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updating this scipy to match the master #3

Merged
merged 123 commits into from
Mar 11, 2020

Commits on Dec 18, 2019

  1. 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.
    mdhaber committed Dec 18, 2019
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Commits on Dec 19, 2019

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  2. Revert "ENH: optimize: redundancy removal - efficiently initialize A/…

    …B in Fortran order"
    
    This reverts commit f065d85 to undo
    changes to doc/scipy-sphinx-theme.
    mdhaber committed Dec 19, 2019
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Commits on Dec 29, 2019

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Commits on Jan 16, 2020

  1. 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.
    Kai-Striega committed Jan 16, 2020
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  2. 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.
    Kai-Striega committed Jan 16, 2020
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  5. 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.
    Kai-Striega committed Jan 16, 2020
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  6. 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).
    Kai-Striega committed Jan 16, 2020
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  9. 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.
    Kai-Striega committed Jan 16, 2020
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  11. 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).
    Kai-Striega committed Jan 16, 2020
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Commits on Jan 18, 2020

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Commits on Jan 21, 2020

  1. 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.
    Kai-Striega committed Jan 21, 2020
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Commits on Feb 12, 2020

  1. 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.
    Jiacheng-Liu committed Feb 12, 2020
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Commits on Feb 14, 2020

  1. ENH: improve sparse.lil.tocsr performance

    Critical sections (indptr, indices and data array creations) are now
    implemented in Cython.
    smola committed Feb 14, 2020
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Commits on Feb 15, 2020

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  3. 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.
    pvanmulbregt committed Feb 15, 2020
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  6. 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.
    pvanmulbregt committed Feb 15, 2020
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  10. Removed an extraneous comment in _continuous_distns.py.

    A commit message had been inserted as a comment during rebasing. Now removed.
    pvanmulbregt committed Feb 15, 2020
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  13. 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.
    pvanmulbregt committed Feb 15, 2020
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  18. Addressing reviewer comments.

    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.
    pvanmulbregt committed Feb 15, 2020
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Commits on Feb 17, 2020

  1. MAINT: Fixed several unused imports and unused assignments.

    5 unused imports, 5 unused assignments;
    7 in test code, 3 in main library.
    pvanmulbregt committed Feb 17, 2020
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  4. Addressing comments of reviewer.

    Replaced "_ = func(...)"  with  "func(...)"
    pvanmulbregt committed Feb 17, 2020
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Commits on Feb 18, 2020

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  5. fix explicit import

    Jiacheng-Liu committed Feb 18, 2020
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Commits on Feb 19, 2020

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  2. Merge pull request #11541 from pvanmulbregt/warnings_special

    MAINT: Fixed several unused imports and unused assignments in scipy/special
    person142 committed Feb 19, 2020
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  3. Merge pull request #11538 from pvanmulbregt/warnings_fft

    MAINT: Fixed several unused imports in scipy/fft.
    tylerjereddy committed Feb 19, 2020
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Commits on Feb 20, 2020

  1. Merge pull request #11548 from pvanmulbregt/warnings_sparse

    MAINT: Removed unused imports; fixed unused assignments in scipy.sparse.
    tylerjereddy committed Feb 20, 2020
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  3. 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.
    ev-br committed Feb 20, 2020
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  4. Merge pull request #11547 from pvanmulbregt/warnings_spatial

    MAINT: Removed unused imports; fixed unused assignments in scipy/spatial
    tylerjereddy committed Feb 20, 2020
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Commits on Feb 21, 2020

  1. Merge pull request #11560 from ev-br/rv_frozen_argcheck

    MAINT: stats: remove an _argcheck call
    tylerjereddy committed Feb 21, 2020
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Commits on Feb 22, 2020

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  3. TST: Add test for 1d sytrd

    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.
    Kai-Striega committed Feb 22, 2020
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  6. TST: Add test for 1d hetrd

    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.
    Kai-Striega committed Feb 22, 2020
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Commits on Feb 23, 2020

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  2. 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.
    arokem committed Feb 23, 2020
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  3. Merge pull request #11245 from mdhaber/dense_rr_speedup

    ENH: optimize: dense redundancy removal routine optimizations
    Kai-Striega committed Feb 23, 2020
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  4. Merge pull request #11378 from Kai-Striega/lapack_support_tbtrs

    ENH: linalg: Python wrapper for ?tbtrs
    Kai-Striega committed Feb 23, 2020
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  6. Merge pull request #11573 from pvanmulbregt/warnings_stats

    MAINT: Removed unused imports; fixed unused assignments in scipy/stats.
    ev-br committed Feb 23, 2020
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  7. Merge pull request #11574 from arokem/error-msg-nnls

    MAINT: Small change to `optimize.nnls` error messages.
    ev-br committed Feb 23, 2020
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  8. Merge pull request #11532 from pvanmulbregt/warnings_linalg

    MAINT: Fixed several unused imports and unused assignments from linalg
    ev-br committed Feb 23, 2020
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  9. fix import numpy

    Jiacheng-Liu committed Feb 23, 2020
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  10. Merge pull request #11510 from Jiacheng-Liu/sparse-doc-improvement

    DOC: sparse: An ex. for creating arbitrary size tri-diagonal
    ev-br committed Feb 23, 2020
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  11. Merge pull request #11575 from Kai-Striega/tidy_sytrd_test

    MAINT: Update sytrd/hetrd tests
    mdhaber committed Feb 23, 2020
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Commits on Feb 24, 2020

  1. 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.
    fuglede authored and tylerjereddy committed Feb 24, 2020
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  2. Merge pull request #11534 from peterbell10/fft-byte-order

    FIX: Allow non-native byte order inputs to scipy.fft
    tylerjereddy committed Feb 24, 2020
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Commits on Feb 25, 2020

  1. Merge pull request #9719 from pvanmulbregt/kstwo_rebase

    ENH: Added kstwo probability distribution for two-sided one-sample Kolmogorov-Smirnov tests.
    chrisb83 committed Feb 25, 2020
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  2. BUG: Differential evolution with LinearConstraint with sparse matrix (#…

    …11587)
    
    BUG: Differential evolution with LinearConstraint with sparse matrix
    santiher committed Feb 25, 2020
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  5. Merge pull request #11549 from sethtroisi/range

    MAINT: Replace xrange with range
    andyfaff committed Feb 25, 2020
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Commits on Feb 26, 2020

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Commits on Feb 27, 2020

  1. Merge pull request #11459 from fuglede/fix-augmentation

    BUG: fix augmentation being broken in maximum_bipartite_matching
    Kai-Striega committed Feb 27, 2020
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Commits on Feb 28, 2020

  1. Merge pull request #11188 from chrisb83/argus_rvs

    MAINT: add rvs method to argus in scipy.stats
    tylerjereddy committed Feb 28, 2020
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  2. ENH: improve docstring of weibull_min_gen and weibull_max_gen to fix #…

    …10014 (#11527)
    
    * ENH: improve docstring of weibull_min_gen and weibull_max_gen function to fix #10014.
    
    * minor fix of docstrings.
    
    * fix docstring based on review.
    
    * fix docstring based on code review:
    
    * fixed URL.
    AtsushiSakai committed Feb 28, 2020
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  3. Merge pull request #11517 from smola/lil-tocsr

    ENH: improve sparse.lil.tocsr performance
    tylerjereddy committed Feb 28, 2020
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Commits on Feb 29, 2020

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Commits on Mar 1, 2020

  1. 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.
    cycentum committed Mar 1, 2020
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Commits on Mar 3, 2020

  1. Merge pull request #11590 from sethtroisi/py_version

    MAINT: Remove Python2 module init
    tylerjereddy committed Mar 3, 2020
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Commits on Mar 4, 2020

  1. Merge pull request #11539 from pvanmulbregt/warnings_interpolate

    MAINT: Fixed several unused imports and unused assignments in scipy/interpolate
    ev-br committed Mar 4, 2020
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  4. Merge pull request #11589 from sethtroisi/sys_version_2

    MAINT: Remove Python 2 workarounds
    rgommers committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. 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
    tylerjereddy committed Mar 5, 2020
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  2. Merge pull request #11628 from tylerjereddy/azure_matplotlib_remove_g…

    …uards
    
    MAINT, TST: adjust azure for matplotlib release
    tylerjereddy committed Mar 5, 2020
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  3. TST: add openblas_support.py

    * 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
    tylerjereddy committed Mar 5, 2020
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Commits on Mar 6, 2020

  1. 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.
    alexhenrie committed Mar 6, 2020
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Commits on Mar 7, 2020

  1. Merge pull request #11632 from alexhenrie/array_anyorder

    MAINT: Define ARRAY_ANYORDER with DEF instead of cdef
    ilayn committed Mar 7, 2020
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  3. Merge pull request #11631 from pmla/lsap-constant-cost

    Revert to old behaviour for constant cost matrices in `linear_sum_assignment`
    tylerjereddy committed Mar 7, 2020
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  4. Merge pull request #11621 from sethtroisi/PY_VERSION_HEX_1

    MAINT: Cleanup uses of PY_VERSION_HEX, NPY_PY3K in ndimage
    tylerjereddy committed Mar 7, 2020
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  5. Merge pull request #11585 from tylerjereddy/treddy_openblas_support

    TST: add openblas_support.py
    tylerjereddy committed Mar 7, 2020
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Commits on Mar 8, 2020

  1. Merge pull request #11623 from sethtroisi/__future_part1

    MAINT: Remove unnecessary 'from __future__ import ...' statements
    tylerjereddy committed Mar 8, 2020
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  2. 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()
    tylerjereddy committed Mar 8, 2020
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  3. Merge pull request #11643 from tylerjereddy/fix_numpy_int_dep_conv

    MAINT: fix conversion in binom_test
    WarrenWeckesser committed Mar 8, 2020
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Commits on Mar 9, 2020

  1. Merge pull request #11651 from jrwrigh/patch-2

    DOC: Update paper URL in lambertw documentation
    rgommers committed Mar 9, 2020
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Commits on Mar 10, 2020

  1. Merge pull request #11626 from sethtroisi/PY_VERSION_HEX_3

    MAINT: Cleanup uses of PY_VERSION_HEX
    tylerjereddy committed Mar 10, 2020
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  2. Merge pull request #11646 from sethtroisi/__future

    MAINT: Remove unnecessary 'from __future__ import ...' statements
    rgommers committed Mar 10, 2020
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Commits on Mar 11, 2020

  1. Merge pull request #11640 from ilayn/trmmfix

    MAINT: Fix BLAS3 trmm wrapper for "side" arg
    ilayn committed Mar 11, 2020
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