diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml index 6af3dd3f9dc..3152caabe76 100644 --- a/.github/actions/setup-deps/action.yaml +++ b/.github/actions/setup-deps/action.yaml @@ -33,6 +33,8 @@ inputs: default: 'hypothesis' matplotlib: default: 'matplotlib-base' + mda_xdrlib: + default: 'mda-xdrlib' mmtf-python: default: 'mmtf-python' networkx: @@ -111,6 +113,7 @@ runs: ${{ inputs.griddataformats }} ${{ inputs.hypothesis }} ${{ inputs.matplotlib }} + ${{ inputs.mda_xdrlib }} ${{ inputs.mmtf-python }} ${{ inputs.networkx }} ${{ inputs.numpy }} diff --git a/package/CHANGELOG b/package/CHANGELOG index f201a0045fd..92a5baff309 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -22,6 +22,9 @@ Fixes Enhancements Changes + * The `mda-xdrlib` module is now a core dependency of MDAnalysis + replacing the now deprecated `xdrlib` core Python library + (PR #4271) * ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404) Deprecations diff --git a/package/MDAnalysis/topology/TPRParser.py b/package/MDAnalysis/topology/TPRParser.py index 733d8bd994f..6e0093304b7 100644 --- a/package/MDAnalysis/topology/TPRParser.py +++ b/package/MDAnalysis/topology/TPRParser.py @@ -158,7 +158,6 @@ __author__ = "Zhuyi Xue" __copyright__ = "GNU Public Licence, v2" -import xdrlib from . import guessers from ..lib.util import openany diff --git a/package/MDAnalysis/topology/tpr/utils.py b/package/MDAnalysis/topology/tpr/utils.py index a72fb5dce71..cbe4e47fe8d 100644 --- a/package/MDAnalysis/topology/tpr/utils.py +++ b/package/MDAnalysis/topology/tpr/utils.py @@ -48,7 +48,7 @@ """ import numpy as np -import xdrlib +from mda_xdrlib import xdrlib import struct from . import obj diff --git a/package/pyproject.toml b/package/pyproject.toml index 6d81f5be713..159f3155397 100644 --- a/package/pyproject.toml +++ b/package/pyproject.toml @@ -46,6 +46,7 @@ dependencies = [ 'threadpoolctl', 'packaging', 'fasteners', + 'mda-xdrlib', ] keywords = [ "python", "science", "chemistry", "biophysics", "molecular-dynamics", diff --git a/package/setup.py b/package/setup.py index 505b55e6546..ff5c864b315 100755 --- a/package/setup.py +++ b/package/setup.py @@ -604,6 +604,7 @@ def long_description(readme): 'threadpoolctl', 'packaging', 'fasteners', + 'mda-xdrlib', ] setup(name='MDAnalysis',