From df352e8b5f2b651d75e9e4f5defdfa0dc8cdce10 Mon Sep 17 00:00:00 2001 From: fiona-naughton Date: Sat, 19 Oct 2024 01:43:16 +1100 Subject: [PATCH 1/4] add deprecation messages --- package/MDAnalysis/analysis/encore/__init__.py | 8 ++++++++ package/MDAnalysis/analysis/encore/bootstrap.py | 5 +++++ .../analysis/encore/clustering/ClusterCollection.py | 5 +++++ .../analysis/encore/clustering/ClusteringMethod.py | 5 +++++ package/MDAnalysis/analysis/encore/clustering/cluster.py | 5 +++++ package/MDAnalysis/analysis/encore/confdistmatrix.py | 5 +++++ package/MDAnalysis/analysis/encore/covariance.py | 6 ++++++ .../DimensionalityReductionMethod.py | 5 +++++ .../dimensionality_reduction/reduce_dimensionality.py | 5 +++++ package/MDAnalysis/analysis/encore/similarity.py | 5 +++++ 10 files changed, 54 insertions(+) diff --git a/package/MDAnalysis/analysis/encore/__init__.py b/package/MDAnalysis/analysis/encore/__init__.py index 2017188580f..34b70dd28d0 100644 --- a/package/MDAnalysis/analysis/encore/__init__.py +++ b/package/MDAnalysis/analysis/encore/__init__.py @@ -34,6 +34,14 @@ __all__ = ['covariance', 'similarity', 'confdistmatrix', 'clustering'] +import warnings + +wmsg = ("Deprecation in version 2.8.0\n" + "MDAnalysis.analysis.encore is deprecated in favour of the " + "MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) " + "and will be removed in MDAnalysis version 3.0.0.") +warnings.warn(wmsg, category=DeprecationWarning) + from ...due import due, Doi due.cite(Doi("10.1371/journal.pcbi.1004415"), diff --git a/package/MDAnalysis/analysis/encore/bootstrap.py b/package/MDAnalysis/analysis/encore/bootstrap.py index 22287d98fc7..2d50d486dcb 100644 --- a/package/MDAnalysis/analysis/encore/bootstrap.py +++ b/package/MDAnalysis/analysis/encore/bootstrap.py @@ -32,6 +32,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np import logging diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py index 35b48219abf..87879ba1077 100644 --- a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py +++ b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py @@ -31,6 +31,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py index b18d6a54350..df13aaff570 100644 --- a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py +++ b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py @@ -32,6 +32,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np import warnings diff --git a/package/MDAnalysis/analysis/encore/clustering/cluster.py b/package/MDAnalysis/analysis/encore/clustering/cluster.py index 9e0ea01fc45..0ad713775d6 100644 --- a/package/MDAnalysis/analysis/encore/clustering/cluster.py +++ b/package/MDAnalysis/analysis/encore/clustering/cluster.py @@ -31,6 +31,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np from ..utils import ParallelCalculation, merge_universes diff --git a/package/MDAnalysis/analysis/encore/confdistmatrix.py b/package/MDAnalysis/analysis/encore/confdistmatrix.py index 483964d5594..2f3e83b94ff 100644 --- a/package/MDAnalysis/analysis/encore/confdistmatrix.py +++ b/package/MDAnalysis/analysis/encore/confdistmatrix.py @@ -34,6 +34,11 @@ class to compute an RMSD matrix in such a way is also available. .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ from joblib import Parallel, delayed import numpy as np diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py index 1fb77b10785..e6768bf698d 100644 --- a/package/MDAnalysis/analysis/encore/covariance.py +++ b/package/MDAnalysis/analysis/encore/covariance.py @@ -30,6 +30,12 @@ :Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen .. versionadded:: 0.16.0 + +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py index 10cd28ce4d6..cef202843d7 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py @@ -32,6 +32,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import logging import warnings diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py index 1432c4a06de..1a35548fbf6 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py @@ -31,6 +31,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + """ import numpy as np from ..confdistmatrix import get_distance_matrix diff --git a/package/MDAnalysis/analysis/encore/similarity.py b/package/MDAnalysis/analysis/encore/similarity.py index 9e1ee2a6749..2f41d233d48 100644 --- a/package/MDAnalysis/analysis/encore/similarity.py +++ b/package/MDAnalysis/analysis/encore/similarity.py @@ -29,6 +29,11 @@ .. versionadded:: 0.16.0 +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + The module contains implementations of similarity measures between protein ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and examples are described in :footcite:p:`Tiberti2015`. From cc12da3f032cd8379a8af78ec5aadceb40337e55 Mon Sep 17 00:00:00 2001 From: fiona-naughton Date: Sat, 19 Oct 2024 01:57:23 +1100 Subject: [PATCH 2/4] add doc deprecation messages --- .../sphinx/source/documentation_pages/analysis/encore.rst | 6 ++++++ .../source/documentation_pages/analysis/encore/utils.rst | 5 +++++ 2 files changed, 11 insertions(+) diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst index 2051a2e3352..d4da4612601 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst @@ -9,6 +9,12 @@ .. versionadded:: 0.16.0 + +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + The module contains implementations of similarity measures between protein ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and examples are described in :footcite:p:`Tiberti2015`. diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst index 85a2f6cd414..e1b1e27b717 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst @@ -2,6 +2,11 @@ Utility functions for ENCORE ============================== +.. deprecated:: 2.8.0 + This module is deprecated in favour of the + MDAKit `mdaencore `_ and will be removed + in MDAnalysis 3.0.0. + .. automodule:: MDAnalysis.analysis.encore.utils :members: From 573097207f40698a077c601a7600656d12ff0fef Mon Sep 17 00:00:00 2001 From: fiona-naughton Date: Sat, 19 Oct 2024 02:22:44 +1100 Subject: [PATCH 3/4] add test --- testsuite/MDAnalysisTests/analysis/test_encore.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index bc07c21af73..424aae54278 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -30,6 +30,7 @@ import os import warnings import platform +from importlib import reload import pytest from numpy.testing import assert_equal, assert_allclose @@ -46,6 +47,11 @@ def function(x): return x**2 +def test_moved_to_mdakit_warning(): + wmsg = "MDAnalysis.analysis.encore is deprecated" + with pytest.warns(DeprecationWarning, match=wmsg): + reload(encore) + class TestEncore(object): @pytest.fixture(scope='class') def ens1_template(self): From 669f6b69ff3561aef1d29d886ab74be32718d900 Mon Sep 17 00:00:00 2001 From: fiona-naughton Date: Sat, 19 Oct 2024 02:56:54 +1100 Subject: [PATCH 4/4] update changelog --- package/CHANGELOG | 2 ++ 1 file changed, 2 insertions(+) diff --git a/package/CHANGELOG b/package/CHANGELOG index de7fddd2660..7fa3a3501a2 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -99,6 +99,8 @@ Changes numpy.testing.assert_allclose #4438) Deprecations + * The MDAnalysis.anaylsis.encore module has been deprecated in favour of the + mdaencore MDAKit and will be removed in version 3.0.0 (PR #4737) * The MMTF Reader is deprecated and will be removed in version 3.0 as the MMTF format is no longer supported (Issue #4634) * The MDAnalysis.analysis.waterdynamics module has been deprecated in favour