization: Aasen’s tridiagonalization 2 stage A contribution from Ichitaro Yamazaki (University of Tennessee). LAPACKE interfaces A contribution from Julie Langou (University of Tennessee).
2020-02-26superlu: remove unused patchwiz1-54/+0
2020-02-26superlu: update to 5.2.1.wiz4-44/+28
Changes not found, previous version was from 2003.
2020-02-24fix build error if PKGSRC_FORTRAN=gfortran: add --tag=FC to libtoolplunky1-2/+2
2020-02-17gnumeric: update to 1.12.46nb1.wiz1-2/+3
Remove mk/omf-scrollkeeper.mk, unneeded since 1.12.33.
2020-02-16math/py-arviz: Update to 0.6.1minskim3-13/+152
Highlights: - Initial bokeh support. - Fully support numpyro - log_likelihood and observed data from pyro - ArviZ.jl - improve rcparams - fix az.concat functionality - distplot docstring plotting example
2020-02-14math/py-pandas: Update to 0.25.3minskim3-104/+288
Highlights: - Groupby aggregation with relabeling - Better repr for MultiIndex - Better truncated repr for Series and DataFrame - Series.explode to split list-like values to rows
2020-02-11math/py-scikit-learn: Update to 0.22.1minskim4-90/+538
Highlights: - New plotting API - Stacking Classifier and Regressor - Permutation-based feature importance - Native support for missing values for gradient boosting - Precomputed sparse nearest neighbors graph - KNN Based Imputation - Tree pruning - Retrieve dataframes from OpenML - Checking scikit-learn compatibility of an estimator - ROC AUC now supports multiclass classification
2020-02-10Added devel/R-lintr version 2.0.0mef1-1/+2
Added devel/R-cyclocomp version 1.1.0 Added textproc/R-xmlparsedata version 1.0.3 Added math/R-stringdist version 0.9.5.5
2020-02-10(math/R-stringdist) import R-stringdist-0.9.5.5mef3-0/+29
Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences. This package is built for speed and runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
2020-02-09(math/ellipsis) Updated to 0.3.0mef2-7/+7
# ellipsis 0.3.0 * `check_dots_used()`, `check_dots_unnamed()`, and `check_dots_empty()` gain an `action` argument, to specify if they should error, warn, message or signal when the dots meet the condition.
2020-02-05libixion, py-libixion: Update to 0.15.0ryoon9-51/+95
Changelog: ixion 0.15.0 * fill_down_cells() method has been added to model_context, to fill duplicate values downward from an arbitrary cell position. For now, it always duplicate the value of the source cell; cell value enumerations are not supported. Also, filling down of formula cells is not yet supported. * cell iterator has been aded to model_context, for efficient horizontal and vertical iterations of cell values in an arbitrary range within a sheet. * improved the cmake-based build, with all test cases integrated. * switched to spdlog for compile-time debug log outputs. * improved performance by removing repeated fetching of each formula cell prior to interpretation. * reworked topological sorting of formula cells to avoid having to unnecessarily build dependency relations twice; once during the dirty cell determination and twice prior to interpretation of formula cells. The new code performs topological sorting during the dirty cell determination phase. * reworked the cell reference tracker to use R-tree. This allows more accurate tracking of references involving grouped formulas. * fixed a resource leak with dynamic loading of compute engine modules.
2020-02-02Revbump all Go packages after go113 update.bsiegert2-4/+4
2020-02-02math: update kde release service to 19.12.1markd10-33/+56
builds with qt 5.14, other changes unknown.
2020-02-01py-numba: updated to 0.48.0adam3-14/+11
Version 0.48.0 This release is particularly small as it was present to catch anything that missed the 0.47.0 deadline (the deadline deliberately coincided with the end of support for Python 2.7). The next release will be considerably larger. The core changes in this release are dominated by the start of the clean up needed for the end of Python 2.7 support, improvements to the CUDA target and support for numerous additional unicode string methods. Enhancements from user contributed PRs (with thanks!): Brian Wignall fixed more spelling typos in. Denis Smirnov added support for string methods capitalize, casefold, swapcase , rsplit , partition and splitlines . Elena Totmenina extended support for string methods startswith and added endswith . Eric Wieser made type_callable return the decorated function itself in Ethan Pronovost added support for np.argwhere in Graham Markall contributed a large number of CUDA enhancements and fixes, namely: * Remove Python 3.4 backports from utils * Make device_array_like create contiguous arrays * Don’t launch ForAll kernels with 0 elements * Fix various issues in CUDA library search * Enable use of records and bools for shared memory, remove ddt, add additional transpose tests * Fix: Add more appropriate typing for CUDA device arrays * test_consuming_strides: Keep dev array alive * State that CUDA Toolkit 8.0 required in docs James Bourbeau added the Python 3.8 classifier to setup.py in. John Kirkham added a clarification to the __cuda_array_interface__ documentation in. Leo Fang Fixed an indexing problem in dummyarray in. Marcel Bargull fixed a build and test issue for Python 3.8 in. Maria Rubtsov added support for string methods isdecimal , isdigit , isnumeric and replace . General Enhancements: * Make type_callable return the decorated function * merge string prs This merge PR included the following: * Implement str.capitalize() based on CPython * Implement str.casefold() based on CPython * Implement str.swapcase() based on CPython * Implement str.rsplit() based on CPython * Implement str.isdecimal * Implement str.isdigit * Implement str.isnumeric * Implement str.partition() based on CPython * Implement str.splitlines() based on CPython * Implement str.replace * Functionality extension str.startswith() based on CPython * Add functionality for str.endswith() * Disable help messages. * Add coverage for np.argwhere Fixes: * Only use lives (and not aliases) to create post parfor live set. * Fix more spelling typos * Propagate semantic constants ahead of static rewrites. * Add Python 3.8 classifier to setup.py * Update setup.py and buildscripts for dependency requirements * Convert from arrays to names in define() and don’t invalidate for multiple consistent defines. * Permit mixed int types in wrap_index * Catch the use of global typed-list in JITed functions * Fix, bug in bytecode analysis. CUDA Enhancements/Fixes: * Fix: Add more appropriate typing for CUDA device arrays * Make device_array_like create contiguous arrays * State that CUDA Toolkit 8.0 required in docs * test_consuming_strides: Keep dev array alive * Fix IndexError when accessing the “-1” element of dummyarray * Enable use of records and bools for shared memory, remove ddt, add additional transpose tests * Fix various issues in CUDA library search * Don’t launch ForAll kernels with 0 elements * Remove Python 3.4 backports from utils Documentation Updates: * Clarify what dictionary means * Update docs for updated version requirements * Update deprecation notices for 0.48.0 CI updates: * Install optional dependencies for Python 3.8 tests * Drop Py2.7 and Py3.5 from public CI * Fix CI py38
2020-01-31math/py-sympy: Update to 1.5.1minskim2-8/+8
Changes: - Fix a regression in 1.5 that allowed expressions to compare equal to strings, and caused == to call str() on the other object. - Avoid using scipy versions of numpy functions, which are deprecated, in lambdify. Take MAINTAINERship.
2020-01-30math/py-numpy: Update to 1.16.6minskim2-7/+7
Changes: - The np.testing.utils functions have been updated from 1.19.0-dev0. This improves the function documentation and error messages as well extending the assert_array_compare function to additional types. - Allow matmul (@) to work with object arrays. - Fix regression in matmul (@) for boolean types. - Array comparison assertions include maximum differences.
2020-01-30math/py-pandas-datareader: Fix dependenciesminskim1-4/+4
2020-01-30math/py-pandas-datareader: Update HOMEPAGEminskim1-2/+2
2020-01-28sc-im: Bump for breaking libxlsxwriter changesjmulder1-2/+2
2020-01-26all: migrate homepages from http to httpsrillig37-75/+75
pkglint -r --network --only "migrate" As a side-effect of migrating the homepages, pkglint also fixed a few indentations in unrelated lines. These and the new homepages have been checked manually.
2020-01-26all: migrate some SourceForge homepage URLs back from https to httprillig1-2/+2
https://mail-index.netbsd.org/pkgsrc-changes/2020/01/18/msg205146.html In the above commit, the homepage URLs were migrated from http to https, assuming that SourceForge would use the same host names for both http and https connections. This assumption was wrong. Their documentation at https://sourceforge.net/p/forge/documentation/Custom%20VHOSTs/ states that the https URLs use the domain sourceforge.io instead. To make the homepages from the above commit reachable again, pkglint has been extended to check for reachable homepages. This check is only enabled when the --network command line option is given. Each of the homepages that referred to https://$project.sourceforge.net before was migrated to https://$project.sourceforge.io (27), and if that was not reachable, to the fallback URL http://$project.sourceforge.net (163).
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