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UGentBiomath / wwdata

Python package to analyse, validate, fill and visualise data acquired in the context of (waste) water treatment
GNU General Public License v3.0
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Bug #12345 Scheduled daily dependency update on Tuesday #2375

Closed pyup-bot closed 2 months ago

pyup-bot commented 2 months ago

Update pandas from 0.24.2 to 2.2.2.

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

Links - PyPI: https://pypi.org/project/pandas - Homepage: https://pandas.pydata.org

Update numpy from 1.16.2 to 2.1.0.

Changelog ### 2.1 ``` 3.13. This support was enabled by fixing a number of C thread-safety issues in NumPy. Before NumPy 2.1, NumPy used a large number of C global static variables to store runtime caches and other state. We have either refactored to avoid the need for global state, converted the global state to thread-local state, or added locking. Support for free-threaded Python does not mean that NumPy is thread safe. Read-only shared access to ndarray should be safe. NumPy exposes shared mutable state and we have not added any locking to the array object itself to serialize access to shared state. Care must be taken in user code to avoid races if you would like to mutate the same array in multiple threads. It is certainly possible to crash NumPy by mutating an array simultaneously in multiple threads, for example by calling a ufunc and the `resize` method simultaneously. For now our guidance is: \"don\'t do that\". In the future we would like to provide stronger guarantees. Object arrays in particular need special care, since the GIL previously provided locking for object array access and no longer does. See [Issue 27199](https://github.com/numpy/numpy/issues/27199) for more information about object arrays in the free-threaded build. If you are interested in free-threaded Python, for example because you have a multiprocessing-based workflow that you are interested in running with Python threads, we encourage testing and experimentation. If you run into problems that you suspect are because of NumPy, please [open an issue](https://github.com/numpy/numpy/issues/new/choose), checking first if the bug also occurs in the \"regular\" non-free-threaded CPython 3.13 build. Many threading bugs can also occur in code that releases the GIL; disabling the GIL only makes it easier to hit threading bugs. ([gh-26157](https://github.com/numpy/numpy/issues/26157#issuecomment-2233864940)) `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)) - `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)) 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)) Type hinting `numpy.polynomial` Starting from the 2.1 release, PEP 484 type annotations have been included for the functions and convenience classes in `numpy.polynomial` and its sub-packages. ([gh-26897](https://github.com/numpy/numpy/pull/26897)) Improved `numpy.dtypes` type hints The type annotations for `numpy.dtypes` are now a better reflection of the runtime: The `numpy.dtype` type-aliases have been replaced with specialized `dtype` *subtypes*, and the previously missing annotations for `numpy.dtypes.StringDType` have been added. ([gh-27008](https://github.com/numpy/numpy/pull/27008)) 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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624884b572dff8ca8f60fab591413f077471de64e376b17d291b19f56504b2bb numpy-2.1.0-cp313-cp313t-musllinux_1_2_aarch64.whl 15ef8b2177eeb7e37dd5ef4016f30b7659c57c2c0b57a779f1d537ff33a72c7b numpy-2.1.0-pp310-pypy310_pp73-macosx_10_15_x86_64.whl e5f0642cdf4636198a4990de7a71b693d824c56a757862230454629cf62e323d numpy-2.1.0-pp310-pypy310_pp73-macosx_14_0_x86_64.whl f15976718c004466406342789f31b6673776360f3b1e3c575f25302d7e789575 numpy-2.1.0-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 6c1de77ded79fef664d5098a66810d4d27ca0224e9051906e634b3f7ead134c2 numpy-2.1.0-pp310-pypy310_pp73-win_amd64.whl 7dc90da0081f7e1da49ec4e398ede6a8e9cc4f5ebe5f9e06b443ed889ee9aaa2 numpy-2.1.0.tar.gz ``` ### 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` Bot
pyup-bot commented 2 months ago

Closing this in favor of #2376