CVS commit: pkgsrc/math/py-scipy

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Fri May  5 14:59:26 UTC 2023

Modified Files:
        pkgsrc/math/py-scipy: Makefile PLIST distinfo
        pkgsrc/math/py-scipy/patches:
            patch-scipy_spatial_ckdtree_src_ckdtree__decl.h
            patch-scipy_stats__unuran_setup.py
Added Files:
        pkgsrc/math/py-scipy/patches: patch-scipy_special_sf__error.c
Removed Files:
        pkgsrc/math/py-scipy/patches: patch-scipy_special___logit.h

Log Message:
py-scipy: updated to 1.10.1

SciPy 1.10.1 is a bug-fix release with no new features
compared to 1.10.0.

SciPy 1.10.0 Release Notes
==========================

SciPy 1.10.0 is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. 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
1.10.x branch, and on adding new features on the main branch.

This release requires Python 3.8+ and NumPy 1.19.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

**************************
Highlights of this release
**************************

- A new dedicated datasets submodule (`scipy.datasets`) has been added, and is
  now preferred over usage of `scipy.misc` for dataset retrieval.
- A new `scipy.interpolate.make_smoothing_spline` function was added. This
  function constructs a smoothing cubic spline from noisy data, using the
  generalized cross-validation (GCV) criterion to find the tradeoff between
  smoothness and proximity to data points.
- `scipy.stats` has three new distributions, two new hypothesis tests, three
  new sample statistics, a class for greater control over calculations
  involving covariance matrices, and many other enhancements.

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

`scipy.datasets` introduction
=============================
- A new dedicated ``datasets`` submodule has been added. The submodules
  is meant for datasets that are relevant to other SciPy submodules ands
  content (tutorials, examples, tests), as well as contain a curated
  set of datasets that are of wider interest. As of this release, all
  the datasets from `scipy.misc` have been added to `scipy.datasets`
  (and deprecated in `scipy.misc`).
- The submodule is based on [Pooch](https://www.fatiando.org/pooch/latest/)
  (a new optional dependency for SciPy), a Python package to simplify fetching
  data files. This move will, in a subsequent release, facilitate SciPy
  to trim down the sdist/wheel sizes, by decoupling the data files and
  moving them out of the SciPy repository, hosting them externally and
  downloading them when requested. After downloading the datasets once,
  the files are cached to avoid network dependence and repeated usage.
- Added datasets from ``scipy.misc``: `scipy.datasets.face`,
  `scipy.datasets.ascent`, `scipy.datasets.electrocardiogram`
- Added download and caching functionality:

  - `scipy.datasets.download_all`: a function to download all the `scipy.datasets`
    associated files at once.
  - `scipy.datasets.clear_cache`: a simple utility function to clear cached dataset
    files from the file system.
  - ``scipy/datasets/_download_all.py`` can be run as a standalone script for
    packaging purposes to avoid any external dependency at build or test time.
    This can be used by SciPy packagers (e.g., for Linux distros) which may
    have to adhere to rules that forbid downloading sources from external
    repositories at package build time.

`scipy.integrate` improvements
==============================
- Added parameter ``complex_func`` to `scipy.integrate.quad`, which can be set
  ``True`` to integrate a complex integrand.

`scipy.interpolate` improvements
================================
- `scipy.interpolate.interpn` now supports tensor-product interpolation methods
  (``slinear``, ``cubic``, ``quintic`` and ``pchip``)
- Tensor-product interpolation methods (``slinear``, ``cubic``, ``quintic`` and
  ``pchip``) in `scipy.interpolate.interpn` and
  `scipy.interpolate.RegularGridInterpolator` now allow values with trailing
  dimensions.
- `scipy.interpolate.RegularGridInterpolator` has a new fast path for
  ``method="linear"`` with 2D data, and ``RegularGridInterpolator`` is now
  easier to subclass
- `scipy.interpolate.interp1d` now can take a single value for non-spline
  methods.
- A new ``extrapolate`` argument is available to `scipy.interpolate.BSpline.design_matrix`,
  allowing extrapolation based on the first and last intervals.
- A new function `scipy.interpolate.make_smoothing_spline` has been added. It is an
  implementation of the generalized cross-validation spline smoothing
  algorithm. The ``lam=None`` (default) mode of this function is a clean-room
  reimplementation of the classic ``gcvspl.f`` Fortran algorithm for
  constructing GCV splines.
- A new ``method="pchip"`` mode was aded to
  `scipy.interpolate.RegularGridInterpolator`. This mode constructs an
  interpolator using tensor products of C1-continuous monotone splines
  (essentially, a `scipy.interpolate.PchipInterpolator` instance per
  dimension).

`scipy.sparse.linalg` improvements
==================================
- The spectral 2-norm is now available in `scipy.sparse.linalg.norm`.
- The performance of `scipy.sparse.linalg.norm` for the default case (Frobenius
  norm) has been improved.
- LAPACK wrappers were added for ``trexc`` and ``trsen``.
- The `scipy.sparse.linalg.lobpcg` algorithm was rewritten, yielding
  the following improvements:

  - a simple tunable restart potentially increases the attainable
    accuracy for edge cases,
  - internal postprocessing runs one final exact Rayleigh-Ritz method
    giving more accurate and orthonormal eigenvectors,
  - output the computed iterate with the smallest max norm of the residual
    and drop the history of subsequent iterations,
  - remove the check for ``LinearOperator`` format input and thus allow
    a simple function handle of a callable object as an input,
  - better handling of common user errors with input data, rather
    than letting the algorithm fail.

`scipy.linalg` improvements
===========================
- `scipy.linalg.lu_factor` now accepts rectangular arrays instead of being restricted
  to square arrays.

`scipy.ndimage` improvements
============================
- The new `scipy.ndimage.value_indices` function provides a time-efficient method to
  search for the locations of individual values with an array of image data.
- A new ``radius`` argument is supported by `scipy.ndimage.gaussian_filter1d` and
  `scipy.ndimage.gaussian_filter` for adjusting the kernel size of the filter.

`scipy.optimize` improvements
=============================
- `scipy.optimize.brute` now coerces non-iterable/single-value ``args`` into a
  tuple.
- `scipy.optimize.least_squares` and `scipy.optimize.curve_fit` now accept
  `scipy.optimize.Bounds` for bounds constraints.
- Added a tutorial for `scipy.optimize.milp`.
- Improved the pretty-printing of `scipy.optimize.OptimizeResult` objects.
- Additional options (``parallel``, ``threads``, ``mip_rel_gap``) can now
  be passed to `scipy.optimize.linprog` with ``method='highs'``.

`scipy.signal` improvements
===========================
- The new window function `scipy.signal.windows.lanczos` was added to compute a
  Lanczos window, also known as a sinc window.

`scipy.sparse.csgraph` improvements
===================================
- the performance of `scipy.sparse.csgraph.dijkstra` has been improved, and
  star graphs in particular see a marked performance improvement

`scipy.special` improvements
============================
- The new function `scipy.special.powm1`, a ufunc with signature
  ``powm1(x, y)``, computes ``x**y - 1``. The function avoids the loss of
  precision that can result when ``y`` is close to 0 or when ``x`` is close to
  1.
- `scipy.special.erfinv` is now more accurate as it leverages the Boost equivalent under
  the hood.

`scipy.stats` improvements
==========================
- Added `scipy.stats.goodness_of_fit`, a generalized goodness-of-fit test for
  use with any univariate distribution, any combination of known and unknown
  parameters, and several choices of test statistic (Kolmogorov-Smirnov,
  Cramer-von Mises, and Anderson-Darling).
- Improved `scipy.stats.bootstrap`: Default method ``'BCa'`` now supports
  multi-sample statistics. Also, the bootstrap distribution is returned in the
  result object, and the result object can be passed into the function as
  parameter ``bootstrap_result`` to add additional resamples or change the
  confidence interval level and type.
- Added maximum spacing estimation to `scipy.stats.fit`.
- Added the Poisson means test ("E-test") as `scipy.stats.poisson_means_test`.
- Added new sample statistics.

  - Added `scipy.stats.contingency.odds_ratio` to compute both the conditional
    and unconditional odds ratios and corresponding confidence intervals for
    2x2 contingency tables.
  - Added `scipy.stats.directional_stats` to compute sample statistics of
    n-dimensional directional data.
  - Added `scipy.stats.expectile`, which generalizes the expected value in the
    same way as quantiles are a generalization of the median.

- Added new statistical distributions.

  - Added `scipy.stats.uniform_direction`, a multivariate distribution to
    sample uniformly from the surface of a hypersphere.
  - Added `scipy.stats.random_table`, a multivariate distribution to sample
    uniformly from m x n contingency tables with provided marginals.
  - Added `scipy.stats.truncpareto`, the truncated Pareto distribution.

- Improved the ``fit`` method of several distributions.

  - `scipy.stats.skewnorm` and `scipy.stats.weibull_min` now use an analytical
    solution when ``method='mm'``, which also serves a starting guess to
    improve the performance of ``method='mle'``.
  - `scipy.stats.gumbel_r` and `scipy.stats.gumbel_l`: analytical maximum
    likelihood estimates have been extended to the cases in which location or
    scale are fixed by the user.
  - Analytical maximum likelihood estimates have been added for
    `scipy.stats.powerlaw`.

- Improved random variate sampling of several distributions.

  - Drawing multiple samples from `scipy.stats.matrix_normal`,
    `scipy.stats.ortho_group`, `scipy.stats.special_ortho_group`, and
    `scipy.stats.unitary_group` is faster.
  - The ``rvs`` method of `scipy.stats.vonmises` now wraps to the interval
    ``[-np.pi, np.pi]``.
  - Improved the reliability of `scipy.stats.loggamma` ``rvs`` method for small
    values of the shape parameter.

- Improved the speed and/or accuracy of functions of several statistical
  distributions.

  - Added `scipy.stats.Covariance` for better speed, accuracy, and user control
    in multivariate normal calculations.
  - `scipy.stats.skewnorm` methods ``cdf``, ``sf``, ``ppf``, and ``isf``
    methods now use the implementations from Boost, improving speed while
    maintaining accuracy. The calculation of higher-order moments is also
    faster and more accurate.
  - `scipy.stats.invgauss` methods ``ppf`` and ``isf`` methods now use the
    implementations from Boost, improving speed and accuracy.
  - `scipy.stats.invweibull` methods ``sf`` and ``isf`` are more accurate for
    small probability masses.
  - `scipy.stats.nct` and `scipy.stats.ncx2` now rely on the implementations
    from Boost, improving speed and accuracy.
  - Implemented the ``logpdf`` method of `scipy.stats.vonmises` for reliability
    in extreme tails.
  - Implemented the ``isf`` method of `scipy.stats.levy` for speed and
    accuracy.
  - Improved the robustness of `scipy.stats.studentized_range` for large ``df``
    by adding an infinite degree-of-freedom approximation.
  - Added a parameter ``lower_limit`` to `scipy.stats.multivariate_normal`,
    allowing the user to change the integration limit from -inf to a desired
    value.
  - Improved the robustness of ``entropy`` of `scipy.stats.vonmises` for large
    concentration values.

- Enhanced `scipy.stats.gaussian_kde`.

  - Added `scipy.stats.gaussian_kde.marginal`, which returns the desired
    marginal distribution of the original kernel density estimate distribution.
  - The ``cdf`` method of `scipy.stats.gaussian_kde` now accepts a
    ``lower_limit`` parameter for integrating the PDF over a rectangular region.
  - Moved calculations for `scipy.stats.gaussian_kde.logpdf` to Cython,
    improving speed.
  - The global interpreter lock is released by the ``pdf`` method of
    `scipy.stats.gaussian_kde` for improved multithreading performance.
  - Replaced explicit matrix inversion with Cholesky decomposition for speed
    and accuracy.

- Enhanced the result objects returned by many `scipy.stats` functions

  - Added a ``confidence_interval`` method to the result object returned by
    `scipy.stats.ttest_1samp` and `scipy.stats.ttest_rel`.
  - The `scipy.stats` functions ``combine_pvalues``, ``fisher_exact``,
    ``chi2_contingency``, ``median_test`` and ``mood`` now return
    bunch objects rather than plain tuples, allowing attributes to be
    accessed by name.
  - Attributes of the result objects returned by ``multiscale_graphcorr``,
    ``anderson_ksamp``, ``binomtest``, ``crosstab``, ``pointbiserialr``,
    ``spearmanr``, ``kendalltau``, and ``weightedtau`` have been renamed to
    ``statistic`` and ``pvalue`` for consistency throughout `scipy.stats`.
    Old attribute names are still allowed for backward compatibility.
  - `scipy.stats.anderson` now returns the parameters of the fitted
    distribution in a `scipy.stats._result_classes.FitResult` object.
  - The ``plot`` method of `scipy.stats._result_classes.FitResult` now accepts
    a ``plot_type`` parameter; the options are ``'hist'`` (histogram, default),
    ``'qq'`` (Q-Q plot), ``'pp'`` (P-P plot), and ``'cdf'`` (empirical CDF
    plot).
  - Kolmogorov-Smirnov tests (e.g. `scipy.stats.kstest`) now return the
    location (argmax) at which the statistic is calculated and the variant
    of the statistic used.

- Improved the performance of several `scipy.stats` functions.

  - Improved the performance of `scipy.stats.cramervonmises_2samp` and
    `scipy.stats.ks_2samp` with ``method='exact'``.
  - Improved the performance of `scipy.stats.siegelslopes`.
  - Improved the performance of `scipy.stats.mstats.hdquantile_sd`.
  - Improved the performance of `scipy.stats.binned_statistic_dd` for several
    NumPy statistics, and binned statistics methods now support complex data.

- Added the ``scramble`` optional argument to `scipy.stats.qmc.LatinHypercube`.
  It replaces ``centered``, which is now deprecated.
- Added a parameter ``optimization`` to all `scipy.stats.qmc.QMCEngine`
  subclasses to improve characteristics of the quasi-random variates.
- Added tie correction to `scipy.stats.mood`.
- Added tutorials for resampling methods in `scipy.stats`.
- `scipy.stats.bootstrap`, `scipy.stats.permutation_test`, and
  `scipy.stats.monte_carlo_test` now automatically detect whether the provided
  ``statistic`` is vectorized, so passing the ``vectorized`` argument
  explicitly is no longer required to take advantage of vectorized statistics.
- Improved the speed of `scipy.stats.permutation_test` for permutation types
  ``'samples'`` and ``'pairings'``.
- Added ``axis``, ``nan_policy``, and masked array support to
  `scipy.stats.jarque_bera`.
- Added the ``nan_policy`` optional argument to `scipy.stats.rankdata`.

*******************
Deprecated features
*******************
- `scipy.misc` module and all the methods in ``misc`` are deprecated in v1.10
  and will be completely removed in SciPy v2.0.0. Users are suggested to
  utilize the `scipy.datasets` module instead for the dataset methods.
- `scipy.stats.qmc.LatinHypercube` parameter ``centered`` has been deprecated.
  It is replaced by the ``scramble`` argument for more consistency with other
  QMC engines.
- `scipy.interpolate.interp2d` class has been deprecated.  The docstring of the
  deprecated routine lists recommended replacements.

********************
Expired Deprecations
********************
- There is an ongoing effort to follow through on long-standing deprecations.
- The following previously deprecated features are affected:

  - Removed ``cond`` & ``rcond`` kwargs in ``linalg.pinv``
  - Removed wrappers ``scipy.linalg.blas.{clapack, flapack}``
  - Removed ``scipy.stats.NumericalInverseHermite`` and removed ``tol`` & ``max_intervals`` kwargs from ``scipy.stats.sampling.NumericalInverseHermite``
  - Removed ``local_search_options`` kwarg frrom ``scipy.optimize.dual_annealing``.

*************
Other changes
*************
- `scipy.stats.bootstrap`, `scipy.stats.permutation_test`, and
  `scipy.stats.monte_carlo_test` now automatically detect whether the provided
  ``statistic`` is vectorized by looking for an ``axis`` parameter in the
  signature of ``statistic``. If an ``axis`` parameter is present in
  ``statistic`` but should not be relied on for vectorized calls, users must
  pass option ``vectorized==False`` explicitly.
- `scipy.stats.multivariate_normal` will now raise a ``ValueError`` when the
  covariance matrix is not positive semidefinite, regardless of which method
  is called.


To generate a diff of this commit:
cvs rdiff -u -r1.64 -r1.65 pkgsrc/math/py-scipy/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/math/py-scipy/PLIST
cvs rdiff -u -r1.41 -r1.42 pkgsrc/math/py-scipy/distinfo
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h
cvs rdiff -u -r1.2 -r0 \
    pkgsrc/math/py-scipy/patches/patch-scipy_special___logit.h
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/math/py-scipy/patches/patch-scipy_special_sf__error.c
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-scipy/Makefile
diff -u pkgsrc/math/py-scipy/Makefile:1.64 pkgsrc/math/py-scipy/Makefile:1.65
--- pkgsrc/math/py-scipy/Makefile:1.64  Wed Jan 25 09:08:20 2023
+++ pkgsrc/math/py-scipy/Makefile       Fri May  5 14:59:25 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.64 2023/01/25 09:08:20 wiz Exp $
+# $NetBSD: Makefile,v 1.65 2023/05/05 14:59:25 adam Exp $
 
-DISTNAME=      scipy-1.9.3
+DISTNAME=      scipy-1.10.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scipy/}
@@ -12,12 +12,17 @@ LICENSE=    modified-bsd
 
 DEPENDS+=      ${PYPKGPREFIX}-pybind11-[0-9]*:../../devel/py-pybind11
 DEPENDS+=      ${PYPKGPREFIX}-pythran>=0.9.11:../../math/py-pythran
+TEST_DEPENDS+= ${PYPKGPREFIX}-mpmath-[0-9]*:../../math/py-mpmath
 TEST_DEPENDS+= ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
+TEST_DEPENDS+= ${PYPKGPREFIX}-pooch-[0-9]*:../../devel/py-pooch
 TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-cov-[0-9]*:../../devel/py-test-cov
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-timeout-[0-9]*:../../devel/py-test-timeout
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-xdist-[0-9]*:../../devel/py-test-xdist
 
-USE_LANGUAGES+=        c c++ fortran
+USE_LANGUAGES+=        c99 c++11 fortran
 MAKE_ENV+=     ATLAS=None
-
+GCC_REQD+=     8
 EGG_NAME=      ${DISTNAME:S/scipy/SciPy/}
 
 # XXX Avoid picking up other compilers when installed

Index: pkgsrc/math/py-scipy/PLIST
diff -u pkgsrc/math/py-scipy/PLIST:1.23 pkgsrc/math/py-scipy/PLIST:1.24
--- pkgsrc/math/py-scipy/PLIST:1.23     Wed Oct  5 20:54:31 2022
+++ pkgsrc/math/py-scipy/PLIST  Fri May  5 14:59:25 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.23 2022/10/05 20:54:31 adam Exp $
+@comment $NetBSD: PLIST,v 1.24 2023/05/05 14:59:25 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -24,12 +24,6 @@ ${PYSITELIB}/scipy/_build_utils/_fortran
 ${PYSITELIB}/scipy/_build_utils/compiler_helper.py
 ${PYSITELIB}/scipy/_build_utils/compiler_helper.pyc
 ${PYSITELIB}/scipy/_build_utils/compiler_helper.pyo
-${PYSITELIB}/scipy/_build_utils/copyfiles.py
-${PYSITELIB}/scipy/_build_utils/copyfiles.pyc
-${PYSITELIB}/scipy/_build_utils/copyfiles.pyo
-${PYSITELIB}/scipy/_build_utils/cythoner.py
-${PYSITELIB}/scipy/_build_utils/cythoner.pyc
-${PYSITELIB}/scipy/_build_utils/cythoner.pyo
 ${PYSITELIB}/scipy/_build_utils/gcc_build_bitness.py
 ${PYSITELIB}/scipy/_build_utils/gcc_build_bitness.pyc
 ${PYSITELIB}/scipy/_build_utils/gcc_build_bitness.pyo
@@ -66,6 +60,9 @@ ${PYSITELIB}/scipy/_lib/_disjoint_set.py
 ${PYSITELIB}/scipy/_lib/_docscrape.py
 ${PYSITELIB}/scipy/_lib/_docscrape.pyc
 ${PYSITELIB}/scipy/_lib/_docscrape.pyo
+${PYSITELIB}/scipy/_lib/_finite_differences.py
+${PYSITELIB}/scipy/_lib/_finite_differences.pyc
+${PYSITELIB}/scipy/_lib/_finite_differences.pyo
 ${PYSITELIB}/scipy/_lib/_fpumode.so
 ${PYSITELIB}/scipy/_lib/_gcutils.py
 ${PYSITELIB}/scipy/_lib/_gcutils.pyc
@@ -180,6 +177,27 @@ ${PYSITELIB}/scipy/constants/tests/__ini
 ${PYSITELIB}/scipy/constants/tests/meson.build
 ${PYSITELIB}/scipy/constants/tests/test_codata.py
 ${PYSITELIB}/scipy/constants/tests/test_constants.py
+${PYSITELIB}/scipy/datasets/__init__.py
+${PYSITELIB}/scipy/datasets/__init__.pyc
+${PYSITELIB}/scipy/datasets/__init__.pyo
+${PYSITELIB}/scipy/datasets/_download_all.py
+${PYSITELIB}/scipy/datasets/_download_all.pyc
+${PYSITELIB}/scipy/datasets/_download_all.pyo
+${PYSITELIB}/scipy/datasets/_fetchers.py
+${PYSITELIB}/scipy/datasets/_fetchers.pyc
+${PYSITELIB}/scipy/datasets/_fetchers.pyo
+${PYSITELIB}/scipy/datasets/_registry.py
+${PYSITELIB}/scipy/datasets/_registry.pyc
+${PYSITELIB}/scipy/datasets/_registry.pyo
+${PYSITELIB}/scipy/datasets/_utils.py
+${PYSITELIB}/scipy/datasets/_utils.pyc
+${PYSITELIB}/scipy/datasets/_utils.pyo
+${PYSITELIB}/scipy/datasets/setup.py
+${PYSITELIB}/scipy/datasets/setup.pyc
+${PYSITELIB}/scipy/datasets/setup.pyo
+${PYSITELIB}/scipy/datasets/tests/__init__.py
+${PYSITELIB}/scipy/datasets/tests/meson.build
+${PYSITELIB}/scipy/datasets/tests/test_data.py
 ${PYSITELIB}/scipy/doc_requirements.txt
 ${PYSITELIB}/scipy/fft/__init__.py
 ${PYSITELIB}/scipy/fft/__init__.pyc
@@ -323,6 +341,7 @@ ${PYSITELIB}/scipy/integrate/_ivp/rk.pyo
 ${PYSITELIB}/scipy/integrate/_ivp/setup.py
 ${PYSITELIB}/scipy/integrate/_ivp/setup.pyc
 ${PYSITELIB}/scipy/integrate/_ivp/setup.pyo
+${PYSITELIB}/scipy/integrate/_ivp/tests/__init__.py
 ${PYSITELIB}/scipy/integrate/_ivp/tests/meson.build
 ${PYSITELIB}/scipy/integrate/_ivp/tests/test_ivp.py
 ${PYSITELIB}/scipy/integrate/_ivp/tests/test_rk.py
@@ -426,6 +445,7 @@ ${PYSITELIB}/scipy/interpolate/_rbfinter
 ${PYSITELIB}/scipy/interpolate/_rgi.py
 ${PYSITELIB}/scipy/interpolate/_rgi.pyc
 ${PYSITELIB}/scipy/interpolate/_rgi.pyo
+${PYSITELIB}/scipy/interpolate/_rgi_cython.so
 ${PYSITELIB}/scipy/interpolate/dfitpack.so
 ${PYSITELIB}/scipy/interpolate/fitpack.py
 ${PYSITELIB}/scipy/interpolate/fitpack.pyc
@@ -452,6 +472,7 @@ ${PYSITELIB}/scipy/interpolate/setup.pyo
 ${PYSITELIB}/scipy/interpolate/tests/__init__.py
 ${PYSITELIB}/scipy/interpolate/tests/data/bug-1310.npz
 ${PYSITELIB}/scipy/interpolate/tests/data/estimate_gradients_hang.npy
+${PYSITELIB}/scipy/interpolate/tests/data/gcvspl.npz
 ${PYSITELIB}/scipy/interpolate/tests/meson.build
 ${PYSITELIB}/scipy/interpolate/tests/test_bsplines.py
 ${PYSITELIB}/scipy/interpolate/tests/test_fitpack.py
@@ -1014,6 +1035,7 @@ ${PYSITELIB}/scipy/misc/setup.pyo
 ${PYSITELIB}/scipy/misc/tests/__init__.py
 ${PYSITELIB}/scipy/misc/tests/meson.build
 ${PYSITELIB}/scipy/misc/tests/test_common.py
+${PYSITELIB}/scipy/misc/tests/test_config.py
 ${PYSITELIB}/scipy/misc/tests/test_doccer.py
 ${PYSITELIB}/scipy/mypy_requirements.txt
 ${PYSITELIB}/scipy/ndimage/__init__.py
@@ -1770,7 +1792,6 @@ ${PYSITELIB}/scipy/sparse/linalg/_isolve
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/setup.pyc
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/setup.pyo
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/tests/__init__.py
-${PYSITELIB}/scipy/sparse/linalg/_isolve/tests/demo_lgmres.py
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/tests/meson.build
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py
 ${PYSITELIB}/scipy/sparse/linalg/_isolve/tests/test_iterative.py
@@ -2048,8 +2069,8 @@ ${PYSITELIB}/scipy/special/_spfun_stats.
 ${PYSITELIB}/scipy/special/_spherical_bessel.py
 ${PYSITELIB}/scipy/special/_spherical_bessel.pyc
 ${PYSITELIB}/scipy/special/_spherical_bessel.pyo
-${PYSITELIB}/scipy/special/_test_round.pyi
-${PYSITELIB}/scipy/special/_test_round.so
+${PYSITELIB}/scipy/special/_test_internal.pyi
+${PYSITELIB}/scipy/special/_test_internal.so
 ${PYSITELIB}/scipy/special/_testutils.py
 ${PYSITELIB}/scipy/special/_testutils.pyc
 ${PYSITELIB}/scipy/special/_testutils.pyo
@@ -2093,6 +2114,7 @@ ${PYSITELIB}/scipy/special/tests/test_cd
 ${PYSITELIB}/scipy/special/tests/test_cosine_distr.py
 ${PYSITELIB}/scipy/special/tests/test_cython_special.py
 ${PYSITELIB}/scipy/special/tests/test_data.py
+${PYSITELIB}/scipy/special/tests/test_dd.py
 ${PYSITELIB}/scipy/special/tests/test_digamma.py
 ${PYSITELIB}/scipy/special/tests/test_ellip_harm.py
 ${PYSITELIB}/scipy/special/tests/test_erfinv.py
@@ -2117,6 +2139,7 @@ ${PYSITELIB}/scipy/special/tests/test_or
 ${PYSITELIB}/scipy/special/tests/test_owens_t.py
 ${PYSITELIB}/scipy/special/tests/test_pcf.py
 ${PYSITELIB}/scipy/special/tests/test_pdtr.py
+${PYSITELIB}/scipy/special/tests/test_powm1.py
 ${PYSITELIB}/scipy/special/tests/test_precompute_expn_asy.py
 ${PYSITELIB}/scipy/special/tests/test_precompute_gammainc.py
 ${PYSITELIB}/scipy/special/tests/test_precompute_utils.py
@@ -2151,11 +2174,15 @@ ${PYSITELIB}/scipy/stats/_boost/__init__
 ${PYSITELIB}/scipy/stats/_boost/beta_ufunc.so
 ${PYSITELIB}/scipy/stats/_boost/binom_ufunc.so
 ${PYSITELIB}/scipy/stats/_boost/hypergeom_ufunc.so
+${PYSITELIB}/scipy/stats/_boost/invgauss_ufunc.so
 ${PYSITELIB}/scipy/stats/_boost/nbinom_ufunc.so
 ${PYSITELIB}/scipy/stats/_boost/ncf_ufunc.so
+${PYSITELIB}/scipy/stats/_boost/nct_ufunc.so
+${PYSITELIB}/scipy/stats/_boost/ncx2_ufunc.so
 ${PYSITELIB}/scipy/stats/_boost/setup.py
 ${PYSITELIB}/scipy/stats/_boost/setup.pyc
 ${PYSITELIB}/scipy/stats/_boost/setup.pyo
+${PYSITELIB}/scipy/stats/_boost/skewnorm_ufunc.so
 ${PYSITELIB}/scipy/stats/_common.py
 ${PYSITELIB}/scipy/stats/_common.pyc
 ${PYSITELIB}/scipy/stats/_common.pyo
@@ -2165,6 +2192,9 @@ ${PYSITELIB}/scipy/stats/_constants.pyo
 ${PYSITELIB}/scipy/stats/_continuous_distns.py
 ${PYSITELIB}/scipy/stats/_continuous_distns.pyc
 ${PYSITELIB}/scipy/stats/_continuous_distns.pyo
+${PYSITELIB}/scipy/stats/_covariance.py
+${PYSITELIB}/scipy/stats/_covariance.pyc
+${PYSITELIB}/scipy/stats/_covariance.pyo
 ${PYSITELIB}/scipy/stats/_crosstab.py
 ${PYSITELIB}/scipy/stats/_crosstab.pyc
 ${PYSITELIB}/scipy/stats/_crosstab.pyo
@@ -2189,10 +2219,6 @@ ${PYSITELIB}/scipy/stats/_generate_pyx.p
 ${PYSITELIB}/scipy/stats/_hypotests.py
 ${PYSITELIB}/scipy/stats/_hypotests.pyc
 ${PYSITELIB}/scipy/stats/_hypotests.pyo
-${PYSITELIB}/scipy/stats/_hypotests_pythran.py
-${PYSITELIB}/scipy/stats/_hypotests_pythran.pyc
-${PYSITELIB}/scipy/stats/_hypotests_pythran.pyo
-${PYSITELIB}/scipy/stats/_hypotests_pythran.so
 ${PYSITELIB}/scipy/stats/_kde.py
 ${PYSITELIB}/scipy/stats/_kde.pyc
 ${PYSITELIB}/scipy/stats/_kde.pyo
@@ -2222,6 +2248,9 @@ ${PYSITELIB}/scipy/stats/_multivariate.p
 ${PYSITELIB}/scipy/stats/_multivariate.pyc
 ${PYSITELIB}/scipy/stats/_multivariate.pyo
 ${PYSITELIB}/scipy/stats/_mvn.so
+${PYSITELIB}/scipy/stats/_odds_ratio.py
+${PYSITELIB}/scipy/stats/_odds_ratio.pyc
+${PYSITELIB}/scipy/stats/_odds_ratio.pyo
 ${PYSITELIB}/scipy/stats/_page_trend_test.py
 ${PYSITELIB}/scipy/stats/_page_trend_test.pyc
 ${PYSITELIB}/scipy/stats/_page_trend_test.pyo
@@ -2230,6 +2259,13 @@ ${PYSITELIB}/scipy/stats/_qmc.pyc
 ${PYSITELIB}/scipy/stats/_qmc.pyo
 ${PYSITELIB}/scipy/stats/_qmc_cy.pyi
 ${PYSITELIB}/scipy/stats/_qmc_cy.so
+${PYSITELIB}/scipy/stats/_rcont/__init__.py
+${PYSITELIB}/scipy/stats/_rcont/__init__.pyc
+${PYSITELIB}/scipy/stats/_rcont/__init__.pyo
+${PYSITELIB}/scipy/stats/_rcont/rcont.so
+${PYSITELIB}/scipy/stats/_rcont/setup.py
+${PYSITELIB}/scipy/stats/_rcont/setup.pyc
+${PYSITELIB}/scipy/stats/_rcont/setup.pyo
 ${PYSITELIB}/scipy/stats/_relative_risk.py
 ${PYSITELIB}/scipy/stats/_relative_risk.pyc
 ${PYSITELIB}/scipy/stats/_relative_risk.pyo
@@ -2253,6 +2289,10 @@ ${PYSITELIB}/scipy/stats/_stats_mstats_c
 ${PYSITELIB}/scipy/stats/_stats_py.py
 ${PYSITELIB}/scipy/stats/_stats_py.pyc
 ${PYSITELIB}/scipy/stats/_stats_py.pyo
+${PYSITELIB}/scipy/stats/_stats_pythran.py
+${PYSITELIB}/scipy/stats/_stats_pythran.pyc
+${PYSITELIB}/scipy/stats/_stats_pythran.pyo
+${PYSITELIB}/scipy/stats/_stats_pythran.so
 ${PYSITELIB}/scipy/stats/_tukeylambda_stats.py
 ${PYSITELIB}/scipy/stats/_tukeylambda_stats.pyc
 ${PYSITELIB}/scipy/stats/_tukeylambda_stats.pyo
@@ -2315,6 +2355,7 @@ ${PYSITELIB}/scipy/stats/stats.pyc
 ${PYSITELIB}/scipy/stats/stats.pyo
 ${PYSITELIB}/scipy/stats/tests/__init__.py
 ${PYSITELIB}/scipy/stats/tests/common_tests.py
+${PYSITELIB}/scipy/stats/tests/data/fisher_exact_results_from_r.py
 ${PYSITELIB}/scipy/stats/tests/data/levy_stable/meson.build
 ${PYSITELIB}/scipy/stats/tests/data/levy_stable/stable-Z1-cdf-sample-data.npy
 ${PYSITELIB}/scipy/stats/tests/data/levy_stable/stable-Z1-pdf-sample-data.npy
@@ -2336,7 +2377,6 @@ ${PYSITELIB}/scipy/stats/tests/data/nist
 ${PYSITELIB}/scipy/stats/tests/data/nist_linregress/meson.build
 ${PYSITELIB}/scipy/stats/tests/data/studentized_range_mpmath_ref.json
 ${PYSITELIB}/scipy/stats/tests/meson.build
-${PYSITELIB}/scipy/stats/tests/studentized_range_mpmath_ref.py
 ${PYSITELIB}/scipy/stats/tests/test_axis_nan_policy.py
 ${PYSITELIB}/scipy/stats/tests/test_binned_statistic.py
 ${PYSITELIB}/scipy/stats/tests/test_boost_ufuncs.py
@@ -2348,12 +2388,16 @@ ${PYSITELIB}/scipy/stats/tests/test_disc
 ${PYSITELIB}/scipy/stats/tests/test_distributions.py
 ${PYSITELIB}/scipy/stats/tests/test_entropy.py
 ${PYSITELIB}/scipy/stats/tests/test_fit.py
+${PYSITELIB}/scipy/stats/tests/test_generation/generate_fisher_exact_results_from_r.R
+${PYSITELIB}/scipy/stats/tests/test_generation/meson.build
+${PYSITELIB}/scipy/stats/tests/test_generation/studentized_range_mpmath_ref.py
 ${PYSITELIB}/scipy/stats/tests/test_hypotests.py
 ${PYSITELIB}/scipy/stats/tests/test_kdeoth.py
 ${PYSITELIB}/scipy/stats/tests/test_morestats.py
 ${PYSITELIB}/scipy/stats/tests/test_mstats_basic.py
 ${PYSITELIB}/scipy/stats/tests/test_mstats_extras.py
 ${PYSITELIB}/scipy/stats/tests/test_multivariate.py
+${PYSITELIB}/scipy/stats/tests/test_odds_ratio.py
 ${PYSITELIB}/scipy/stats/tests/test_qmc.py
 ${PYSITELIB}/scipy/stats/tests/test_rank.py
 ${PYSITELIB}/scipy/stats/tests/test_relative_risk.py

Index: pkgsrc/math/py-scipy/distinfo
diff -u pkgsrc/math/py-scipy/distinfo:1.41 pkgsrc/math/py-scipy/distinfo:1.42
--- pkgsrc/math/py-scipy/distinfo:1.41  Tue May  2 06:14:35 2023
+++ pkgsrc/math/py-scipy/distinfo       Fri May  5 14:59:25 2023
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.41 2023/05/02 06:14:35 wiz Exp $
+$NetBSD: distinfo,v 1.42 2023/05/05 14:59:25 adam Exp $
 
-BLAKE2s (scipy-1.9.3.tar.gz) = a36ff01b49b034093dfdd43040a7bd1228fb5fbe823852f7fc4413d60e4c637e
-SHA512 (scipy-1.9.3.tar.gz) = 119f9a5e1ce3b4268ba38a0eb82dff78837593d9a5c5e464663925a4b3b1de060201fe568236e19ed0996a045754333c580e181c4cdec2cc707e57060f59364e
-Size (scipy-1.9.3.tar.gz) = 42075414 bytes
-SHA1 (patch-scipy_spatial_ckdtree_src_ckdtree__decl.h) = ad0e4a79af2a3b0667e61f205f5b8453ea440498
-SHA1 (patch-scipy_special___logit.h) = c729c2b73de00cad4c9ad834a79b80dea7b05af3
-SHA1 (patch-scipy_stats__unuran_setup.py) = 9839f589fdfe7f1f74e84f32526a2ce96a28d04a
+BLAKE2s (scipy-1.10.1.tar.gz) = 0ba22381e66ccc4017de0042a14410af34e44455f4c4a12b80ed3f670c0d2d72
+SHA512 (scipy-1.10.1.tar.gz) = 767e1dee6285d98e4d58d8d8d1e3654b00e3216e9ad55455fc9473f1d044bef80ecce749bcd24d8f331367b882c9c3e6b652a6e901bb4296ddc7cc44699215b6
+Size (scipy-1.10.1.tar.gz) = 42407997 bytes
+SHA1 (patch-scipy_spatial_ckdtree_src_ckdtree__decl.h) = c5684427731eef00c012b1ebc7fba00da560f493
+SHA1 (patch-scipy_special_sf__error.c) = 416489193a6ff90caaa95f489a452f23f0a27bbe
+SHA1 (patch-scipy_stats__unuran_setup.py) = ea6651d6e07781a5a600f33e5f0d251213e6c614

Index: pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h
diff -u pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h:1.2 pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h:1.3
--- pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h:1.2    Fri May 27 16:59:50 2022
+++ pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h        Fri May  5 14:59:25 2023
@@ -1,11 +1,11 @@
-$NetBSD: patch-scipy_spatial_ckdtree_src_ckdtree__decl.h,v 1.2 2022/05/27 16:59:50 tnn Exp $
+$NetBSD: patch-scipy_spatial_ckdtree_src_ckdtree__decl.h,v 1.3 2023/05/05 14:59:25 adam Exp $
 
 Many errors like this:
 scipy/spatial/ckdtree/src/query_pairs.cxx:110:16: error: argument to '__builtin_prefetch' must be a constant integer
 
---- scipy/spatial/ckdtree/src/ckdtree_decl.h.orig      2022-04-29 21:14:38.041529700 +0000
+--- scipy/spatial/ckdtree/src/ckdtree_decl.h.orig      1970-01-01 00:00:00.000000000 +0000
 +++ scipy/spatial/ckdtree/src/ckdtree_decl.h
-@@ -10,7 +10,11 @@
+@@ -9,7 +9,11 @@
  #include <numpy/npy_common.h>
  #define CKDTREE_LIKELY(x) NPY_LIKELY(x)
  #define CKDTREE_UNLIKELY(x)  NPY_UNLIKELY(x)
@@ -16,4 +16,4 @@ scipy/spatial/ckdtree/src/query_pairs.cx
 +#endif
  
  #define ckdtree_intp_t npy_intp
- #define ckdtree_isinf(x)   sc_isinf(x)
+ #define ckdtree_fmin(x, y)   fmin(x, y)

Index: pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py
diff -u pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py:1.1 pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py:1.2
--- pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py:1.1 Sat Jul 30 16:13:48 2022
+++ pkgsrc/math/py-scipy/patches/patch-scipy_stats__unuran_setup.py     Fri May  5 14:59:25 2023
@@ -1,11 +1,11 @@
-$NetBSD: patch-scipy_stats__unuran_setup.py,v 1.1 2022/07/30 16:13:48 he Exp $
+$NetBSD: patch-scipy_stats__unuran_setup.py,v 1.2 2023/05/05 14:59:25 adam Exp $
 
 On NetBSD/powerpc, you can't build with _ISOC99_SOURCE defined,
 the include of <ieeefp.h> deep down in the python headers will fail
 with undefined types.
 
---- ./scipy/stats/_unuran/setup.py.orig        2022-05-16 12:36:53.864307900 +0000
-+++ ./scipy/stats/_unuran/setup.py
+--- scipy/stats/_unuran/setup.py.orig  2022-05-16 12:36:53.864307900 +0000
++++ scipy/stats/_unuran/setup.py
 @@ -95,7 +95,6 @@ def configuration(parent_package="", top
          ("UNUR_ENABLE_INFO", "1"),
          ("VERSION", '"%s"' % UNURAN_VERSION),

Added files:

Index: pkgsrc/math/py-scipy/patches/patch-scipy_special_sf__error.c
diff -u /dev/null pkgsrc/math/py-scipy/patches/patch-scipy_special_sf__error.c:1.1
--- /dev/null   Fri May  5 14:59:26 2023
+++ pkgsrc/math/py-scipy/patches/patch-scipy_special_sf__error.c        Fri May  5 14:59:25 2023
@@ -0,0 +1,26 @@
+$NetBSD: patch-scipy_special_sf__error.c,v 1.1 2023/05/05 14:59:25 adam Exp $
+
+Workaround for https://github.com/numpy/numpy/issues/23379
+Add hack here, because sf_error.c is compiled in both _ufuncs.so and _ufuncs_cxx.so.
+
+--- scipy/special/sf_error.c.orig      2023-05-05 14:40:42.972802223 +0000
++++ scipy/special/sf_error.c
+@@ -5,6 +5,18 @@
+ 
+ #include "sf_error.h"
+ 
++#ifdef __NetBSD__
++long double log2l(long double arg) {
++    return log2(arg);
++}
++long double log1pl(long double arg) {
++    return log1p(arg);
++}
++long double expm1l(long double arg) {
++    return expm1(arg);
++}
++#endif
++
+ const char *sf_error_messages[] = {
+     "no error",
+     "singularity",