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abrahamnunes / fitr

Tools for computational psychiatry research.
https://computationalpsychiatry.github.io/fitr
GNU General Public License v3.0
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Pin numpy to latest version 2.1.0 #469

Open pyup-bot opened 2 months ago

pyup-bot commented 2 months ago

This PR pins numpy to the latest release 2.1.0.

Changelog ### 2.1.0 ``` NumPy 2.1.0 provides support for the upcoming Python 3.13 release and drops support for Python 3.9. In addition to the usual bug fixes and updated Python support, it helps get us back into our usual release cycle after the extended development of 2.0. The highlights for this release are: - Support for the array-api 2023.12 standard. - Support for Python 3.13. - Preliminary support for free threaded Python 3.13. Python versions 3.10-3.13 are supported in this release. New functions New function `numpy.unstack` A new function `np.unstack(array, axis=...)` was added, which splits an array into a tuple of arrays along an axis. It serves as the inverse of [numpy.stack]{.title-ref}. ([gh-26579](https://github.com/numpy/numpy/pull/26579)) Deprecations - The `fix_imports` keyword argument in `numpy.save` is deprecated. Since NumPy 1.17, `numpy.save` uses a pickle protocol that no longer supports Python 2, and ignored `fix_imports` keyword. This keyword is kept only for backward compatibility. It is now deprecated. ([gh-26452](https://github.com/numpy/numpy/pull/26452)) - Passing non-integer inputs as the first argument of [bincount]{.title-ref} is now deprecated, because such inputs are silently cast to integers with no warning about loss of precision. ([gh-27076](https://github.com/numpy/numpy/pull/27076)) Expired deprecations - Scalars and 0D arrays are disallowed for `numpy.nonzero` and `numpy.ndarray.nonzero`. ([gh-26268](https://github.com/numpy/numpy/pull/26268)) - `set_string_function` internal function was removed and `PyArray_SetStringFunction` was stubbed out. ([gh-26611](https://github.com/numpy/numpy/pull/26611)) C API changes API symbols now hidden but customizable NumPy now defaults to hide the API symbols it adds to allow all NumPy API usage. This means that by default you cannot dynamically fetch the NumPy API from another library (this was never possible on windows). If you are experiencing linking errors related to `PyArray_API` or `PyArray_RUNTIME_VERSION`, you can define the `NPY_API_SYMBOL_ATTRIBUTE` to opt-out of this change. If you are experiencing problems due to an upstream header including NumPy, the solution is to make sure you `include "numpy/ndarrayobject.h"` before their header and import NumPy yourself based on `including-the-c-api`. ([gh-26103](https://github.com/numpy/numpy/pull/26103)) Many shims removed from npy_3kcompat.h Many of the old shims and helper functions were removed from `npy_3kcompat.h`. If you find yourself in need of these, vendor the previous version of the file into your codebase. ([gh-26842](https://github.com/numpy/numpy/pull/26842)) New `PyUFuncObject` field `process_core_dims_func` The field `process_core_dims_func` was added to the structure `PyUFuncObject`. For generalized ufuncs, this field can be set to a function of type `PyUFunc_ProcessCoreDimsFunc` that will be called when the ufunc is called. It allows the ufunc author to check that core dimensions satisfy additional constraints, and to set output core dimension sizes if they have not been provided. ([gh-26908](https://github.com/numpy/numpy/pull/26908)) New Features - `numpy.reshape` and `numpy.ndarray.reshape` now support `shape` and `copy` arguments. ([gh-26292](https://github.com/numpy/numpy/pull/26292)) - NumPy now supports DLPack v1, support for older versions will be deprecated in the future. ([gh-26501](https://github.com/numpy/numpy/pull/26501)) - `numpy.asanyarray` now supports `copy` and `device` arguments, matching `numpy.asarray`. ([gh-26580](https://github.com/numpy/numpy/pull/26580)) - `numpy.printoptions`, `numpy.get_printoptions`, and `numpy.set_printoptions` now support a new option, `override_repr`, for defining custom `repr(array)` behavior. ([gh-26611](https://github.com/numpy/numpy/pull/26611)) - `numpy.cumulative_sum` and `numpy.cumulative_prod` were added as Array API compatible alternatives for `numpy.cumsum` and `numpy.cumprod`. The new functions can include a fixed initial (zeros for `sum` and ones for `prod`) in the result. ([gh-26724](https://github.com/numpy/numpy/pull/26724)) - `numpy.clip` now supports `max` and `min` keyword arguments which are meant to replace `a_min` and `a_max`. Also, for `np.clip(a)` or `np.clip(a, None, None)` a copy of the input array will be returned instead of raising an error. ([gh-26724](https://github.com/numpy/numpy/pull/26724)) - `numpy.astype` now supports `device` argument. ([gh-26724](https://github.com/numpy/numpy/pull/26724)) `f2py` can generate freethreading-compatible C extensions Pass `--freethreading-compatible` to the f2py CLI tool to produce a C extension marked as compatible with the free threading CPython interpreter. Doing so prevents the interpreter from re-enabling the GIL at runtime when it imports the C extension. Note that `f2py` does not analyze fortran code for thread safety, so you must verify that the wrapped fortran code is thread safe before marking the extension as compatible. ([gh-26981](https://github.com/numpy/numpy/pull/26981)) Improvements `histogram` auto-binning now returns bin sizes \>=1 for integer input data For integer input data, bin sizes smaller than 1 result in spurious empty bins. This is now avoided when the number of bins is computed using one of the algorithms provided by `histogram_bin_edges`. ([gh-12150](https://github.com/numpy/numpy/pull/12150)) `ndarray` shape-type parameter is now covariant and bound to `tuple[int, ...]` Static typing for `ndarray` is a long-term effort that continues with this change. It is a generic type with type parameters for the shape and the data type. Previously, the shape type parameter could be any value. This change restricts it to a tuple of ints, as one would expect from using `ndarray.shape`. Further, the shape-type parameter has been changed from invariant to covariant. This change also applies to the subtypes of `ndarray`, e.g. `numpy.ma.MaskedArray`. See the [typing docs](https://typing.readthedocs.io/en/latest/reference/generics.html#variance-of-generic-types) for more information. ([gh-26081](https://github.com/numpy/numpy/pull/26081)) `np.quantile` with method `closest_observation` chooses nearest even order statistic This changes the definition of nearest for border cases from the nearest odd order statistic to nearest even order statistic. The numpy implementation now matches other reference implementations. ([gh-26656](https://github.com/numpy/numpy/pull/26656)) `lapack_lite` is now thread safe NumPy provides a minimal low-performance version of LAPACK named `lapack_lite` that can be used if no BLAS/LAPACK system is detected at build time. Until now, `lapack_lite` was not thread safe. Single-threaded use cases did not hit any issues, but running linear algebra operations in multiple threads could lead to errors, incorrect results, or segfaults due to data races. We have added a global lock, serializing access to `lapack_lite` in multiple threads. ([gh-26750](https://github.com/numpy/numpy/pull/26750)) The `numpy.printoptions` context manager is now thread and async-safe In prior versions of NumPy, the printoptions were defined using a combination of Python and C global variables. We have refactored so the state is stored in a python `ContextVar`, making the context manager thread and async-safe. ([gh-26846](https://github.com/numpy/numpy/pull/26846)) Performance improvements and changes - `numpy.save` now uses pickle protocol version 4 for saving arrays with object dtype, which allows for pickle objects larger than 4GB and improves saving speed by about 5% for large arrays. ([gh-26388](https://github.com/numpy/numpy/pull/26388)) - OpenBLAS on x86_64 and i686 is built with fewer kernels. Based on benchmarking, there are 5 clusters of performance around these kernels: `PRESCOTT NEHALEM SANDYBRIDGE HASWELL SKYLAKEX`. ([gh-27147](https://github.com/numpy/numpy/pull/27147)) - OpenBLAS on windows is linked without quadmath, simplifying licensing ([gh-27147](https://github.com/numpy/numpy/pull/27147)) - Due to a regression in OpenBLAS on windows, the performance improvements when using multiple threads for OpenBLAS 0.3.26 were reverted. ([gh-27147](https://github.com/numpy/numpy/pull/27147)) `ma.cov` and `ma.corrcoef` are now significantly faster The private function has been refactored along with `ma.cov` and `ma.corrcoef`. They are now significantly faster, particularly on large, masked arrays. ([gh-26285](https://github.com/numpy/numpy/pull/26285)) Changes - As `numpy.vecdot` is now a ufunc it has a less precise signature. This is due to the limitations of ufunc\'s typing stub. ([gh-26313](https://github.com/numpy/numpy/pull/26313)) - `numpy.floor`, `numpy.ceil`, and `numpy.trunc` now won\'t perform casting to a floating dtype for integer and boolean dtype input arrays. ([gh-26766](https://github.com/numpy/numpy/pull/26766)) `ma.corrcoef` may return a slightly different result A pairwise observation approach is currently used in `ma.corrcoef` to calculate the standard deviations for each pair of variables. This has been changed as it is being used to normalise the covariance, estimated using `ma.cov`, which does not consider the observations for each variable in a pairwise manner, rendering it unnecessary. The normalisation has been replaced by the more appropriate standard deviation for each variable, which significantly reduces the wall time, but will return slightly different estimates of the correlation coefficients in cases where the observations between a pair of variables are not aligned. However, it will return the same estimates in all other cases, including returning the same correlation matrix as `corrcoef` when using a masked array with no masked values. ([gh-26285](https://github.com/numpy/numpy/pull/26285)) Cast-safety fixes in `copyto` and `full` `copyto` now uses NEP 50 correctly and applies this to its cast safety. Python integer to NumPy integer casts and Python float to NumPy float casts are now considered \"safe\" even if assignment may fail or precision may be lost. This means the following examples change slightly: - `np.copyto(int8_arr, 1000)` previously performed an unsafe/same-kind cast : of the Python integer. It will now always raise, to achieve an unsafe cast you must pass an array or NumPy scalar. - `np.copyto(uint8_arr, 1000, casting="safe")` will raise an OverflowError rather than a TypeError due to same-kind casting. - `np.copyto(float32_arr, 1e300, casting="safe")` will overflow to `inf` (float32 cannot hold `1e300`) rather raising a TypeError. Further, only the dtype is used when assigning NumPy scalars (or 0-d arrays), meaning that the following behaves differently: - `np.copyto(float32_arr, np.float64(3.0), casting="safe")` raises. - `np.coptyo(int8_arr, np.int64(100), casting="safe")` raises. Previously, NumPy checked whether the 100 fits the `int8_arr`. This aligns `copyto`, `full`, and `full_like` with the correct NumPy 2 behavior. 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dc7ce867d277aa74555c67b93ef2a6f78bd7bd73e6c2bbafeb96f8bccd05b9d9 numpy-2.1.0rc1.tar.gz ``` ### 2.0.1 ``` discovered after the 2.0.0 release. NumPy 2.0.1 is the last planned release in the 2.0.x series, 2.1.0rc1 should be out shortly. The Python versions supported by this release are 3.9-3.12. **_NOTE:_** Do not use the GitHub generated "Source code" files listed in the "Assets", they are garbage. Improvements `np.quantile` with method `closest_observation` chooses nearest even order statistic This changes the definition of nearest for border cases from the nearest odd order statistic to nearest even order statistic. The numpy implementation now matches other reference implementations. ([gh-26656](https://github.com/numpy/numpy/pull/26656)) Contributors A total of 15 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - \vahidmech + - Alex Herbert + - Charles Harris - Giovanni Del Monte + - Leo Singer - Lysandros Nikolaou - Matti Picus - Nathan Goldbaum - Patrick J. Roddy + - Raghuveer Devulapalli - Ralf Gommers - Rostan Tabet + - Sebastian Berg - Tyler Reddy - Yannik Wicke + Pull requests merged A total of 24 pull requests were merged for this release. - [26711](https://github.com/numpy/numpy/pull/26711): MAINT: prepare 2.0.x for further development - [26792](https://github.com/numpy/numpy/pull/26792): TYP: fix incorrect import in `ma/extras.pyi` stub - [26793](https://github.com/numpy/numpy/pull/26793): DOC: Mention \'1.25\' legacy printing mode in `set_printoptions` - [26794](https://github.com/numpy/numpy/pull/26794): DOC: Remove mention of NaN and NAN aliases from constants - [26821](https://github.com/numpy/numpy/pull/26821): BLD: Fix x86-simd-sort build failure on openBSD - [26822](https://github.com/numpy/numpy/pull/26822): BUG: Ensure output order follows input in numpy.fft - [26823](https://github.com/numpy/numpy/pull/26823): TYP: fix missing sys import in numeric.pyi - [26832](https://github.com/numpy/numpy/pull/26832): DOC: remove hack to override \_add_newdocs_scalars - [26835](https://github.com/numpy/numpy/pull/26835): BUG: avoid side-effect of \'include complex.h\' - [26836](https://github.com/numpy/numpy/pull/26836): BUG: fix max_rows and chunked string/datetime reading in `loadtxt` - [26837](https://github.com/numpy/numpy/pull/26837): BUG: fix PyArray_ImportNumPyAPI under -Werror=strict-prototypes - [26856](https://github.com/numpy/numpy/pull/26856): DOC: Update some documentation - [26868](https://github.com/numpy/numpy/pull/26868): BUG: fancy indexing copy - [26869](https://github.com/numpy/numpy/pull/26869): BUG: Mismatched allocation domains in `PyArray_FillWithScalar` - [26870](https://github.com/numpy/numpy/pull/26870): BUG: Handle \--f77flags and \--f90flags for meson \[wheel build\] - [26887](https://github.com/numpy/numpy/pull/26887): BUG: Fix new DTypes and new string promotion when signature is\... - [26888](https://github.com/numpy/numpy/pull/26888): BUG: remove numpy.f2py from excludedimports - [26959](https://github.com/numpy/numpy/pull/26959): BUG: Quantile closest_observation to round to nearest even order - [26960](https://github.com/numpy/numpy/pull/26960): BUG: Fix off-by-one error in amount of characters in strip - [26961](https://github.com/numpy/numpy/pull/26961): API: Partially revert unique with return_inverse - [26962](https://github.com/numpy/numpy/pull/26962): BUG,MAINT: Fix utf-8 character stripping memory access - [26963](https://github.com/numpy/numpy/pull/26963): BUG: Fix out-of-bound minimum offset for in1d table method - [26971](https://github.com/numpy/numpy/pull/26971): BUG: fix f2py tests to work with v2 API - [26995](https://github.com/numpy/numpy/pull/26995): BUG: Add object cast to avoid warning with limited API Checksums MD5 a3e7d0f361ee7302448cae3c10844dd3 numpy-2.0.1-cp310-cp310-macosx_10_9_x86_64.whl cff8546b69e43ae7b5050f05bdc25df2 numpy-2.0.1-cp310-cp310-macosx_11_0_arm64.whl 1713d23342528f4f8f4027970f010068 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numpy-2.0.1-cp39-cp39-musllinux_1_1_x86_64.whl 24a0e1befbfa14615b49ba9659d3d8818a0f4d8a1c5822af8696706fbda7310c numpy-2.0.1-cp39-cp39-musllinux_1_2_aarch64.whl f9cf5ea551aec449206954b075db819f52adc1638d46a6738253a712d553c7b4 numpy-2.0.1-cp39-cp39-win32.whl e9e81fa9017eaa416c056e5d9e71be93d05e2c3c2ab308d23307a8bc4443c368 numpy-2.0.1-cp39-cp39-win_amd64.whl 61728fba1e464f789b11deb78a57805c70b2ed02343560456190d0501ba37b0f numpy-2.0.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 12f5d865d60fb9734e60a60f1d5afa6d962d8d4467c120a1c0cda6eb2964437d numpy-2.0.1-pp39-pypy39_pp73-macosx_14_0_x86_64.whl eacf3291e263d5a67d8c1a581a8ebbcfd6447204ef58828caf69a5e3e8c75990 numpy-2.0.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2c3a346ae20cfd80b6cfd3e60dc179963ef2ea58da5ec074fd3d9e7a1e7ba97f numpy-2.0.1-pp39-pypy39_pp73-win_amd64.whl 485b87235796410c3519a699cfe1faab097e509e90ebb05dcd098db2ae87e7b3 numpy-2.0.1.tar.gz ``` ### 2.0 ``` - `npy_interrupt.h` and the corresponding macros like `NPY_SIGINT_ON` have been removed. We recommend querying `PyErr_CheckSignals()` or `PyOS_InterruptOccurred()` periodically (these do currently require holding the GIL though). - The `noprefix.h` header has been removed. Replace missing symbols with their prefixed counterparts (usually an added `NPY_` or `npy_`). ([gh-23919](https://github.com/numpy/numpy/pull/23919)) - `PyUFunc_GetPyVals`, `PyUFunc_handlefperr`, and `PyUFunc_checkfperr` have been removed. If needed, a new backwards compatible function to raise floating point errors could be restored. Reason for removal: there are no known users and the functions would have made `with np.errstate()` fixes much more difficult). ([gh-23922](https://github.com/numpy/numpy/pull/23922)) - The `numpy/old_defines.h` which was part of the API deprecated since NumPy 1.7 has been removed. This removes macros of the form `PyArray_CONSTANT`. The [replace_old_macros.sed](https://github.com/numpy/numpy/blob/main/tools/replace_old_macros.sed) script may be useful to convert them to the `NPY_CONSTANT` version. ([gh-24011](https://github.com/numpy/numpy/pull/24011)) - The `legacy_inner_loop_selector` member of the ufunc struct is removed to simplify improvements to the dispatching system. There are no known users overriding or directly accessing this member. ([gh-24271](https://github.com/numpy/numpy/pull/24271)) - `NPY_INTPLTR` has been removed to avoid confusion (see `intp` redefinition). ([gh-24888](https://github.com/numpy/numpy/pull/24888)) - The advanced indexing `MapIter` and related API has been removed. The (truly) public part of it was not well tested and had only one known user (Theano). Making it private will simplify improvements to speed up `ufunc.at`, make advanced indexing more maintainable, and was important for increasing the maximum number of dimensions of arrays to 64. Please let us know if this API is important to you so we can find a solution together. ([gh-25138](https://github.com/numpy/numpy/pull/25138)) - The `NPY_MAX_ELSIZE` macro has been removed, as it only ever reflected builtin numeric types and served no internal purpose. ([gh-25149](https://github.com/numpy/numpy/pull/25149)) - `PyArray_REFCNT` and `NPY_REFCOUNT` are removed. Use `Py_REFCNT` instead. ([gh-25156](https://github.com/numpy/numpy/pull/25156)) - `PyArrayFlags_Type` and `PyArray_NewFlagsObject` as well as `PyArrayFlagsObject` are private now. There is no known use-case; use the Python API if needed. - `PyArray_MoveInto`, `PyArray_CastTo`, `PyArray_CastAnyTo` are removed use `PyArray_CopyInto` and if absolutely needed `PyArray_CopyAnyInto` (the latter does a flat copy). - `PyArray_FillObjectArray` is removed, its only true use was for implementing `np.empty`. Create a new empty array or use `PyArray_FillWithScalar()` (decrefs existing objects). - `PyArray_CompareUCS4` and `PyArray_CompareString` are removed. Use the standard C string comparison functions. - `PyArray_ISPYTHON` is removed as it is misleading, has no known use-cases, and is easy to replace. - `PyArray_FieldNames` is removed, as it is unclear what it would be useful for. It also has incorrect semantics in some possible use-cases. - `PyArray_TypestrConvert` is removed, since it seems a misnomer and unlikely to be used by anyone. If you know the size or are limited to few types, just use it explicitly, otherwise go via Python strings. ([gh-25292](https://github.com/numpy/numpy/pull/25292)) - `PyDataType_GetDatetimeMetaData` is removed, it did not actually do anything since at least NumPy 1.7. ([gh-25802](https://github.com/numpy/numpy/pull/25802)) - `PyArray_GetCastFunc` is removed. Note that custom legacy user dtypes can still provide a castfunc as their implementation, but any access to them is now removed. The reason for this is that NumPy never used these internally for many years. If you use simple numeric types, please just use C casts directly. In case you require an alternative, please let us know so we can create new API such as `PyArray_CastBuffer()` which could use old or new cast functions depending on the NumPy version. ([gh-25161](https://github.com/numpy/numpy/pull/25161)) New Features `np.add` was extended to work with `unicode` and `bytes` dtypes. > ([gh-24858](https://github.com/numpy/numpy/pull/24858)) A new `bitwise_count` function This new function counts the number of 1-bits in a number. `numpy.bitwise_count` works on all the numpy integer types and integer-like objects. python >>> a = np.array([2**i - 1 for i in range(16)]) >>> np.bitwise_count(a) array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15], dtype=uint8) ([gh-19355](https://github.com/numpy/numpy/pull/19355)) macOS Accelerate support, including the ILP64 Support for the updated Accelerate BLAS/LAPACK library, including ILP64 (64-bit integer) support, in macOS 13.3 has been added. This brings arm64 support, and significant performance improvements of up to 10x for commonly used linear algebra operations. When Accelerate is selected at build time, or if no explicit BLAS library selection is done, the 13.3+ version will automatically be used if available. ([gh-24053](https://github.com/numpy/numpy/pull/24053)) Binary wheels are also available. On macOS \>=14.0, users who install NumPy from PyPI will get wheels built against Accelerate rather than OpenBLAS. ([gh-25255](https://github.com/numpy/numpy/pull/25255)) Option to use weights for quantile and percentile functions A `weights` keyword is now available for `numpy.quantile`, `numpy.percentile`, `numpy.nanquantile` and `numpy.nanpercentile`. Only `method="inverted_cdf"` supports weights. ([gh-24254](https://github.com/numpy/numpy/pull/24254)) Improved CPU optimization tracking A new tracer mechanism is available which enables tracking of the enabled targets for each optimized function (i.e., that uses hardware-specific SIMD instructions) in the NumPy library. With this enhancement, it becomes possible to precisely monitor the enabled CPU dispatch targets for the dispatched functions. A new function named `opt_func_info` has been added to the new namespace `numpy.lib.introspect`, offering this tracing capability. This function allows you to retrieve information about the enabled targets based on function names and data type signatures. ([gh-24420](https://github.com/numpy/numpy/pull/24420)) A new Meson backend for `f2py` `f2py` in compile mode (i.e. `f2py -c`) now accepts the `--backend meson` option. This is the default option for Python \>=3.12. For older Python versions, `f2py` will still default to `--backend distutils`. To support this in realistic use-cases, in compile mode `f2py` takes a `--dep` flag one or many times which maps to `dependency()` calls in the `meson` backend, and does nothing in the `distutils` backend. There are no changes for users of `f2py` only as a code generator, i.e. without `-c`. ([gh-24532](https://github.com/numpy/numpy/pull/24532)) `bind(c)` support for `f2py` Both functions and subroutines can be annotated with `bind(c)`. `f2py` will handle both the correct type mapping, and preserve the unique label for other C interfaces. **Note:** `bind(c, name = 'routine_name_other_than_fortran_routine')` is not honored by the `f2py` bindings by design, since `bind(c)` with the `name` is meant to guarantee only the same name in C and Fortran, not in Python and Fortran. ([gh-24555](https://github.com/numpy/numpy/pull/24555)) A new `strict` option for several testing functions The `strict` keyword is now available for `numpy.testing.assert_allclose`, `numpy.testing.assert_equal`, and `numpy.testing.assert_array_less`. Setting `strict=True` will disable the broadcasting behaviour for scalars and ensure that input arrays have the same data type. ([gh-24680](https://github.com/numpy/numpy/pull/24680), [gh-24770](https://github.com/numpy/numpy/pull/24770), [gh-24775](https://github.com/numpy/numpy/pull/24775)) Add `np.core.umath.find` and `np.core.umath.rfind` UFuncs Add two `find` and `rfind` UFuncs that operate on unicode or byte strings and are used in `np.char`. They operate similar to `str.find` and `str.rfind`. ([gh-24868](https://github.com/numpy/numpy/pull/24868)) `diagonal` and `trace` for `numpy.linalg` `numpy.linalg.diagonal` and `numpy.linalg.trace` have been added, which are array API standard-compatible variants of `numpy.diagonal` and `numpy.trace`. They differ in the default axis selection which define 2-D sub-arrays. ([gh-24887](https://github.com/numpy/numpy/pull/24887)) New `long` and `ulong` dtypes `numpy.long` and `numpy.ulong` have been added as NumPy integers mapping to C\'s `long` and `unsigned long`. Prior to NumPy 1.24, `numpy.long` was an alias to Python\'s `int`. ([gh-24922](https://github.com/numpy/numpy/pull/24922)) `svdvals` for `numpy.linalg` `numpy.linalg.svdvals` has been added. It computes singular values for (a stack of) matrices. Executing `np.svdvals(x)` is the same as calling `np.svd(x, compute_uv=False, hermitian=False)`. This function is compatible with the array API standard. ([gh-24940](https://github.com/numpy/numpy/pull/24940)) A new `isdtype` function `numpy.isdtype` was added to provide a canonical way to classify NumPy\'s dtypes in compliance with the array API standard. ([gh-25054](https://github.com/numpy/numpy/pull/25054)) A new `astype` function `numpy.astype` was added to provide an array API standard-compatible alternative to the `numpy.ndarray.astype` method. ([gh-25079](https://github.com/numpy/numpy/pull/25079)) Array API compatible functions\' aliases 13 aliases for existing functions were added to improve compatibility with the array API standard: - Trigonometry: `acos`, `acosh`, `asin`, `asinh`, `atan`, `atanh`, `atan2`. - Bitwise: `bitwise_left_shift`, `bitwise_invert`, `bitwise_right_shift`. - Misc: `concat`, `permute_dims`, `pow`. - In `numpy.linalg`: `tensordot`, `matmul`. ([gh-25086](https://github.com/numpy/numpy/pull/25086)) New `unique_*` functions The `numpy.unique_all`, `numpy.unique_counts`, `numpy.unique_inverse`, and `numpy.unique_values` functions have been added. They provide functionality of `numpy.unique` with different sets of flags. They are array API standard-compatible, and because the number of arrays they return does not depend on the values of input arguments, they are easier to target for JIT compilation. ([gh-25088](https://github.com/numpy/numpy/pull/25088)) Matrix transpose support for ndarrays NumPy now offers support for calculating the matrix transpose of an array (or stack of arrays). The matrix transpose is equivalent to swapping the last two axes of an array. Both `np.ndarray` and `np.ma.MaskedArray` now expose a `.mT` attribute, and there is a matching new `numpy.matrix_transpose` function. ([gh-23762](https://github.com/numpy/numpy/pull/23762)) Array API compatible functions for `numpy.linalg` Six new functions and two aliases were added to improve compatibility with the Array API standard for \`numpy.linalg\`: - `numpy.linalg.matrix_norm` - Computes the matrix norm of a matrix (or a stack of matrices). - `numpy.linalg.vector_norm` - Computes the vector norm of a vector (or batch of vectors). - `numpy.vecdot` - Computes the (vector) dot product of two arrays. - `numpy.linalg.vecdot` - An alias for `numpy.vecdot`. - `numpy.linalg.matrix_transpose` - An alias for `numpy.matrix_transpose`. ([gh-25155](https://github.com/numpy/numpy/pull/25155)) - `numpy.linalg.outer` has been added. It computes the outer product of two vectors. It differs from `numpy.outer` by accepting one-dimensional arrays only. This function is compatible with the array API standard. ([gh-25101](https://github.com/numpy/numpy/pull/25101)) - `numpy.linalg.cross` has been added. It computes the cross product of two (arrays of) 3-dimensional vectors. It differs from `numpy.cross` by accepting three-dimensional vectors only. This function is compatible with the array API standard. ([gh-25145](https://github.com/numpy/numpy/pull/25145)) A `correction` argument for `var` and `std` A `correction` argument was added to `numpy.var` and `numpy.std`, which is an array API standard compatible alternative to `ddof`. As both arguments serve a similar purpose, only one of them can be provided at the same time. ([gh-25169](https://github.com/numpy/numpy/pull/25169)) `ndarray.device` and `ndarray.to_device` An `ndarray.device` attribute and `ndarray.to_device` method were added to `numpy.ndarray` for array API standard compatibility. Additionally, `device` keyword-only arguments were added to: `numpy.asarray`, `numpy.arange`, `numpy.empty`, `numpy.empty_like`, `numpy.eye`, `numpy.full`, `numpy.full_like`, `numpy.linspace`, `numpy.ones`, `numpy.ones_like`, `numpy.zeros`, and `numpy.zeros_like`. For all these new arguments, only `device="cpu"` is supported. ([gh-25233](https://github.com/numpy/numpy/pull/25233)) StringDType has been added to NumPy We have added a new variable-width UTF-8 encoded string data type, implementing a \"NumPy array of Python strings\", including support for a user-provided missing data sentinel. It is intended as a drop-in replacement for arrays of Python strings and missing data sentinels using the object dtype. See [NEP 55](https://numpy.org/neps/nep-0055-string_dtype.html) and the documentation of stringdtype for more details. ([gh-25347](https://github.com/numpy/numpy/pull/25347)) New keywords for `cholesky` and `pinv` The `upper` and `rtol` keywords were added to `numpy.linalg.cholesky` and `numpy.linalg.pinv`, respectively, to improve array API standard compatibility. For `numpy.linalg.pinv`, if neither `rcond` nor `rtol` is specified, the `rcond`\'s default is used. We plan to deprecate and remove `rcond` in the future. ([gh-25388](https://github.com/numpy/numpy/pull/25388)) New keywords for `sort`, `argsort` and `linalg.matrix_rank` New keyword parameters were added to improve array API standard compatibility: - `rtol` was added to `numpy.linalg.matrix_rank`. - `stable` was added to `numpy.sort` and `numpy.argsort`. ([gh-25437](https://github.com/numpy/numpy/pull/25437)) New `numpy.strings` namespace for string ufuncs NumPy now implements some string operations as ufuncs. The old `np.char` namespace is still available, and where possible the string manipulation functions in that namespace have been updated to use the new ufuncs, substantially improving their performance. Where possible, we suggest updating code to use functions in `np.strings` instead of `np.char`. In the future we may deprecate `np.char` in favor of `np.strings`. ([gh-25463](https://github.com/numpy/numpy/pull/25463)) `numpy.fft` support for different precisions and in-place calculations The various FFT routines in `numpy.fft` now do their calculations natively in float, double, or long double precision, depending on the input precision, instead of always calculating in double precision. Hence, the calculation will now be less precise for single and more precise for long double precision. The data type of the output array will now be adjusted accordingly. Furthermore, all FFT routines have gained an `out` argument that can be used for in-place calculations. ([gh-25536](https://github.com/numpy/numpy/pull/25536)) configtool and pkg-config support A new `numpy-config` CLI script is available that can be queried for the NumPy version and for compile flags needed to use the NumPy C API. This will allow build systems to better support the use of NumPy as a dependency. Also, a `numpy.pc` pkg-config file is now included with Numpy. In order to find its location for use with `PKG_CONFIG_PATH`, use `numpy-config --pkgconfigdir`. ([gh-25730](https://github.com/numpy/numpy/pull/25730)) Array API standard support in the main namespace The main `numpy` namespace now supports the array API standard. See `array-api-standard-compatibility` for details. ([gh-25911](https://github.com/numpy/numpy/pull/25911)) Improvements Strings are now supported by `any`, `all`, and the logical ufuncs. > ([gh-25651](https://github.com/numpy/numpy/pull/25651)) Integer sequences as the shape argument for `memmap` `numpy.memmap` can now be created with any integer sequence as the `shape` argument, such as a list or numpy array of integers. Previously, only the types of tuple and int could be used without raising an error. ([gh-23729](https://github.com/numpy/numpy/pull/23729)) `errstate` is now faster and context safe The `numpy.errstate` context manager/decorator is now faster and safer. Previously, it was not context safe and had (rare) issues with thread-safety. ([gh-23936](https://github.com/numpy/numpy/pull/23936)) AArch64 quicksort speed improved by using Highway\'s VQSort The first introduction of the Google Highway library, using VQSort on AArch64. Execution time is improved by up to 16x in some cases, see the PR for benchmark results. Extensions to other platforms will be done in the future. ([gh-24018](https://github.com/numpy/numpy/pull/24018)) Complex types - underlying C type changes - The underlying C types for all of NumPy\'s complex types have been changed to use C99 complex types. - While this change does not affect the memory layout of complex types, it changes the API to be used to directly retrieve or write the real or complex part of the complex number, since direct field access (as in `c.real` or `c.imag`) is no longer an option. You can now use utilities provided in `numpy/npy_math.h` to do these operations, like this: c npy_cdouble c; npy_csetreal(&c, 1.0); npy_csetimag(&c, 0.0); printf("%d + %di\n", npy_creal(c), npy_cimag(c)); - To ease cross-version compatibility, equivalent macros and a compatibility layer have been added which can be used by downstream packages to continue to support both NumPy 1.x and 2.x. See `complex-numbers` for more info. - `numpy/npy_common.h` now includes `complex.h`, which means that `complex` is now a reserved keyword. ([gh-24085](https://github.com/numpy/numpy/pull/24085)) `iso_c_binding` support and improved common blocks for `f2py` Previously, users would have to define their own custom `f2cmap` file to use type mappings defined by the Fortran2003 `iso_c_binding` intrinsic module. These type maps are now natively supported by `f2py` ([gh-24555](https://github.com/numpy/numpy/pull/24555)) `f2py` now handles `common` blocks which have `kind` specifications from modules. This further expands the usability of intrinsics like `iso_fortran_env` and `iso_c_binding`. ([gh-25186](https://github.com/numpy/numpy/pull/25186)) Call `str` automatically on third argument to functions like `assert_equal` The third argument to functions like `numpy.testing.assert_equal` now has `str` called on it automatically. This way it mimics the built-in `assert` statement, where `assert_equal(a, b, obj)` works like `assert a == b, obj`. ([gh-24877](https://github.com/numpy/numpy/pull/24877)) Support for array-like `atol`/`rtol` in `isclose`, `allclose` The keywords `atol` and `rtol` in `numpy.isclose` and `numpy.allclose` now accept both scalars and arrays. An array, if given, must broadcast to the shapes of the first two array arguments. ([gh-24878](https://github.com/numpy/numpy/pull/24878)) Consistent failure messages in test functions Previously, some `numpy.testing` assertions printed messages that referred to the actual and desired results as `x` and `y`. Now, these values are consistently referred to as `ACTUAL` and `DESIRED`. ([gh-24931](https://github.com/numpy/numpy/pull/24931)) n-D FFT transforms allow `s[i] == -1` The `numpy.fft.fftn`, `numpy.fft.ifftn`, `numpy.fft.rfftn`, `numpy.fft.irfftn`, `numpy.fft.fft2`, `numpy.fft.ifft2`, `numpy.fft.rfft2` and `numpy.fft.irfft2` functions now use the whole input array along the axis `i` if `s[i] == -1`, in line with the array API standard. ([gh-25495](https://github.com/numpy/numpy/pull/25495)) Guard PyArrayScalar_VAL and PyUnicodeScalarObject for the limited API `PyUnicodeScalarObject` holds a `PyUnicodeObject`, which is not available when using `Py_LIMITED_API`. Add guards to hide it and consequently also make the `PyArrayScalar_VAL` macro hidden. ([gh-25531](https://github.com/numpy/numpy/pull/25531)) Changes - `np.gradient()` now returns a tuple rather than a list making the return value immutable. ([gh-23861](https://github.com/numpy/numpy/pull/23861)) - Being fully context and thread-safe, `np.errstate` can only be entered once now. - `np.setbufsize` is now tied to `np.errstate()`: leaving an `np.errstate` context will also reset the `bufsize`. ([gh-23936](https://github.com/numpy/numpy/pull/23936)) - A new public `np.lib.array_utils` submodule has been introduced and it currently contains three functions: `byte_bounds` (moved from `np.lib.utils`), `normalize_axis_tuple` and `normalize_axis_index`. ([gh-24540](https://github.com/numpy/numpy/pull/24540)) - Introduce `numpy.bool` as the new canonical name for NumPy\'s boolean dtype, and make `numpy.bool\_` an alias to it. Note that until NumPy 1.24, `np.bool` was an alias to Python\'s builtin `bool`. The new name helps with array API standard compatibility and is a more intuitive name. ([gh-25080](https://github.com/numpy/numpy/pull/25080)) - The `dtype.flags` value was previously stored as a signed integer. This means that the aligned dtype struct flag lead to negative flags being set (-128 rather than 128). This flag is now stored unsigned (positive). Code which checks flags manually may need to adapt. This may include code compiled with Cython 0.29.x. ([gh-25816](https://github.com/numpy/numpy/pull/25816)) Representation of NumPy scalars changed As per NEP 51, the scalar representation has been updated to include the type information to avoid confusion with Python scalars. Scalars are now printed as `np.float64(3.0)` rather than just `3.0`. This may disrupt workflows that store representations of numbers (e.g., to files) making it harder to read them. They should be stored as explicit strings, for example by using `str()` or `f"{scalar!s}"`. For the time being, affected users can use `np.set_printoptions(legacy="1.25")` to get the old behavior (with possibly a few exceptions). Documentation of downstream projects may require larger updates, if code snippets are tested. We are working on tooling for [doctest-plus](https://github.com/scientific-python/pytest-doctestplus/issues/107) to facilitate updates. ([gh-22449](https://github.com/numpy/numpy/pull/22449)) Truthiness of NumPy strings changed NumPy strings previously were inconsistent about how they defined if the string is `True` or `False` and the definition did not match the one used by Python. Strings are now considered `True` when they are non-empty and `False` when they are empty. This changes the following distinct cases: - Casts from string to boolean were previously roughly equivalent to `string_array.astype(np.int64).astype(bool)`, meaning that only valid integers could be cast. Now a string of `"0"` will be considered `True` since it is not empty. If you need the old behavior, you may use the above step (casting to integer first) or `string_array == "0"` (if the input is only ever `0` or `1`). To get the new result on old NumPy versions use `string_array != ""`. - `np.nonzero(string_array)` previously ignored whitespace so that a string only containing whitespace was considered `False`. Whitespace is now considered `True`. This change does not affect `np.loadtxt`, `np.fromstring`, or `np.genfromtxt`. The first two still use the integer definition, while `genfromtxt` continues to match for `"true"` (ignoring case). However, if `np.bool_` is used as a converter the result will change. The change does affect `np.fromregex` as it uses direct assignments. ([gh-23871](https://github.com/numpy/numpy/pull/23871)) A `mean` keyword was added to var and std function Often when the standard deviation is needed the mean is also needed. The same holds for the variance and the mean. Until now the mean is then calculated twice, the change introduced here for the `numpy.var` and `numpy.std` functions allows for passing in a precalculated mean as an keyword argument. See the docstrings for details and an example illustrating the speed-up. ([gh-24126](https://github.com/numpy/numpy/pull/24126)) Remove datetime64 deprecation warning when constructing with timezone The `numpy.datetime64` method now issues a UserWarning rather than a DeprecationWarning whenever a timezone is included in the datetime string that is provided. ([gh-24193](https://github.com/numpy/numpy/pull/24193)) Default integer dtype is now 64-bit on 64-bit Windows The default NumPy integer is now 64-bit on all 64-bit systems as the historic 32-bit default on Windows was a common source of issues. Most users should not notice this. The main issues may occur with code interfacing with libraries written in a compiled language like C. For more information see `migration_windows_int64`. ([gh-24224](https://github.com/numpy/numpy/pull/24224)) Renamed `numpy.core` to `numpy._core` Accessing `numpy.core` now emits a DeprecationWarning. In practice we have found that most downstream usage of `numpy.core` was to access functionality that is available in the main `numpy` namespace. If for some reason you are using functionality in `numpy.core` that is not available in the main `numpy` namespace, this means you are likely using private NumPy internals. You can still access these internals via `numpy._core` without a deprecation warning but we do not provide any backward compatibility guarantees for NumPy internals. Please open an issue if you think a mistake was made and something needs to be made public. ([gh-24634](https://github.com/numpy/numpy/pull/24634)) The \"relaxed strides\" debug build option, which was previously enabled through the `NPY_RELAXED_STRIDES_DEBUG` environment variable or the `-Drelaxed-strides-debug` config-settings flag has been removed. ([gh-24717](https://github.com/numpy/numpy/pull/24717)) Redefinition of `np.intp`/`np.uintp` (almost never a change) Due to the actual use of these types almost always matching the use of `size_t`/`Py_ssize_t` this is now the definition in C. Previously, it matched `intptr_t` and `uintptr_t` which would often have been subtly incorrect. This has no effect on the vast majority of machines since the size of these types only differ on extremely niche platforms. However, it means that: - Pointers may not necessarily fit into an `intp` typed array anymore. The `p` and `P` character codes can still be used, however. - Creating `intptr_t` or `uintptr_t` typed arrays in C remains possible in a cross-platform way via `PyArray_DescrFromType('p')`. - The new character codes `nN` were introduced. - It is now correct to use the Python C-API functions when parsing to `npy_intp` typed arguments. ([gh-24888](https://github.com/numpy/numpy/pull/24888)) `numpy.fft.helper` made private `numpy.fft.helper` was renamed to `numpy.fft._helper` to indicate that it is a private submodule. All public functions exported by it should be accessed from `numpy.fft`. ([gh-24945](https://github.com/numpy/numpy/pull/24945)) `numpy.linalg.linalg` made private `numpy.linalg.linalg` was renamed to `numpy.linalg._linalg` to indicate that it is a private submodule. All public functions exported by it should be accessed from `numpy.linalg`. ([gh-24946](https://github.com/numpy/numpy/pull/24946)) Out-of-bound axis not the same as `axis=None` In some cases `axis=32` or for concatenate any large value was the same as `axis=None`. Except for `concatenate` this was deprecate. Any out of bound axis value will now error, make sure to use `axis=None`. ([gh-25149](https://github.com/numpy/numpy/pull/25149)) New `copy` keyword meaning for `array` and `asarray` constructors Now `numpy.array` and `numpy.asarray` support three values for `copy` parameter: - `None` - A copy will only be made if it is necessary. - `True` - Always make a copy. - `False` - Never make a copy. If a copy is required a `ValueError` is raised. The meaning of `False` changed as it now raises an exception if a copy is needed. ([gh-25168](https://github.com/numpy/numpy/pull/25168)) The `__array__` special method now takes a `copy` keyword argument. NumPy will pass `copy` to the `__array__` special method in situations where it would be set to a non-default value (e.