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Cache modification resolvers (temporary patch); version bump #79

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Apr 16, 2024
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Cache modification resolvers (temporary patch); version bump #79

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7 changes: 7 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [0.8.3] - 2024-04-16

### Added

- Speed up mass calculation for large datasets by caching Proforma modification resolvers.
Temporary patch until implemented in Pyteomics (see levitsky/pyteomics#147).

## [0.8.2] - 2024-04-05

### Added
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21 changes: 17 additions & 4 deletions psm_utils/__init__.py
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@@ -1,7 +1,9 @@
"""Common utilities for parsing and handling PSMs, and search engine results."""

__version__ = "0.8.2"
__version__ = "0.8.3"
__all__ = ["Peptidoform", "PSM", "PSMList"]

from functools import lru_cache
from warnings import filterwarnings

# mzmlb is not used, so hdf5plugin is not needed
Expand All @@ -12,6 +14,17 @@
module="psims.mzmlb",
)

from psm_utils.peptidoform import Peptidoform # noqa: E402, F401
from psm_utils.psm import PSM # noqa: E402, F401
from psm_utils.psm_list import PSMList # noqa: E402, F401
from pyteomics.proforma import ( # noqa: E402
GenericResolver,
PSIModResolver,
UnimodResolver,
)

from psm_utils.peptidoform import Peptidoform # noqa: E402
from psm_utils.psm import PSM # noqa: E402
from psm_utils.psm_list import PSMList # noqa: E402

# Temporary patch until released in pyteomics (see levitsky/pyteomics#147)
UnimodResolver.resolve = lru_cache(maxsize=None)(UnimodResolver.resolve)
PSIModResolver.resolve = lru_cache(maxsize=None)(PSIModResolver.resolve)
GenericResolver.resolve = lru_cache(maxsize=None)(GenericResolver.resolve)
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