Mailman 3 May 2019 - NumPy-Discussion

ANN: SciPy 1.3.0rc2 -- please test
by Tyler Reddy May 9, 2019

May 9, 2019

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.3.0rc2. Please help us test this pre-release. The primary motivation for the second release candidate to is to update wheels to use a more recent OpenBLAS with fixes for SkylakeX AVX kernel problems. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.3.0rc2 One of a few ways to install the release candidate with pip: pip install scipy==1.3.0rc2 ========================== SciPy 1.3.0 Release Notes ========================== Note: Scipy 1.3.0 is not released yet! SciPy 1.3.0 is the culmination of 5 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been some 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. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with ``python -Wd`` and check for ``DeprecationWarning`` s). Our development attention will now shift to bug-fix releases on the 1.3.x branch, and on adding new features on the master branch. This release requires Python 3.5+ and NumPy 1.13.3 or greater. For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release - -------------------------- - - Three new ``stats`` functions, a rewrite of ``pearsonr``, and an exact computation of the Kolmogorov-Smirnov two-sample test - - A new Cython API for bounded scalar-function root-finders in `scipy.optimize` - - Substantial ``CSR`` and ``CSC`` sparse matrix indexing performance improvements - - Added support for interpolation of rotations with continuous angular rate and acceleration in ``RotationSpline`` New features ============ `scipy.interpolate` improvements - -------------------------------- A new class ``CubicHermiteSpline`` is introduced. It is a piecewise-cubic interpolator which matches observed values and first derivatives. Existing cubic interpolators ``CubicSpline``, ``PchipInterpolator`` and ``Akima1DInterpolator`` were made subclasses of ``CubicHermiteSpline``. `scipy.io` improvements - ----------------------- For the Attribute-Relation File Format (ARFF) `scipy.io.arff.loadarff` now supports relational attributes. `scipy.io.mmread` can now parse Matrix Market format files with empty lines. `scipy.linalg` improvements - --------------------------- Added wrappers for ``?syconv`` routines, which convert a symmetric matrix given by a triangular matrix factorization into two matrices and vice versa. `scipy.linalg.clarkson_woodruff_transform` now uses an algorithm that leverages sparsity. This may provide a 60-90 percent speedup for dense input matrices. Truly sparse input matrices should also benefit from the improved sketch algorithm, which now correctly runs in ``O(nnz(A))`` time. Added new functions to calculate symmetric Fiedler matrices and Fiedler companion matrices, named `scipy.linalg.fiedler` and `scipy.linalg.fiedler_companion`, respectively. These may be used for root finding. `scipy.ndimage` improvements - ---------------------------- Gaussian filter performances may improve by an order of magnitude in some cases, thanks to removal of a dependence on ``np.polynomial``. This may impact `scipy.ndimage.gaussian_filter` for example. `scipy.optimize` improvements - ----------------------------- The `scipy.optimize.brute` minimizer obtained a new keyword ``workers``, which can be used to parallelize computation. A Cython API for bounded scalar-function root-finders in `scipy.optimize` is available in a new module `scipy.optimize.cython_optimize` via ``cimport``. This API may be used with ``nogil`` and ``prange`` to loop over an array of function arguments to solve for an array of roots more quickly than with pure Python. ``'interior-point'`` is now the default method for ``linprog``, and ``'interior-point'`` now uses SuiteSparse for sparse problems when the required scikits (scikit-umfpack and scikit-sparse) are available. On benchmark problems (gh-10026), execution time reductions by factors of 2-3 were typical. Also, a new ``method='revised simplex'`` has been added. It is not as fast or robust as ``method='interior-point'``, but it is a faster, more robust, and equally accurate substitute for the legacy ``method='simplex'``. ``differential_evolution`` can now use a ``Bounds`` class to specify the bounds for the optimizing argument of a function. `scipy.optimize.dual_annealing` performance improvements related to vectorisation of some internal code. `scipy.signal` improvements - --------------------------- Two additional methods of discretization are now supported by `scipy.signal.cont2discrete`: ``impulse`` and ``foh``. `scipy.signal.firls` now uses faster solvers `scipy.signal.detrend` now has a lower physical memory footprint in some cases, which may be leveraged using the new ``overwrite_data`` keyword argument `scipy.signal.firwin` ``pass_zero`` argument now accepts new string arguments that allow specification of the desired filter type: ``'bandpass'``, ``'lowpass'``, ``'highpass'``, and ``'bandstop'`` `scipy.signal.sosfilt` may have improved performance due to lower retention of the global interpreter lock (GIL) in algorithm `scipy.sparse` improvements - --------------------------- A new keyword was added to ``csgraph.dijsktra`` that allows users to query the shortest path to ANY of the passed in indices, as opposed to the shortest path to EVERY passed index. `scipy.sparse.linalg.lsmr` performance has been improved by roughly 10 percent on large problems Improved performance and reduced physical memory footprint of the algorithm used by `scipy.sparse.linalg.lobpcg` ``CSR`` and ``CSC`` sparse matrix fancy indexing performance has been improved substantially `scipy.spatial` improvements - ---------------------------- `scipy.spatial.ConvexHull` now has a ``good`` attribute that can be used alongsize the ``QGn`` Qhull options to determine which external facets of a convex hull are visible from an external query point. `scipy.spatial.cKDTree.query_ball_point` has been modernized to use some newer Cython features, including GIL handling and exception translation. An issue with ``return_sorted=True`` and scalar queries was fixed, and a new mode named ``return_length`` was added. ``return_length`` only computes the length of the returned indices list instead of allocating the array every time. `scipy.spatial.transform.RotationSpline` has been added to enable interpolation of rotations with continuous angular rates and acceleration `scipy.stats` improvements - -------------------------- Added a new function to compute the Epps-Singleton test statistic, `scipy.stats.epps_singleton_2samp`, which can be applied to continuous and discrete distributions. New functions `scipy.stats.median_absolute_deviation` and `scipy.stats.gstd` (geometric standard deviation) were added. The `scipy.stats.combine_pvalues` method now supports ``pearson``, ``tippett`` and ``mudholkar_george`` pvalue combination methods. The `scipy.stats.ortho_group` and `scipy.stats.special_ortho_group` ``rvs(dim)`` functions' algorithms were updated from a ``O(dim^4)`` implementation to a ``O(dim^3)`` which gives large speed improvements for ``dim>100``. A rewrite of `scipy.stats.pearsonr` to use a more robust algorithm, provide meaningful exceptions and warnings on potentially pathological input, and fix at least five separate reported issues in the original implementation. Improved the precision of ``hypergeom.logcdf`` and ``hypergeom.logsf``. Added exact computation for Kolmogorov-Smirnov (KS) two-sample test, replacing the previously approximate computation for the two-sided test `stats.ks_2samp`. Also added a one-sided, two-sample KS test, and a keyword ``alternative`` to `stats.ks_2samp`. Backwards incompatible changes ============================== `scipy.interpolate` changes - --------------------------- Functions from ``scipy.interpolate`` (``spleval``, ``spline``, ``splmake``, and ``spltopp``) and functions from ``scipy.misc`` (``bytescale``, ``fromimage``, ``imfilter``, ``imread``, ``imresize``, ``imrotate``, ``imsave``, ``imshow``, ``toimage``) have been removed. The former set has been deprecated since v0.19.0 and the latter has been deprecated since v1.0.0. Similarly, aliases from ``scipy.misc`` (``comb``, ``factorial``, ``factorial2``, ``factorialk``, ``logsumexp``, ``pade``, ``info``, ``source``, ``who``) which have been deprecated since v1.0.0 are removed. `SciPy documentation for v1.1.0 <https://docs.scipy.org/doc/scipy-1.1.0/reference/misc.html>`__ can be used to track the new import locations for the relocated functions. `scipy.linalg` changes - ---------------------- For ``pinv``, ``pinv2``, and ``pinvh``, the default cutoff values are changed for consistency (see the docs for the actual values). `scipy.stats` changes - --------------------- Previously, ``ks_2samp(data1, data2)`` would run a two-sided test and return the approximated p-value. The new signature, ``ks_2samp(data1, data2, alternative="two-sided", method="auto")``, still runs the two-sided test by default but returns the exact p-value for small samples and the approximated value for large samples. ``method="asymp"`` would be equivalent to the old version but ``auto`` is the better choice. Other changes ============= Our tutorial has been expanded with a new section on global optimizers There has been a rework of the ``stats.distributions`` tutorials. `scipy.optimize` now correctly sets the convergence flag of the result to ``CONVERR``, a convergence error, for bounded scalar-function root-finders if the maximum iterations has been exceeded, ``disp`` is false, and ``full_output`` is true. `scipy.optimize.curve_fit` no longer fails if ``xdata`` and ``ydata`` dtypes differ; they are both now automatically cast to ``float64``. `scipy.ndimage` functions including ``binary_erosion``, ``binary_closing``, and ``binary_dilation`` now require an integer value for the number of iterations, which alleviates a number of reported issues. Fixed normal approximation in case ``zero_method == "pratt"`` in `scipy.stats.wilcoxon`. Fixes for incorrect probabilities, broadcasting issues and thread-safety related to stats distributions setting member variables inside ``_argcheck()``. `scipy.optimize.newton` now correctly raises a ``RuntimeError``, when default arguments are used, in the case that a derivative of value zero is obtained, which is a special case of failing to converge. A draft toolchain roadmap is now available, laying out a compatibility plan including Python versions, C standards, and NumPy versions. Authors ======= * ananyashreyjain + * ApamNapat + * Scott Calabrese Barton + * Christoph Baumgarten * Peter Bell + * Jacob Blomgren + * Doctor Bob + * Mana Borwornpadungkitti + * Matthew Brett * Evgeni Burovski * CJ Carey * Vega Theil Carstensen + * Robert Cimrman * Forrest Collman + * Pietro Cottone + * David + * Idan David + * Christoph Deil * Dieter Werthmüller * Conner DiPaolo + * Dowon * Michael Dunphy + * Peter Andreas Entschev + * Gökçen Eraslan + * Johann Faouzi + * Yu Feng * Piotr Figiel + * Matthew H Flamm * Franz Forstmayr + * Christoph Gohlke * Richard Janis Goldschmidt + * Ralf Gommers * Lars Grueter * Sylvain Gubian * Matt Haberland * Yaroslav Halchenko * Charles Harris * Lindsey Hiltner * JakobStruye + * He Jia + * Jwink3101 + * Greg Kiar + * Julius Bier Kirkegaard * John Kirkham + * Thomas Kluyver * Vladimir Korolev + * Joseph Kuo + * Michael Lamparski + * Eric Larson * Denis Laxalde * Katrin Leinweber * Jesse Livezey * ludcila + * Dhruv Madeka + * Magnus + * Nikolay Mayorov * Mark Mikofski * Jarrod Millman * Markus Mohrhard + * Eric Moore * Andrew Nelson * Aki Nishimura + * OGordon100 + * Petar Mlinarić + * Stefan Peterson * Matti Picus + * Ilhan Polat * Aaron Pries + * Matteo Ravasi + * Tyler Reddy * Ashton Reimer + * Joscha Reimer * rfezzani + * Riadh + * Lucas Roberts * Heshy Roskes + * Mirko Scholz + * Taylor D. Scott + * Srikrishna Sekhar + * Kevin Sheppard + * Sourav Singh * skjerns + * Kai Striega * SyedSaifAliAlvi + * Gopi Manohar T + * Albert Thomas + * Timon + * Paul van Mulbregt * Jacob Vanderplas * Daniel Vargas + * Pauli Virtanen * VNMabus + * Stefan van der Walt * Warren Weckesser * Josh Wilson * Nate Yoder + * Roman Yurchak A total of 97 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 1.3.0 - ----------------------- * `#1320 <https://github.com/scipy/scipy/issues/1320>`__: scipy.stats.distribution: problem with self.a, self.b if they... * `#2002 <https://github.com/scipy/scipy/issues/2002>`__: members set in scipy.stats.distributions.##._argcheck (Trac #1477) * `#2823 <https://github.com/scipy/scipy/issues/2823>`__: distribution methods add tmp * `#3220 <https://github.com/scipy/scipy/issues/3220>`__: Scipy.opimize.fmin_powell direc argument syntax unclear * `#3728 <https://github.com/scipy/scipy/issues/3728>`__: scipy.stats.pearsonr: possible bug with zero variance input * `#6805 <https://github.com/scipy/scipy/issues/6805>`__: error-in-scipy-wilcoxon-signed-rank-test-for-equal-series * `#6873 <https://github.com/scipy/scipy/issues/6873>`__: 'stats.boxcox' return all same values * `#7117 <https://github.com/scipy/scipy/issues/7117>`__: Warn users when using float32 input data to curve_fit and friends * `#7632 <https://github.com/scipy/scipy/issues/7632>`__: it's not possible to tell the \`optimize.least_squares\` solver... * `#7730 <https://github.com/scipy/scipy/issues/7730>`__: stats.pearsonr: Potential division by zero for dataset of length... * `#7933 <https://github.com/scipy/scipy/issues/7933>`__: stats.truncnorm fails when providing values outside truncation... * `#8033 <https://github.com/scipy/scipy/issues/8033>`__: Add standard filter types to firwin to set pass_zero intuitively... * `#8600 <https://github.com/scipy/scipy/issues/8600>`__: lfilter.c.src zfill has erroneous header * `#8692 <https://github.com/scipy/scipy/issues/8692>`__: Non-negative values of \`stats.hypergeom.logcdf\` * `#8734 <https://github.com/scipy/scipy/issues/8734>`__: Enable pip build isolation * `#8861 <https://github.com/scipy/scipy/issues/8861>`__: scipy.linalg.pinv gives wrong result while scipy.linalg.pinv2... * `#8915 <https://github.com/scipy/scipy/issues/8915>`__: need to fix macOS build against older numpy versions * `#8980 <https://github.com/scipy/scipy/issues/8980>`__: scipy.stats.pearsonr overflows with high values of x and y * `#9226 <https://github.com/scipy/scipy/issues/9226>`__: BUG: signal: SystemError: <built-in function _linear_filter>... * `#9254 <https://github.com/scipy/scipy/issues/9254>`__: BUG: root finders brentq, etc, flag says "converged" even if... * `#9308 <https://github.com/scipy/scipy/issues/9308>`__: Test failure - test_initial_constraints_as_canonical * `#9353 <https://github.com/scipy/scipy/issues/9353>`__: scipy.stats.pearsonr returns r=1 if r_num/r_den = inf * `#9359 <https://github.com/scipy/scipy/issues/9359>`__: Planck distribution is a geometric distribution * `#9381 <https://github.com/scipy/scipy/issues/9381>`__: linregress should warn user in 2x2 array case * `#9406 <https://github.com/scipy/scipy/issues/9406>`__: BUG: stats: In pearsonr, when r is nan, the p-value must also... * `#9437 <https://github.com/scipy/scipy/issues/9437>`__: Cannot create sparse matrix from size_t indexes * `#9518 <https://github.com/scipy/scipy/issues/9518>`__: Relational attributes in loadarff * `#9551 <https://github.com/scipy/scipy/issues/9551>`__: BUG: scipy.optimize.newton says the root of x^2+1 is zero. * `#9564 <https://github.com/scipy/scipy/issues/9564>`__: rv_sample accepts invalid input in scipy.stats * `#9565 <https://github.com/scipy/scipy/issues/9565>`__: improper handling of multidimensional input in stats.rv_sample * `#9581 <https://github.com/scipy/scipy/issues/9581>`__: Least-squares minimization fails silently when x and y data are... * `#9587 <https://github.com/scipy/scipy/issues/9587>`__: Outdated value for scipy.constants.au * `#9611 <https://github.com/scipy/scipy/issues/9611>`__: Overflow error with new way of p-value calculation in kendall... * `#9645 <https://github.com/scipy/scipy/issues/9645>`__: \`scipy.stats.mode\` crashes with variable length arrays (\`dtype=object\`) * `#9734 <https://github.com/scipy/scipy/issues/9734>`__: PendingDeprecationWarning for np.matrix with pytest * `#9786 <https://github.com/scipy/scipy/issues/9786>`__: stats.ks_2samp() misleading for small data sets. * `#9790 <https://github.com/scipy/scipy/issues/9790>`__: Excessive memory usage on detrend * `#9801 <https://github.com/scipy/scipy/issues/9801>`__: dual_annealing does not set the success attribute in OptimizeResult * `#9833 <https://github.com/scipy/scipy/issues/9833>`__: IntegrationWarning from mielke.stats() during build of html doc. * `#9835 <https://github.com/scipy/scipy/issues/9835>`__: scipy.signal.firls seems to be inefficient versus MATLAB firls * `#9864 <https://github.com/scipy/scipy/issues/9864>`__: Curve_fit does not check for empty input data if called with... * `#9869 <https://github.com/scipy/scipy/issues/9869>`__: scipy.ndimage.label: Minor documentation issue * `#9882 <https://github.com/scipy/scipy/issues/9882>`__: format at the wrong paranthesis in scipy.spatial.transform * `#9889 <https://github.com/scipy/scipy/issues/9889>`__: scipy.signal.find_peaks minor documentation issue * `#9890 <https://github.com/scipy/scipy/issues/9890>`__: Minkowski p-norm Issues in cKDTree For Values Other Than 2 Or... * `#9896 <https://github.com/scipy/scipy/issues/9896>`__: scipy.stats._argcheck sets (not just checks) values * `#9905 <https://github.com/scipy/scipy/issues/9905>`__: Memory error in ndimage.binary_erosion * `#9909 <https://github.com/scipy/scipy/issues/9909>`__: binary_dilation/erosion/closing crashes when iterations is float * `#9919 <https://github.com/scipy/scipy/issues/9919>`__: BUG: \`coo_matrix\` does not validate the \`shape\` argument. * `#9982 <https://github.com/scipy/scipy/issues/9982>`__: lsq_linear hangs/infinite loop with 'trf' method * `#10003 <https://github.com/scipy/scipy/issues/10003>`__: exponnorm.pdf returns NAN for small K * `#10011 <https://github.com/scipy/scipy/issues/10011>`__: Incorrect check for invalid rotation plane in scipy.ndimage.rotate * `#10024 <https://github.com/scipy/scipy/issues/10024>`__: Fails to build from git * `#10048 <https://github.com/scipy/scipy/issues/10048>`__: DOC: scipy.optimize.root_scalar * `#10068 <https://github.com/scipy/scipy/issues/10068>`__: DOC: scipy.interpolate.splev * `#10074 <https://github.com/scipy/scipy/issues/10074>`__: BUG: \`expm\` calculates the wrong coefficients in the backward... Pull requests for 1.3.0 - ----------------------- * `#7827 <https://github.com/scipy/scipy/pull/7827>`__: ENH: sparse: overhaul of sparse matrix indexing * `#8431 <https://github.com/scipy/scipy/pull/8431>`__: ENH: Cython optimize zeros api * `#8743 <https://github.com/scipy/scipy/pull/8743>`__: DOC: Updated linalg.pinv, .pinv2, .pinvh docstrings * `#8744 <https://github.com/scipy/scipy/pull/8744>`__: DOC: added examples to remez docstring * `#9227 <https://github.com/scipy/scipy/pull/9227>`__: DOC: update description of "direc" parameter of "fmin_powell" * `#9263 <https://github.com/scipy/scipy/pull/9263>`__: ENH: optimize: added "revised simplex" for scipy.optimize.linprog * `#9325 <https://github.com/scipy/scipy/pull/9325>`__: DEP: Remove deprecated functions for 1.3.0 * `#9330 <https://github.com/scipy/scipy/pull/9330>`__: Add note on push and pull affine transformations * `#9423 <https://github.com/scipy/scipy/pull/9423>`__: DOC: Clearly state how 2x2 input arrays are handled in stats.linregress * `#9428 <https://github.com/scipy/scipy/pull/9428>`__: ENH: parallelised brute * `#9438 <https://github.com/scipy/scipy/pull/9438>`__: BUG: Initialize coo matrix with size_t indexes * `#9455 <https://github.com/scipy/scipy/pull/9455>`__: MAINT: Speed up get_(lapack,blas)_func * `#9465 <https://github.com/scipy/scipy/pull/9465>`__: MAINT: Clean up optimize.zeros C solvers interfaces/code. * `#9477 <https://github.com/scipy/scipy/pull/9477>`__: DOC: linalg: fix lstsq docstring on residues shape * `#9478 <https://github.com/scipy/scipy/pull/9478>`__: DOC: Add docstring examples for rosen functions * `#9479 <https://github.com/scipy/scipy/pull/9479>`__: DOC: Add docstring example for ai_zeros and bi_zeros * `#9480 <https://github.com/scipy/scipy/pull/9480>`__: MAINT: linalg: lstsq clean up * `#9489 <https://github.com/scipy/scipy/pull/9489>`__: DOC: roadmap update for changes over the last year. * `#9492 <https://github.com/scipy/scipy/pull/9492>`__: MAINT: stats: Improve implementation of chi2 ppf method. * `#9497 <https://github.com/scipy/scipy/pull/9497>`__: DOC: Improve docstrings sparse.linalg.isolve * `#9499 <https://github.com/scipy/scipy/pull/9499>`__: DOC: Replace "Scipy" with "SciPy" in the .rst doc files for consistency. * `#9500 <https://github.com/scipy/scipy/pull/9500>`__: DOC: Document the toolchain and its roadmap. * `#9505 <https://github.com/scipy/scipy/pull/9505>`__: DOC: specify which definition of skewness is used * `#9511 <https://github.com/scipy/scipy/pull/9511>`__: DEP: interpolate: remove deprecated interpolate_wrapper * `#9517 <https://github.com/scipy/scipy/pull/9517>`__: BUG: improve error handling in stats.iqr * `#9522 <https://github.com/scipy/scipy/pull/9522>`__: ENH: Add Fiedler and fiedler companion to special matrices * `#9526 <https://github.com/scipy/scipy/pull/9526>`__: TST: relax precision requirements in signal.correlate tests * `#9529 <https://github.com/scipy/scipy/pull/9529>`__: DOC: fix missing random seed in optimize.newton example * `#9533 <https://github.com/scipy/scipy/pull/9533>`__: MAINT: Use list comprehension when possible * `#9537 <https://github.com/scipy/scipy/pull/9537>`__: DOC: add a "big picture" roadmap * `#9538 <https://github.com/scipy/scipy/pull/9538>`__: DOC: Replace "Numpy" with "NumPy" in .py, .rst and .txt doc files... * `#9539 <https://github.com/scipy/scipy/pull/9539>`__: ENH: add two-sample test (Epps-Singleton) to scipy.stats * `#9559 <https://github.com/scipy/scipy/pull/9559>`__: DOC: add section on global optimizers to tutorial * `#9561 <https://github.com/scipy/scipy/pull/9561>`__: ENH: remove noprefix.h, change code appropriately * `#9562 <https://github.com/scipy/scipy/pull/9562>`__: MAINT: stats: Rewrite pearsonr. * `#9563 <https://github.com/scipy/scipy/pull/9563>`__: BUG: Minor bug fix Callback in linprog(method='simplex') * `#9568 <https://github.com/scipy/scipy/pull/9568>`__: MAINT: raise runtime error for newton with zeroder if disp true,... * `#9570 <https://github.com/scipy/scipy/pull/9570>`__: Correct docstring in show_options in optimize. Fixes #9407 * `#9573 <https://github.com/scipy/scipy/pull/9573>`__: BUG fixes range of pk variable pre-check * `#9577 <https://github.com/scipy/scipy/pull/9577>`__: TST: fix minor issue in a signal.stft test. * `#9580 <https://github.com/scipy/scipy/pull/9580>`__: Included blank line before list - Fixes #8658 * `#9582 <https://github.com/scipy/scipy/pull/9582>`__: MAINT: drop Python 2.7 and 3.4 * `#9588 <https://github.com/scipy/scipy/pull/9588>`__: MAINT: update \`constants.astronomical_unit\` to new 2012 value. * `#9592 <https://github.com/scipy/scipy/pull/9592>`__: TST: Add 32-bit testing to CI * `#9593 <https://github.com/scipy/scipy/pull/9593>`__: DOC: Replace cumulative density with cumulative distribution * `#9596 <https://github.com/scipy/scipy/pull/9596>`__: TST: remove VC 9.0 from Azure CI * `#9599 <https://github.com/scipy/scipy/pull/9599>`__: Hyperlink DOI to preferred resolver * `#9601 <https://github.com/scipy/scipy/pull/9601>`__: DEV: try to limit GC memory use on PyPy * `#9603 <https://github.com/scipy/scipy/pull/9603>`__: MAINT: improve logcdf and logsf of hypergeometric distribution * `#9605 <https://github.com/scipy/scipy/pull/9605>`__: Reference to pylops in LinearOperator notes and ARPACK example * `#9617 <https://github.com/scipy/scipy/pull/9617>`__: TST: reduce max memory usage for sparse.linalg.lgmres test * `#9619 <https://github.com/scipy/scipy/pull/9619>`__: FIX: Sparse matrix addition/subtraction eliminates explicit zeros * `#9621 <https://github.com/scipy/scipy/pull/9621>`__: bugfix in rv_sample in scipy.stats * `#9622 <https://github.com/scipy/scipy/pull/9622>`__: MAINT: Raise error in directed_hausdorff distance * `#9623 <https://github.com/scipy/scipy/pull/9623>`__: DOC: Build docs with warnings as errors * `#9625 <https://github.com/scipy/scipy/pull/9625>`__: Return the number of calls to 'hessp' (not just 'hess') in trust... * `#9627 <https://github.com/scipy/scipy/pull/9627>`__: BUG: ignore empty lines in mmio * `#9637 <https://github.com/scipy/scipy/pull/9637>`__: Function to calculate the MAD of an array * `#9646 <https://github.com/scipy/scipy/pull/9646>`__: BUG: stats: mode for objects w/ndim > 1 * `#9648 <https://github.com/scipy/scipy/pull/9648>`__: Add \`stats.contingency\` to refguide-check * `#9650 <https://github.com/scipy/scipy/pull/9650>`__: ENH: many lobpcg() algorithm improvements * `#9652 <https://github.com/scipy/scipy/pull/9652>`__: Move misc.doccer to _lib.doccer * `#9660 <https://github.com/scipy/scipy/pull/9660>`__: ENH: add pearson, tippett, and mudholkar-george to combine_pvalues * `#9661 <https://github.com/scipy/scipy/pull/9661>`__: BUG: Fix ksone right-hand endpoint, documentation and tests. * `#9664 <https://github.com/scipy/scipy/pull/9664>`__: ENH: adding multi-target dijsktra performance enhancement * `#9670 <https://github.com/scipy/scipy/pull/9670>`__: MAINT: link planck and geometric distribution in scipy.stats * `#9676 <https://github.com/scipy/scipy/pull/9676>`__: ENH: optimize: change default linprog method to interior-point * `#9685 <https://github.com/scipy/scipy/pull/9685>`__: Added reference to ndimage.filters.median_filter * `#9705 <https://github.com/scipy/scipy/pull/9705>`__: Fix coefficients in expm helper function * `#9711 <https://github.com/scipy/scipy/pull/9711>`__: Release the GIL during sosfilt processing for simple types * `#9721 <https://github.com/scipy/scipy/pull/9721>`__: ENH: Convexhull visiblefacets * `#9723 <https://github.com/scipy/scipy/pull/9723>`__: BLD: Modify rv_generic._construct_doc to print out failing distribution... * `#9726 <https://github.com/scipy/scipy/pull/9726>`__: BUG: Fix small issues with \`signal.lfilter' * `#9729 <https://github.com/scipy/scipy/pull/9729>`__: BUG: Typecheck iterations for binary image operations * `#9730 <https://github.com/scipy/scipy/pull/9730>`__: ENH: reduce sizeof(NI_WatershedElement) by 20% * `#9731 <https://github.com/scipy/scipy/pull/9731>`__: ENH: remove suspicious sequence of type castings * `#9739 <https://github.com/scipy/scipy/pull/9739>`__: BUG: qr_updates fails if u is exactly in span Q * `#9749 <https://github.com/scipy/scipy/pull/9749>`__: BUG: MapWrapper.__exit__ should terminate * `#9753 <https://github.com/scipy/scipy/pull/9753>`__: ENH: Added exact computation for Kolmogorov-Smirnov two-sample... * `#9755 <https://github.com/scipy/scipy/pull/9755>`__: DOC: Added example for signal.impulse, copied from impulse2 * `#9756 <https://github.com/scipy/scipy/pull/9756>`__: DOC: Added docstring example for iirdesign * `#9757 <https://github.com/scipy/scipy/pull/9757>`__: DOC: Added examples for step functions * `#9759 <https://github.com/scipy/scipy/pull/9759>`__: ENH: Allow pass_zero to act like btype * `#9760 <https://github.com/scipy/scipy/pull/9760>`__: DOC: Added docstring for lp2bs * `#9761 <https://github.com/scipy/scipy/pull/9761>`__: DOC: Added docstring and example for lp2bp * `#9764 <https://github.com/scipy/scipy/pull/9764>`__: BUG: Catch internal warnings for matrix * `#9766 <https://github.com/scipy/scipy/pull/9766>`__: ENH: Speed up _gaussian_kernel1d by removing dependence on np.polynomial * `#9769 <https://github.com/scipy/scipy/pull/9769>`__: BUG: Fix Cubic Spline Read Only issues * `#9773 <https://github.com/scipy/scipy/pull/9773>`__: DOC: Several docstrings * `#9774 <https://github.com/scipy/scipy/pull/9774>`__: TST: bump Azure CI OpenBLAS version to match wheels * `#9775 <https://github.com/scipy/scipy/pull/9775>`__: DOC: Improve clarity of cov_x documentation for scipy.optimize.leastsq * `#9779 <https://github.com/scipy/scipy/pull/9779>`__: ENH: dual_annealing vectorise visit_fn * `#9788 <https://github.com/scipy/scipy/pull/9788>`__: TST, BUG: f2py-related issues with NumPy < 1.14.0 * `#9791 <https://github.com/scipy/scipy/pull/9791>`__: BUG: fix amax constraint not enforced in scalar_search_wolfe2 * `#9792 <https://github.com/scipy/scipy/pull/9792>`__: ENH: Allow inplace copying in place in "detrend" function * `#9795 <https://github.com/scipy/scipy/pull/9795>`__: DOC: Fix/update docstring for dstn and dst * `#9796 <https://github.com/scipy/scipy/pull/9796>`__: MAINT: Allow None tolerances in least_squares * `#9798 <https://github.com/scipy/scipy/pull/9798>`__: BUG: fixes abort trap 6 error in scipy issue 9785 in unit tests * `#9807 <https://github.com/scipy/scipy/pull/9807>`__: MAINT: improve doc and add alternative keyword to wilcoxon in... * `#9808 <https://github.com/scipy/scipy/pull/9808>`__: Fix PPoly integrate and test for CubicSpline * `#9810 <https://github.com/scipy/scipy/pull/9810>`__: ENH: Add the geometric standard deviation function * `#9811 <https://github.com/scipy/scipy/pull/9811>`__: MAINT: remove invalid derphi default None value in scalar_search_wolfe2 * `#9813 <https://github.com/scipy/scipy/pull/9813>`__: Adapt hamming distance in C to support weights * `#9817 <https://github.com/scipy/scipy/pull/9817>`__: DOC: Copy solver description to solver modules * `#9829 <https://github.com/scipy/scipy/pull/9829>`__: ENH: Add FOH and equivalent impulse response discretizations... * `#9831 <https://github.com/scipy/scipy/pull/9831>`__: ENH: Implement RotationSpline * `#9834 <https://github.com/scipy/scipy/pull/9834>`__: DOC: Change mielke distribution default parameters to ensure... * `#9838 <https://github.com/scipy/scipy/pull/9838>`__: ENH: Use faster solvers for firls * `#9854 <https://github.com/scipy/scipy/pull/9854>`__: ENH: loadarff now supports relational attributes. * `#9856 <https://github.com/scipy/scipy/pull/9856>`__: integrate.bvp - improve handling of nonlinear boundary conditions * `#9862 <https://github.com/scipy/scipy/pull/9862>`__: TST: reduce Appveyor CI load * `#9874 <https://github.com/scipy/scipy/pull/9874>`__: DOC: Update requirements in release notes * `#9883 <https://github.com/scipy/scipy/pull/9883>`__: BUG: fixed parenthesis in spatial.rotation * `#9884 <https://github.com/scipy/scipy/pull/9884>`__: ENH: Use Sparsity in Clarkson-Woodruff Sketch * `#9888 <https://github.com/scipy/scipy/pull/9888>`__: MAINT: Replace NumPy aliased functions * `#9892 <https://github.com/scipy/scipy/pull/9892>`__: BUG: Fix 9890 query_ball_point returns wrong result when p is... * `#9893 <https://github.com/scipy/scipy/pull/9893>`__: BUG: curve_fit doesn't check for empty input if called with bounds * `#9894 <https://github.com/scipy/scipy/pull/9894>`__: scipy.signal.find_peaks documentation error * `#9898 <https://github.com/scipy/scipy/pull/9898>`__: BUG: Set success attribute in OptimizeResult. See #9801 * `#9900 <https://github.com/scipy/scipy/pull/9900>`__: BUG: Restrict rv_generic._argcheck() and its overrides from setting... * `#9906 <https://github.com/scipy/scipy/pull/9906>`__: fixed a bug in kde logpdf * `#9911 <https://github.com/scipy/scipy/pull/9911>`__: DOC: replace example for "np.select" with the one from numpy... * `#9912 <https://github.com/scipy/scipy/pull/9912>`__: BF(DOC): point to numpy.select instead of plain (python) .select * `#9914 <https://github.com/scipy/scipy/pull/9914>`__: DOC: change ValueError message in _validate_pad of signaltools. * `#9915 <https://github.com/scipy/scipy/pull/9915>`__: cKDTree query_ball_point improvements * `#9918 <https://github.com/scipy/scipy/pull/9918>`__: Update ckdtree.pyx with boxsize argument in docstring * `#9920 <https://github.com/scipy/scipy/pull/9920>`__: BUG: sparse: Validate explicit shape if given with dense argument... * `#9924 <https://github.com/scipy/scipy/pull/9924>`__: BLD: add back pyproject.toml * `#9931 <https://github.com/scipy/scipy/pull/9931>`__: Fix empty constraint * `#9935 <https://github.com/scipy/scipy/pull/9935>`__: DOC: fix references for stats.f_oneway * `#9936 <https://github.com/scipy/scipy/pull/9936>`__: Revert gh-9619: "FIX: Sparse matrix addition/subtraction eliminates... * `#9937 <https://github.com/scipy/scipy/pull/9937>`__: MAINT: fix PEP8 issues and update to pycodestyle 2.5.0 * `#9939 <https://github.com/scipy/scipy/pull/9939>`__: DOC: correct \`structure\` description in \`ndimage.label\` docstring * `#9940 <https://github.com/scipy/scipy/pull/9940>`__: MAINT: remove extraneous distutils copies * `#9945 <https://github.com/scipy/scipy/pull/9945>`__: ENH: differential_evolution can use Bounds object * `#9949 <https://github.com/scipy/scipy/pull/9949>`__: Added 'std' to add doctstrings since it is a \`known_stats\`... * `#9953 <https://github.com/scipy/scipy/pull/9953>`__: DOC: Documentation cleanup for stats tutorials. * `#9962 <https://github.com/scipy/scipy/pull/9962>`__: __repr__ for Bounds * `#9971 <https://github.com/scipy/scipy/pull/9971>`__: ENH: Improve performance of lsmr * `#9987 <https://github.com/scipy/scipy/pull/9987>`__: CI: pin Sphinx version to 1.8.5 * `#9990 <https://github.com/scipy/scipy/pull/9990>`__: ENH: constraint violation * `#9991 <https://github.com/scipy/scipy/pull/9991>`__: BUG: Avoid inplace modification of input array in newton * `#9995 <https://github.com/scipy/scipy/pull/9995>`__: MAINT: sparse.csgraph: Add cdef to stop build warning. * `#9996 <https://github.com/scipy/scipy/pull/9996>`__: BUG: Make minimize_quadratic_1d work with infinite bounds correctly * `#10004 <https://github.com/scipy/scipy/pull/10004>`__: BUG: Fix unbound local error in linprog - simplex. * `#10007 <https://github.com/scipy/scipy/pull/10007>`__: BLD: fix Python 3.7 build with build isolation * `#10009 <https://github.com/scipy/scipy/pull/10009>`__: BUG: Make sure that _binary_erosion only accepts an integer number... * `#10016 <https://github.com/scipy/scipy/pull/10016>`__: Update link to airspeed-velocity * `#10017 <https://github.com/scipy/scipy/pull/10017>`__: DOC: Update \`interpolate.LSQSphereBivariateSpline\` to include... * `#10018 <https://github.com/scipy/scipy/pull/10018>`__: MAINT: special: Fix a few warnings that occur when compiling... * `#10019 <https://github.com/scipy/scipy/pull/10019>`__: TST: Azure summarizes test failures * `#10021 <https://github.com/scipy/scipy/pull/10021>`__: ENH: Introduce CubicHermiteSpline * `#10022 <https://github.com/scipy/scipy/pull/10022>`__: BENCH: Increase cython version in asv to fix benchmark builds * `#10023 <https://github.com/scipy/scipy/pull/10023>`__: BUG: Avoid exponnorm producing nan for small K values. * `#10025 <https://github.com/scipy/scipy/pull/10025>`__: BUG: optimize: tweaked linprog status 4 error message * `#10026 <https://github.com/scipy/scipy/pull/10026>`__: ENH: optimize: use SuiteSparse in linprog interior-point when... * `#10027 <https://github.com/scipy/scipy/pull/10027>`__: MAINT: cluster: clean up the use of malloc() in the function... * `#10028 <https://github.com/scipy/scipy/pull/10028>`__: Fix rotate invalid plane check * `#10040 <https://github.com/scipy/scipy/pull/10040>`__: MAINT: fix pratt method of wilcox test in scipy.stats * `#10041 <https://github.com/scipy/scipy/pull/10041>`__: MAINT: special: Fix a warning generated when building the AMOS... * `#10044 <https://github.com/scipy/scipy/pull/10044>`__: DOC: fix up spatial.transform.Rotation docstrings * `#10047 <https://github.com/scipy/scipy/pull/10047>`__: MAINT: interpolate: Fix a few build warnings. * `#10051 <https://github.com/scipy/scipy/pull/10051>`__: Add project_urls to setup * `#10052 <https://github.com/scipy/scipy/pull/10052>`__: don't set flag to "converged" if max iter exceeded * `#10054 <https://github.com/scipy/scipy/pull/10054>`__: MAINT: signal: Fix a few build warnings and modernize some C... * `#10056 <https://github.com/scipy/scipy/pull/10056>`__: BUG: Ensure factorial is not too large in kendaltau * `#10058 <https://github.com/scipy/scipy/pull/10058>`__: Small speedup in samping from ortho and special_ortho groups * `#10059 <https://github.com/scipy/scipy/pull/10059>`__: BUG: optimize: fix #10038 by increasing tol * `#10061 <https://github.com/scipy/scipy/pull/10061>`__: BLD: DOC: make building docs easier by parsing python version. * `#10064 <https://github.com/scipy/scipy/pull/10064>`__: ENH: Significant speedup for ortho and special ortho group * `#10065 <https://github.com/scipy/scipy/pull/10065>`__: DOC: Reword parameter descriptions in \`optimize.root_scalar\` * `#10066 <https://github.com/scipy/scipy/pull/10066>`__: BUG: signal: Fix error raised by savgol_coeffs when deriv > polyorder. * `#10067 <https://github.com/scipy/scipy/pull/10067>`__: MAINT: Fix the cutoff value inconsistency for pinv2 and pinvh * `#10072 <https://github.com/scipy/scipy/pull/10072>`__: BUG: stats: Fix boxcox_llf to avoid loss of precision. * `#10075 <https://github.com/scipy/scipy/pull/10075>`__: ENH: Add wrappers for ?syconv routines * `#10076 <https://github.com/scipy/scipy/pull/10076>`__: BUG: optimize: fix curve_fit for mixed float32/float64 input * `#10077 <https://github.com/scipy/scipy/pull/10077>`__: DOC: Replace undefined \`k\` in \`interpolate.splev\` docstring * `#10079 <https://github.com/scipy/scipy/pull/10079>`__: DOC: Fixed typo, rearranged some doc of stats.morestats.wilcoxon. * `#10080 <https://github.com/scipy/scipy/pull/10080>`__: TST: install scikit-sparse for full TravisCI tests * `#10083 <https://github.com/scipy/scipy/pull/10083>`__: Clean \`\`_clean_inputs\`\` in optimize.linprog * `#10088 <https://github.com/scipy/scipy/pull/10088>`__: ENH: optimize: linprog test CHOLMOD/UMFPACK solvers when available * `#10090 <https://github.com/scipy/scipy/pull/10090>`__: MAINT: Fix CubicSplinerInterpolator for pandas * `#10091 <https://github.com/scipy/scipy/pull/10091>`__: MAINT: improve logcdf and logsf of hypergeometric distribution * `#10095 <https://github.com/scipy/scipy/pull/10095>`__: MAINT: Clean \`\`_clean_inputs\`\` in linprog * `#10116 <https://github.com/scipy/scipy/pull/10116>`__: MAINT: update scipy-sphinx-theme * `#10135 <https://github.com/scipy/scipy/pull/10135>`__: BUG: fix linprog revised simplex docstring problem failure Checksums ========= MD5 ~~~ 11305bc9940ca76568a1c7e46ea0ff05 scipy-1.3.0rc2-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 7cef904e09aff64d5207064bb61e1a6b scipy-1.3.0rc2-cp35-cp35m-manylinux1_i686.whl 63ba156855e33b971dc94206ecbdd7f3 scipy-1.3.0rc2-cp35-cp35m-manylinux1_x86_64.whl 00e48cb29dbb88e56730a59285c463ec scipy-1.3.0rc2-cp35-cp35m-win32.whl 232eb3104f19d1559e30e749a92707cd scipy-1.3.0rc2-cp35-cp35m-win_amd64.whl 559b152a8b438825ba0352a3303e2651 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1 0

Style guide for numpy code?
by Chris Barker May 9, 2019

May 9, 2019

Hey all, Do any of you know of a style guide for computational / numpy code? I don't mean code that will go into numpy itself, but rather, users code that uses numpy (and scipy, and...) I know about (am a proponent -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

2 1

Preparation for 1.17.x branch
by Charles R Harris May 8, 2019

May 8, 2019

Hi All, It's time to look forward to branching 1.17.x and the first rc. Please note of any issues that you think fixing or PRs that should be merged before the first release. It would also help if some folks would review the release notes for completeness. I figure the branch should take place in a week or so. Chuck

3 3

NumPy Community Meeting May 8/ 2019
by Tyler Reddy May 7, 2019

May 7, 2019

Hi, There will be a NumPy Community meeting at 12 pm Pacific Time on May 8/ 2019. Anyone is welcome to join and edit the work in progress meeting document: https://hackmd.io/M-ef_Fu5QOOitACnyoO0kQ?view Best wishes, Tyler

1 0

Contributing: NumPy Documentation
by Bhanu Bhandari May 7, 2019

May 7, 2019

Hello, I’m Bhanu, a third year student of Electronics and Computers Engineering. I’d like to get started with contributing into the NumPy documentation. I’m a writer who is actively machine learning research as well, and have used NumPy extensively for my coding assignments and research work. Thanks, Bhanu Bhandari

2 1

GSoD'19 project discussion
by Oishika Pradhan May 6, 2019

May 6, 2019

Hi, I am Oishika Pradhan, a research student at IIIT Hyderabad, India. I am interested in machine learning and neural networks and hence have used numpy very regularly in my projects and assignments. This is why I'm interested in becoming a contributor to this organization. I have some prior experience in technical documentation. I am interested in working on the following project: Improving the structure and content of https://numpy.org/ Please provide pointers on how to get started with this project. Thanks, Oishika Pradhan

2 1

type and kind for custom dtypes
by Alex Samuel May 6, 2019

May 6, 2019

Hi, I'm working on building a number of related custom dtypes, and I'm not sure how to set the type and kind fields in PyArray_Descr. I tried using type='V' and choosing a single unused kind for all my dtypes; this mostly worked, except I found that coercions would sometimes treat values of two different dtypes as if they were the same. But not always... sometimes my registered cast functions would be called. Through trial and error, I've found that if I choose an unused type code for each dtype, coercion seems to work as I expect it to (no coercion unless I've provided a cast). The kind doesn't seem to matter. I couldn't find any guidance in the docs for how to choose these values. Apologies if I've overlooked something. Could someone please advise me? More widely, is there some global registry of these codes? Is the number of NumPy dtypes limited to the number of (UTF-8-encodable) chars? It seems like common practice to use dtype.kind in user code. If I use one or more for my custom dtypes, is there any mechanism to ensure they do not collide with others'? Are there any other semantics for either field I should take into account? Thanks, Alex

2 5

Re: [Numpy-discussion] grant proposal for core scientific Python projects (rejected)
by Chris Barker - NOAA Federal May 5, 2019

May 5, 2019

Thanks for the update — this is great stuff! -CHB On May 3, 2019, at 3:13 PM, Joe Harrington <jh(a)physics.ucf.edu> wrote: Just to keep people in the loop, Ralf and I are in discussion with people at NASA HQ about a funding stream for core development.ï¿½ Ralf has put together a short description of the development and funding model (5 core projects, 10-20 core developers each, nearly all volunteer now, how NumFOCUS fits in, what we hope to establish from NASA vs. from other agencies, industry, other countries' science entities, etc.).ï¿½ That will circulate within the agency, to see what can be scraped together.ï¿½ Program managers in NASA's Science Mission Directorate (SMD) gave quite-positive feedback on how vital the Python ecosystem is to NASA's mission.ï¿½ We're emphasizing the need for both new functionality and maintenance (e.g., docs, web site, bug fixing).ï¿½ If this is ultimately successful, it can be a model for approaching other agencies in the US and elsewhere. To Steve's point, regarding how hard it is for Civil Servants to contribute to OSS (due to NASA's lengthy internal review process for releasing software), this problem was clearly called out in the Academies report.ï¿½ We proposed some solutions to streamline things.ï¿½ What's needed now is for NASA Civil Servants to take that report and the relevant white papers (cited in the report and posted online) to their center's senior management, and to NASA HQ, and similarly for others in government agencies.ï¿½ You may wish to start from NASA's (or your agency's) mission, which includes sharing technology openly to boost the economy, and how you are encountering unreasonable barriers to that goal.ï¿½ This is mandated by the National Air and Space Act of 1958. For example, there is little reason to conduct an export-control review with lawyers looking at code emerging from a group that has nothing to do with anything near an export-controlled topic.ï¿½ Universities and contractors are subject to the same export-control laws as NASA, and they have not routinely conducted similar reviews of every line of code released.ï¿½ This has not led to a pattern of export violations.ï¿½ (Whether there is any benefit at all to the export control laws as applied to software is debatable, since it's usually easy for coders elsewhere to write the same codes, but the law is the law.) --jh-- On 5/3/19 12:48 PM, numpy-discussion-request(a)python.org wrote: Subject: Re: [Numpy-discussion] grant proposal for core scientific Python projects (rejected) From: Mark Mikofski <mikofski(a)berkeley.edu> <mikofski(a)berkeley.edu> Date: 5/3/19, 12:47 PM To: Discussion of Numerical Python <numpy-discussion(a)python.org> <numpy-discussion(a)python.org> Sorry, that last attachment was just a slide show of the topic 3 recording, here is the full funding opportunity announcement - letter with 200 word abstract are due May 7th On Fri, May 3, 2019 at 8:40 AM Mark Mikofski <mikofski(a)berkeley.edu> wrote: > Hi Ralf, and others, > > Sorry for the late notice, but there is are several funding opportunities > in solar, including one for $350,000 to develop open source software to > lower soft costs of solar. > https://eere-exchange.energy.gov/#FoaId45eda43a-e826-4481-ae7a-cc6e8ed4fdae > ï¿½ > see topic 3.4 specifically in attached PDF - also note to view the > recording the password is "*Setofoa2019"*ï¿½it's about 30 minutes long. > > I know that this is a extremely niche, but as a few others have said, [the > DOE] grants tend to be very specific, but perhaps we can creatively think > of ways to channel funds to NumPy and SciPy. > > Also there is a cost share that is typically 20%, which would be a > non-starter for volunteer projects. > > But here's an idea, perhaps partnering with a company, like mine (DNV GL) > who is applying for the grant, and who uses NumPy,and could pay the cost > share, and then we collaborate on something that is required to complete > theï¿½project, which is contributed to NumPy (or SciPy) - but we would have > to figure what we could align on. > > Seems like NumFOCUS, Quantsight, or some other company in the OSS space > could figure out ways to help connect companies, OSS projects, and funding > opportunities like these, where there's a possibility of alignment and > mutual benefit? > > The full list of funding opportunities is here: > https://eere-exchange.energy.gov/ï¿½ > > Best Regards, > Markï¿½ > ï¿½ > > On Thu, May 2, 2019 at 11:52 PM Ralf Gommers <ralf.gommers(a)gmail.com> > wrote: > >> >> >> On Fri, May 3, 2019 at 3:49 AM Stephen Waterbury <waterbug(a)pangalactic.us> >> wrote: >> >>> P.S.ï¿½ If anyone wants to continue this discussion at SciPy 2019, >>> I will be there (on my own nickel!ï¿½ ;) ... >>> >> >> Thanks for the input Stephen, and looking forward to see you at SciPy'19! >> >> Ralf >> >> >> Steve >>> >>> On 5/2/19 9:45 PM, Stephen Waterbury wrote: >>> >>> I am a NASA pythonista (for 20+ years ;), but you can now say you know >>> yet another person at NASA who has no idea this even exists ... :) >>> Not only do I not know of that, but I know of NASA policies that make >>> it very difficult for NASA civil servants to contribute to open source >>> projects -- quite hypocritical, given the amount of open source >>> code that NASA (like all other large organizations) depends critically >>> on, but it's a fact. >>> >>> Cheers, >>> Steve Waterbury >>> >>> (CLEARLY **NOT** SPEAKING IN ANY OFFICIAL CAPACITY FOR NASA OR >>> THE U.S. GOVERNMENT AS A WHOLE!ï¿½ Hence the personal email >>> address. :) >>> >>> On 5/2/19 9:31 PM, Chris Barker - NOAA Federal wrote: >>> >>> Sounds like this is a NASA specific thing, in which case, I guess >>> someone at NASA would need to step up. >>> >>> Iï¿½m afraid I know no pythonistas at NASA.ï¿½ >>> >>> But Iï¿½ll poke around NOAA to see if thereï¿½s anything similar. >>> >>> -CHB >>> >>> On Apr 25, 2019, at 1:04 PM, Ralf Gommers <ralf.gommers(a)gmail.com> >>> wrote: >>> >>> >>> >>> On Sat, Apr 20, 2019 at 12:41 PM Ralf Gommers <ralf.gommers(a)gmail.com> >>> wrote: >>> >>>> >>>> >>>> On Thu, Apr 18, 2019 at 10:03 PM Joe Harrington <jh(a)physics.ucf.edu> >>>> wrote: >>>> >>>> >>>>> 3. There's such a thing as a share-in-savings contract at NASA, in >>>>> which >>>>> you calculate a savings, such as from avoided costs of licensing IDL >>>>> or >>>>> Matlab, and say you'll develop a replacement for that product that >>>>> costs >>>>> less, in exchange for a portion of the savings.ï¿½ These are rare and >>>>> few >>>>> people know about them, but one presenter to the committee did discuss >>>>> them and thought they'd be appropriate.ï¿½ I've always felt that we >>>>> could >>>>> get a chunk of change this way, and was surprised to find that the >>>>> approach exists and has a name.ï¿½ About 3 of 4 people I talk to at >>>>> NASA >>>>> have no idea this even exists, though, and I haven't pursued it to its >>>>> logical end to see if it's viable. >>>>> >>>> >>>> I've heard of these. Definitely worth looking into. >>>> >>> >>> It seems to be hard to find any information about these share-in-savings >>> contracts. The closest thing I found is this: >>> https://www.federalregister.gov/documents/2018/06/22/2018-13463/nasa-federa… >>> >>> It is called "Shared Savings" there, and was replaced last year by >>> something called "Value Engineering Change Proposal". If anyone can comment >>> on whether that's the same thing as Joe meant and whether this is worth >>> following up on, that would be very helpful. >>> >>> Cheers, >>> Ralf >>> >>> _______________________________________________ >>> NumPy-Discussion mailing list >>> NumPy-Discussion(a)python.org >>> https://mail.python.org/mailman/listinfo/numpy-discussion >>> >>> >>> _______________________________________________ >>> NumPy-Discussion mailing listNumPy-Discussion@python.orghttps://mail.python.org/mailman/listinfo/numpy-discussion >>> >>> >>> >>> _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion(a)python.org https://mail.python.org/mailman/listinfo/numpy-discussion

1 0

Re: [Numpy-discussion] grant proposal for core scientific Python projects (rejected)
by Joe Harrington May 4, 2019

May 4, 2019

Hi Ralf, The rejection is disappointing, for sure. Some good ammo for next time might be the recommendations in this report from the US National Academies of Science, Engineering, and Medicine: http://sites.nationalacademies.org/SSB/CurrentProjects/SSB_178892 https://www.nap.edu/read/25217/chapter/1#ii You can download a free PDF if you click around and give them an email address. There is some code on the cover that might raise a smile. Lorena Barba, Kelle Cruz, and many other community members contributed, both as committee members and as white-paper authors. While it's a report for NASA, the conclusions are strong and there is explicit support of investment in community resources like numpy, scipy, astropy, matplotlib, etc. Other agencies are asking similar questions, so I expect the report to get somewhat of a look at NSF, etc. A note on the Academies' process: A consensus study report must only include statements that no single member of the committee objects to, and the committee generally only includes senior members or people with a lot of relevant experience. There were stakeholders from some large modeling shops for whom openness might be a threat to their business model, in their eyes, and some of the senior members had never experienced the open-source environment and had bad experiences sharing software. This made for an interesting social dynamic, and prevented an all-out recommendation to forcibly open everything immediately. Given all that, I was ultimately pleased that we got full agreement on the recommendations we did make. So, some general thoughts on fundraising, not specific to this proposal: 1. Try NASA. The Administrator for Space Science, Thomas Zurbuchen, is pushing "open" very hard, given the success of open data in NASA Earth Science, and its positive impact on the economy in fields like agriculture and weather forecasting. He paid for the study above. Many grant programs specifically solicit proposals for open-source tools. There are also technology development programs in other parts of NASA than the Science Mission Directorate. Try contacting Dr. Michael New, who is Zurbuchen's deputy, and could direct you to appropriate programs. (Please, let's be coordinated and not all deluge the guy.) 2. As suggested in another message, it's often easier to get support for a specific, targeted item as part of a big project or institute using that item, such as LSST or the black-hole group. There's a certain way to wend into those projects, usually originating from within. STScI has long devoted programmer resources, for example. 3. There's such a thing as a share-in-savings contract at NASA, in which you calculate a savings, such as from avoided costs of licensing IDL or Matlab, and say you'll develop a replacement for that product that costs less, in exchange for a portion of the savings. These are rare and few people know about them, but one presenter to the committee did discuss them and thought they'd be appropriate. I've always felt that we could get a chunk of change this way, and was surprised to find that the approach exists and has a name. About 3 of 4 people I talk to at NASA have no idea this even exists, though, and I haven't pursued it to its logical end to see if it's viable. 4. I mostly lurk here, since being more actively involved in the early days of numpy docs, so maybe this one has been tried already, or is in the works. My apologies if so. Think of development as a product to buy. You could put chunks of development up for sale, advertise them, and coordinate one or more groups buying them together. For something like an efficiency boost, you could price it according to the avoided cost of CPU resources for a project of a given size (e.g., somewhat below the net present value of avoided future AWS cycles for the projects buying it). It would be like buying a custom-built data pipeline, except that once you buy it, everyone gets it. This might mean scoping out a roadmap of improvements, packaging them into fundable projects with teams ready to go, pricing them, advertising them to specific customers and in trade media and shows, and making sales pitches. This sounds really weird to us scientists, but it would work just like a regular purchase for services, which the government and industry are much more used to doing than donations to open-source projects. Don't just sell what the customer is buying, sell in the manner that the customer likes to buy. 5. And, keep trying grant proposals to NSF! --jh-- On 4/18/19 6:36 AM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > A number of core projects (NumPy, SciPy, Matplotlib, Pandas, > scikit-learn) got together and put in a proposal to NSF for a large 5 > year grant, and it was unfortunately just rejected. We now published > the proposal, which may be of interest: > https://figshare.com/articles/Mid-Scale_Research_Infrastructure_-_The_Scien….

7 16

Re: [Numpy-discussion] grant proposal for core scientific Python projects (rejected)
by Joe Harrington May 3, 2019

May 3, 2019

Just to keep people in the loop, Ralf and I are in discussion with people at NASA HQ about a funding stream for core development. Ralf has put together a short description of the development and funding model (5 core projects, 10-20 core developers each, nearly all volunteer now, how NumFOCUS fits in, what we hope to establish from NASA vs. from other agencies, industry, other countries' science entities, etc.). That will circulate within the agency, to see what can be scraped together. Program managers in NASA's Science Mission Directorate (SMD) gave quite-positive feedback on how vital the Python ecosystem is to NASA's mission. We're emphasizing the need for both new functionality and maintenance (e.g., docs, web site, bug fixing). If this is ultimately successful, it can be a model for approaching other agencies in the US and elsewhere. To Steve's point, regarding how hard it is for Civil Servants to contribute to OSS (due to NASA's lengthy internal review process for releasing software), this problem was clearly called out in the Academies report. We proposed some solutions to streamline things. What's needed now is for NASA Civil Servants to take that report and the relevant white papers (cited in the report and posted online) to their center's senior management, and to NASA HQ, and similarly for others in government agencies. You may wish to start from NASA's (or your agency's) mission, which includes sharing technology openly to boost the economy, and how you are encountering unreasonable barriers to that goal. This is mandated by the National Air and Space Act of 1958. For example, there is little reason to conduct an export-control review with lawyers looking at code emerging from a group that has nothing to do with anything near an export-controlled topic. Universities and contractors are subject to the same export-control laws as NASA, and they have not routinely conducted similar reviews of every line of code released. This has not led to a pattern of export violations. (Whether there is any benefit at all to the export control laws as applied to software is debatable, since it's usually easy for coders elsewhere to write the same codes, but the law is the law.) --jh-- On 5/3/19 12:48 PM, numpy-discussion-request(a)python.org wrote: > Subject: > Re: [Numpy-discussion] grant proposal for core scientific Python > projects (rejected) > From: > Mark Mikofski <mikofski(a)berkeley.edu> > Date: > 5/3/19, 12:47 PM > > To: > Discussion of Numerical Python <numpy-discussion(a)python.org> > > > Sorry, that last attachment was just a slide show of the topic 3 > recording, here is the full funding opportunity announcement - letter > with 200 word abstract are due May 7th > > On Fri, May 3, 2019 at 8:40 AM Mark Mikofski <mikofski(a)berkeley.edu > <mailto:mikofski@berkeley.edu>> wrote: > > Hi Ralf, and others, > > Sorry for the late notice, but there is are several funding > opportunities in solar, including one for $350,000 to develop open > source software to lower soft costs of solar. > https://eere-exchange.energy.gov/#FoaId45eda43a-e826-4481-ae7a-cc6e8ed4fdae > > see topic 3.4 specifically in attached PDF - also note to view the > recording the password is "*Setofoa2019"* it's about 30 minutes long. > > I know that this is a extremely niche, but as a few others have > said, [the DOE] grants tend to be very specific, but perhaps we > can creatively think of ways to channel funds to NumPy and SciPy. > > Also there is a cost share that is typically 20%, which would be a > non-starter for volunteer projects. > > But here's an idea, perhaps partnering with a company, like mine > (DNV GL) who is applying for the grant, and who uses NumPy,and > could pay the cost share, and then we collaborate on something > that is required to complete the project, which is contributed to > NumPy (or SciPy) - but we would have to figure what we could align on. > > Seems like NumFOCUS, Quantsight, or some other company in the OSS > space could figure out ways to help connect companies, OSS > projects, and funding opportunities like these, where there's a > possibility of alignment and mutual benefit? > > The full list of funding opportunities is here: > https://eere-exchange.energy.gov/ > > Best Regards, > Mark > > > On Thu, May 2, 2019 at 11:52 PM Ralf Gommers > <ralf.gommers(a)gmail.com <mailto:ralf.gommers@gmail.com>> wrote: > > > > On Fri, May 3, 2019 at 3:49 AM Stephen Waterbury > <waterbug(a)pangalactic.us <mailto:waterbug@pangalactic.us>> wrote: > > P.S. If anyone wants to continue this discussion at SciPy > 2019, > I will be there (on my own nickel! ;) ... > > > Thanks for the input Stephen, and looking forward to see you > at SciPy'19! > > Ralf > > > Steve > > On 5/2/19 9:45 PM, Stephen Waterbury wrote: > >> I am a NASA pythonista (for 20+ years ;), but you can now >> say you know >> yet another person at NASA who has no idea this even >> exists ... :) >> Not only do I not know of that, but I know of NASA >> policies that make >> it very difficult for NASA civil servants to contribute >> to open source >> projects -- quite hypocritical, given the amount of open >> source >> code that NASA (like all other large organizations) >> depends critically >> on, but it's a fact. >> >> Cheers, >> Steve Waterbury >> >> (CLEARLY **NOT** SPEAKING IN ANY OFFICIAL CAPACITY FOR >> NASA OR >> THE U.S. GOVERNMENT AS A WHOLE! Hence the personal email >> address. :) >> >> On 5/2/19 9:31 PM, Chris Barker - NOAA Federal wrote: >> >>> Sounds like this is a NASA specific thing, in which >>> case, I guess someone at NASA would need to step up. >>> >>> I’m afraid I know no pythonistas at NASA. >>> >>> But I’ll poke around NOAA to see if there’s anything >>> similar. >>> >>> -CHB >>> >>> On Apr 25, 2019, at 1:04 PM, Ralf Gommers >>> <ralf.gommers(a)gmail.com <mailto:ralf.gommers@gmail.com>> >>> wrote: >>> >>>> >>>> >>>> On Sat, Apr 20, 2019 at 12:41 PM Ralf Gommers >>>> <ralf.gommers(a)gmail.com >>>> <mailto:ralf.gommers@gmail.com>> wrote: >>>> >>>> >>>> >>>> On Thu, Apr 18, 2019 at 10:03 PM Joe Harrington >>>> <jh(a)physics.ucf.edu <mailto:jh@physics.ucf.edu>> wrote: >>>> >>>> >>>> 3. There's such a thing as a share-in-savings >>>> contract at NASA, in which >>>> you calculate a savings, such as from avoided >>>> costs of licensing IDL or >>>> Matlab, and say you'll develop a replacement >>>> for that product that costs >>>> less, in exchange for a portion of the savings. >>>> These are rare and few >>>> people know about them, but one presenter to >>>> the committee did discuss >>>> them and thought they'd be appropriate. I've >>>> always felt that we could >>>> get a chunk of change this way, and was >>>> surprised to find that the >>>> approach exists and has a name. About 3 of 4 >>>> people I talk to at NASA >>>> have no idea this even exists, though, and I >>>> haven't pursued it to its >>>> logical end to see if it's viable. >>>> >>>> >>>> I've heard of these. Definitely worth looking into. >>>> >>>> >>>> It seems to be hard to find any information about these >>>> share-in-savings contracts. The closest thing I found >>>> is this: >>>> https://www.federalregister.gov/documents/2018/06/22/2018-13463/nasa-federa… >>>> >>>> It is called "Shared Savings" there, and was replaced >>>> last year by something called "Value Engineering Change >>>> Proposal". If anyone can comment on whether that's the >>>> same thing as Joe meant and whether this is worth >>>> following up on, that would be very helpful. >>>> >>>> Cheers, >>>> Ralf >>>> >>>> _______________________________________________ >>>> NumPy-Discussion mailing list >>>> NumPy-Discussion(a)python.org >>>> <mailto:NumPy-Discussion@python.org> >>>> https://mail.python.org/mailman/listinfo/numpy-discussion >>> >>> _______________________________________________ >>> NumPy-Discussion mailing list >>> NumPy-Discussion(a)python.org <mailto:NumPy-Discussion@python.org> >>> https://mail.python.org/mailman/listinfo/numpy-discussion >> >> >

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