diff --git a/CHANGELOG.md b/CHANGELOG.md index ad12218..f54d0fd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Upgrade Pydantic dependency to v2. The PSM `spectrum_id` field is now always coerced to a string. - `io.proteoscape`: Use pyarrow to iteratively read from Parquet instead of first reading an entire dataframe with Pandas. - `io.sage`: Update compatibility to Sage v0.14 +- Remove temporary patch for caching Proforma modification resolvers (now in Pyteomics v4.7.2). ## [0.8.3] - 2024-04-16 diff --git a/psm_utils/__init__.py b/psm_utils/__init__.py index 7e9087d..4cf394e 100644 --- a/psm_utils/__init__.py +++ b/psm_utils/__init__.py @@ -3,7 +3,6 @@ __version__ = "0.9.0" __all__ = ["Peptidoform", "PSM", "PSMList"] -from functools import lru_cache from warnings import filterwarnings # mzmlb is not used, so hdf5plugin is not needed @@ -14,17 +13,6 @@ module="psims.mzmlb", ) -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) diff --git a/pyproject.toml b/pyproject.toml index a2f3629..edaf8b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ dependencies = [ "pyarrow", "pydantic >= 2", "pyopenms", - "pyteomics >= 4, <4.7", + "pyteomics >= 4", "rich", "sqlalchemy", ]