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Bump pyteomics from 4.4.2 to 4.5.3 #416

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merged 1 commit into from
Apr 14, 2022

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Bumps pyteomics from 4.4.2 to 4.5.3.

Release notes

Sourced from pyteomics's releases.

Version 4.5.3

Version 4.5.2

  • Support Python 3.10.

Version 4.5.1

  • Add max_length parameter in pyteomics.parser.cleave.
  • Bugfix in pyteomics.parser.cleave for semi=True.
  • Add regex parameter in pyteomics.parser.cleave and warn for possible typos in cleavage rule names.
  • Add functions parser.icleave (generator) and parser.xcleave (list) to produce peptide sequences with indices and possible repetitions.
  • Bugfixes (#63 and #64 by @​mobiusklein).

Version 4.5

Changelog

Sourced from pyteomics's changelog.

4.5.3

  • Fix ThreadPool shutdown and add new parameter ephemeral_pool in :py:class:pyteomics.usi.PROXIAggregator ([#67](https://github.com/levitsky/pyteomics/issues/67) <https://github.com/levitsky/pyteomics/pull/67>_ by Joshua Klein).
  • Bugfix in pyteomics.proforma.GenericModificationResolver ([#68](https://github.com/levitsky/pyteomics/issues/68) <https://github.com/levitsky/pyteomics/issues/68>_) by Joshua Klein.
  • New helper function :py:func:pyteomics.fasta.decoy_entries.
  • New arguments charge_carrier, absolute in :py:func:mass.calculate_mass and :py:meth:mass.Composition.mass ([#61](https://github.com/levitsky/pyteomics/issues/61) <https://github.com/levitsky/pyteomics/pull/61>_). Charge is now only handled in :py:meth:Composition.mass and not :py:meth:Composition.__init__.
  • Bugfix in :py:mod:pyteomics.tandem ([#71](https://github.com/levitsky/pyteomics/issues/71) <https://github.com/levitsky/pyteomics/pull/71>_ by @​superrino130).

4.5.2

  • Support Python 3.10.

4.5.1

  • Add max_length parameter in :py:func:pyteomics.parser.cleave.
  • Bugfix in :py:func:pyteomics.parser.cleave for semi=True.
  • Add regex parameter in :py:func:pyteomics.parser.cleave and warn for possible typos in cleavage rule names.
  • Add functions :py:func:parser.icleave (generator) and :py:func:parser.xcleave (list) to produce peptide sequences with indices and possible repetitions.
  • Bugfixes ([#63](https://github.com/levitsky/pyteomics/issues/63) <https://github.com/levitsky/pyteomics/pull/63>_ and [#64](https://github.com/levitsky/pyteomics/issues/64) <https://github.com/levitsky/pyteomics/pull/64>_ by Joshua Klein).

4.5

  • Add support for mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>_ ([#35](https://github.com/levitsky/pyteomics/issues/35) <https://github.com/levitsky/pyteomics/pull/35>_ and [#38](https://github.com/levitsky/pyteomics/issues/38) <https://github.com/levitsky/pyteomics/pull/38>_ by Joshua Klein) with new module :py:mod:pyteomics.mzmlb.

  • Add ProteomeExchange backend for PROXI requests and implement an aggregator for responses from all backends ([#36](https://github.com/levitsky/pyteomics/issues/36) <https://github.com/levitsky/pyteomics/pull/36>, [#45](https://github.com/levitsky/pyteomics/issues/45) <https://github.com/levitsky/pyteomics/pull/45>, and [#55](https://github.com/levitsky/pyteomics/issues/55) <https://github.com/levitsky/pyteomics/pull/55>_ by Joshua Klein) in :py:mod:pyteomics.usi.

  • Add support for ProForma <https://www.psidev.info/proforma>_ ([#37](https://github.com/levitsky/pyteomics/issues/37) <https://github.com/levitsky/pyteomics/pull/37>_ by Joshua Klein) in new module :py:mod:pyteomics.proforma.

  • New arguments keep_nterm_M and fix_aa in :py:func:pyteomics.fasta.shuffle ([#54](https://github.com/levitsky/pyteomics/issues/54) <https://github.com/levitsky/pyteomics/pull/54>_ by Vladimir Gorshkov).

  • Fx for unwanted warnings in :py:func:pyteomics.auxiliary.file_helpers._check_use_index when

... (truncated)

Commits
  • e125123 Version 4.5.3
  • a889f0b Improve exception message in Composition._from_parsed_sequence
  • 6d5c0f9 Update changelog, version and authors
  • 10b12ac Merge pull request #71 from superrino130/master
  • 2d901a9 typo?
  • 2ac9e6d Future-proof protxml test
  • 8e58049 Update changelog
  • 057798d Merge pull request #61 from levitsky/feature/charge_carrier
  • 527f641 Merge branch 'master' into feature/charge_carrier
  • 5784e0a Merge pull request #70 from mobiusklein/usi_test_backend
  • Additional commits viewable in compare view

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Bumps [pyteomics](https://github.com/levitsky/pyteomics) from 4.4.2 to 4.5.3.
- [Release notes](https://github.com/levitsky/pyteomics/releases)
- [Changelog](https://github.com/levitsky/pyteomics/blob/master/CHANGELOG)
- [Commits](levitsky/pyteomics@v4.4.2...v4.5.3)

---
updated-dependencies:
- dependency-name: pyteomics
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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dependabot bot commented on behalf of github Apr 14, 2022

The following labels could not be found: pip dependencies.

@straussmaximilian straussmaximilian merged commit 843bfb4 into develop Apr 14, 2022
@dependabot dependabot bot deleted the dependabot/pip/develop/pyteomics-4.5.3 branch April 14, 2022 09:53
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