compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
37 stars 18 forks source link

Bump cython from 0.29.17 to 0.29.18 #76

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

⚠️ Dependabot is rebasing this PR ⚠️

If you make any changes to it yourself then they will take precedence over the rebase.


Bumps cython from 0.29.17 to 0.29.18.

Changelog

Sourced from cython's changelog.

0.29.18 (2020-05-18)

Bugs fixed

  • Exception position reporting could run into race conditions on threaded code. It now uses function-local variables again.
  • Error handling early in the module init code could lead to a crash.
  • Error handling in cython.array creation was improved to avoid calling C-API functions with an error held.
  • A memory corruption was fixed when garbage collection was triggered during calls to PyType_Ready() of extension type subclasses. (Github issue #3603)
  • Memory view slicing generated unused error handling code which could negatively impact the C compiler optimisations for parallel OpenMP code etc. Also, it is now helped by static branch hints. (Github issue #2987)
  • Cython's built-in OpenMP functions were not translated inside of call arguments. Original patch by Celelibi and David Woods. (Github issue #3594)
  • Complex buffer item types of structs of arrays could fail to validate. Patch by Leo and smutch. (Github issue #1407)
  • Decorators were not allowed on nested async def functions. (Github issue #1462)
  • C-tuples could use invalid C struct casting. Patch by MegaIng. (Github issue #3038)
  • Optimised %d string formatting into f-strings failed on float values. (Github issue #3092)
  • Optimised aligned string formatting (%05s, %-5s) failed. (Github issue #3476)
  • When importing the old Cython build_ext integration with distutils, the additional command line arguments leaked into the regular command. Patch by Kamekameha. (Github issue #2209)
  • When using the CYTHON_NO_PYINIT_EXPORT option in C++, the module init function was not declared as extern "C". (Github issue #3414)
  • Three missing timedelta access macros were added in cpython.datetime.
  • The signature of the NumPy C-API function PyArray_SearchSorted() was fixed. Patch by Brock Mendel. (Github issue #3606)
Commits
  • a57de92 Prepare release of 0.29.18.
  • c0031d9 Add ticket reference explaining why a work-around is needed.
  • 4bf6a29 Update changelog.
  • f7ca5ef Disable GC during hacked calls to PyType_Ready() that simulate a heap type fo...
  • b177f22 Uncomment timedelta macros in datetime.pxd, because why not have them?
  • 98baa2f Update changelog.
  • a50be2a Also mark the case of an uninitialised memory view slice as "unlikely()" when...
  • fc09a6d Mark the last deletion of a memory view slice as "unlikely()" to ask the C co...
  • 8bcd238 Sprinkle "unlikely()" branch hints in all places where the memory view C code...
  • cc40053 Mark the first creation of a memory view slice as "unlikely()" to ask the C c...
  • Additional commits viewable in compare view


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