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   2024-10-14 08:46:10 by Thomas Klausner | Files touched by this commit (325)
Log message:
*: clean-up after python38 removal
   2024-08-21 12:11:44 by Adam Ciarcinski | Files touched by this commit (3) | Package updated
Log message:
py-scipy: updated to 1.14.1

Issues closed for 1.14.1

BUG: doccer: \`test_decorator\` fails with Python 3.13 due to...
BUG: open_memstream unavailable with glibc >= 2.10 + C99
ENH: 3.13 wheels
BUG: spsolve prints "dgstrf info" to stdout on singular matrices
BUG: \`special.pro_rad1\`: incorrect results
BUG: sparse: \`hstack/vstack\` between a sparse and ndarray breaks...
MAINT: \`cluster\`/\`stats\`: array API test failures in main
BUG: unable to securely deploy app as scipy 1.14.0 requires write...
BUG: signal: crash in \`signaltools\` on free-threaded Python,...
CI: documentation build failing?
BUG: \`fft.hfftn\` fails on list inputs
BUG: Files in SuperLU under LGPL license
BUG: io/scipy.sparse.csgraph: refguide check failure in main
DOC: \`sampling_tdr.rst\` failing in CircleCI smoke-tutorials...
BUG: dtype changed for argument to \`rv_discrete._pmf\`
BUG: odr: pickling is not possible
DOC: build failing in CI
BLD, CI: Cirrus 3.13 wheels?

Pull requests for 1.14.1

BLD: make cp313 wheels [wheel build]
REL, MAINT: prep for 1.14.1
BUG: special: Fixes for pro_rad1
BUG: special: remove type punning to avoid warnings in LTO builds
MAINT: uarray: fix typo in \`small_dynamic_array.h\`
MAINT: adapt to array-api-strict 2.0
BLD: Enable \`open_memstream()\` on newer glibc
MAINT: Unskip \`scipy.misc.test.test_decorator\` for Python 3.13+
DOC: add release note for 1.14 sparse section about sparse array...
BUG: sparse: fix 1D for vstack/hstack and Improve 1D error msgs...
BUG: signal: fix crash under free-threaded CPython in medfilt2d
BUG: sparse.linalg: Update \`SuperLU\` to fix unfilterable output...
DOC: Fix type of \`\`html_sidebars\`\` value in \`\`conf.py\`\`
BUG: fft: fix array-like input
BUG: sparse: fix failing doctests in io and csgraph that print...
DOC: stats: silence the doctest error
MAINT: sparse.linalg: update \`SuperLU/colamd.c\` to fix license...
BUG: stats: adapt to \`np.floor\` type promotion removal
MAINT: \`stats.bartlett\`: ensure statistic is non-negative
CI: Update to cibuildwheel 2.20.0
BUG: odr: fix pickling
DOC: Don't use Sphinx 8.0.0 until gh-21323 is resolved.
BUG: sparse: Fix 1D specialty hstack codes
MAINT: special: Accommodate changed integer handling in NumPy...
BLD: cp313 wheels on \`manylinux_aarch64\`
   2024-08-06 11:46:17 by Adam Ciarcinski | Files touched by this commit (1)
Log message:
py-scipy: bump GCC_REQD
   2024-07-31 20:16:11 by Adam Ciarcinski | Files touched by this commit (1)
Log message:
py-scipy: remove unused patch
   2024-07-31 20:15:38 by Adam Ciarcinski | Files touched by this commit (9) | Package updated
Log message:
py-scipy: updated to 1.14.0

SciPy 1.14.0 is the culmination of 3 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. 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
1.14.x branch, and on adding new features on the main branch.
   2024-06-12 10:57:43 by Adam Ciarcinski | Files touched by this commit (2) | Package updated
Log message:
py-scipy: updated to 1.13.1

Issues closed for 1.13.1

BUG: \`scipy.ndimage.value_indices\` returns empty dict for \`intc\`/\`uintc\` \ 
dtype on Windows
DOC, MAINT: .jupyterlite.doit.db shows up untracked
DOC: optimize.root(method='lm') option
BUG: csr_array can no longer be initialized with 1D array
BUG: \`TestEig.test_falker\` fails on windows + MKL as well as...
BUG: Cannot find \`OpenBLAS\` on Cygwin
BUG: special.spherical_in: derivative at \`z=0, n=1\` incorrect
BUG: \`eigh\` fails for size 1 array with driver=evd
BUG: warning from \`optimize.least_squares\` for astropy with...
BUG: spatial: error in \`Rotation.align_vectors()\` with an infinite...
MAINT, TST: two types of failures observed on maintenance/1.13.x...
BUG: scipy.special.factorial2 doesn't handle \`uint32\` dtypes
BUG: scipy.stats.wilcoxon in 1.13 fails on 2D array with nan...
BUG: scipy.spatial.Delaunay, scipy.interpolate.LinearNDInterpolator...
BUG: stats.yulesimon: incorrect kurtosis values
BUG: incorrect origin tuple handling in ndimage \`minimum_filter\`...
BUG: spatial: \`Rotation.align_vectors()\` incorrect for anti-parallel...
BUG: sparse matrix creation in 1.13 with indices not summing...
BUG: stats.zipf: incorrect pmf values
CI: scipy installation failing in umfpack tests

Pull requests for 1.13.1

MAINT: added doc/source/.jupyterlite.doit.db to .gitignore See...
BUG: sparse: align dok_array.pop() to dict.pop() for case with...
BUG: sync pocketfft again
REL, MAINT: prep for 1.13.1
DOC: optimize: fix wrong optional argument name in \`root(method="lm")\`.
DOC: add missing deprecations from 1.13.0 release notes
MAINT/DOC: fix syntax in 1.13.0 release notes
BUG: sparse: Clean up 1D input handling to sparse array/matrix...
DOC: remove spurious backtick from release notes
BUG: linalg: fix ordering of complex conj gen eigenvalues
TST: tolerance bumps for the conda-forge builds
TST: compare absolute values of U and VT in pydata-sparse SVD...
BUG: Include Python.h before system headers.
BUG: linalg: fix eigh(1x1 array, driver='evd') f2py check
BUG: \`spherical_in\` for \`n=0\` and \`z=0\`
BLD: Fix error message for f2py generation fail
TST: Adapt to \`__array__(copy=True)\`
BLD: Move Python-including files to start of source.
REV: 1.13.x: revert changes to f2py and tempita handling in meson.build...
update openblas to 0.3.27
BUG: Fix error with 180 degree rotation in Rotation.align_vectors()...
MAINT: optimize.linprog: fix bug when integrality is a list of...
MAINT: stats.wilcoxon: fix failure with multidimensional \`x\`...
MAINT: lint: temporarily disable UP031
BUG: handle uint arrays in factorial{,2,k}
BUG: prevent QHull message stream being closed twice
MAINT/DEV: lint: disable UP032
BUG: fix Vor/Delaunay segfaults
BUG: ndimage.value_indices: deal with unfixed types
BUG: ndimage: fix origin handling for \`{minimum, maximum}_filter\`
MAINT: stats.yulesimon: fix kurtosis
BUG: sparse: Fix summing duplicates for CSR/CSC creation from...
BUG: stats: Fix \`zipf.pmf\` and \`zipfian.pmf\` for int32 \`k\`
CI: pin Python for MacOS conda
   2024-06-04 22:46:45 by Mark Davies | Files touched by this commit (1)
Log message:
py-scipy: drop maintainership
   2024-05-05 21:02:05 by Thomas Klausner | Files touched by this commit (1)
Log message:
py-scipy: fix build
   2024-04-30 01:01:39 by David H. Gutteridge | Files touched by this commit (1)
Log message:
py-scipy: reflect correct minimum dependencies

1.13 requires newer versions of py-cython and py-pybind11 than what was
previously specified in order to build at all.
   2024-04-19 21:24:25 by Adam Ciarcinski | Files touched by this commit (7) | Package updated
Log message:
py-scipy: updated to 1.13.0

SciPy 1.13.0 is the culmination of 3 months of hard work. This
out-of-band release aims to support NumPy ``2.0.0``, and is backwards
compatible to NumPy ``1.22.4``. The version of OpenBLAS used to build
the PyPI wheels has been increased to ``0.3.26.dev``.

This release requires Python 3.9+ and NumPy 1.22.4 or greater.

For running on PyPy, PyPy3 6.0+ is required.

**************************
Highlights of this release
**************************
- Support for NumPy ``2.0.0``.
- Interactive examples have been added to the documentation, allowing users
  to run the examples locally on embedded Jupyterlite notebooks in their
  browser.
- Preliminary 1D array support for the COO and DOK sparse formats.
- Several `scipy.stats` functions have gained support for additional
  ``axis``, ``nan_policy``, and ``keepdims`` arguments. `scipy.stats` also
  has several performance and accuracy improvements.

************
New features
************

`scipy.integrate` improvements
==============================
- The ``terminal`` attribute of `scipy.integrate.solve_ivp` ``events``
  callables now additionally accepts integer values to specify a number
  of occurrences required for termination, rather than the previous restriction
  of only accepting a ``bool`` value to terminate on the first registered
  event.

`scipy.io` improvements
=======================
- `scipy.io.wavfile.write` has improved ``dtype`` input validation.

`scipy.interpolate` improvements
================================
- The Modified Akima Interpolation has been added to
  ``interpolate.Akima1DInterpolator``, available via the new ``method``
  argument.
- New method ``BSpline.insert_knot`` inserts a knot into a ``BSpline`` instance.
  This routine is similar to the module-level `scipy.interpolate.insert`
  function, and works with the BSpline objects instead of ``tck`` tuples.
- ``RegularGridInterpolator`` gained the functionality to compute derivatives
  in place. For instance, ``RegularGridInterolator((x, y), values,
  method="cubic")(xi, nu=(1, 1))`` evaluates the mixed second derivative,
  :math:`\partial^2 / \partial x \partial y` at ``xi``.
- Performance characteristics of tensor-product spline methods of
  ``RegularGridInterpolator`` have been changed: evaluations should be
  significantly faster, while construction might be slower. If you experience
  issues with construction times, you may need to experiment with optional
  keyword arguments ``solver`` and ``solver_args``. Previous behavior (fast
  construction, slow evaluations) can be obtained via `"*_legacy"` methods:
  ``method="cubic_legacy"`` is exactly equivalent to \ 
``method="cubic"`` in
  previous releases. See ``gh-19633`` for details.

`scipy.signal` improvements
===========================
- Many filter design functions now have improved input validation for the
  sampling frequency (``fs``).

`scipy.sparse` improvements
===========================
- ``coo_array`` now supports 1D shapes, and has additional 1D support for
  ``min``, ``max``, ``argmin``, and ``argmax``. The DOK format now has
  preliminary 1D support as well, though only supports simple integer indices
  at the time of writing.
- Experimental support has been added for ``pydata/sparse`` array inputs to
  `scipy.sparse.csgraph`.
- ``dok_array`` and ``dok_matrix`` now have proper implementations of
  ``fromkeys``.
- ``csr`` and ``csc`` formats now have improved ``setdiag`` performance.

`scipy.spatial` improvements
============================
- ``voronoi_plot_2d`` now draws Voronoi edges to infinity more clearly
  when the aspect ratio is skewed.

`scipy.special` improvements
============================
- All Fortran code, namely, ``AMOS``, ``specfun``, and ``cdflib`` libraries
  that the majority of special functions depend on, is ported to Cython/C.
- The function ``factorialk`` now also supports faster, approximate
  calculation using ``exact=False``.

`scipy.stats` improvements
==========================
- `scipy.stats.rankdata` and `scipy.stats.wilcoxon` have been vectorized,
  improving their performance and the performance of hypothesis tests that
  depend on them.
- ``stats.mannwhitneyu`` should now be faster due to a vectorized statistic
  calculation, improved caching, improved exploitation of symmetry, and a
  memory reduction. ``PermutationMethod`` support was also added.
- `scipy.stats.mood` now has ``nan_policy`` and ``keepdims`` support.
- `scipy.stats.brunnermunzel` now has ``axis`` and ``keepdims`` support.
- `scipy.stats.friedmanchisquare`, `scipy.stats.shapiro`,
  `scipy.stats.normaltest`, `scipy.stats.skewtest`,
  `scipy.stats.kurtosistest`, `scipy.stats.f_oneway`,
  `scipy.stats.alexandergovern`, `scipy.stats.combine_pvalues`, and
  `scipy.stats.kstest` have gained ``axis``, ``nan_policy`` and
  ``keepdims`` support.
- `scipy.stats.boxcox_normmax` has gained a ``ymax`` parameter to allow user
  specification of the maximum value of the transformed data.
- `scipy.stats.vonmises` ``pdf`` method has been extended to support
  ``kappa=0``. The ``fit`` method is also more performant due to the use of
  non-trivial bounds to solve for ``kappa``.
- High order ``moment`` calculations for `scipy.stats.powerlaw` are now more
  accurate.
- The ``fit`` methods of  `scipy.stats.gamma` (with ``method='mm'``) and
  `scipy.stats.loglaplace` are faster and more reliable.
- `scipy.stats.goodness_of_fit` now supports the use of a custom ``statistic``
  provided by the user.
- `scipy.stats.wilcoxon` now supports ``PermutationMethod``, enabling
  calculation of accurate p-values in the presence of ties and zeros.
- `scipy.stats.monte_carlo_test` now has improved robustness in the face of
  numerical noise.
- `scipy.stats.wasserstein_distance_nd` was introduced to compute the
  Wasserstein-1 distance between two N-D discrete distributions.

*******************
Deprecated features
*******************
- Complex dtypes in ``PchipInterpolator`` and ``Akima1DInterpolator`` have
  been deprecated and will raise an error in SciPy 1.15.0. If you are trying
  to use the real components of the passed array, use ``np.real`` on ``y``.

******************************
Backwards incompatible changes
******************************

*************
Other changes
*************
- The second argument of `scipy.stats.moment` has been renamed to ``order``
  while maintaining backward compatibility.

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