Mailman 3 January 2016 - NumPy-Discussion

Bump warning stacklevel
by Sebastian Berg 28 Jan '16

28 Jan '16

Hi all, in my PR about warnings suppression, I currently also have a commit which bumps the warning stacklevel to two (or three), i.e. use: warnings.warn(..., stacklevel=2) (almost) everywhere. This means that for example (take only the empty warning): np.mean([]) would not print: /usr/lib/python2.7/dist-packages/numpy/core/_methods.py:55: RuntimeWarning: Mean of empty slice. warnings.warn("Mean of empty slice.", RuntimeWarning) but instead print the actual `np.mean([])` code line (the repetition of the warning command is always a bit funny). The advantage is nicer printing for the user. The disadvantage would probably mostly be that existing warning filters that use the `module` keyword argument, will fail. Any objections/thoughts about doing this change to try to better report the offending code line? Frankly, I am not sure whether there might be a python standard about this, but I would expect that for a library such as numpy, it makes sense to change. But, if downstream uses warning filters with modules, we might want to reconsider for example. - Sebastian

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Re: [Numpy-discussion] Building Numpy with OpenBLAS
by G Young 27 Jan '16

27 Jan '16

Hello all, I'm trying to update the documentation for building Numpy from source, and I've hit a brick wall in trying to build the library using OpenBLAS because I can't seem to link the libopenblas.dll file. I tried following the suggestion of placing the DLL in numpy/core as suggested here <https://github.com/numpy/numpy/wiki/Mingw-static-toolchain#notes> but it still doesn't pick it up. What am I doing wrong? Thanks, Greg

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Re: [Numpy-discussion] Appveyor Testing Changes
by G Young 26 Jan '16

26 Jan '16

Hello all, I currently have a branch on my fork (not PR) where I am experimenting with running Appveyor CI via Virtualenv instead of Conda. I have build running here <https://ci.appveyor.com/project/gfyoung/numpy-dr74v/build/1.0.14>. What do people think of using Virtualenv (as we do on Travis) instead of Conda for testing? Thanks, Greg

5 7

Testing warnings
by Sebastian Berg 26 Jan '16

26 Jan '16

Hi all, so I have been thinking about this a little more, and I do not think there is a truly nice solution to the python bug: http://bugs.python.org/issue4180 (does not create problems for new pythons). However, I have been so annoyed by trying to test FutureWarnings or DeprecationWarnings in the past that I want *some* improvement. You can do quite a lot by adding some new features, but there are also some limitations. I think that we must be able to: o Filter out warnings on the global test run level. o Find all not explicitly filtered warnings during development easily. o We should be able to test any (almost any?) warnings, even those that would be filtered globally. The next line of considerations for me is, whether we want: o To be able to *print* warnings during test runs? (in release mode) o Be able to not repeat filtering of globally filtered warnings when filtering additional warnings in an individual test? o Be able to count warnings, but ignore other warnings (not the global ones, though). o Filter warnings by module? (might be hard to impossible) And one further option: o Could we accept that testing warnings is *only* possible reliable in Python 3.4+? It would however even mean that we have to fully *skip* tests that would ensure specific warnings to be given. The first things can be achieved setting all warnings to errors on the global level and trying to make the local tests as specific specific as possible. I could go ahead with it. There will likely be some uglier points, but it should work. They do not require funnier new hacks. For all I can see, the second bunch of things requires new features such as in my current PR. So, I want to know whether we can/want to go ahead with this kind of idea [1]. For me personally, I cannot accept we do not provide the first points. The second bunch, I would like some of them (I do not know about printing warnings in release mode?), and skipping tests on Python 2, seems to me even worse then ugly hacks. Getting there is a bit uglier (requires a new context manager for all I see), an I tend to think it is worth the trouble, but I don't think it is vital. In other words, I don't care too much about those points, but I want to get somewhere because I have been bitten often enough by the annoying and in my opinion simply unacceptable (on python 2) use of "ignore" warnings filters in tests. The current state makes finding warnings given in our own tests almost impossible, in the best case they will have to be fixed much much later when the change actually occurs, in the worst case we never find our own real bugs. So where to go? :) - Sebastian [1] I need to fix the module filtering point, the module filtering does not work reliably currently, I think it can be fixed at least 99.5%, but it is not too pretty (not that the user should notice).

1 0

Inconsistent behavior for ufuncs in numpy v1.10.X
by Solbrig,Jeremy 26 Jan '16

26 Jan '16

Hello, <http://stackoverflow.com/questions/35005569/behavior-of-ufuncs-and-mathemat…> Much of what is below was copied from this stack overflow question. I am attempting to subclass numpy.ma.MaskedArray. I am currently using Python v2.7.10. The problem discussed below does not occur in Numpy v1.9.2, but does occur in all versions of Numpy v1.10.x. In all versions of Numpy v1.10.x, using mathematical operators on my subclass behaves differently than using the analogous ufunc. When using the ufunc directly (e.g. np.subtract(arr1, arr2)), __array_prepare__, __array_finalize__, and __array_wrap__ are all called as expected, however, when using the symbolic operator (e.g. arr1-arr2) only __array_finalize__ is called. As a consequence, I lose any information stored in arr._optinfo when a mathematical operator is used. Here is a code snippet that illustrates the issue. #!/bin/env python import numpy as np from numpy.ma import MaskedArray, nomask class InfoArray(MaskedArray): def __new__(cls, info=None, data=None, mask=nomask, dtype=None, copy=False, subok=True, ndmin=0, fill_value=None, keep_mask=True, hard_mask=None, shrink=True, **kwargs): obj = super(InfoArray, cls).__new__(cls, data=data, mask=mask, dtype=dtype, copy=copy, subok=subok, ndmin=ndmin, fill_value=fill_value, hard_mask=hard_mask, shrink=shrink, **kwargs) obj._optinfo['info'] = info return obj def __array_prepare__(self, out, context=None): print '__array_prepare__' return super(InfoArray, self).__array_prepare__(out, context) def __array_wrap__(self, out, context=None): print '__array_wrap__' return super(InfoArray, self).__array_wrap__(out, context) def __array_finalize__(self, obj): print '__array_finalize__' return super(InfoArray, self).__array_finalize__(obj) if __name__ == "__main__": arr1 = InfoArray('test', data=[1,2,3,4,5,6]) arr2 = InfoArray(data=[0,1,2,3,4,5]) diff1 = np.subtract(arr1, arr2) print diff1._optinfo diff2 = arr1-arr2 print diff2._optinfo If run, the output looks like this: $ python test_ma_sub.py #Call to np.subtract(arr1, arr2) here __array_finalize__ __array_finalize__ __array_prepare__ __array_finalize__ __array_wrap__ __array_finalize__ {'info': 'test'} #Executing arr1-arr2 here __array_finalize__ {} Currently I have simply downgraded to 1.9.2 to solve the problem for myself, but have been having difficulty figuring out where the difference lies between 1.9.2 and 1.10.0. Thanks, Jeremy

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Make as_strided result writeonly
by Sebastian Berg 25 Jan '16

25 Jan '16

Hi all, I have just opened a PR, to make as_strided writeonly (as default). The reasoning for this change is that an `as_strided` array often have self overlapping memory. However, writing to an array where multiple elements have the identical memory address can be confusing, and the results are typically unpredictable. Considering the danger, the proposal is to add a `readonly=True`. A poweruser (who that function is designed for anyway), could thus still get a writeable array. For the moment, writing to the result would raise a FutureWarning with `readonly="warn"`. Do you agree with this, or would it be a major inconvenience? - Sebastian

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PR #7090: ENH: Added 'doane' and 'sqrt' estimators to np.histogram
by Joseph Fox-Rabinovitz 24 Jan '16

24 Jan '16

As someone very new to relatively large projects such as numpy, I was wondering how the process works. I have announced my PR with some small enhancements to the histogram function and fixed up all of the comments that were made (originally to PR 7083). What happens next? All I have to go on is http://docs.scipy.org/doc/numpy-1.10.1/dev/gitwash/development_workflow.htm…, but that does not go into detail about what happens after the point I have already reached. Regards, -Joe On Thu, Jan 21, 2016 at 3:37 PM, Joseph Fox-Rabinovitz <jfoxrabinovitz(a)gmail.com> wrote: > Due to a mistake I made in my branch structure, I have replaced this > PR with #7090: https://github.com/numpy/numpy/pull/7090. All of the > changes and fixes so far are squashed into the new request. > > -Joe > > On Thu, Jan 21, 2016 at 1:51 AM, Joseph Fox-Rabinovitz > <jfoxrabinovitz(a)gmail.com> wrote: >> Please let me know if there is anything wrong or missing. I have added >> a couple of estimators that I find useful sometimes. >> >> -Joe

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ANN: scipy 0.17.0 release
by Evgeni Burovski 23 Jan '16

23 Jan '16

Hi, On behalf of the Scipy development team I am pleased to announce the availability of Scipy 0.17.0. This release contains several new features, detailed in the release notes below. 101 people contributed to this release over the course of six months. This release requires Python 2.6, 2.7 or 3.2-3.4 and NumPy 1.6.2 or greater. Source tarballs and release notes can be found at https://github.com/scipy/scipy/releases/tag/v0.17.0. Thanks to everyone who contributed to this release. Cheers, Evgeni -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 ========================== SciPy 0.17.0 Release Notes ========================== .. contents:: SciPy 0.17.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Moreover, our development attention will now shift to bug-fix releases on the 0.17.x branch, and on adding new features on the master branch. This release requires Python 2.6, 2.7 or 3.2-3.5 and NumPy 1.6.2 or greater. Release highlights: - New functions for linear and nonlinear least squares optimization with constraints: `scipy.optimize.lsq_linear` and `scipy.optimize.least_squares` - Support for fitting with bounds in `scipy.optimize.curve_fit`. - Significant improvements to `scipy.stats`, providing many functions with better handing of inputs which have NaNs or are empty, improved documentation, and consistent behavior between `scipy.stats` and `scipy.stats.mstats`. - Significant performance improvements and new functionality in `scipy.spatial.cKDTree`. New features ============ `scipy.cluster` improvements - ---------------------------- A new function `scipy.cluster.hierarchy.cut_tree`, which determines a cut tree from a linkage matrix, was added. `scipy.io` improvements - ----------------------- `scipy.io.mmwrite` gained support for symmetric sparse matrices. `scipy.io.netcdf` gained support for masking and scaling data based on data attributes. `scipy.optimize` improvements - ----------------------------- Linear assignment problem solver ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ `scipy.optimize.linear_sum_assignment` is a new function for solving the linear sum assignment problem. It uses the Hungarian algorithm (Kuhn-Munkres). Least squares optimization ~~~~~~~~~~~~~~~~~~~~~~~~~~ A new function for *nonlinear* least squares optimization with constraints was added: `scipy.optimize.least_squares`. It provides several methods: Levenberg-Marquardt for unconstrained problems, and two trust-region methods for constrained ones. Furthermore it provides different loss functions. New trust-region methods also handle sparse Jacobians. A new function for *linear* least squares optimization with constraints was added: `scipy.optimize.lsq_linear`. It provides a trust-region method as well as an implementation of the Bounded-Variable Least-Squares (BVLS) algorithm. `scipy.optimize.curve_fit` now supports fitting with bounds. `scipy.signal` improvements - --------------------------- A ``mode`` keyword was added to `scipy.signal.spectrogram`, to let it return other spectrograms than power spectral density. `scipy.stats` improvements - -------------------------- Many functions in `scipy.stats` have gained a ``nan_policy`` keyword, which allows specifying how to treat input with NaNs in them: propagate the NaNs, raise an error, or omit the NaNs. Many functions in `scipy.stats` have been improved to correctly handle input arrays that are empty or contain infs/nans. A number of functions with the same name in `scipy.stats` and `scipy.stats.mstats` were changed to have matching signature and behavior. See `gh-5474 <https://github.com/scipy/scipy/issues/5474>`__ for details. `scipy.stats.binom_test` and `scipy.stats.mannwhitneyu` gained a keyword ``alternative``, which allows specifying the hypothesis to test for. Eventually all hypothesis testing functions will get this keyword. For methods of many continuous distributions, complex input is now accepted. Matrix normal distribution has been implemented as `scipy.stats.matrix_normal`. `scipy.sparse` improvements - --------------------------- The `axis` keyword was added to sparse norms, `scipy.sparse.linalg.norm`. `scipy.spatial` improvements - ---------------------------- `scipy.spatial.cKDTree` was partly rewritten for improved performance and several new features were added to it: - - the ``query_ball_point`` method became significantly faster - - ``query`` and ``query_ball_point`` gained an ``n_jobs`` keyword for parallel execution - - build and query methods now release the GIL - - full pickling support - - support for periodic spaces - - the ``sparse_distance_matrix`` method can now return and sparse matrix type `scipy.interpolate` improvements - -------------------------------- Out-of-bounds behavior of `scipy.interpolate.interp1d` has been improved. Use a two-element tuple for the ``fill_value`` argument to specify separate fill values for input below and above the interpolation range. Linear and nearest interpolation kinds of `scipy.interpolate.interp1d` support extrapolation via the ``fill_value="extrapolate"`` keyword. ``fill_value`` can also be set to an array-like (or a two-element tuple of array-likes for separate below and above values) so long as it broadcasts properly to the non-interpolated dimensions of an array. This was implicitly supported by previous versions of scipy, but support has now been formalized and gets compatibility-checked before use. For example, a set of ``y`` values to interpolate with shape ``(2, 3, 5)`` interpolated along the last axis (2) could accept a ``fill_value`` array with shape ``()`` (singleton), ``(1,)``, ``(2, 1)``, ``(1, 3)``, ``(3,)``, or ``(2, 3)``; or it can be a 2-element tuple to specify separate below and above bounds, where each of the two tuple elements obeys proper broadcasting rules. `scipy.linalg` improvements - --------------------------- The default algorithm for `scipy.linalg.leastsq` has been changed to use LAPACK's function ``*gelsd``. Users wanting to get the previous behavior can use a new keyword ``lapack_driver="gelss"`` (allowed values are "gelss", "gelsd" and "gelsy"). ``scipy.sparse`` matrices and linear operators now support the matmul (``@``) operator when available (Python 3.5+). See [PEP 465](http://legacy.python.org/dev/peps/pep-0465/) A new function `scipy.linalg.ordqz`, for QZ decomposition with reordering, has been added. Deprecated features =================== ``scipy.stats.histogram`` is deprecated in favor of ``np.histogram``, which is faster and provides the same functionality. ``scipy.stats.threshold`` and ``scipy.mstats.threshold`` are deprecated in favor of ``np.clip``. See issue #617 for details. ``scipy.stats.ss`` is deprecated. This is a support function, not meant to be exposed to the user. Also, the name is unclear. See issue #663 for details. ``scipy.stats.square_of_sums`` is deprecated. This too is a support function not meant to be exposed to the user. See issues #665 and #663 for details. ``scipy.stats.f_value``, ``scipy.stats.f_value_multivariate``, ``scipy.stats.f_value_wilks_lambda``, and ``scipy.mstats.f_value_wilks_lambda`` are deprecated. These are related to ANOVA, for which ``scipy.stats`` provides quite limited functionality and these functions are not very useful standalone. See issues #660 and #650 for details. ``scipy.stats.chisqprob`` is deprecated. This is an alias. ``stats.chi2.sf`` should be used instead. ``scipy.stats.betai`` is deprecated. This is an alias for ``special.betainc`` which should be used instead. Backwards incompatible changes ============================== The functions ``stats.trim1`` and ``stats.trimboth`` now make sure the elements trimmed are the lowest and/or highest, depending on the case. Slicing without at least partial sorting was previously done, but didn't make sense for unsorted input. When ``variable_names`` is set to an empty list, ``scipy.io.loadmat`` now correctly returns no values instead of all the contents of the MAT file. Element-wise multiplication of sparse matrices now returns a sparse result in all cases. Previously, multiplying a sparse matrix with a dense matrix or array would return a dense matrix. The function ``misc.lena`` has been removed due to license incompatibility. The constructor for ``sparse.coo_matrix`` no longer accepts ``(None, (m,n))`` to construct an all-zero matrix of shape ``(m,n)``. This functionality was deprecated since at least 2007 and was already broken in the previous SciPy release. Use ``coo_matrix((m,n))`` instead. The Cython wrappers in ``linalg.cython_lapack`` for the LAPACK routines ``*gegs``, ``*gegv``, ``*gelsx``, ``*geqpf``, ``*ggsvd``, ``*ggsvp``, ``*lahrd``, ``*latzm``, ``*tzrqf`` have been removed since these routines are not present in the new LAPACK 3.6.0 release. With the exception of the routines ``*ggsvd`` and ``*ggsvp``, these were all deprecated in favor of routines that are currently present in our Cython LAPACK wrappers. Because the LAPACK ``*gegv`` routines were removed in LAPACK 3.6.0. The corresponding Python wrappers in ``scipy.linalg.lapack`` are now deprecated and will be removed in a future release. The source files for these routines have been temporarily included as a part of ``scipy.linalg`` so that SciPy can be built against LAPACK versions that do not provide these deprecated routines. Other changes ============= Html and pdf documentation of development versions of Scipy is now automatically rebuilt after every merged pull request. `scipy.constants` is updated to the CODATA 2014 recommended values. Usage of `scipy.fftpack` functions within Scipy has been changed in such a way that `PyFFTW <http://hgomersall.github.io/pyFFTW/>`__ can easily replace `scipy.fftpack` functions (with improved performance). See `gh-5295 <https://github.com/scipy/scipy/pull/5295>`__ for details. The ``imread`` functions in `scipy.misc` and `scipy.ndimage` were unified, for which a ``mode`` argument was added to `scipy.misc.imread`. Also, bugs for 1-bit and indexed RGB image formats were fixed. ``runtests.py``, the development script to build and test Scipy, now allows building in parallel with ``--parallel``. Authors ======= * @cel4 + * @chemelnucfin + * @endolith * @mamrehn + * @tosh1ki + * Joshua L. Adelman + * Anne Archibald * Hervé Audren + * Vincent Barrielle + * Bruno Beltran + * Sumit Binnani + * Joseph Jon Booker * Olga Botvinnik + * Michael Boyle + * Matthew Brett * Zaz Brown + * Lars Buitinck * Pete Bunch + * Evgeni Burovski * CJ Carey * Ien Cheng + * Cody + * Jaime Fernandez del Rio * Ales Erjavec + * Abraham Escalante * Yves-Rémi Van Eycke + * Yu Feng + * Eric Firing * Francis T. O'Donovan + * André Gaul * Christoph Gohlke * Ralf Gommers * Alex Griffing * Alexander Grigorievskiy * Charles Harris * Jörn Hees + * Ian Henriksen * Derek Homeier + * David Menéndez Hurtado * Gert-Ludwig Ingold * Aakash Jain + * Rohit Jamuar + * Jan Schlüter * Johannes Ballé * Luke Zoltan Kelley + * Jason King + * Andreas Kopecky + * Eric Larson * Denis Laxalde * Antony Lee * Gregory R. Lee * Josh Levy-Kramer + * Sam Lewis + * François Magimel + * Martín Gaitán + * Sam Mason + * Andreas Mayer * Nikolay Mayorov * Damon McDougall + * Robert McGibbon * Sturla Molden * Will Monroe + * Eric Moore * Maniteja Nandana * Vikram Natarajan + * Andrew Nelson * Marti Nito + * Behzad Nouri + * Daisuke Oyama + * Giorgio Patrini + * Fabian Paul + * Christoph Paulik + * Mad Physicist + * Irvin Probst * Sebastian Pucilowski + * Ted Pudlik + * Eric Quintero * Yoav Ram + * Joscha Reimer + * Juha Remes * Frederik Rietdijk + * Rémy Léone + * Christian Sachs + * Skipper Seabold * Sebastian Skoupý + * Alex Seewald + * Andreas Sorge + * Bernardo Sulzbach + * Julian Taylor * Louis Tiao + * Utkarsh Upadhyay + * Jacob Vanderplas * Gael Varoquaux + * Pauli Virtanen * Fredrik Wallner + * Stefan van der Walt * James Webber + * Warren Weckesser * Raphael Wettinger + * Josh Wilson + * Nat Wilson + * Peter Yin + A total of 101 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. Issues closed for 0.17.0 - ------------------------ - - `#1923 <https://github.com/scipy/scipy/issues/1923>`__: problem with numpy 0's in stats.poisson.rvs (Trac #1398) - - `#2138 <https://github.com/scipy/scipy/issues/2138>`__: scipy.misc.imread segfaults on 1 bit png (Trac #1613) - - `#2237 <https://github.com/scipy/scipy/issues/2237>`__: distributions do not accept complex arguments (Trac #1718) - - `#2282 <https://github.com/scipy/scipy/issues/2282>`__: scipy.special.hyp1f1(0.5, 1.5, -1000) fails (Trac #1763) - - `#2618 <https://github.com/scipy/scipy/issues/2618>`__: poisson.pmf returns NaN if mu is 0 - - `#2957 <https://github.com/scipy/scipy/issues/2957>`__: hyp1f1 precision issue - - `#2997 <https://github.com/scipy/scipy/issues/2997>`__: FAIL: test_qhull.TestUtilities.test_more_barycentric_transforms - - `#3129 <https://github.com/scipy/scipy/issues/3129>`__: No way to set ranges for fitting parameters in Optimize functions - - `#3191 <https://github.com/scipy/scipy/issues/3191>`__: interp1d should contain a fill_value_below and a fill_value_above... - - `#3453 <https://github.com/scipy/scipy/issues/3453>`__: PchipInterpolator sets slopes at edges differently than Matlab's... - - `#4106 <https://github.com/scipy/scipy/issues/4106>`__: ndimage._ni_support._normalize_sequence() fails with numpy.int64 - - `#4118 <https://github.com/scipy/scipy/issues/4118>`__: `scipy.integrate.ode.set_solout` called after `scipy.integrate.ode.set_initial_value` fails silently - - `#4233 <https://github.com/scipy/scipy/issues/4233>`__: 1D scipy.interpolate.griddata using method=nearest produces nans... - - `#4375 <https://github.com/scipy/scipy/issues/4375>`__: All tests fail due to bad file permissions - - `#4580 <https://github.com/scipy/scipy/issues/4580>`__: scipy.ndimage.filters.convolve documenation is incorrect - - `#4627 <https://github.com/scipy/scipy/issues/4627>`__: logsumexp with sign indicator - enable calculation with negative... - - `#4702 <https://github.com/scipy/scipy/issues/4702>`__: logsumexp with zero scaling factor - - `#4834 <https://github.com/scipy/scipy/issues/4834>`__: gammainc should return 1.0 instead of NaN for infinite x - - `#4838 <https://github.com/scipy/scipy/issues/4838>`__: enh: exprel special function - - `#4862 <https://github.com/scipy/scipy/issues/4862>`__: the scipy.special.boxcox function is inaccurate for denormal... - - `#4887 <https://github.com/scipy/scipy/issues/4887>`__: Spherical harmonic incongruences - - `#4895 <https://github.com/scipy/scipy/issues/4895>`__: some scipy ufuncs have inconsistent output dtypes? - - `#4923 <https://github.com/scipy/scipy/issues/4923>`__: logm does not aggressively convert complex outputs to float - - `#4932 <https://github.com/scipy/scipy/issues/4932>`__: BUG: stats: The `fit` method of the distributions silently ignores... - - `#4956 <https://github.com/scipy/scipy/issues/4956>`__: Documentation error in `scipy.special.bi_zeros` - - `#4957 <https://github.com/scipy/scipy/issues/4957>`__: Docstring for `pbvv_seq` is wrong - - `#4967 <https://github.com/scipy/scipy/issues/4967>`__: block_diag should look at dtypes of all arguments, not only the... - - `#5037 <https://github.com/scipy/scipy/issues/5037>`__: scipy.optimize.minimize error messages are printed to stdout... - - `#5039 <https://github.com/scipy/scipy/issues/5039>`__: Cubic interpolation: On entry to DGESDD parameter number 12 had... - - `#5163 <https://github.com/scipy/scipy/issues/5163>`__: Base case example of Hierarchical Clustering (offer) - - `#5181 <https://github.com/scipy/scipy/issues/5181>`__: BUG: stats.genextreme.entropy should use the explicit formula - - `#5184 <https://github.com/scipy/scipy/issues/5184>`__: Some? wheels don't express a numpy dependency - - `#5197 <https://github.com/scipy/scipy/issues/5197>`__: mstats: test_kurtosis fails (ULP max is 2) - - `#5260 <https://github.com/scipy/scipy/issues/5260>`__: Typo causing an error in splrep - - `#5263 <https://github.com/scipy/scipy/issues/5263>`__: Default epsilon in rbf.py fails for colinear points - - `#5276 <https://github.com/scipy/scipy/issues/5276>`__: Reading empty (no data) arff file fails - - `#5280 <https://github.com/scipy/scipy/issues/5280>`__: 1d scipy.signal.convolve much slower than numpy.convolve - - `#5326 <https://github.com/scipy/scipy/issues/5326>`__: Implementation error in scipy.interpolate.PchipInterpolator - - `#5370 <https://github.com/scipy/scipy/issues/5370>`__: Test issue with test_quadpack and libm.so as a linker script - - `#5426 <https://github.com/scipy/scipy/issues/5426>`__: ERROR: test_stats.test_chisquare_masked_arrays - - `#5427 <https://github.com/scipy/scipy/issues/5427>`__: Automate installing correct numpy versions in numpy-vendor image - - `#5430 <https://github.com/scipy/scipy/issues/5430>`__: Python3 : Numpy scalar types "not iterable"; specific instance... - - `#5450 <https://github.com/scipy/scipy/issues/5450>`__: BUG: spatial.ConvexHull triggers a seg. fault when given nans. - - `#5478 <https://github.com/scipy/scipy/issues/5478>`__: clarify the relation between matrix normal distribution and `multivariate_normal` - - `#5539 <https://github.com/scipy/scipy/issues/5539>`__: lstsq related test failures on windows binaries from numpy-vendor - - `#5560 <https://github.com/scipy/scipy/issues/5560>`__: doc: scipy.stats.burr pdf issue - - `#5571 <https://github.com/scipy/scipy/issues/5571>`__: lstsq test failure after lapack_driver change - - `#5577 <https://github.com/scipy/scipy/issues/5577>`__: ordqz segfault on Python 3.4 in Wine - - `#5578 <https://github.com/scipy/scipy/issues/5578>`__: scipy.linalg test failures on python 3 in Wine - - `#5607 <https://github.com/scipy/scipy/issues/5607>`__: Overloaded ‘isnan(double&)’ is ambiguous when compiling with... - - `#5629 <https://github.com/scipy/scipy/issues/5629>`__: Test for lstsq randomly failed - - `#5630 <https://github.com/scipy/scipy/issues/5630>`__: memory leak with scipy 0.16 spatial cKDEtree - - `#5689 <https://github.com/scipy/scipy/issues/5689>`__: isnan errors compiling scipy/special/Faddeeva.cc with clang++ - - `#5694 <https://github.com/scipy/scipy/issues/5694>`__: fftpack test failure in test_import - - `#5719 <https://github.com/scipy/scipy/issues/5719>`__: curve_fit(method!="lm") ignores initial guess Pull requests for 0.17.0 - ------------------------ - - `#3022 <https://github.com/scipy/scipy/pull/3022>`__: hyp1f1: better handling of large negative arguments - - `#3107 <https://github.com/scipy/scipy/pull/3107>`__: ENH: Add ordered QZ decomposition - - `#4390 <https://github.com/scipy/scipy/pull/4390>`__: ENH: Allow axis and keepdims arguments to be passed to scipy.linalg.norm. - - `#4671 <https://github.com/scipy/scipy/pull/4671>`__: ENH: add axis to sparse norms - - `#4796 <https://github.com/scipy/scipy/pull/4796>`__: ENH: Add cut tree function to scipy.cluster.hierarchy - - `#4809 <https://github.com/scipy/scipy/pull/4809>`__: MAINT: cauchy moments are undefined - - `#4821 <https://github.com/scipy/scipy/pull/4821>`__: ENH: stats: make distribution instances picklable - - `#4839 <https://github.com/scipy/scipy/pull/4839>`__: ENH: Add scipy.special.exprel relative error exponential ufunc - - `#4859 <https://github.com/scipy/scipy/pull/4859>`__: Logsumexp fixes - allows sign flags and b==0 - - `#4865 <https://github.com/scipy/scipy/pull/4865>`__: BUG: scipy.io.mmio.write: error with big indices and low precision - - `#4869 <https://github.com/scipy/scipy/pull/4869>`__: add as_inexact option to _lib._util._asarray_validated - - `#4884 <https://github.com/scipy/scipy/pull/4884>`__: ENH: Finite difference approximation of Jacobian matrix - - `#4890 <https://github.com/scipy/scipy/pull/4890>`__: ENH: Port cKDTree query methods to C++, allow pickling on Python... - - `#4892 <https://github.com/scipy/scipy/pull/4892>`__: how much doctesting is too much? - - `#4896 <https://github.com/scipy/scipy/pull/4896>`__: MAINT: work around a possible numpy ufunc loop selection bug - - `#4898 <https://github.com/scipy/scipy/pull/4898>`__: MAINT: A bit of pyflakes-driven cleanup. - - `#4899 <https://github.com/scipy/scipy/pull/4899>`__: ENH: add 'alternative' keyword to hypothesis tests in stats - - `#4903 <https://github.com/scipy/scipy/pull/4903>`__: BENCH: Benchmarks for interpolate module - - `#4905 <https://github.com/scipy/scipy/pull/4905>`__: MAINT: prepend underscore to mask_to_limits; delete masked_var. - - `#4906 <https://github.com/scipy/scipy/pull/4906>`__: MAINT: Benchmarks for optimize.leastsq - - `#4910 <https://github.com/scipy/scipy/pull/4910>`__: WIP: Trimmed statistics functions have inconsistent API. - - `#4912 <https://github.com/scipy/scipy/pull/4912>`__: MAINT: fix typo in stats tutorial. Closes gh-4911. - - `#4914 <https://github.com/scipy/scipy/pull/4914>`__: DEP: deprecate `scipy.stats.ss` and `scipy.stats.square_of_sums`. - - `#4924 <https://github.com/scipy/scipy/pull/4924>`__: MAINT: if the imaginary part of logm of a real matrix is small,... - - `#4930 <https://github.com/scipy/scipy/pull/4930>`__: BENCH: Benchmarks for signal module - - `#4941 <https://github.com/scipy/scipy/pull/4941>`__: ENH: update `find_repeats`. - - `#4942 <https://github.com/scipy/scipy/pull/4942>`__: MAINT: use np.float64_t instead of np.float_t in cKDTree - - `#4944 <https://github.com/scipy/scipy/pull/4944>`__: BUG: integer overflow in correlate_nd - - `#4951 <https://github.com/scipy/scipy/pull/4951>`__: do not ignore invalid kwargs in distributions fit method - - `#4958 <https://github.com/scipy/scipy/pull/4958>`__: Add some detail to docstrings for special functions - - `#4961 <https://github.com/scipy/scipy/pull/4961>`__: ENH: stats.describe: add bias kw and empty array handling - - `#4963 <https://github.com/scipy/scipy/pull/4963>`__: ENH: scipy.sparse.coo.coo_matrix.__init__: less memory needed - - `#4968 <https://github.com/scipy/scipy/pull/4968>`__: DEP: deprecate ``stats.f_value*`` and ``mstats.f_value*`` functions. - - `#4969 <https://github.com/scipy/scipy/pull/4969>`__: ENH: review `stats.relfreq` and `stats.cumfreq`; fixes to `stats.histogram` - - `#4971 <https://github.com/scipy/scipy/pull/4971>`__: Extend github source links to line ranges - - `#4972 <https://github.com/scipy/scipy/pull/4972>`__: MAINT: impove the error message in validate_runtests_log - - `#4976 <https://github.com/scipy/scipy/pull/4976>`__: DEP: deprecate `scipy.stats.threshold` - - `#4977 <https://github.com/scipy/scipy/pull/4977>`__: MAINT: more careful dtype treatment in block diagonal matrix... - - `#4979 <https://github.com/scipy/scipy/pull/4979>`__: ENH: distributions, complex arguments - - `#4984 <https://github.com/scipy/scipy/pull/4984>`__: clarify dirichlet distribution error handling - - `#4992 <https://github.com/scipy/scipy/pull/4992>`__: ENH: `stats.fligner` and `stats.bartlett` empty input handling. - - `#4996 <https://github.com/scipy/scipy/pull/4996>`__: DOC: fix stats.spearmanr docs - - `#4997 <https://github.com/scipy/scipy/pull/4997>`__: Fix up boxcox for underflow / loss of precision - - `#4998 <https://github.com/scipy/scipy/pull/4998>`__: DOC: improved documentation for `stats.ppcc_max` - - `#5000 <https://github.com/scipy/scipy/pull/5000>`__: ENH: added empty input handling `scipy.moment`; doc enhancements - - `#5003 <https://github.com/scipy/scipy/pull/5003>`__: ENH: improves rankdata algorithm - - `#5005 <https://github.com/scipy/scipy/pull/5005>`__: scipy.stats: numerical stability improvement - - `#5007 <https://github.com/scipy/scipy/pull/5007>`__: ENH: nan handling in functions that use `stats._chk_asarray` - - `#5009 <https://github.com/scipy/scipy/pull/5009>`__: remove coveralls.io - - `#5010 <https://github.com/scipy/scipy/pull/5010>`__: Hypergeometric distribution log survival function - - `#5014 <https://github.com/scipy/scipy/pull/5014>`__: Patch to compute the volume and area of convex hulls - - `#5015 <https://github.com/scipy/scipy/pull/5015>`__: DOC: Fix mistaken variable name in sawtooth - - `#5016 <https://github.com/scipy/scipy/pull/5016>`__: DOC: resample example - - `#5017 <https://github.com/scipy/scipy/pull/5017>`__: DEP: deprecate `stats.betai` and `stats.chisqprob` - - `#5018 <https://github.com/scipy/scipy/pull/5018>`__: ENH: Add test on random inpu to volume computations - - `#5026 <https://github.com/scipy/scipy/pull/5026>`__: BUG: Fix return dtype of lil_matrix.getnnz(axis=0) - - `#5030 <https://github.com/scipy/scipy/pull/5030>`__: DOC: resample slow for prime output too - - `#5033 <https://github.com/scipy/scipy/pull/5033>`__: MAINT: integrate, special: remove unused R1MACH and Makefile - - `#5034 <https://github.com/scipy/scipy/pull/5034>`__: MAINT: signal: lift max_len_seq validation out of Cython - - `#5035 <https://github.com/scipy/scipy/pull/5035>`__: DOC/MAINT: refguide / doctest drudgery - - `#5041 <https://github.com/scipy/scipy/pull/5041>`__: BUG: fixing some small memory leaks detected by cppcheck - - `#5044 <https://github.com/scipy/scipy/pull/5044>`__: [GSoC] ENH: New least-squares algorithms - - `#5050 <https://github.com/scipy/scipy/pull/5050>`__: MAINT: C fixes, trimmed a lot of dead code from Cephes - - `#5057 <https://github.com/scipy/scipy/pull/5057>`__: ENH: sparse: avoid densifying on sparse/dense elementwise mult - - `#5058 <https://github.com/scipy/scipy/pull/5058>`__: TST: stats: add a sample distribution to the test loop - - `#5061 <https://github.com/scipy/scipy/pull/5061>`__: ENH: spatial: faster 2D Voronoi and Convex Hull plotting - - `#5065 <https://github.com/scipy/scipy/pull/5065>`__: TST: improve test coverage for `stats.mvsdist` and `stats.bayes_mvs` - - `#5066 <https://github.com/scipy/scipy/pull/5066>`__: MAINT: fitpack: remove a noop - - `#5067 <https://github.com/scipy/scipy/pull/5067>`__: ENH: empty and nan input handling for `stats.kstat` and `stats.kstatvar` - - `#5071 <https://github.com/scipy/scipy/pull/5071>`__: DOC: optimize: Correct paper reference, add doi - - `#5072 <https://github.com/scipy/scipy/pull/5072>`__: MAINT: scipy.sparse cleanup - - `#5073 <https://github.com/scipy/scipy/pull/5073>`__: DOC: special: Add an example showing the relation of diric to... - - `#5075 <https://github.com/scipy/scipy/pull/5075>`__: DOC: clarified parameterization of stats.lognorm - - `#5076 <https://github.com/scipy/scipy/pull/5076>`__: use int, float, bool instead of np.int, np.float, np.bool - - `#5078 <https://github.com/scipy/scipy/pull/5078>`__: DOC: Rename fftpack docs to README - - `#5081 <https://github.com/scipy/scipy/pull/5081>`__: BUG: Correct handling of scalar 'b' in lsmr and lsqr - - `#5082 <https://github.com/scipy/scipy/pull/5082>`__: loadmat variable_names: don't confuse [] and None. - - `#5083 <https://github.com/scipy/scipy/pull/5083>`__: Fix integrate.fixed_quad docstring to indicate None return value - - `#5086 <https://github.com/scipy/scipy/pull/5086>`__: Use solve() instead of inv() for gaussian_kde - - `#5090 <https://github.com/scipy/scipy/pull/5090>`__: MAINT: stats: add explicit _sf, _isf to gengamma distribution - - `#5094 <https://github.com/scipy/scipy/pull/5094>`__: ENH: scipy.interpolate.NearestNDInterpolator: cKDTree configurable - - `#5098 <https://github.com/scipy/scipy/pull/5098>`__: DOC: special: fix typesetting in ``*_roots quadrature`` functions - - `#5099 <https://github.com/scipy/scipy/pull/5099>`__: DOC: make the docstring of stats.moment raw - - `#5104 <https://github.com/scipy/scipy/pull/5104>`__: DOC/ENH fixes and micro-optimizations for scipy.linalg - - `#5105 <https://github.com/scipy/scipy/pull/5105>`__: enh: made l-bfgs-b parameter for the maximum number of line search... - - `#5106 <https://github.com/scipy/scipy/pull/5106>`__: TST: add NIST test cases to `stats.f_oneway` - - `#5110 <https://github.com/scipy/scipy/pull/5110>`__: [GSoC]: Bounded linear least squares - - `#5111 <https://github.com/scipy/scipy/pull/5111>`__: MAINT: special: Cephes cleanup - - `#5118 <https://github.com/scipy/scipy/pull/5118>`__: BUG: FIR path failed if len(x) < len(b) in lfilter. - - `#5124 <https://github.com/scipy/scipy/pull/5124>`__: ENH: move the filliben approximation to a publicly visible function - - `#5126 <https://github.com/scipy/scipy/pull/5126>`__: StatisticsCleanup: `stats.kruskal` review - - `#5130 <https://github.com/scipy/scipy/pull/5130>`__: DOC: update PyPi trove classifiers. Beta -> Stable. Add license. - - `#5131 <https://github.com/scipy/scipy/pull/5131>`__: DOC: differential_evolution, improve docstring for mutation and... - - `#5132 <https://github.com/scipy/scipy/pull/5132>`__: MAINT: differential_evolution improve init_population_lhs comments... - - `#5133 <https://github.com/scipy/scipy/pull/5133>`__: MRG: rebased mmio refactoring - - `#5135 <https://github.com/scipy/scipy/pull/5135>`__: MAINT: `stats.mstats` consistency with `stats.stats` - - `#5139 <https://github.com/scipy/scipy/pull/5139>`__: TST: linalg: add a smoke test for gh-5039 - - `#5140 <https://github.com/scipy/scipy/pull/5140>`__: EHN: Update constants.codata to CODATA 2014 - - `#5145 <https://github.com/scipy/scipy/pull/5145>`__: added ValueError to docstring as possible error raised - - `#5146 <https://github.com/scipy/scipy/pull/5146>`__: MAINT: Improve implementation details and doc in `stats.shapiro` - - `#5147 <https://github.com/scipy/scipy/pull/5147>`__: [GSoC] ENH: Upgrades to curve_fit - - `#5150 <https://github.com/scipy/scipy/pull/5150>`__: Fix misleading wavelets/cwt example - - `#5152 <https://github.com/scipy/scipy/pull/5152>`__: BUG: cluster.hierarchy.dendrogram: missing font size doesn't... - - `#5153 <https://github.com/scipy/scipy/pull/5153>`__: add keywords to control the summation in discrete distributions... - - `#5156 <https://github.com/scipy/scipy/pull/5156>`__: DOC: added comments on algorithms used in Legendre function - - `#5158 <https://github.com/scipy/scipy/pull/5158>`__: ENH: optimize: add the Hungarian algorithm - - `#5162 <https://github.com/scipy/scipy/pull/5162>`__: FIX: Remove lena - - `#5164 <https://github.com/scipy/scipy/pull/5164>`__: MAINT: fix cluster.hierarchy.dendrogram issues and docs - - `#5166 <https://github.com/scipy/scipy/pull/5166>`__: MAINT: changed `stats.pointbiserialr` to delegate to `stats.pearsonr` - - `#5167 <https://github.com/scipy/scipy/pull/5167>`__: ENH: add nan_policy to `stats.kendalltau`. - - `#5168 <https://github.com/scipy/scipy/pull/5168>`__: TST: added nist test case (Norris) to `stats.linregress`. - - `#5169 <https://github.com/scipy/scipy/pull/5169>`__: update lpmv docstring - - `#5171 <https://github.com/scipy/scipy/pull/5171>`__: Clarify metric parameter in linkage docstring - - `#5172 <https://github.com/scipy/scipy/pull/5172>`__: ENH: add mode keyword to signal.spectrogram - - `#5177 <https://github.com/scipy/scipy/pull/5177>`__: DOC: graphical example for KDTree.query_ball_point - - `#5179 <https://github.com/scipy/scipy/pull/5179>`__: MAINT: stats: tweak the formula for ncx2.pdf - - `#5188 <https://github.com/scipy/scipy/pull/5188>`__: MAINT: linalg: A bit of clean up. - - `#5189 <https://github.com/scipy/scipy/pull/5189>`__: BUG: stats: Use the explicit formula in stats.genextreme.entropy - - `#5193 <https://github.com/scipy/scipy/pull/5193>`__: BUG: fix uninitialized use in lartg - - `#5194 <https://github.com/scipy/scipy/pull/5194>`__: BUG: properly return error to fortran from ode_jacobian_function - - `#5198 <https://github.com/scipy/scipy/pull/5198>`__: TST: Fix TestCtypesQuad failure on Python 3.5 for Windows - - `#5201 <https://github.com/scipy/scipy/pull/5201>`__: allow extrapolation in interp1d - - `#5209 <https://github.com/scipy/scipy/pull/5209>`__: MAINT: Change complex parameter to boolean in Y_() - - `#5213 <https://github.com/scipy/scipy/pull/5213>`__: BUG: sparse: fix logical comparison dtype conflicts - - `#5216 <https://github.com/scipy/scipy/pull/5216>`__: BUG: sparse: fixing unbound local error - - `#5218 <https://github.com/scipy/scipy/pull/5218>`__: DOC and BUG: Bessel function docstring improvements, fix array_like,... - - `#5222 <https://github.com/scipy/scipy/pull/5222>`__: MAINT: sparse: fix COO ctor - - `#5224 <https://github.com/scipy/scipy/pull/5224>`__: DOC: optimize: type of OptimizeResult.hess_inv varies - - `#5228 <https://github.com/scipy/scipy/pull/5228>`__: ENH: Add maskandscale support to netcdf; based on pupynere and... - - `#5229 <https://github.com/scipy/scipy/pull/5229>`__: DOC: sparse.linalg.svds doc typo fixed - - `#5234 <https://github.com/scipy/scipy/pull/5234>`__: MAINT: sparse: simplify COO ctor - - `#5235 <https://github.com/scipy/scipy/pull/5235>`__: MAINT: sparse: warn on todia() with many diagonals - - `#5236 <https://github.com/scipy/scipy/pull/5236>`__: MAINT: ndimage: simplify thread handling/recursion + constness - - `#5239 <https://github.com/scipy/scipy/pull/5239>`__: BUG: integrate: Fixed issue 4118 - - `#5241 <https://github.com/scipy/scipy/pull/5241>`__: qr_insert fixes, closes #5149 - - `#5246 <https://github.com/scipy/scipy/pull/5246>`__: Doctest tutorial files - - `#5247 <https://github.com/scipy/scipy/pull/5247>`__: DOC: optimize: typo/import fix in linear_sum_assignment - - `#5248 <https://github.com/scipy/scipy/pull/5248>`__: remove inspect.getargspec and test python 3.5 on Travis CI - - `#5250 <https://github.com/scipy/scipy/pull/5250>`__: BUG: Fix sparse multiply by single-element zero - - `#5261 <https://github.com/scipy/scipy/pull/5261>`__: Fix bug causing a TypeError in splrep when a runtime warning... - - `#5262 <https://github.com/scipy/scipy/pull/5262>`__: Follow up to 4489 (Addition LAPACK routines in linalg.lstsq) - - `#5264 <https://github.com/scipy/scipy/pull/5264>`__: ignore zero-length edges for default epsilon - - `#5269 <https://github.com/scipy/scipy/pull/5269>`__: DOC: Typos and spell-checking - - `#5272 <https://github.com/scipy/scipy/pull/5272>`__: MAINT: signal: Convert array syntax to memoryviews - - `#5273 <https://github.com/scipy/scipy/pull/5273>`__: DOC: raw strings for docstrings with math - - `#5274 <https://github.com/scipy/scipy/pull/5274>`__: MAINT: sparse: update cython code for MST - - `#5278 <https://github.com/scipy/scipy/pull/5278>`__: BUG: io: Stop guessing the data delimiter in ARFF files. - - `#5289 <https://github.com/scipy/scipy/pull/5289>`__: BUG: misc: Fix the Pillow work-around for 1-bit images. - - `#5291 <https://github.com/scipy/scipy/pull/5291>`__: ENH: call np.correlate for 1d in scipy.signal.correlate - - `#5294 <https://github.com/scipy/scipy/pull/5294>`__: DOC: special: Remove a potentially misleading example from the... - - `#5295 <https://github.com/scipy/scipy/pull/5295>`__: Simplify replacement of fftpack by pyfftw - - `#5296 <https://github.com/scipy/scipy/pull/5296>`__: ENH: Add matrix normal distribution to stats - - `#5297 <https://github.com/scipy/scipy/pull/5297>`__: Fixed leaf_rotation and leaf_font_size in Python 3 - - `#5303 <https://github.com/scipy/scipy/pull/5303>`__: MAINT: stats: rewrite find_repeats - - `#5307 <https://github.com/scipy/scipy/pull/5307>`__: MAINT: stats: remove unused Fortran routine - - `#5313 <https://github.com/scipy/scipy/pull/5313>`__: BUG: sparse: fix diags for nonsquare matrices - - `#5315 <https://github.com/scipy/scipy/pull/5315>`__: MAINT: special: Cephes cleanup - - `#5316 <https://github.com/scipy/scipy/pull/5316>`__: fix input check for sparse.linalg.svds - - `#5319 <https://github.com/scipy/scipy/pull/5319>`__: MAINT: Cython code maintenance - - `#5328 <https://github.com/scipy/scipy/pull/5328>`__: BUG: Fix place_poles return values - - `#5329 <https://github.com/scipy/scipy/pull/5329>`__: avoid a spurious divide-by-zero in Student t stats - - `#5334 <https://github.com/scipy/scipy/pull/5334>`__: MAINT: integrate: miscellaneous cleanup - - `#5340 <https://github.com/scipy/scipy/pull/5340>`__: MAINT: Printing Error Msg to STDERR and Removing iterate.dat - - `#5347 <https://github.com/scipy/scipy/pull/5347>`__: ENH: add Py3.5-style matmul operator (e.g. A @ B) to sparse linear... - - `#5350 <https://github.com/scipy/scipy/pull/5350>`__: FIX error, when reading 32-bit float wav files - - `#5351 <https://github.com/scipy/scipy/pull/5351>`__: refactor the PCHIP interpolant's algorithm - - `#5354 <https://github.com/scipy/scipy/pull/5354>`__: MAINT: construct csr and csc matrices from integer lists - - `#5359 <https://github.com/scipy/scipy/pull/5359>`__: add a fast path to interp1d - - `#5364 <https://github.com/scipy/scipy/pull/5364>`__: Add two fill_values to interp1d. - - `#5365 <https://github.com/scipy/scipy/pull/5365>`__: ABCD docstrings - - `#5366 <https://github.com/scipy/scipy/pull/5366>`__: Fixed typo in the documentation for scipy.signal.cwt() per #5290. - - `#5367 <https://github.com/scipy/scipy/pull/5367>`__: DOC updated scipy.spatial.Delaunay example - - `#5368 <https://github.com/scipy/scipy/pull/5368>`__: ENH: Do not create a throwaway class at every function call - - `#5372 <https://github.com/scipy/scipy/pull/5372>`__: DOC: spectral: fix reference formatting - - `#5375 <https://github.com/scipy/scipy/pull/5375>`__: PEP8 amendments to ffpack_basic.py - - `#5377 <https://github.com/scipy/scipy/pull/5377>`__: BUG: integrate: builtin name no longer shadowed - - `#5381 <https://github.com/scipy/scipy/pull/5381>`__: PEP8ified fftpack_pseudo_diffs.py - - `#5385 <https://github.com/scipy/scipy/pull/5385>`__: BLD: fix Bento build for changes to optimize and spatial - - `#5386 <https://github.com/scipy/scipy/pull/5386>`__: STY: PEP8 amendments to interpolate.py - - `#5387 <https://github.com/scipy/scipy/pull/5387>`__: DEP: deprecate stats.histogram - - `#5388 <https://github.com/scipy/scipy/pull/5388>`__: REL: add "make upload" command to doc/Makefile. - - `#5389 <https://github.com/scipy/scipy/pull/5389>`__: DOC: updated origin param of scipy.ndimage.filters.convolve - - `#5395 <https://github.com/scipy/scipy/pull/5395>`__: BUG: special: fix a number of edge cases related to `x = np.inf`. - - `#5398 <https://github.com/scipy/scipy/pull/5398>`__: MAINT: stats: avoid spurious warnings in lognorm.pdf(0, s) - - `#5407 <https://github.com/scipy/scipy/pull/5407>`__: ENH: stats: Handle mu=0 in stats.poisson - - `#5409 <https://github.com/scipy/scipy/pull/5409>`__: Fix the behavior of discrete distributions at the right-hand... - - `#5412 <https://github.com/scipy/scipy/pull/5412>`__: TST: stats: skip a test to avoid a spurious log(0) warning - - `#5413 <https://github.com/scipy/scipy/pull/5413>`__: BUG: linalg: work around LAPACK single-precision lwork computation... - - `#5414 <https://github.com/scipy/scipy/pull/5414>`__: MAINT: stats: move creation of namedtuples outside of function... - - `#5415 <https://github.com/scipy/scipy/pull/5415>`__: DOC: fix up sections in ToC in the pdf reference guide - - `#5416 <https://github.com/scipy/scipy/pull/5416>`__: TST: fix issue with a ctypes test for integrate on Fedora. - - `#5418 <https://github.com/scipy/scipy/pull/5418>`__: DOC: fix bugs in signal.TransferFunction docstring. Closes gh-5287. - - `#5419 <https://github.com/scipy/scipy/pull/5419>`__: MAINT: sparse: fix usage of NotImplementedError - - `#5420 <https://github.com/scipy/scipy/pull/5420>`__: Raise proper error if maxiter < 1 - - `#5422 <https://github.com/scipy/scipy/pull/5422>`__: DOC: changed documentation of brent to be consistent with bracket - - `#5444 <https://github.com/scipy/scipy/pull/5444>`__: BUG: gaussian_filter, BPoly.from_derivatives fail on numpy int... - - `#5445 <https://github.com/scipy/scipy/pull/5445>`__: MAINT: stats: fix incorrect deprecation warnings and test noise - - `#5446 <https://github.com/scipy/scipy/pull/5446>`__: DOC: add note about PyFFTW in fftpack tutorial. - - `#5459 <https://github.com/scipy/scipy/pull/5459>`__: DOC: integrate: Some improvements to the differential equation... - - `#5465 <https://github.com/scipy/scipy/pull/5465>`__: BUG: Relax mstats kurtosis test tolerance by a few ulp - - `#5471 <https://github.com/scipy/scipy/pull/5471>`__: ConvexHull should raise ValueError for NaNs. - - `#5473 <https://github.com/scipy/scipy/pull/5473>`__: MAINT: update decorators.py module to version 4.0.5 - - `#5476 <https://github.com/scipy/scipy/pull/5476>`__: BUG: imsave searches for wrong channel axis if image has 3 or... - - `#5477 <https://github.com/scipy/scipy/pull/5477>`__: BLD: add numpy to setup/install_requires for OS X wheels - - `#5479 <https://github.com/scipy/scipy/pull/5479>`__: ENH: return Jacobian/Hessian from BasinHopping - - `#5484 <https://github.com/scipy/scipy/pull/5484>`__: BUG: fix ttest zero division handling - - `#5486 <https://github.com/scipy/scipy/pull/5486>`__: Fix crash on kmeans2 - - `#5491 <https://github.com/scipy/scipy/pull/5491>`__: MAINT: Expose parallel build option to runtests.py - - `#5494 <https://github.com/scipy/scipy/pull/5494>`__: Sort OptimizeResult.__repr__ by key - - `#5496 <https://github.com/scipy/scipy/pull/5496>`__: DOC: update the author name mapping - - `#5497 <https://github.com/scipy/scipy/pull/5497>`__: Enhancement to binned_statistic: option to unraveled returned... - - `#5498 <https://github.com/scipy/scipy/pull/5498>`__: BUG: sparse: fix a bug in sparsetools input dtype resolution - - `#5500 <https://github.com/scipy/scipy/pull/5500>`__: DOC: detect unprintable characters in docstrings - - `#5505 <https://github.com/scipy/scipy/pull/5505>`__: BUG: misc: Ensure fromimage converts mode 'P' to 'RGB' or 'RGBA'. - - `#5514 <https://github.com/scipy/scipy/pull/5514>`__: DOC: further update the release notes - - `#5515 <https://github.com/scipy/scipy/pull/5515>`__: ENH: optionally disable fixed-point acceleration - - `#5517 <https://github.com/scipy/scipy/pull/5517>`__: DOC: Improvements and additions to the matrix_normal doc - - `#5518 <https://github.com/scipy/scipy/pull/5518>`__: Remove wrappers for LAPACK deprecated routines - - `#5521 <https://github.com/scipy/scipy/pull/5521>`__: TST: skip a linalg.orth memory test on 32-bit platforms. - - `#5523 <https://github.com/scipy/scipy/pull/5523>`__: DOC: change a few floats to integers in docstring examples - - `#5524 <https://github.com/scipy/scipy/pull/5524>`__: DOC: more updates to 0.17.0 release notes. - - `#5525 <https://github.com/scipy/scipy/pull/5525>`__: Fix to minor typo in documentation for scipy.integrate.ode - - `#5527 <https://github.com/scipy/scipy/pull/5527>`__: TST: bump arccosh tolerance to allow for inaccurate numpy or... - - `#5535 <https://github.com/scipy/scipy/pull/5535>`__: DOC: signal: minor clarification to docstring of TransferFunction. - - `#5538 <https://github.com/scipy/scipy/pull/5538>`__: DOC: signal: fix find_peaks_cwt documentation - - `#5545 <https://github.com/scipy/scipy/pull/5545>`__: MAINT: Fix typo in linalg/basic.py - - `#5547 <https://github.com/scipy/scipy/pull/5547>`__: TST: mark TestEig.test_singular as knownfail in master. - - `#5550 <https://github.com/scipy/scipy/pull/5550>`__: MAINT: work around lstsq driver selection issue - - `#5556 <https://github.com/scipy/scipy/pull/5556>`__: BUG: Fixed broken dogbox trust-region radius update - - `#5561 <https://github.com/scipy/scipy/pull/5561>`__: BUG: eliminate warnings, exception (on Win) in test_maskandscale;... - - `#5567 <https://github.com/scipy/scipy/pull/5567>`__: TST: a few cleanups in the test suite; run_module_suite and clearer... - - `#5568 <https://github.com/scipy/scipy/pull/5568>`__: MAINT: simplify poisson's _argcheck - - `#5569 <https://github.com/scipy/scipy/pull/5569>`__: TST: bump GMean test tolerance to make it pass on Wine - - `#5572 <https://github.com/scipy/scipy/pull/5572>`__: TST: lstsq: bump test tolerance for TravisCI - - `#5573 <https://github.com/scipy/scipy/pull/5573>`__: TST: remove use of np.fromfile from cluster.vq tests - - `#5576 <https://github.com/scipy/scipy/pull/5576>`__: Lapack deprecations - - `#5579 <https://github.com/scipy/scipy/pull/5579>`__: TST: skip tests of linalg.norm axis keyword on numpy <= 1.7.x - - `#5582 <https://github.com/scipy/scipy/pull/5582>`__: Clarify language of survival function documentation - - `#5583 <https://github.com/scipy/scipy/pull/5583>`__: MAINT: stats/tests: A bit of clean up. - - `#5588 <https://github.com/scipy/scipy/pull/5588>`__: DOC: stats: Add a note that stats.burr is the Type III Burr distribution. - - `#5595 <https://github.com/scipy/scipy/pull/5595>`__: TST: fix test_lamch failures on Python 3 - - `#5600 <https://github.com/scipy/scipy/pull/5600>`__: MAINT: Ignore spatial/ckdtree.cxx and .h - - `#5602 <https://github.com/scipy/scipy/pull/5602>`__: Explicitly numbered replacement fields for maintainability - - `#5605 <https://github.com/scipy/scipy/pull/5605>`__: MAINT: collection of small fixes to test suite - - `#5614 <https://github.com/scipy/scipy/pull/5614>`__: Minor doc change. - - `#5624 <https://github.com/scipy/scipy/pull/5624>`__: FIX: Fix interpolate - - `#5625 <https://github.com/scipy/scipy/pull/5625>`__: BUG: msvc9 binaries crash when indexing std::vector of size 0 - - `#5635 <https://github.com/scipy/scipy/pull/5635>`__: BUG: misspelled __dealloc__ in cKDTree. - - `#5642 <https://github.com/scipy/scipy/pull/5642>`__: STY: minor fixup of formatting of 0.17.0 release notes. - - `#5643 <https://github.com/scipy/scipy/pull/5643>`__: BLD: fix a build issue in special/Faddeeva.cc with isnan. - - `#5661 <https://github.com/scipy/scipy/pull/5661>`__: TST: linalg tests used stdlib random instead of numpy.random. - - `#5682 <https://github.com/scipy/scipy/pull/5682>`__: backports for 0.17.0 - - `#5696 <https://github.com/scipy/scipy/pull/5696>`__: Minor improvements to least_squares' docstring. - - `#5697 <https://github.com/scipy/scipy/pull/5697>`__: BLD: fix for isnan/isinf issues in special/Faddeeva.cc - - `#5720 <https://github.com/scipy/scipy/pull/5720>`__: TST: fix for file opening error in fftpack test_import.py - - `#5722 <https://github.com/scipy/scipy/pull/5722>`__: BUG: Make curve_fit respect an initial guess with bounds - - `#5726 <https://github.com/scipy/scipy/pull/5726>`__: Backports for v0.17.0rc2 - - `#5727 <https://github.com/scipy/scipy/pull/5727>`__: API: Changes to least_squares API Checksums ========= MD5 ~~~ 5ff2971e1ce90e762c59d2cd84837224 scipy-0.17.0.tar.gz ef0949640ee73f845dde6dd7f84d7691 scipy-0.17.0.tar.xz 28a4fe29e980804db162524f10873211 scipy-0.17.0.zip SHA256 ~~~~~~ f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089 scipy-0.17.0.tar.gz 2bc03ea36cd55bfd80869d87f690334b4cad240373e05857ddfa7a4d1e2f9a7a scipy-0.17.0.tar.xz ede6820030b2e5796126aa1571d86738b14bbd670d68c83378877b1d9eb9894d scipy-0.17.0.zip -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJWokWbAAoJEIp0pQ0zQcu+JUgH/16Qqurptl3jUU11+4pl+8ji 3AFZN+dgzGLyiMz9s+V+OyL4hcdZY4++WM2QizF5uD3hDDFNi+aJRHAYySMAZeIZ O8y//v+DXDVOLZpKwcPFq5E5ZebTDh1jO4zZzpuyi1PnKgTAEKZeSyBSMd0RMx/p kZ0URTcAa/tPgkNZz3+i8By9b/zBWOlbI+v6fCVwV8E20YWfGBSp2s0KAtQk787D Q88ylnc3Zfv4IR1hgCFZz6oJA0RgmpH4USKi7guyg+fIKjf1nFe64zIuV3C2r/Uj y9Qbs/8x/HTteDp5owkRiSwnpTZHOtx/jqeh2z/w9aQe0i8Nag5Ere6JZ2kixG4= =jZUn -----END PGP SIGNATURE-----

3 4

deprecating assignment to ndarray.data
by Nathaniel Smith 22 Jan '16

22 Jan '16

So it turns out that ndarray.data supports assignment at the Python level, and what it does is just assign to the ->data field of the ndarray object: https://github.com/numpy/numpy/blob/master/numpy/core/src/multiarray/getset… This kind of assignment been deprecated at the C level since 1.7, and is totally unsafe -- if there are any views pointing to the array when this happens, then they'll be left pointing off into unallocated memory. E.g.: a = np.arange(10) b = np.linspace(0, 1, 10) c = a.view() a.data = b.data # Now c points into free'd memory Can we deprecate or just remove this? (Also filed issue: https://github.com/numpy/numpy/issues/7093) -n -- Nathaniel J. Smith -- https://vorpus.org

3 4

Set FutureWarnings to error in (dev) tests?
by Sebastian Berg 21 Jan '16

21 Jan '16

Hi all, should we try to set FutureWarnings to errors in dev tests? I am seriously annoyed by FutureWarnings getting lost all over for two reasons. First, it is hard to impossible to find even our own errors for our own FutureWarning changes. Secondly, we currently would not even see any Futurewarnings from someone else. For numpy that may not be a big issue, but still. So, I was starting to try it, and it is annoying obviously. The only serious issue, though, seems actually MA [1]. Sometimes one would add a filter for a whole test file (for my start I did this for the NaT stuff) [2]. Anyway, should we attempt to do this? I admit that trying to make it work, even *with* the change FutureWarnings suddenly pop up when you make the warnings being given less often (I will guess that warning was already issued at import time somewhere). - Sebastian [1] And at that a brand new future warning there, which seems too agressive in any case, though that won't change much. [2] One annoying thing about this, the filter might never be removed. One could add a canary maybe to error out when the filter is not needed anymore.

2 6