search

malramsay64 / statdyn-analysis

Collection of tools for the statistical dynamics analysis of Molecular Dynamics trajectories.
MIT License
6 stars 0 forks source link

chore(deps): Update joblib requirement from ~=0.13.2 to >=0.13.2,<0.15.0 #118

Closed dependabot-preview[bot] closed 5 years ago

dependabot-preview[bot] commented 5 years ago

Updates the requirements on joblib to permit the latest version.

Changelog *Sourced from [joblib's changelog](https://github.com/joblib/joblib/blob/master/CHANGES.rst).* > 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). > - 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). > - 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. > - Upgrade to cloudpickle 1.1.1 that add supports for the upcoming Python 3.8 release among other things. > - Fix semaphore availability checker to avoid spawning resource trackers on module import. > - Fix the oversubscription protection to only protect against nested Parallel calls. This allows joblib to be run in background threads. > - Fix ValueError (negative dimensions) when pickling large numpy arrays on Windows. > - Upgrade to loky 2.6.0 that add supports for the setting environment variables in child before loading any module. > - 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`. > > Release 0.13.2 > ============== > > Pierre Glaser > > > Upgrade to cloudpickle 0.8.0 > > > > Add a non-regression test related to joblib issues [#836](https://github-redirect.dependabot.com/joblib/joblib/issues/836) and [#833](https://github-redirect.dependabot.com/joblib/joblib/issues/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 > > Release 0.13.1 > ============== > > Pierre Glaser > > > Memory now accepts pathlib.Path objects as `location` parameter. Also, a warning is raised if the returned backend is None while `location` is not None. > > Olivier Grisel > > > Make `Parallel` raise an informative `RuntimeError` when the active parallel backend has zero worker. > > > > Make the `DaskDistributedBackend` wait for workers before trying to schedule work. This is useful in particular when the workers are provisionned dynamically but provisionning is not immediate (for instance using Kubernetes, Yarn or an HPC job queue). > > Release 0.13.0 > ============== > > Thomas Moreau > > > Include loky 2.4.2 with default serialization with `cloudpickle`. This can be tweaked with the environment variable `LOKY_PICKLER`. > > Thomas Moreau > > > Fix nested backend in SequentialBackend to avoid changing the default backend to Sequential. ([#792](https://github-redirect.dependabot.com/joblib/joblib/issues/792)) > > Thomas Moreau, Olivier Grisel > > > Fix nested\_backend behavior to avoid setting the default number of workers to -1 when the backend is not dask. ([#784](https://github-redirect.dependabot.com/joblib/joblib/issues/784)) > ... (truncated)
Commits - [`a07df3b`](https://github.com/joblib/joblib/commit/a07df3beb6565909e660b677922ecd1e6c000d43) Release 0.14.0 - [`1940e57`](https://github.com/joblib/joblib/commit/1940e57af5900375704adc690fa5500de0edd06a) DOC fix typo in documentation - [`a41bd5a`](https://github.com/joblib/joblib/commit/a41bd5a71a1889a46fb635831fdf2767e2dc89fe) ENH over-subscription mitigation + MTN vendor loky 2.6 ([#940](https://github-redirect.dependabot.com/joblib/joblib/issues/940)) - [`dec1595`](https://github.com/joblib/joblib/commit/dec1595b6610d312b0e23ed78e8f4d5233674bbb) ENH Improve load-balancing between workers for large batch sizes. ([#899](https://github-redirect.dependabot.com/joblib/joblib/issues/899)) - [`470a637`](https://github.com/joblib/joblib/commit/470a6372dbae826b2f6107a77f6457e956249fef) Missing entry in changelog - [`f7f3c33`](https://github.com/joblib/joblib/commit/f7f3c33ce0e938943a60841f94818076fe9c8bb0) prevent overflow when pickling large numpy arrays ([#920](https://github-redirect.dependabot.com/joblib/joblib/issues/920)) - [`79847c5`](https://github.com/joblib/joblib/commit/79847c5fa6701da47f8a20e880fa744950fee109) Change setup.py to import setup from setuptools which supports ([#924](https://github-redirect.dependabot.com/joblib/joblib/issues/924)) - [`5397271`](https://github.com/joblib/joblib/commit/5397271c8f5de205304e691b5efc4066d4bcceb7) Upgrade to cloudpickle 1.2.2 ([#938](https://github-redirect.dependabot.com/joblib/joblib/issues/938)) - [`591a8e6`](https://github.com/joblib/joblib/commit/591a8e683f5a4a4e7ce4bb382024234315abc505) Fix dask scatter deadlock ([#914](https://github-redirect.dependabot.com/joblib/joblib/issues/914)) - [`eb7a949`](https://github.com/joblib/joblib/commit/eb7a9496efe43bec04a5b430f1f6b169691e79a6) ENH only protect against nested call in Parallel ([#934](https://github-redirect.dependabot.com/joblib/joblib/issues/934)) - Additional commits viewable in [compare view](https://github.com/joblib/joblib/compare/0.13.2...0.14.0)


Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language - `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com): - Update frequency (including time of day and day of week) - Pull request limits (per update run and/or open at any time) - Out-of-range updates (receive only lockfile updates, if desired) - Security updates (receive only security updates, if desired) Finally, you can contact us by mentioning @dependabot.
codecov[bot] commented 5 years ago

Codecov Report

Merging #118 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #118   +/-   ##
=======================================
  Coverage   84.35%   84.35%           
=======================================
  Files          19       19           
  Lines        1547     1547           
=======================================
  Hits         1305     1305           
  Misses        242      242

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update d3e2826...e726b7f. Read the comment docs.

dependabot-preview[bot] commented 5 years ago

Looks like joblib is up-to-date now, so this is no longer needed.