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malramsay64 / statdyn-analysis

Collection of tools for the statistical dynamics analysis of Molecular Dynamics trajectories.
MIT License
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chore(deps): Update joblib requirement from <0.15,>=0.13.2 to >=0.13.2,<0.16 #177

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Updates the requirements on joblib to permit the latest version.

Changelog

Sourced from joblib's changelog.

Release 0.15.1

  • Make joblib work on Python 3 installation that do not ship with the lzma package in their standard library.

Release 0.15.0

  • Drop support for Python 2 and Python 3.5. All objects in joblib.my_exceptions and joblib.format_stack are now deprecated and will be removed in joblib 0.16. Note that no deprecation warning will be raised for these objects Python < 3.7. joblib/joblib#1018
  • Fix many bugs related to the temporary files and folder generated when automatically memory mapping large numpy arrays for efficient inter-process communication. In particular, this would cause PermissionError exceptions to be raised under Windows and large leaked files in /dev/shm under Linux in case of crash. joblib/joblib#966
  • Make the dask backend collect results as soon as they complete leading to a performance improvement: joblib/joblib#1025
  • Fix the number of jobs reported by effective_n_jobs when n_jobs=None called in a parallel backend context. joblib/joblib#985
  • Upgraded vendored cloupickle to 1.4.1 and loky to 2.8.0. This allows for Parallel calls of dynamically defined functions with type annotations in particular.

Release 0.14.1

  • Configure the loky workers' environment to mitigate oversubsription with nested multi-threaded code in the following case:

    • allow for a suitable number of threads for numba (NUMBA_NUM_THREADS);
    • enable Interprocess Communication for scheduler coordination when the nested code uses Threading Building Blocks (TBB) (ENABLE_IPC=1)

    joblib/joblib#951

  • Fix a regression where the loky backend was not reusing previously spawned workers. joblib/joblib#968

  • Revert joblib/joblib#847 to avoid using pkg_resources that introduced a performance regression under Windows: joblib/joblib#965

Release 0.14.0

  • Improved the load balancing between workers to avoid stranglers caused by an excessively large batch size when the task duration is varying significantly (because of the combined use of joblib.Parallel and joblib.Memory with a partially warmed cache for instance). joblib/joblib#899
  • Add official support for Python 3.8: fixed protocol number in Hasher and updated tests.
  • Fix a deadlock when using the dask backend (when scattering large numpy arrays). joblib/joblib#914
  • Warn users that they should never use joblib.load with files from untrusted sources. Fix security related API change introduced in numpy 1.6.3 that would prevent using joblib with recent numpy versions. joblib/joblib#879
  • Upgrade to cloudpickle 1.1.1 that add supports for the upcoming Python 3.8 release among other things. joblib/joblib#878
  • Fix semaphore availability checker to avoid spawning resource trackers on module import. joblib/joblib#893
  • Fix the oversubscription protection to only protect against nested Parallel calls. This allows joblib to be run in background threads. joblib/joblib#934
  • Fix ValueError (negative dimensions) when pickling large numpy arrays on Windows. joblib/joblib#920
  • Upgrade to loky 2.6.0 that add supports for the setting environment variables in child before loading any module. joblib/joblib#940
  • Fix the oversubscription protection for native libraries using threadpools (OpenBLAS, MKL, Blis and OpenMP runtimes). The maximal number of threads is can now be set in children using the inner_max_num_threads in parallel_backend. It defaults to cpu_count() // n_jobs. joblib/joblib#940

Release 0.13.2

Pierre Glaser

Upgrade to cloudpickle 0.8.0

Add a non-regression test related to joblib issues #836 and #833, reporting that cloudpickle versions between 0.5.4 and 0.7 introduced a bug where global variables changes in a parent process between two calls to joblib.Parallel would not be propagated into the workers

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codecov[bot] commented 4 years ago

Codecov Report

Merging #177 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #177   +/-   ##
=======================================
  Coverage   85.08%   85.08%           
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  Files          22       22           
  Lines        1602     1602           
=======================================
  Hits         1363     1363           
  Misses        239      239

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dependabot-preview[bot] commented 4 years ago

Superseded by #179.