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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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Scheduled monthly dependency update for November #402

Closed pyup-bot closed 8 months ago

pyup-bot commented 9 months ago

Update pomegranate from 0.14.9 to 1.0.3.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/pomegranate - Repo: https://github.com/jmschrei/torchegranate

Update cython from 0.29.34 to 3.0.5.

Changelog ### 3.0.5 ``` ================== Bugs fixed ---------- * A compiler crash was fixed. (Github issue :issue:`5771`) * A typo in the ``always_allow_keywords`` directive for Python code was fixed. Patch by lk-1984. (Github issue :issue:`5772`) ``` ### 3.0.4 ``` ================== Features added -------------- * A new compiler directive ``show_performance_hints`` was added to disable the newly added performance hint output. (Github issue :issue:`5748`) Bugs fixed ---------- * cythonize` required ``distutils`` even for operations that did not build binaries. (Github issue :issue:`5751`) * A regression in 3.0.3 was fixed that prevented calling inline functions from another inline function in ``.pxd`` files. (Github issue :issue:`5748`) * Some C compiler warnings were resolved. Patch by Pierre Jolivet. (Github issue :issue:`5756`) ``` ### 3.0.3 ``` ================== Features added -------------- * More warnings were added to help users migrate and avoid bugs. (Github issue :issue:`5650`) * A warning-like category for performance hints was added that bypasses ``-Werror``. (Github issue :issue:`5673`) * FastGIL now uses standard ``thread_local`` in C++. (Github issue :issue:`5640`) * ``reference_wrapper`` was added to ``libcpp.functional``. Patch by Vyas Ramasubramani. (Github issue :issue:`5671`) * The ``cythonize`` command now supports the ``--cplus`` option known from the ``cython`` command. (Github issue :issue:`5736`) Bugs fixed ---------- * Performance regressions where the GIL was needlessly acquired were fixed. (Github issues :issue:`5670`, :issue:`5700`) * A reference leak for exceptions in Python 3.12 was resolved. Patch by Eric Johnson. (Github issue :issue:`5724`) * ``fastcall`` calls with keyword arguments generated incorrect C code. (Github issue :issue:`5665`) * Assigning the type converted result of a conditional (if-else) expression to ``int`` or ``bool`` variables could lead to incorrect C code. (Github issue :issue:`5731`) * Early (unlikely) failures in Python function wrappers no longer set a traceback in order to simplify the C code flow. Being mostly memory allocation errors, they probably would never have created a traceback anyway. (Github issue :issue:`5681`) * Relative cimports from packages with ``__init__.py`` files could fail. (Github issue :issue:`5715`) * Several issues with the Limited API support were resolved. (Github issues :issue:`5641`, :issue:`5648`, :issue:`5689`) * The code generated for special-casing both Cython functions and PyCFunctions was cleaned up to avoid calling C-API functions that were not meant for the other type respectively. This could previously trigger assertions in CPython debug builds and now also plays better with the Limited API. (Github issues :issue:`4804`, :issue:`5739`) * Fix some C compiler warnings. Patches by Ralf Gommers, Oleksandr Pavlyk, Sebastian Koslowski et al. (Github issues :issue:`5651`, :issue:`5663`, :issue:`5668`, :issue:`5717`, :issue:`5726`, :issue:`5734`) * Generating gdb debugging information failed when using generator expressions. Patch by Oleksandr Pavlyk. (Github issue :issue:`5552`) * Passing a ``setuptools.Extension`` into ``cythonize()`` instead of a ``distutils.Extension`` could make it miss the matching extensions. * ``cython -M`` needlessly required ``distutils``, which made it fail in Python 3.12. (Github issue :issue:`5681`) Other changes ------------- * The visible deprecation warning for ``DEF`` was removed again since it proved difficult for some users to migrate away from it. The statement is still meant to be removed at some point (and thus, like ``IF``, should not be used in new code), but the time for sunset is probably not around the corner. (Github issue :issue:`4310`) * The ``np_pythran`` option raise a ``DeprecationWarning`` if it receives other values than ``True`` and ``False``. This will eventually be disallowed (in line with all other boolean options). ``` ### 3.0.2 ``` ================== Bugs fixed ---------- * Using ``None`` as default value for arguments annotated as ``int`` could crash Cython. (Github issue :issue:`5643`) * Default values of fused types that include ``complex`` could generate invalid C code with ``-DCYTHON_CCOMPLEX=0``. (Github issue :issue:`5644`) * Using C++ enum class types in extension type method signatures could generate invalid C code. (Github issue :issue:`5637`) ``` ### 3.0.1 ``` ================== Features added -------------- * The error messages regarding exception declarations were improved in order to give better help about possible reasons and fixes. (Github issue :issue:`5547`) Bugs fixed ---------- * Memory view types in Python argument annotations no longer accept ``None``. They now require an explicit ``Optional[]`` or a ``None`` default value in order to allow ``None`` to be passed. This was an oversight in the 3.0.0 release and is a BACKWARDS INCOMPATIBLE change. However, since it only applies to code using Python syntax, it probably only applies to newly written code that was written for Cython 3.0 and can easily be adapted. In most cases, we expect that this change will avoid bugs in user code rather than produce problems. (Github issue :issue:`5612`) * ``nogil`` functions using parallel code could freeze when called with the GIL held. (Github issues :issue:`5564`, :issue:`5573`) * Relative cimports could end up searching globally and find the same package installed elsewhere, potentially in another version. (Github issue :issue:`5511`) * Attribute lookups on known standard library modules could accidentally search in the module namespace instead. (Github issue :issue:`5536`) * Using constructed C++ default arguments could generate invalid C++ code. (Github issue :issue:`5553`) * ``libcpp.memory.make_unique()`` was lacking C++ exception handling. (Github issue :issue:`5560`) * Some non-public and deprecated CAPI usages were replaced by public (and thus more future proof) API code. * Many issues with the Limited API support were resolved. Patches by Lisandro Dalcin et al. (Github issues :issue:`5549`, :issue:`5550`, :issue:`5556`, :issue:`5605`, :issue:`5617`) * Some C compiler warnings were resolved. Patches by Matti Picus et al. (Github issues :issue:`5557`, :issue:`5555`) * Large Python integers are now stored in hex instead of decimal strings to work around security limits in Python and generally speed up their Python object creation. * ``NULL`` could not be used as default for fused type pointer arguments. (Github issue :issue:`5554`) * C functions that return pointer types now return ``NULL`` as default exception value. Previously, calling code wasn't aware of this and always tested for raised exceptions. (Github issue :issue:`5554`) * Untyped literal default arguments in fused functions could generate invalid C code. (Github issue :issue:`5614`) * C variables declared as ``const`` could generate invalid C code when used in closures, generator expressions, ctuples, etc. (Github issues :issue:`5558`, :issue:`5333`) * Enums could not refer to previously defined enums in their definition. (Github issue :issue:`5602`) * The Python conversion code for anonymous C enums conflicted with regular int conversion. (Github issue :issue:`5623`) * Using memory views for property methods (and other special methods) could lead to refcounting problems. (Github issue :issue:`5571`) * Star-imports could generate code that tried to assign to constant C macros like ``PY_SSIZE_T_MAX`` and ``PY_SSIZE_T_MIN``. Patch by Philipp Wagner. (Github issue :issue:`5562`) * ``CYTHON_USE_TYPE_SPECS`` can now be (explicitly) enabled in PyPy. * The template parameter "delimeters" in the Tempita ``Template`` class was corrected to "delimiters". The old spelling is still available in the main template API but now issues a ``DeprecationWarning``. (Github issue :issue:`5608`) * The ``cython --version`` output is now less likely to reach both stdout and stderr. Patch by Eli Schwartz. (Github issue :issue:`5504`) * The sdist was missing the `Shadow.pyi` stub file. ``` ### 3.0.0 ``` ========================== Features added -------------- * Cython functions now use the `PEP-590`_ vectorcall protocol in Py3.7+. Patch by Jeroen Demeyer. (Github issue :issue:`2263`) * Unicode identifiers are supported in Cython code (`PEP-3131`_). Patch by David Woods. (Github issue :issue:`2601`) * Unicode module names and imports are supported. Patch by David Woods. (Github issue :issue:`3119`) * Annotations are no longer parsed, keeping them as strings following `PEP-563`_. Patch by David Woods. (Github issue :issue:`3285`) * Preliminary support for the CPython's ``Py_LIMITED_API`` (stable ABI) is available by setting the ``CYTHON_LIMITED_API`` C macro. Note that the support is currently in an early stage and many features do not yet work. You currently still have to define ``Py_LIMITED_API`` externally in order to restrict the API usage. This will change when the feature stabilises. Patches by Eddie Elizondo and David Woods. (Github issues :issue:`3223`, :issue:`3311`, :issue:`3501`) * The dispatch to fused functions is now linear in the number of arguments, which makes it much faster, often 2x or more, and several times faster for larger fused types with many specialisations. Patch by will-ca. (Github issue :issue:`1385`) * ``with gil/nogil`` statements can be conditional based on compile-time constants, e.g. fused type checks. Patch by Noam Hershtig. (Github issue :issue:`2579`) * ``const`` can be used together with fused types. Patch by Thomas Vincent. (Github issue :issue:`1772`) * Reimports of already imported modules are substantially faster. (Github issue :issue:`2854`) * Positional-only arguments are supported in Python functions (`PEP-570`_). Patch by Josh Tobin. (Github issue :issue:`2915`) * The ``volatile`` C modifier is supported in Cython code. Patch by Jeroen Demeyer. (Github issue :issue:`1667`) * ``cython.trashcan(True)`` can be used on an extension type to enable the CPython :ref:`trashcan`. This allows deallocating deeply recursive objects without overflowing the stack. Patch by Jeroen Demeyer. (Github issue :issue:`2842`) * Inlined properties can be defined for external extension types. Patch by Matti Picus. (Github issue :issue:`2640`, redone later in :issue:`3571`) * The ``str()`` builtin now calls ``PyObject_Str()`` instead of going through a Python call. Patch by William Ayd. (Github issue :issue:`3279`) * String concatenation can now happen in place if possible, by extending the existing string rather than always creating a new one. Patch by David Woods. (Github issue :issue:`3453`) * Multiplication of Python numbers with small constant integers is faster. (Github issue :issue:`2808`) * Some list copying is avoided internally when a new list needs to be created but we already have a fresh one. (Github issue :issue:`3494`) * Extension types that do not need their own ``tp_new`` implementation (because they have no object attributes etc.) directly inherit the implementation of their parent type if possible. (Github issue :issue:`1555`) * The attributes ``gen.gi_frame`` and ``coro.cr_frame`` of Cython compiled generators and coroutines now return an actual frame object for introspection. (Github issue :issue:`2306`) * Several declarations in ``cpython.*``, ``libc.*`` and ``libcpp.*`` were added. Patches by Jeroen Demeyer, Matthew Edwards, Chris Gyurgyik, Jerome Kieffer and Zackery Spytz. (Github issues :issue:`3468`, :issue:`3332`, :issue:`3202`, :issue:`3188`, :issue:`3179`, :issue:`2891`, :issue:`2826`, :issue:`2713`) * Deprecated NumPy API usages were removed from ``numpy.pxd``. Patch by Matti Picus. (Github issue :issue:`3365`) * ``cython.inline()`` now sets the ``NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION`` C macro automatically when ``numpy`` is imported in the code, to avoid C compiler warnings about deprecated NumPy C-API usage. * The builtin ``abs()`` function can now be used on C numbers in nogil code. Patch by Elliott Sales de Andrade. (Github issue :issue:`2748`) * `PEP-479`_ (``generator_stop``) is now enabled by default with language level 3. (Github issue :issue:`2580`) * The ``cython.view.array`` type supports inheritance. Patch by David Woods. (Github issue :issue:`3413`) * Code annotation accepts a new debugging argument ``--annotate-fullc`` that will include the complete syntax highlighted C file in the HTML output. (Github issue :issue:`2855`) * ``--no-capture`` added to ``runtests.py`` to prevent stdout/stderr capturing during srctree tests. Patch by Matti Picus. (Github issue :issue:`2701`) * ``--no-docstrings`` option added to ``cythonize`` script. Original patch by mo-han. (Github issue :issue:`2889`) * ``cygdb`` gives better error messages when it fails to initialise the Python runtime support in gdb. Patch by Volker Weissmann. (Github issue :issue:`3489`) * The Pythran ``shape`` attribute is supported. Patch by Serge Guelton. (Github issue :issue:`3307`) Bugs fixed ---------- * The unicode methods ``.upper()``, ``.lower()`` and ``.title()`` were incorrectly optimised for single character input values and only returned the first character if multiple characters should have been returned. They now use the original Python methods again. * Fused argument types were not correctly handled in type annotations and ``cython.locals()``. Patch by David Woods. (Github issues :issue:`3391`, :issue:`3142`) * Diverging from the usual behaviour, ``len(memoryview)``, ``len(char*)`` and ``len(Py_UNICODE*)`` returned an unsigned ``size_t`` value. They now return a signed ``Py_ssize_t``, like other usages of ``len()``. * Nested dict literals in function call kwargs could incorrectly raise an error about duplicate keyword arguments, which are allowed when passing them from dict literals. (Github issue :issue:`2963`) * Item access (subscripting) with integer indices/keys always tried the Sequence protocol before the Mapping protocol, which diverged from Python semantics. It now passes through the Mapping protocol first when supported. (Github issue :issue:`1807`) * Name lookups in class bodies no longer go through an attribute lookup. Patch by Jeroen Demeyer. (Github issue :issue:`3100`) * Broadcast assignments to a multi-dimensional memory view slice could end up in the wrong places when the underlying memory view is known to be contiguous but the slice is not. (Github issue :issue:`2941`) * Pickling unbound methods of Python classes failed. Patch by Pierre Glaser. (Github issue :issue:`2972`) * The ``Py_hash_t`` type failed to accept arbitrary "index" values. (Github issue :issue:`2752`) * The first function line number of functions with decorators pointed to the signature line and not the first decorator line, as in Python. Patch by Felix Kohlgrüber. (Github issue :issue:`2536`) * Constant integer expressions that used a negative exponent were evaluated as integer 0 instead of the expected float value. Patch by Kryštof Pilnáček. (Github issue :issue:`2133`) * The ``cython.declare()`` and ``cython.cast()`` functions could fail in pure mode. Patch by Dmitry Shesterkin. (Github issue :issue:`3244`) * ``__doc__`` was not available inside of the class body during class creation. (Github issue :issue:`1635`) * Setting ``language_level=2`` in a file did not work if ``language_level=3`` was enabled globally before. Patch by Jeroen Demeyer. (Github issue :issue:`2791`) * ``__init__.pyx`` files were not always considered as package indicators. (Github issue :issue:`2665`) * Compiling package ``__init__`` files could fail under Windows due to an undefined export symbol. (Github issue :issue:`2968`) * A C compiler cast warning was resolved. Patch by Michael Buesch. (Github issue :issue:`2775`) * Binding staticmethods of Cython functions were not behaving like Python methods. Patch by Jeroen Demeyer. (Github issue :issue:`3106`, :issue:`3102`) * Memoryviews failed to compile when the ``cache_builtins`` feature was disabled. Patch by David Woods. (Github issue :issue:`3406`) Other changes ------------- * The default language level was changed to ``3str``, i.e. Python 3 semantics, but with ``str`` literals (also in Python 2.7). This is a backwards incompatible change from the previous default of Python 2 semantics. The previous behaviour is available through the directive ``language_level=2``. (Github issue :issue:`2565`) * Cython no longer generates ``__qualname__`` attributes for classes in Python 2.x since they are problematic there and not correctly maintained for subclasses. Patch by Jeroen Demeyer. (Github issue :issue:`2772`) * Source file fingerprinting now uses SHA-1 instead of MD5 since the latter tends to be slower and less widely supported these days. (Github issue :issue:`2790`) * The long deprecated include files ``python_*``, ``stdio``, ``stdlib`` and ``stl`` in ``Cython/Includes/Deprecated/`` were removed. Use the ``libc.*`` and ``cpython.*`` pxd modules instead. Patch by Jeroen Demeyer. (Github issue :issue:`2904`) * The search order for include files was changed. Previously it was ``include_directories``, ``Cython/Includes``, ``sys.path``. Now it is ``include_directories``, ``sys.path``, ``Cython/Includes``. This was done to allow third-party ``*.pxd`` files to override the ones in Cython. Patch by Matti Picus. (Github issue :issue:`2905`) * The command line parser was rewritten and modernised using ``argparse``. Patch by Egor Dranischnikow. (Github issue :issue:`2952`, :issue:`3001`) * Dotted filenames for qualified module names (``pkg.mod.pyx``) are deprecated. Use the normal Python package directory layout instead. (Github issue :issue:`2686`) * Binary Linux wheels now follow the manylinux2010 standard. Patch by Alexey Stepanov. (Github issue :issue:`3355`) * Support for Python 2.6 was removed. .. _`PEP-560`: https://www.python.org/dev/peps/pep-0560 .. _`PEP-570`: https://www.python.org/dev/peps/pep-0570 .. _`PEP-487`: https://www.python.org/dev/peps/pep-0487 .. _`PEP-590`: https://www.python.org/dev/peps/pep-0590 .. _`PEP-3131`: https://www.python.org/dev/peps/pep-3131 .. _`PEP-563`: https://www.python.org/dev/peps/pep-0563 .. _`PEP-479`: https://www.python.org/dev/peps/pep-0479 ``` ### 0.29.36 ``` ==================== Bugs fixed ---------- * Async generators lost their return value in PyPy. (Github issue :issue:`5465`) * The outdated C macro ``_PyGC_FINALIZED()`` is no longer used in Py3.9+. * The deprecated ``Py_OptimizeFlag`` is no longer used in Python 3.9+. (Github issue :issue:`5343`) * Using the global ``__debug__`` variable but not assertions could lead to compile errors. * The broken HTML template support was removed from Tempita. (Github issue :issue:`3309`) ``` ### 0.29.35 ``` ==================== Bugs fixed ---------- * A garbage collection enabled subtype of a non-GC extension type could call into the deallocation function of the super type with GC tracking enabled. This could lead to crashes during deallocation if GC was triggered on the type at the same time. (Github issue :issue:`5432`) * Some C compile failures and crashes in CPython 3.12 were resolved. * ``except + nogil`` was syntactically not allowed. ``except +nogil`` (i.e. defining a C++ exception handling function called ``nogil``) is now disallowed to prevent typos. (Github issue :issue:`5430`) * A C compile failure in PyPy 3.10 was resolved. Patch by Matti Picus. (Github issue :issue:`5408`) * Cython modules now use PEP-489 multi-phase init by default in PyPy 3.9 and later. Original patch by Matti Picus. (Github issue :issue:`5413`) * API header files generated by different Cython versions can now be included in the same C file. (Github issue :issue:`5383`) * Function signatures containing a type like `tuple[()]` could not be printed. Patch by Lisandro Dalcin. (Github issue :issue:`5355`) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://data.safetycli.com/changelogs/cython/ - Homepage: https://cython.org/

Update numpy from 1.24.3 to 1.26.1.

Changelog ### 1.26.1 ``` discovered after the 1.26.0 release. In addition, it adds new functionality for detecting BLAS and LAPACK when building from source. Highlights are: - Improved detection of BLAS and LAPACK libraries for meson builds - Pickle compatibility with the upcoming NumPy 2.0. The 1.26.release series is the last planned minor release series before NumPy 2.0. The Python versions supported by this release are 3.9-3.12. Build system changes Improved BLAS/LAPACK detection and control Auto-detection for a number of BLAS and LAPACK is now implemented for Meson. By default, the build system will try to detect MKL, Accelerate (on macOS \>=13.3), OpenBLAS, FlexiBLAS, BLIS and reference BLAS/LAPACK. Support for MKL was significantly improved, and support for FlexiBLAS was added. New command-line flags are available to further control the selection of the BLAS and LAPACK libraries to build against. To select a specific library, use the config-settings interface via `pip` or `pypa/build`. E.g., to select `libblas`/`liblapack`, use: $ pip install numpy -Csetup-args=-Dblas=blas -Csetup-args=-Dlapack=lapack $ OR $ python -m build . -Csetup-args=-Dblas=blas -Csetup-args=-Dlapack=lapack This works not only for the libraries named above, but for any library that Meson is able to detect with the given name through `pkg-config` or CMake. Besides `-Dblas` and `-Dlapack`, a number of other new flags are available to control BLAS/LAPACK selection and behavior: - `-Dblas-order` and `-Dlapack-order`: a list of library names to search for in order, overriding the default search order. - `-Duse-ilp64`: if set to `true`, use ILP64 (64-bit integer) BLAS and LAPACK. Note that with this release, ILP64 support has been extended to include MKL and FlexiBLAS. OpenBLAS and Accelerate were supported in previous releases. - `-Dallow-noblas`: if set to `true`, allow NumPy to build with its internal (very slow) fallback routines instead of linking against an external BLAS/LAPACK library. *The default for this flag may be changed to \`\`true\`\` in a future 1.26.x release, however for 1.26.1 we\'d prefer to keep it as \`\`false\`\` because if failures to detect an installed library are happening, we\'d like a bug report for that, so we can quickly assess whether the new auto-detection machinery needs further improvements.* - `-Dmkl-threading`: to select the threading layer for MKL. There are four options: `seq`, `iomp`, `gomp` and `tbb`. The default is `auto`, which selects from those four as appropriate given the version of MKL selected. - `-Dblas-symbol-suffix`: manually select the symbol suffix to use for the library - should only be needed for linking against libraries built in a non-standard way. New features `numpy._core` submodule stubs `numpy._core` submodule stubs were added to provide compatibility with pickled arrays created using NumPy 2.0 when running Numpy 1.26. Contributors A total of 13 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Andrew Nelson - Anton Prosekin + - Charles Harris - Chongyun Lee + - Ivan A. Melnikov + - Jake Lishman + - Mahder Gebremedhin + - Mateusz Sokół - Matti Picus - Munira Alduraibi + - Ralf Gommers - Rohit Goswami - Sayed Adel Pull requests merged A total of 20 pull requests were merged for this release. - [24742](https://github.com/numpy/numpy/pull/24742): MAINT: Update cibuildwheel version - [24748](https://github.com/numpy/numpy/pull/24748): MAINT: fix version string in wheels built with setup.py - [24771](https://github.com/numpy/numpy/pull/24771): BLD, BUG: Fix build failure for host flags e.g. `-march=native`\... - [24773](https://github.com/numpy/numpy/pull/24773): DOC: Updated the f2py docs to remove a note on -fimplicit-none - [24776](https://github.com/numpy/numpy/pull/24776): BUG: Fix SIMD f32 trunc test on s390x when baseline is none - [24785](https://github.com/numpy/numpy/pull/24785): BLD: add libquadmath to licences and other tweaks (#24753) - [24786](https://github.com/numpy/numpy/pull/24786): MAINT: Activate `use-compute-credits` for Cirrus. - [24803](https://github.com/numpy/numpy/pull/24803): BLD: updated vendored-meson/meson for mips64 fix - [24804](https://github.com/numpy/numpy/pull/24804): MAINT: fix licence path win - [24813](https://github.com/numpy/numpy/pull/24813): BUG: Fix order of Windows OS detection macros. - [24831](https://github.com/numpy/numpy/pull/24831): BUG, SIMD: use scalar cmul on bad Apple clang x86_64 (#24828) - [24840](https://github.com/numpy/numpy/pull/24840): BUG: Fix DATA statements for f2py - [24870](https://github.com/numpy/numpy/pull/24870): API: Add `NumpyUnpickler` for backporting - [24872](https://github.com/numpy/numpy/pull/24872): MAINT: Xfail test failing on PyPy. - [24879](https://github.com/numpy/numpy/pull/24879): BLD: fix math func feature checks, fix FreeBSD build, add CI\... - [24899](https://github.com/numpy/numpy/pull/24899): ENH: meson: implement BLAS/LAPACK auto-detection and many CI\... - [24902](https://github.com/numpy/numpy/pull/24902): DOC: add a 1.26.1 release notes section for BLAS/LAPACK build\... - [24906](https://github.com/numpy/numpy/pull/24906): MAINT: Backport `numpy._core` stubs. 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Python 3.12 dropped distutils, consequently supporting it required finding a replacement for the setup.py/distutils based build system NumPy was using. We have chosen to use the Meson build system instead, and this is the first NumPy release supporting it. This is also the first release that supports Cython 3.0 in addition to retaining 0.29.X compatibility. Supporting those two upgrades was a large project, over 100 files have been touched in this release. The changelog doesn\'t capture the full extent of the work, special thanks to Ralf Gommers, Sayed Adel, Stéfan van der Walt, and Matti Picus who did much of the work in the main development branch. The highlights of this release are: - Python 3.12.0 support. - Cython 3.0.0 compatibility. - Use of the Meson build system - Updated SIMD support The Python versions supported in this release are 3.9-3.12. Build system changes In this release, NumPy has switched to Meson as the build system and meson-python as the build backend. Installing NumPy or building a wheel can be done with standard tools like `pip` and `pypa/build`. The following are supported: - Regular installs: `pip install numpy` or (in a cloned repo) `pip install .` - Building a wheel: `python -m build` (preferred), or `pip wheel .` - Editable installs: `pip install -e . --no-build-isolation` - Development builds through the custom CLI implemented with [spin](https://github.com/scientific-python/spin): `spin build`. All the regular `pip` and `pypa/build` flags (e.g., `--no-build-isolation`) should work as expected. NumPy-specific build customization Many of the NumPy-specific ways of customizing builds have changed. The `NPY_*` environment variables which control BLAS/LAPACK, SIMD, threading, and other such options are no longer supported, nor is a `site.cfg` file to select BLAS and LAPACK. Instead, there are command-line flags that can be passed to the build via `pip`/`build`\'s config-settings interface. These flags are all listed in the `meson_options.txt` file in the root of the repo. Detailed documented will be available before the final 1.26.0 release; for now please see [the SciPy \"building from source\"docs](http://scipy.github.io/devdocs/building/index.html) since most build customization works in an almost identical way in SciPy as it does in NumPy. Build dependencies While the runtime dependencies of NumPy have not changed, the build dependencies have. Because we temporarily vendor Meson and meson-python, there are several new dependencies - please see the `[build-system]` section of `pyproject.toml` for details. Troubleshooting This build system change is quite large. In case of unexpected issues, it is still possible to use a `setup.py`-based build as a temporary workaround (on Python 3.9-3.11, not 3.12), by copying `pyproject.toml.setuppy` to `pyproject.toml`. However, please open an issue with details on the NumPy issue tracker. We aim to phase out `setup.py` builds as soon as possible, and therefore would like to see all potential blockers surfaced early on in the 1.26.0 release cycle. Contributors A total of 11 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Bas van Beek - Charles Harris - Matti Picus - Melissa Weber Mendonça - Ralf Gommers - Sayed Adel - Sebastian Berg - Stefan van der Walt - Tyler Reddy - Warren Weckesser Pull requests merged A total of 18 pull requests were merged for this release. - [24305](https://github.com/numpy/numpy/pull/24305): MAINT: Prepare 1.26.x branch for development - [24308](https://github.com/numpy/numpy/pull/24308): MAINT: Massive update of files from main for numpy 1.26 - [24322](https://github.com/numpy/numpy/pull/24322): CI: fix wheel builds on the 1.26.x branch - [24326](https://github.com/numpy/numpy/pull/24326): BLD: update openblas to newer version - [24327](https://github.com/numpy/numpy/pull/24327): TYP: Trim down the `_NestedSequence.__getitem__` signature - [24328](https://github.com/numpy/numpy/pull/24328): BUG: fix choose refcount leak - [24337](https://github.com/numpy/numpy/pull/24337): TST: fix running the test suite in builds without BLAS/LAPACK - [24338](https://github.com/numpy/numpy/pull/24338): BUG: random: Fix generation of nan by dirichlet. - [24340](https://github.com/numpy/numpy/pull/24340): MAINT: Dependabot updates from main - [24342](https://github.com/numpy/numpy/pull/24342): MAINT: Add back NPY_RUN_MYPY_IN_TESTSUITE=1 - [24353](https://github.com/numpy/numpy/pull/24353): MAINT: Update `extbuild.py` from main. - [24356](https://github.com/numpy/numpy/pull/24356): TST: fix distutils tests for deprecations in recent setuptools\... - [24375](https://github.com/numpy/numpy/pull/24375): MAINT: Update cibuildwheel to version 2.15.0 - [24381](https://github.com/numpy/numpy/pull/24381): MAINT: Fix codespaces setup.sh script - [24403](https://github.com/numpy/numpy/pull/24403): ENH: Vendor meson for multi-target build support - [24404](https://github.com/numpy/numpy/pull/24404): BLD: vendor meson-python to make the Windows builds with SIMD\... - 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numpy-1.26.0b1-cp312-cp312-win_amd64.whl 2b258f67ca4a8245c74470da66a87684ddb3f06dde98760efc7ca792a44ee254 numpy-1.26.0b1-cp39-cp39-macosx_10_9_x86_64.whl a31d9109ffed9fc5566e73346a076fffbc7db00e626579ae4d5dfec933b29bfc numpy-1.26.0b1-cp39-cp39-macosx_11_0_arm64.whl 18e29ab806ec5e0b05df900d44b3b257a5901c32fc3ddaeb818c520cd9279b4e numpy-1.26.0b1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 216b47882877ea5272f279c08bf7e42935728f35c6db2e4843b37db7b29ce016 numpy-1.26.0b1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl eea337d6d5ab2b6eb657b3f18e8b57a280f16fb5f94df484d9c1a8d3450d9ae9 numpy-1.26.0b1-cp39-cp39-musllinux_1_1_x86_64.whl db698c9008217c54a8005ea58bd5836241d7b519c8bb16a698a1b4ec4ca296a8 numpy-1.26.0b1-cp39-cp39-win_amd64.whl f250b3099649137f1021f8f95a9404273bcb7539f0bef6d6cf2c91260285edc4 numpy-1.26.0b1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 22584a41b1be30543dd8c030affc90d8cb7ec19a56fda7f27fc33f64f8b0fbaa numpy-1.26.0b1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 8aefe8ab1228e00146e5ae88290c7fdb8221aef45b357aed7f3dff6ac3b3b25a numpy-1.26.0b1-pp39-pypy39_pp73-win_amd64.whl c67eea90827e1e9aa220a3fc380ce8776428deba8ac9e7c931ce7b69e8dce115 numpy-1.26.0b1.tar.gz ``` ### 1.25.2 ``` discovered after the 1.25.1 release. This is the last planned release in the 1.25.x series, the next release will be 1.26.0, which will use the meson build system and support Python 3.12. The Python versions supported by this release are 3.9-3.11. Contributors A total of 13 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Aaron Meurer - Andrew Nelson - Charles Harris - Kevin Sheppard - Matti Picus - Nathan Goldbaum - Peter Hawkins - Ralf Gommers - Randy Eckenrode + - Sam James + - Sebastian Berg - Tyler Reddy - dependabot\[bot\] Pull requests merged A total of 19 pull requests were merged for this release. - [24148](https://github.com/numpy/numpy/pull/24148): MAINT: prepare 1.25.x for further development - [24174](https://github.com/numpy/numpy/pull/24174): ENH: Improve clang-cl compliance - [24179](https://github.com/numpy/numpy/pull/24179): MAINT: Upgrade various build dependencies. - [24182](https://github.com/numpy/numpy/pull/24182): BLD: use `-ftrapping-math` with Clang on macOS - [24183](https://github.com/numpy/numpy/pull/24183): BUG: properly handle negative indexes in ufunc_at fast path - [24184](https://github.com/numpy/numpy/pull/24184): BUG: PyObject_IsTrue and PyObject_Not error handling in setflags - [24185](https://github.com/numpy/numpy/pull/24185): BUG: histogram small range robust - [24186](https://github.com/numpy/numpy/pull/24186): MAINT: Update meson.build files from main branch - [24234](https://github.com/numpy/numpy/pull/24234): MAINT: exclude min, max and round from `np.__all__` - [24241](https://github.com/numpy/numpy/pull/24241): MAINT: Dependabot updates - [24242](https://github.com/numpy/numpy/pull/24242): BUG: Fix the signature for np.array_api.take - [24243](https://github.com/numpy/numpy/pull/24243): BLD: update OpenBLAS to an intermeidate commit - [24244](https://github.com/numpy/numpy/pull/24244): BUG: Fix reference count leak in str(scalar). - [24245](https://github.com/numpy/numpy/pull/24245): BUG: fix invalid function pointer conversion error - [24255](https://github.com/numpy/numpy/pull/24255): BUG: Factor out slow `getenv` call used for memory policy warning - [24292](https://github.com/numpy/numpy/pull/24292): CI: correct URL in cirrus.star - [24293](https://github.com/numpy/numpy/pull/24293): BUG: Fix C types in scalartypes - [24294](https://github.com/numpy/numpy/pull/24294): BUG: do not modify the input to ufunc_at - [24295](https://github.com/numpy/numpy/pull/24295): BUG: Further fixes to indexing loop and added tests Checksums MD5 33518ccb4da8ee11f1dee4b9fef1e468 numpy-1.25.2-cp310-cp310-macosx_10_9_x86_64.whl b5cb0c3b33ef6d93ec2888f25b065636 numpy-1.25.2-cp310-cp310-macosx_11_0_arm64.whl ae027dd38bd73f09c07220b2f516f148 numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 88cf69dc3c0d293492c4c7e75dccf3d8 numpy-1.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 3e4e3ad02375ba71ae2cd05ccd97aba4 numpy-1.25.2-cp310-cp310-musllinux_1_1_x86_64.whl f52bb644682deb26c35ddec77198b65c numpy-1.25.2-cp310-cp310-win32.whl 4944cf36652be7560a6bcd0d5d56e8ea numpy-1.25.2-cp310-cp310-win_amd64.whl 5a56e639defebb7b871c8c5613960ca3 numpy-1.25.2-cp311-cp311-macosx_10_9_x86_64.whl 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1a1329e26f46230bf77b02cc19e900db9b52f398d6722ca853349a782d4cff55 numpy-1.25.2-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 4c3abc71e8b6edba80a01a52e66d83c5d14433cbcd26a40c329ec7ed09f37901 numpy-1.25.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 1b9735c27cea5d995496f46a8b1cd7b408b3f34b6d50459d9ac8fe3a20cc17bf numpy-1.25.2-pp39-pypy39_pp73-win_amd64.whl fd608e19c8d7c55021dffd43bfe5492fab8cc105cc8986f813f8c3c048b38760 numpy-1.25.2.tar.gz ``` ### 1.25.1 ``` discovered after the 1.25.0 release. The Python versions supported by this release are 3.9-3.11. Contributors A total of 10 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Andrew Nelson - Charles Harris - Developer-Ecosystem-Engineering - Hood Chatham - Nathan Goldbaum - Rohit Goswami - Sebastian Berg - Tim Paine + - dependabot\[bot\] - matoro + Pull requests merged A total of 14 pull requests were merged for this release. - [23968](https://github.com/numpy/numpy/pull/23968): MAINT: prepare 1.25.x for further development - [24036](https://github.com/numpy/numpy/pull/24036): BLD: Port long double identification to C for meson - [24037](https://github.com/numpy/numpy/pull/24037): BUG: Fix reduction `return NULL` to be `goto fail` - [24038](https://github.com/numpy/numpy/pull/24038): BUG: Avoid undefined behavior in array.astype() - [24039](https://github.com/numpy/numpy/pull/24039): BUG: Ensure `__array_ufunc__` works without any kwargs passed - [24117](https://github.com/numpy/numpy/pull/24117): MAINT: Pin urllib3 to avoid anaconda-client bug. - [24118](https://github.com/numpy/numpy/pull/24118): TST: Pin pydantic\<2 in Pyodide workflow - [24119](https://github.com/numpy/numpy/pull/24119): MAINT: Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 - [24120](https://github.com/numpy/numpy/pull/24120): MAINT: Bump actions/checkout from 3.5.2 to 3.5.3 - [24122](https://github.com/numpy/numpy/pull/24122): BUG: Multiply or Divides using SIMD without a full vector can\... - [24127](https://github.com/numpy/numpy/pull/24127): MAINT: testing for IS_MUSL closes #24074 - [24128](https://github.com/numpy/numpy/pull/24128): BUG: Only replace dtype temporarily if dimensions changed - [24129](https://github.com/numpy/numpy/pull/24129): MAINT: Bump actions/setup-node from 3.6.0 to 3.7.0 - [24134](https://github.com/numpy/numpy/pull/24134): BUG: Fix private procedures in f2py modules Checksums MD5 d09d98643db31e892fad11b8c2b7af22 numpy-1.25.1-cp310-cp310-macosx_10_9_x86_64.whl d5b8d3b0424e2af41018f35a087c4500 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numpy-1.25.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 20e1266411120a4f16fad8efa8e0454d21d00b8c7cee5b5ccad7565d95eb42dd numpy-1.25.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl f76aebc3358ade9eacf9bc2bb8ae589863a4f911611694103af05346637df1b7 numpy-1.25.1-cp39-cp39-musllinux_1_1_x86_64.whl 247d3ffdd7775bdf191f848be8d49100495114c82c2bd134e8d5d075fb386a1c numpy-1.25.1-cp39-cp39-win32.whl 1d5d3c68e443c90b38fdf8ef40e60e2538a27548b39b12b73132456847f4b631 numpy-1.25.1-cp39-cp39-win_amd64.whl 35a9527c977b924042170a0887de727cd84ff179e478481404c5dc66b4170009 numpy-1.25.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 0d3fe3dd0506a28493d82dc3cf254be8cd0d26f4008a417385cbf1ae95b54004 numpy-1.25.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 012097b5b0d00a11070e8f2e261128c44157a8689f7dedcf35576e525893f4fe numpy-1.25.1-pp39-pypy39_pp73-win_amd64.whl 9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf numpy-1.25.1.tar.gz ``` ### 1.25.0 ``` The NumPy 1.25.0 release continues the ongoing work to improve the handling and promotion of dtypes, increase the execution speed, and clarify the documentation. There has also been work to prepare for the future NumPy 2.0.0 release, resulting in a large number of new and expired deprecation. Highlights are: - Support for MUSL, there are now MUSL wheels. - Support the Fujitsu C/C++ compiler. - Object arrays are now supported in einsum - Support for inplace matrix multiplication (`=`). We will be releasing a NumPy 1.26 when Python 3.12 comes out. That is needed because distutils has been dropped by Python 3.12 and we will be switching to using meson for future builds. The next mainline release will be NumPy 2.0.0. We plan that the 2.0 series will still support downstream projects built against earlier versions of NumPy. The Python versions supported in this release are 3.9-3.11. Deprecations - `np.core.MachAr` is deprecated. It is private API. In names defined in `np.core` should generally be considered private. ([gh-22638](https://github.com/numpy/numpy/pull/22638)) - `np.finfo(None)` is deprecated. ([gh-23011](https://github.com/numpy/numpy/pull/23011)) - `np.round_` is deprecated. Use `np.round` instead. ([gh-23302](https://github.com/numpy/numpy/pull/23302)) - `np.product` is deprecated. Use `np.prod` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.cumproduct` is deprecated. Use `np.cumprod` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.sometrue` is deprecated. Use `np.any` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.alltrue` is deprecated. Use `np.all` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - Only ndim-0 arrays are treated as scalars. NumPy used to treat all arrays of size 1 (e.g., `np.array([3.14])`) as scalars. In the future, this will be limited to arrays of ndim 0 (e.g., `np.array(3.14)`). The following expressions will report a deprecation warning: python a = np.array([3.14]) float(a) better: a[0] to get the numpy.float or a.item() b = np.array([[3.14]]) c = numpy.random.rand(10) c[0] = b better: c[0] = b[0, 0] ([gh-10615](https://github.com/numpy/numpy/pull/10615)) - `numpy.find_common_type` is now deprecated and its use should be replaced with either `numpy.result_type` or `numpy.promote_types`. Most users leave the second `scalar_types` argument to `find_common_type` as `[]` in which case `np.result_type` and `np.promote_types` are both faster and more robust. When not using `scalar_types` the main difference is that the replacement intentionally converts non-native byte-order to native byte order. Further, `find_common_type` returns `object` dtype rather than failing promotion. This leads to differences when the inputs are not all numeric. Importantly, this also happens for e.g. timedelta/datetime for which NumPy promotion rules are currently sometimes surprising. When the `scalar_types` argument is not `[]` things are more complicated. In most cases, using `np.result_type` and passing the Python values `0`, `0.0`, or `0j` has the same result as using `int`, `float`, or `complex` in `scalar_types`. When `scalar_types` is constructed, `np.result_type` is the correct replacement and it may be passed scalar values like `np.float32(0.0)`. Passing values other than 0, may lead to value-inspecting behavior (which `np.find_common_type` never used and NEP 50 may change in the future). The main possible change in behavior in this case, is when the array types are signed integers and scalar types are unsigned. If you are unsure about how to replace a use of `scalar_types` or when non-numeric dtypes are likely, please do not hesitate to open a NumPy issue to ask for help. ([gh-22539](https://github.com/numpy/numpy/pull/22539)) Expired deprecations - `np.core.machar` and `np.finfo.machar` have been removed. ([gh-22638](https://github.com/numpy/numpy/pull/22638)) - `+arr` will now raise an error when the dtype is not numeric (and positive is undefined). ([gh-22998](https://github.com/numpy/numpy/pull/22998)) - A sequence must now be passed into the stacking family of functions (`stack`, `vstack`, `hstack`, `dstack` and `column_stack`). ([gh-23019](https://github.com/numpy/numpy/pull/23019)) - `np.clip` now
pyup-bot commented 8 months ago

Closing this in favor of #404