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updating this scipy to match the master #3
Commits on Dec 18, 2019
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ENH: optimize: redundancy removal replace solve_triangular w/ dtrsv
As reported in gh-10722, solve_triangular can be quite slow. Replacing with direct call to dtrsv is faster.
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Commits on Dec 19, 2019
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Revert "ENH: optimize: redundancy removal - efficiently initialize A/…
…B in Fortran order" This reverts commit f065d85 to undo changes to doc/scipy-sphinx-theme.
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Commits on Dec 29, 2019
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Commits on Jan 16, 2020
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TST: linalg: Add test for ?tbtrs NAG example
This commit adds the tests f07vef and v07vsf from the NAG examples for real and complex cases respectively. These are available at: * https://www.nag.com/numeric/fl/nagdoc_latest/html/f07/f07vef.html * https://www.nag.com/numeric/fl/nagdoc_latest/html/f07/f07vsf.html The function being tested still takes the input matrix `ab` not `a` as prescribed in #gh-11190.
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ENH: linalg: Add wrapper for ?tbtrs
This commit adds a Python wrapper for the set of LAPACK functions ?tbtrs. This solves a triangular system of the form: A * X = B or A**T * X = B, The signature differs from the signature proposed in gh-11190 as the matrix `a` is expected, rather than `ab`. This was chosen to follow the documented signature used in LAPACK.
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ENH: linalg: Allow b to be complex
The test tests whether the system Ax = b is calculated correctly for each of float, double, complex float and complex double type values. Previously the value of b was constrained to being a real value inside a complex datatype (i.e. a + 0j). This has now been fixed such that b may cover all potential complex numbers.
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ENH: linalg: Test trans = {T, C} in ?tbtrs
This commit adds test for the transpose and conjugate transpose arguments these correspond to the systems of: A.T x = b and A.H x = b respectively. Some complexity was added in the parameterization as the complex conjugate does not exist for real data types (float32 and float64).
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TST: linalg: Test ?tbtrs with a zero diagonal
?tbtrs checks for singular matrices by identifying any zero elements in the diagonal. If the i-th diagonal element of A is singular then `info` should be equal to i. Note that this uses Fortran indexing.
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ENH: linalg: Test ldb >= max(1, n) in ?tbtrs
This commit tests the precondition that the leading dimension of b (ldb) is greater than the minimum allowed order of matrix A (n + 1).
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Commits on Jan 18, 2020
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Commits on Jan 21, 2020
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ENH: linalg: Allow ld? to be size 1
This PR changes definitions of the leading dimensions to ``MAX(1, shape(?, n)`` This prevents segfaults in cases where the leading dimension is 0.
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Commits on Feb 12, 2020
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An ex. for creating arbitrary size tri-diagonal
This kind of setting would be used a lot in numerical simulations, like numerical PDE, I was confused a bit on how to get it, so maybe someone else would be confused too. It would be nice to have such an example for them so they can easily plug in and run.
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Commits on Feb 14, 2020
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ENH: improve sparse.lil.tocsr performance
Critical sections (indptr, indices and data array creations) are now implemented in Cython.
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Commits on Feb 15, 2020
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DOC: Added necessary doc for stats.kstwo distribution.
Added a tutorial. Reference kstwo from multiple locations. Added default shape parameters for testing, and added to list of fails_cmplx.
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ENH: Enhance efficiency of some stats.kstwo basic operations.
Change stats.kstwo's momtype from the default of 1, which uses self.ppf(), to 0, which uses self.pdf() when computing the distribution's moments. Added kolmogni(n, q) in _ksstats.py to calculate the ppf/isf for kstwo. Fixed a general bug in rv_continuous._ppf_single(): If self.a is 0, it incorrectly used -10 as the left-hand endpoint of the seach interval passed to optimize.brentq. If a distribution is excluded from the basic entropy calculation in test_continuous_basic.py, also exclude it from the private_entropy, vec_entropy and entropy_vect_scale entropy calculations. Lower n=100 to n=10 in the example parameters for kstwo in _distr_params.py. Inside TestKSTwo: - Add test_isf_of_sf() and test_isf_of_sf_sqrtn() methods. - Keep CDFs and SFs away from 1 when doing round-trip cdf/ppf sf/isf tests, as these are subject to more error due to the extreme flatness of the function at the end-points. (Computing the sf(isf(n, 1-p, n), n) for a CDF probability p close to 1 works fine, as does cdf(ppf(1-p, n), n).) All this reduces the computation time in in the kstwo tests by a factor of ~10.
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Removed an extraneous comment in _continuous_distns.py.
A commit message had been inserted as a comment during rebasing. Now removed.
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Added a test of values computed near the mean of the KSTwo distribution.
The table is from "Computing the Two-Sided Kolmogorov-Smirnov Distribution" by Simard & L'Ecuyer, with values computed using SageMath 500-bit arithmetic.
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Removed special case handling from _kolmogn_DMTW as handled in _kolmogn. Simplified _kolmogn_PelzGood as subtractive cancellation not an issue for the extra terms in K2, K3. Added _log_nfactorial_div_n_pow_n(n) to compute log(n!/n**n). Removed unneeded comments and/or code notived by reviewer. Removed _kolmogn_LCK as not used. Made some function docstrings compliant.
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Commits on Feb 17, 2020
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MAINT: Fixed several unused imports and unused assignments.
5 unused imports, 5 unused assignments; 7 in test code, 3 in main library.
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Addressing comments of reviewer.
Replaced "_ = func(...)" with "func(...)"
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Commits on Feb 18, 2020
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Commits on Feb 19, 2020
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Merge pull request #11541 from pvanmulbregt/warnings_special
MAINT: Fixed several unused imports and unused assignments in scipy/special
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Merge pull request #11538 from pvanmulbregt/warnings_fft
MAINT: Fixed several unused imports in scipy/fft.
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Commits on Feb 20, 2020
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Merge pull request #11548 from pvanmulbregt/warnings_sparse
MAINT: Removed unused imports; fixed unused assignments in scipy.sparse.
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MAINT: stats: remove an _argcheck call
This was needed when _argcheck could set the .a and .b attributes. Since it no longer does, the call is not needed. The attributes are set in _get_support which is, literally, the next line.
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Merge pull request #11547 from pvanmulbregt/warnings_spatial
MAINT: Removed unused imports; fixed unused assignments in scipy/spatial
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Commits on Feb 21, 2020
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Merge pull request #11560 from ev-br/rv_frozen_argcheck
MAINT: stats: remove an _argcheck call
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Commits on Feb 22, 2020
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This test previously failed due to a numpy issue (see gh-9617). This fix had been implemented in numpy version 1.4, which is now the miniumum version used in SciPy.
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This test could not be run previously due to a numpy bug (see gh-9617) as the minimum numpy version (1.14) required by SciPy now includes the fix, we are able to add the requried test.
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Commits on Feb 23, 2020
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MAINT: Small change to
optimize.nnls
error messages.The term "matrix" is ambiguous and can refer to either a two-dimensional array or a numpy `matrix` object (which is deprecated). The changed error message can confuse users to think they need the latter, when the former will do. I also added more detail about the inputs provided by the user, as additional feedback when things go wrong.
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Merge pull request #11245 from mdhaber/dense_rr_speedup
ENH: optimize: dense redundancy removal routine optimizations
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Merge pull request #11378 from Kai-Striega/lapack_support_tbtrs
ENH: linalg: Python wrapper for ?tbtrs
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Merge pull request #11573 from pvanmulbregt/warnings_stats
MAINT: Removed unused imports; fixed unused assignments in scipy/stats.
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Merge pull request #11574 from arokem/error-msg-nnls
MAINT: Small change to `optimize.nnls` error messages.
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Merge pull request #11532 from pvanmulbregt/warnings_linalg
MAINT: Fixed several unused imports and unused assignments from linalg
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Merge pull request #11510 from Jiacheng-Liu/sparse-doc-improvement
DOC: sparse: An ex. for creating arbitrary size tri-diagonal
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Merge pull request #11575 from Kai-Striega/tidy_sytrd_test
MAINT: Update sytrd/hetrd tests
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Commits on Feb 24, 2020
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BUG: fix augmentation being broken in maximum_bipartite_matching
This fixes an issue that would worst case cause infeasible solutions to be produced by maximum_bipartite_matching as the value of the `x`-array would end up containing edges that do not belong to the input graph. The root cause of the issue was a piece broken logic in the DFS part of the Hopcroft--Karp implementation concerned with keeping track of the augmenting path. We fix the issue by replacing this logic with a more standard approach of marking the parents of each vertex on the path (or rather, its grandparent, as we still only deal explicitly with one partition at a time). A regression test has been added to showcase an example of an input that would previously lead to an infeasible solution.
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Merge pull request #11534 from peterbell10/fft-byte-order
FIX: Allow non-native byte order inputs to scipy.fft
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Commits on Feb 25, 2020
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Merge pull request #9719 from pvanmulbregt/kstwo_rebase
ENH: Added kstwo probability distribution for two-sided one-sample Kolmogorov-Smirnov tests.
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BUG: Differential evolution with LinearConstraint with sparse matrix (#…
…11587) BUG: Differential evolution with LinearConstraint with sparse matrix
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Merge pull request #11549 from sethtroisi/range
MAINT: Replace xrange with range
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Commits on Feb 26, 2020
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Commits on Feb 27, 2020
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Merge pull request #11459 from fuglede/fix-augmentation
BUG: fix augmentation being broken in maximum_bipartite_matching
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Commits on Feb 28, 2020
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Merge pull request #11188 from chrisb83/argus_rvs
MAINT: add rvs method to argus in scipy.stats
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ENH: improve docstring of weibull_min_gen and weibull_max_gen to fix #…
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Merge pull request #11517 from smola/lil-tocsr
ENH: improve sparse.lil.tocsr performance
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Commits on Feb 29, 2020
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Commits on Mar 1, 2020
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ENH: special: add
log_softmax
(#11187)Closes gh-11058. Add `log_softmax` to `special/_logsumexp.py` and unit tests for it to special/tests/test_log_softmax.py.
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Commits on Mar 3, 2020
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Merge pull request #11590 from sethtroisi/py_version
MAINT: Remove Python2 module init
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Commits on Mar 4, 2020
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Merge pull request #11539 from pvanmulbregt/warnings_interpolate
MAINT: Fixed several unused imports and unused assignments in scipy/interpolate
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Merge pull request #11589 from sethtroisi/sys_version_2
MAINT: Remove Python 2 workarounds
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Commits on Mar 5, 2020
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MAINT, TST: adjust azure for matplotlib release
* matplotlib 3.2.0 stable is out, so we shouldn't need guards for the release candidate (and Python 3.6 should be ok with it too) * also unpin matplotlib from 3.2.0rc1 in Travis CI * pin matplotlib to 3.1.3 version for 32-bit Linux Azure CI run because of unclear issue with 3.2.0 install there
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Merge pull request #11628 from tylerjereddy/azure_matplotlib_remove_g…
…uards MAINT, TST: adjust azure for matplotlib release
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* borrow/adjust openblas_support.py used in the NumPy project as a common handling point for OpenBLAS-related version checking & downloads * adjust test_version() function to use scipy.linalg instead of NumPy for checking the linked in OpenBLAS version; also, increase the sensitivity of this function so it can distinguish between development & stable releases of OpenBLAS * adjust openblas_support.py to print out the download error for openblas when it fails * openblas_support.py now uses anaconda.org instead of rackspace, as the NumFOCUS ecosystem is migrating off the latter; as part of this, add some logic to overcome the anti-scraping behavior at anaconda.org so we can still download files programmatically * adjust azure pipelines configuration to leverage openblas_support.py to retrieve OpenBLAS & verify version linked to SciPy; version verification is not possible on Windows (this is also true for NumPy) * the version of OpenBLAS used for Azure CI has been bumped to 0.3.8.dev from 0.3.7 stable as part of this change
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Commits on Mar 6, 2020
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MAINT: Define ARRAY_ANYORDER with DEF instead of cdef
This is the only way to tell the compiler that the value is a constant which may be inlined instead of read from memory.
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Commits on Mar 7, 2020
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Merge pull request #11632 from alexhenrie/array_anyorder
MAINT: Define ARRAY_ANYORDER with DEF instead of cdef
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Merge pull request #11631 from pmla/lsap-constant-cost
Revert to old behaviour for constant cost matrices in `linear_sum_assignment`
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Merge pull request #11621 from sethtroisi/PY_VERSION_HEX_1
MAINT: Cleanup uses of PY_VERSION_HEX, NPY_PY3K in ndimage
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Merge pull request #11585 from tylerjereddy/treddy_openblas_support
TST: add openblas_support.py
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Commits on Mar 8, 2020
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Merge pull request #11623 from sethtroisi/__future_part1
MAINT: Remove unnecessary 'from __future__ import ...' statements
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MAINT: fix conversion in binom_test
* Converting `np.integer` or `np.signedinteger` to a dtype is deprecated in NumPy master (and causes failures in our Travis CI NumPy pre-release wheel tests) * repair the single violation of this deprecation in our source code, in binom_test()
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Merge pull request #11643 from tylerjereddy/fix_numpy_int_dep_conv
MAINT: fix conversion in binom_test
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Commits on Mar 9, 2020
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Merge pull request #11651 from jrwrigh/patch-2
DOC: Update paper URL in lambertw documentation
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Commits on Mar 10, 2020
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Merge pull request #11626 from sethtroisi/PY_VERSION_HEX_3
MAINT: Cleanup uses of PY_VERSION_HEX
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Merge pull request #11646 from sethtroisi/__future
MAINT: Remove unnecessary 'from __future__ import ...' statements
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Commits on Mar 11, 2020
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Merge pull request #11640 from ilayn/trmmfix
MAINT: Fix BLAS3 trmm wrapper for "side" arg
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